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Tsai WC, Hueng DY, Nieh S, Gao HW. ARID4B is a good biomarker to predict tumour behaviour and decide WHO grades in gliomas and meningiomas. J Clin Pathol 2016; 70:162-167. [DOI: 10.1136/jclinpath-2016-203804] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/23/2016] [Accepted: 07/02/2016] [Indexed: 12/14/2022]
Abstract
AimsAlthough ARID4B is known to promote tumour metastasis in breast cancer and inhibit transformation and progression in leukaemia, the possible effect of ARID4B on primary brain tumours (PBTs) is not well characterised. We tested the hypothesis that expression of ARID4B correlates with WHO grade and survival in patients with PBTs.MethodsWestern blot analysis was performed on protein lysates prepared from normal brain tissue and glioma cell lines (U87MG, LN229, GBM8401 and U118MG). Subsequently, immunohistochemical analysis of ARID4B was performed on 2 tissue microarrays, including 12 normal brain tissues, 63 meningiomas with different subtypes, 232 gliomas of various grades and degrees of differentiation, 8 central neurocytomas and 4 chordomas. The ARID4B immunostaining score was calculated by multiplying the intensity score by the percentage of tumour cells expressing ARID4B.ResultsIn vitro, ARID4B protein expression was increased in some glioma cell lines. In addition, the average ARID4B immunostaining score was 38.03, 79.09, 129.76 and 119.32, respectively, in gliomas of WHO grade I, II, III and IV. Higher ARID4B immunostaining score was significantly correlated with more advanced WHO grade of gliomas (p=7.4×10–6) and meningiomas. Finally, higher ARID4B expression tended to the shorter survival rates, but did not reach statistical significance.ConclusionsARID4B overexpression presented in most of PBTs, rather than non-neoplastic brain tissue, and correlated with WHO grades in meningiomas and gliomas. Therefore, ARID4B is a satisfactory biomarker to highlight tumour component and predict tumour behaviour in primary brain neoplasms.
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52
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Horton JR, Liu X, Gale M, Wu L, Shanks JR, Zhang X, Webber PJ, Bell JSK, Kales SC, Mott BT, Rai G, Jansen DJ, Henderson MJ, Urban DJ, Hall MD, Simeonov A, Maloney DJ, Johns MA, Fu H, Jadhav A, Vertino PM, Yan Q, Cheng X. Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds. Cell Chem Biol 2016; 23:769-781. [PMID: 27427228 PMCID: PMC4958579 DOI: 10.1016/j.chembiol.2016.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/15/2016] [Accepted: 06/04/2016] [Indexed: 12/12/2022]
Abstract
The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases removes methyl groups from methylated lysine 4 of histone H3. Accumulating evidence supports a role for KDM5 family members as oncogenic drivers. We compare the in vitro inhibitory properties and binding affinity of ten diverse compounds with all four family members, and present the crystal structures of the KDM5A-linked Jumonji domain in complex with eight of these inhibitors in the presence of Mn(II). All eight inhibitors structurally examined occupy the binding site of α-ketoglutarate, but differ in their specific binding interactions, including the number of ligands involved in metal coordination. We also observed inhibitor-induced conformational changes in KDM5A, particularly those residues involved in the binding of α-ketoglutarate, the anticipated peptide substrate, and intramolecular interactions. We discuss how particular chemical moieties contribute to inhibitor potency and suggest strategies that might be utilized in the successful design of selective and potent epigenetic inhibitors.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xu Liu
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Molly Gale
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - John R Shanks
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Philip J Webber
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA
| | - Joshua S K Bell
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Bryan T Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Daniel J Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Daniel J Urban
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Margaret A Johns
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Paula M Vertino
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.
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53
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Zhou D, Kannappan V, Chen X, Li J, Leng X, Zhang J, Xuan S. RBP2 induces stem-like cancer cells by promoting EMT and is a prognostic marker for renal cell carcinoma. Exp Mol Med 2016; 48:e238. [PMID: 27282106 PMCID: PMC4929691 DOI: 10.1038/emm.2016.37] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/30/2015] [Accepted: 01/06/2016] [Indexed: 12/13/2022] Open
Abstract
Renal cell carcinoma (RCC), one of the most common kidney cancers, has a poor prognosis. Epithelial to mesenchymal transition (EMT) is a hallmark of carcinoma invasion and metastasis. Several studies have examined the molecular regulation of EMT, but the relationship between histone demethylases and EMT is little understood. In this study, we investigated the role of retinoblastoma-binding protein-2 (RBP2), a histone demethylase that is highly expressed in RCC and is positively correlated with poor RCC prognosis in the regulation of EMT. We found that ectopic overexpression of RBP2 can induce cancer stem cell-like (CSC) phenotypes through EMT in RCC cells by converting them to a more mesenchymal phenotype. This results in increased resistance to apoptosis, which leads to enhanced tumor growth in xenograft models. Together, our data show that RBP2 is an epigenetic regulator that has an important role in the initiation of CSC phenotypes through EMT, leading to tumor progression. RBP2 is also a novel biomolecule for RCC diagnosis, and prognosis and may be a therapeutic target.
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MESH Headings
- Animals
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/metabolism
- Carcinogenesis/metabolism
- Carcinogenesis/pathology
- Carcinoma, Renal Cell/diagnosis
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cell Line, Tumor
- Epithelial-Mesenchymal Transition
- Follow-Up Studies
- Humans
- Kidney/metabolism
- Kidney/pathology
- Kidney Neoplasms/diagnosis
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Mice, Inbred BALB C
- Mice, Nude
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Prognosis
- Retinol-Binding Proteins, Cellular/analysis
- Retinol-Binding Proteins, Cellular/metabolism
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Affiliation(s)
- Dahai Zhou
- College of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Department of Urology, 401 Hospital of PLA, Qingdao, China
| | - Vinodh Kannappan
- Research Institute in Healthcare Science, Faculty of Science & Engineering, University of Wolverhampton, Wolverhampton, UK
| | | | - Jingqin Li
- Department of Urology, 401 Hospital of PLA, Qingdao, China
| | - Xuefeng Leng
- Department of Urology, 401 Hospital of PLA, Qingdao, China
| | - Jinping Zhang
- Department of Urology, 401 Hospital of PLA, Qingdao, China
| | - Shiying Xuan
- College of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Qingdao Municipal Hospital, Qingdao, China
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54
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Huang C, Cheng J, Bawa-Khalfe T, Yao X, Chin YE, Yeh ETH. SUMOylated ORC2 Recruits a Histone Demethylase to Regulate Centromeric Histone Modification and Genomic Stability. Cell Rep 2016; 15:147-157. [PMID: 27052177 DOI: 10.1016/j.celrep.2016.02.091] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/17/2015] [Accepted: 02/26/2016] [Indexed: 01/25/2023] Open
Abstract
Origin recognition complex 2 (ORC2), a subunit of the ORC, is essential for DNA replication initiation in eukaryotic cells. In addition to a role in DNA replication initiation at the G1/S phase, ORC2 has been shown to localize to the centromere during the G2/M phase. Here, we show that ORC2 is modified by small ubiquitin-like modifier 2 (SUMO2), but not SUMO1, at the G2/M phase of the cell cycle. SUMO2-modification of ORC2 is important for the recruitment of KDM5A in order to convert H3K4me3 to H3K4me2, a "permissive" histone marker for α-satellite transcription at the centromere. Persistent expression of SUMO-less ORC2 led to reduced α-satellite transcription and impaired pericentric heterochromatin silencing, which resulted in re-replication of heterochromatin DNA. DNA re-replication eventually activated the DNA damage response, causing the bypass of mitosis and the formation of polyploid cells. Thus, ORC2 sustains genomic stability by recruiting KDM5A to maintain centromere histone methylation in order to prevent DNA re-replication.
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Affiliation(s)
- Chao Huang
- Texas Heart Institute, Houston, TX 77030, USA; Department of Cardiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; The Central Lab at Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jinke Cheng
- Texas Heart Institute, Houston, TX 77030, USA; Department of Biochemistry and Molecular and Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Tasneem Bawa-Khalfe
- Department of Cardiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Center for Nuclear Receptors and Cell Signaling and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Xuebiao Yao
- Anhui Key Laboratory of Cellular Dynamics and Hefei National Laboratory for Physical Sciences at Nanoscale, University of Science and Technology of China, Hefei 230026, China
| | - Y Eugene Chin
- The Central Lab at Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Edward T H Yeh
- Texas Heart Institute, Houston, TX 77030, USA; Department of Cardiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
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55
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Horton JR, Engstrom A, Zoeller EL, Liu X, Shanks JR, Zhang X, Johns MA, Vertino PM, Fu H, Cheng X. Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases. J Biol Chem 2016; 291:2631-46. [PMID: 26645689 PMCID: PMC4742734 DOI: 10.1074/jbc.m115.698449] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/17/2015] [Indexed: 12/18/2022] Open
Abstract
The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases remove methyl groups from tri- and dimethylated lysine 4 of histone H3. Accumulating evidence from primary tumors and model systems supports a role for KDM5A (JARID1A/RBP2) and KDM5B (JARID1B/PLU1) as oncogenic drivers. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC). Here we demonstrate that internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. We present a crystal structure of the linked JmjN-JmjC domain from KDM5A, which reveals that the linked domain fully reconstitutes the cofactor (metal ion and α-ketoglutarate) binding characteristics of other structurally characterized Jumonji domain demethylases. Docking studies with GSK-J1, a selective inhibitor of the KDM6/KDM5 subfamilies, identify critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. Further, we found that GSK-J1 inhibited the demethylase activity of KDM5C with 8.5-fold increased potency compared with that of KDM5B at 1 mm α-ketoglutarate. In contrast, JIB-04 (a pan-inhibitor of the Jumonji demethylase superfamily) had the opposite effect and was ~8-fold more potent against KDM5B than against KDM5C. Interestingly, the relative selectivity of JIB-04 toward KDM5B over KDM5C in vitro translates to a ~10-50-fold greater growth-inhibitory activity against breast cancer cell lines. These data define the minimal requirements for enzymatic activity of the KDM5 family to be the linked JmjN-JmjC domain coupled with the immediate C-terminal helical zinc-binding domain and provide structural characterization of the linked JmjN-JmjC domain for the KDM5 family, which should prove useful in the design of KDM5 demethylase inhibitors with improved potency and selectivity.
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Affiliation(s)
| | - Amanda Engstrom
- the Graduate Program in Biochemistry, Cell and Developmental Biology
| | | | - Xu Liu
- From the Departments of Biochemistry
| | | | | | | | - Paula M Vertino
- Radiation Oncology, the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Haian Fu
- the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322 Radiation Oncology, the Emory Chemical Biology Discovery Center, and Hematology and Medical Oncology, and
| | - Xiaodong Cheng
- From the Departments of Biochemistry, the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
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56
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Kong LL, Man DM, Wang T, Zhang GA, Cui W. siRNA targeting RBP2 inhibits expression, proliferation, tumorigenicity and invasion in thyroid carcinoma cells. Oncol Lett 2015; 10:3393-3398. [PMID: 26788140 PMCID: PMC4665154 DOI: 10.3892/ol.2015.3782] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022] Open
Abstract
In order to estimate the effects of small interfering RNA (siRNA) targeting retinoblastoma binding protein 2 (RBP2) on the proliferation, expression, invasion, migration and tumorigenicity abilities of papillary thyroid carcinoma K1 cells, siRNA targeting RBP2 (RBP2-siRNA) and negative control siRNA were transfected into K1 cells. The mRNA levels of RBP2 in the transfected cells were estimated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and the protein levels of RBP2 in these cells were evaluated by western blot analysis and immunocytochemical (ICC) analyses. The growth, tumorigenicity, migration and invasion abilities of the transfected cells were measured by Cell Counting Kit-8 (CCK-8), soft agar colony formation and transwell chamber assay, respectively. The ICC results demonstrated that the protein expression levels of RBP2 were lower in the RBP2-siRNA-transfected cells than in the blank and control cells (analysis of variance, F=26.754, P<0.01). RBP2-siRNA downregulated RBP2 at the mRNA (t=8.869) and protein level (F=60.835) (P=0.000 vs. control cells). In addition, the transfection of RBP2-siRNA into K1 cells also suppressed cell proliferation at 24, 48 and 72 h post-transfection (t=7.650, P<0.01; t=2.606, P=0.016; and t=2.377, P=0.027, respectively). Compared with the control group, the number of invasive and migrated cells were significantly reduced in the RBP2-siRNA-transfected group (t=4.774 and t=6.366, respectively; P<0.01). Furthermore, the tumorigenic potential of the cells transfected with RBP2-siRNA was markedly reduced, as indicated by the soft agar formation assay (t=2.749, P=0.014 vs. control cells). In conclusion, the transfection of RBP2-siRNA into papillary thyroid carcinoma K1 cells suppressed the expression of RBP2 in these cells, and reduced their proliferation, invasion, migration and tumorigenic potential. Therefore, targeting RBP2 may be an efficient approach to control thyroid carcinoma.
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Affiliation(s)
- Ling-Ling Kong
- Department of Pathology, Basic Science School, Jining Medical University, Jining, Shandong 272067, P.R. China
| | - Dong-Mei Man
- Department of Gynecology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Tian Wang
- Department of Electrocardiogram, The First Affiliated Hospital of Jining Medical University, Jining, Shandong 272111, P.R. China
| | - Guo-An Zhang
- Department of Pathology, Basic Science School, Jining Medical University, Jining, Shandong 272067, P.R. China
| | - Wen Cui
- Department of Pathology, Basic Science School, Jining Medical University, Jining, Shandong 272067, P.R. China
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57
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Wang Y, Zheng Z, Zhang J, Wang Y, Kong R, Liu J, Zhang Y, Deng H, Du X, Ke Y. A Novel Retinoblastoma Protein (RB) E3 Ubiquitin Ligase (NRBE3) Promotes RB Degradation and Is Transcriptionally Regulated by E2F1 Transcription Factor. J Biol Chem 2015; 290:28200-28213. [PMID: 26442585 DOI: 10.1074/jbc.m115.655597] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Indexed: 12/25/2022] Open
Abstract
Retinoblastoma protein (RB) plays critical roles in tumor suppression and is degraded through the proteasomal pathway. However, E3 ubiquitin ligases responsible for proteasome-mediated degradation of RB are largely unknown. Here we characterize a novel RB E3 ubiquitin ligase (NRBE3) that binds RB and promotes RB degradation. NRBE3 contains an LXCXE motif and bound RB in vitro. NRBE3 interacted with RB in cells when proteasome activity was inhibited. NRBE3 promoted RB ubiquitination and degradation via the ubiquitin-proteasome pathway. Importantly, purified NRBE3 ubiquitinated recombinant RB in vitro, and a U-box was identified as essential for its E3 activity. Surprisingly, NRBE3 was transcriptionally activated by E2F1/DP1. Consequently, NRBE3 affected the cell cycle by promoting G1/S transition. Moreover, NRBE3 was up-regulated in breast cancer tissues. Taken together, we identified NRBE3 as a novel ubiquitin E3 ligase for RB that might play a role as a potential oncoprotein in human cancers.
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Affiliation(s)
- Yingshuang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Zongfang Zheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Jingyi Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education)
| | - You Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Ruirui Kong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Jiangying Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Ying Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Hongkui Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaojuan Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
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58
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Vallianatos CN, Iwase S. Disrupted intricacy of histone H3K4 methylation in neurodevelopmental disorders. Epigenomics 2015; 7:503-19. [PMID: 26077434 DOI: 10.2217/epi.15.1] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4me) is an intricately regulated posttranslational modification, which is broadly associated with enhancers and promoters of actively transcribed genomic loci. Recent advances in next-generation sequencing have identified a number of H3K4me regulators mutated in neurodevelopmental disorders including intellectual disabilities, autism spectrum disorders, and schizophrenia. Here, we aim to summarize the molecular function of H3K4me-regulating enzymes in brain development and function. We describe four H3K4me methyltransferases (KMT2A, KMT2C, KMT2D, KMT2F), four demethylases (KDM1A, KDM5A, KDM5B, KDM5C), and two reader proteins (PHF21A, PHF8) mutated in neurodevelopmental disorders. Understanding the role of these chromatin regulators in the development and maintenance of neural connections will advance therapeutic opportunities for prevention and treatment of these lifelong neurodevelopmental disorders.
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Affiliation(s)
- Christina N Vallianatos
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA.,Predoctoral Training Program in Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
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59
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Jiang XH, Bukhari I, Zheng W, Yin S, Wang Z, Cooke HJ, Shi QH. Blood-testis barrier and spermatogenesis: lessons from genetically-modified mice. Asian J Androl 2015; 16:572-80. [PMID: 24713828 PMCID: PMC4104086 DOI: 10.4103/1008-682x.125401] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The blood-testis barrier (BTB) is found between adjacent Sertoli cells in the testis where it creates a unique microenvironment for the development and maturation of meiotic and postmeiotic germ cells in seminiferous tubes. It is a compound proteinous structure, composed of several types of cell junctions including tight junctions (TJs), adhesion junctions and gap junctions (GJs). Some of the junctional proteins function as structural proteins of BTB and some have regulatory roles. The deletion or functional silencing of genes encoding these proteins may disrupt the BTB, which may cause immunological or other damages to meiotic and postmeiotic cells and ultimately lead to spermatogenic arrest and infertility. In this review, we will summarize the findings on the BTB structure and function from genetically-modified mouse models and discuss the future perspectives.
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Affiliation(s)
| | | | | | | | | | | | - Qing-Hua Shi
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China; Institute of Physics, Chinese Academy of Sciences, Hefei, China,
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60
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Wu RC, Zeng Y, Pan IW, Wu MY. Androgen Receptor Coactivator ARID4B Is Required for the Function of Sertoli Cells in Spermatogenesis. Mol Endocrinol 2015; 29:1334-46. [PMID: 26258622 DOI: 10.1210/me.2015-1089] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Defects in spermatogenesis, a process that produces spermatozoa inside seminiferous tubules of the testis, result in male infertility. Spermatogenic progression is highly dependent on a microenvironment provided by Sertoli cells, the only somatic cells and epithelium of seminiferous tubules. However, genes that regulate such an important activity of Sertoli cells are poorly understood. Here, we found that AT-rich interactive domain 4B (ARID4B), is essential for the function of Sertoli cells to regulate spermatogenesis. Specifically, we generated Sertoli cell-specific Arid4b knockout (Arid4bSCKO) mice, and showed that the Arid4bSCKO male mice were completely infertile with impaired testis development and significantly reduced testis size. Importantly, severe structural defects accompanied by loss of germ cells and Sertoli cell-only phenotype were found in many seminiferous tubules of the Arid4bSCKO testes. In addition, maturation of Sertoli cells was significantly delayed in the Arid4bSCKO mice, associated with delayed onset of spermatogenesis. Spermatogenic progression was also defective, showing an arrest at the round spermatid stage in the Arid4bSCKO testes. Interestingly, we showed that ARID4B functions as a "coactivator" of androgen receptor and is required for optimal transcriptional activation of reproductive homeobox 5, an androgen receptor target gene specifically expressed in Sertoli cells and critical for spermatogenesis. Together, our study identified ARID4B to be a key regulator of Sertoli cell function important for male germ cell development.
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Affiliation(s)
- Ray-Chang Wu
- Department of Biochemistry and Molecular Medicine (R.-C.W., Y.Z., M.-Y.W.), The George Washington University, Washington, DC 20037; and Department of Neurosurgery (I-W.P.), Texas Children's Hospital and Baylor College of Medicine, Houston, Texas 77030
| | - Yang Zeng
- Department of Biochemistry and Molecular Medicine (R.-C.W., Y.Z., M.-Y.W.), The George Washington University, Washington, DC 20037; and Department of Neurosurgery (I-W.P.), Texas Children's Hospital and Baylor College of Medicine, Houston, Texas 77030
| | - I-Wen Pan
- Department of Biochemistry and Molecular Medicine (R.-C.W., Y.Z., M.-Y.W.), The George Washington University, Washington, DC 20037; and Department of Neurosurgery (I-W.P.), Texas Children's Hospital and Baylor College of Medicine, Houston, Texas 77030
| | - Mei-Yi Wu
- Department of Biochemistry and Molecular Medicine (R.-C.W., Y.Z., M.-Y.W.), The George Washington University, Washington, DC 20037; and Department of Neurosurgery (I-W.P.), Texas Children's Hospital and Baylor College of Medicine, Houston, Texas 77030
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Liu H, Liu L, Holowatyj A, Jiang Y, Yang ZQ. Integrated genomic and functional analyses of histone demethylases identify oncogenic KDM2A isoform in breast cancer. Mol Carcinog 2015. [PMID: 26207617 DOI: 10.1002/mc.22341] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Histone lysine demethylases (KDMs) comprise a large class of enzymes that catalyze site-specific demethylation of lysine residues on histones and other proteins. They play critical roles in controlling transcription, chromatin architecture, and cellular differentiation. However, the genomic landscape and clinical significance of KDMs in breast cancer remain poorly characterized. Here, we conducted a meta-analysis of 24 KDMs in breast cancer and identified associations among recurrent copy number alterations, gene expression, breast cancer subtypes, and clinical outcome. Two KDMs, KDM2A and KDM5B, had the highest frequency of genetic amplification and overexpression. Furthermore, among the 24 KDM genes, KDM2A had the highest correlation between copy number and mRNA expression, and high mRNA levels of KDM2A were significantly associated with shorter survival of breast cancer patients. KDM2A has two isoforms: the long isoform is comprised of a JmjC domain, CXXC-zinc finger, PHD zinc finger, F-box, and the AMN1 protein domain; whereas the short isoform of KDM2A lacks the N-terminal JmjC domain but contains all other motifs. Detailed characterization of KDM2A in breast cancer revealed that the short isoform of KDM2A is more abundant than the long isoform at DNA, mRNA, and protein levels in a subset of breast cancers. Furthermore, our data indicate that the short isoform of KDM2A has oncogenic potential and functions as an oncogenic isoform in a subset of breast cancers. Taken together, our findings suggest that amplification and overexpression of the KDM2A short isoform is critical in breast cancer progression.
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Affiliation(s)
- Hui Liu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medicine, Jilin University, Jilin, China.,Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
| | - Lanxin Liu
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
| | - Andreana Holowatyj
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
| | - Yuanyuan Jiang
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
| | - Zeng-Quan Yang
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
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62
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McGrath J, Trojer P. Targeting histone lysine methylation in cancer. Pharmacol Ther 2015; 150:1-22. [PMID: 25578037 DOI: 10.1016/j.pharmthera.2015.01.002] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 02/06/2023]
Abstract
Within the vast landscape of histone modifications lysine methylation has gained increasing attention because of its profound regulatory potential. The methylation of lysine residues on histone proteins modulates chromatin structure and thereby contributes to the regulation of DNA-based nuclear processes such as transcription, replication and repair. Protein families with opposing catalytic activities, lysine methyltransferases (KMTs) and demethylases (KDMs), dynamically control levels of histone lysine methylation and individual enzymes within these families have become candidate oncology targets in recent years. A number of high quality small molecule inhibitors of these enzymes have been identified. Several of these compounds elicit selective cancer cell killing in vitro and robust efficacy in vivo, suggesting that targeting 'histone lysine methylation pathways' may be a relevant, emerging cancer therapeutic strategy. Here, we discuss individual histone lysine methylation pathway targets, the properties of currently available small molecule inhibitors and their application in the context of cancer.
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Affiliation(s)
- John McGrath
- Constellation Pharmaceuticals, 215 1st Street Suite 200, Cambridge, MA, 02142, USA
| | - Patrick Trojer
- Constellation Pharmaceuticals, 215 1st Street Suite 200, Cambridge, MA, 02142, USA.
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63
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Nishibuchi G, Shibata Y, Hayakawa T, Hayakawa N, Ohtani Y, Sinmyozu K, Tagami H, Nakayama JI. Physical and functional interactions between the histone H3K4 demethylase KDM5A and the nucleosome remodeling and deacetylase (NuRD) complex. J Biol Chem 2014; 289:28956-70. [PMID: 25190814 DOI: 10.1074/jbc.m114.573725] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Histone H3K4 methylation has been linked to transcriptional activation. KDM5A (also known as RBP2 or JARID1A), a member of the KDM5 protein family, is an H3K4 demethylase, previously implicated in the regulation of transcription and differentiation. Here, we show that KDM5A is physically and functionally associated with two histone deacetylase complexes. Immunoaffinity purification of KDM5A confirmed a previously described association with the SIN3B-containing histone deacetylase complex and revealed an association with the nucleosome remodeling and deacetylase (NuRD) complex. Sucrose density gradient and sequential immunoprecipitation analyses further confirmed the stable association of KDM5A with these two histone deacetylase complexes. KDM5A depletion led to changes in the expression of hundreds of genes, two-thirds of which were also controlled by CHD4, the NuRD catalytic subunit. Gene ontology analysis confirmed that the genes commonly regulated by both KDM5A and CHD4 were categorized as developmentally regulated genes. ChIP analyses suggested that CHD4 modulates H3K4 methylation levels at the promoter and coding regions of target genes. We further demonstrated that the Caenorhabditis elegans homologues of KDM5 and CHD4 function in the same pathway during vulva development. These results suggest that KDM5A and the NuRD complex cooperatively function to control developmentally regulated genes.
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Affiliation(s)
- Gohei Nishibuchi
- From the Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501
| | - Yukimasa Shibata
- the Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Hyogo 669-1337, and
| | | | | | | | - Kaori Sinmyozu
- Proteomics Support Unit, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Hideaki Tagami
- From the Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501
| | - Jun-ichi Nakayama
- From the Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, the Laboratory for Chromatin Dynamics and
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64
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Cadet JL, Brannock C, Jayanthi S, Krasnova IN. Transcriptional and epigenetic substrates of methamphetamine addiction and withdrawal: evidence from a long-access self-administration model in the rat. Mol Neurobiol 2014; 51:696-717. [PMID: 24939695 PMCID: PMC4359351 DOI: 10.1007/s12035-014-8776-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 06/01/2014] [Indexed: 01/06/2023]
Abstract
Methamphetamine use disorder is a chronic neuropsychiatric disorder characterized by recurrent binge episodes, intervals of abstinence, and relapses to drug use. Humans addicted to methamphetamine experience various degrees of cognitive deficits and other neurological abnormalities that complicate their activities of daily living and their participation in treatment programs. Importantly, models of methamphetamine addiction in rodents have shown that animals will readily learn to give themselves methamphetamine. Rats also accelerate their intake over time. Microarray studies have also shown that methamphetamine taking is associated with major transcriptional changes in the striatum measured within a short or longer time after cessation of drug taking. After a 2-h withdrawal time, there was increased expression of genes that participate in transcription regulation. These included cyclic AMP response element binding (CREB), ETS domain-containing protein (ELK1), and members of the FOS family of transcription factors. Other genes of interest include brain-derived neurotrophic factor (BDNF), tyrosine kinase receptor, type 2 (TrkB), and synaptophysin. Methamphetamine-induced transcription was found to be regulated via phosphorylated CREB-dependent events. After a 30-day withdrawal from methamphetamine self-administration, however, there was mostly decreased expression of transcription factors including junD. There was also downregulation of genes whose protein products are constituents of chromatin-remodeling complexes. Altogether, these genome-wide results show that methamphetamine abuse might be associated with altered regulation of a diversity of gene networks that impact cellular and synaptic functions. These transcriptional changes might serve as triggers for the neuropsychiatric presentations of humans who abuse this drug. Better understanding of the way that gene products interact to cause methamphetamine addiction will help to develop better pharmacological treatment of methamphetamine addicts.
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Affiliation(s)
- Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH, DHHS, 251 Bayview Boulevard, Baltimore, MD, 21224, USA,
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65
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Cao J, Liu Z, Cheung WKC, Zhao M, Chen SY, Chan SW, Booth CJ, Nguyen DX, Yan Q. Histone demethylase RBP2 is critical for breast cancer progression and metastasis. Cell Rep 2014; 6:868-77. [PMID: 24582965 DOI: 10.1016/j.celrep.2014.02.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 12/31/2013] [Accepted: 02/03/2014] [Indexed: 12/20/2022] Open
Abstract
Metastasis is a major clinical challenge for cancer treatment. Emerging evidence suggests that aberrant epigenetic modifications contribute significantly to tumor formation and progression. However, the drivers and roles of such epigenetic changes in tumor metastasis are still poorly understood. Using bioinformatic analysis of human breast cancer gene-expression data sets, we identified histone demethylase RBP2 as a putative mediator of metastatic progression. By using both human breast cancer cells and genetically engineered mice, we demonstrated that RBP2 is critical for breast cancer metastasis to the lung in multiple in vivo models. Mechanistically, RBP2 promotes metastasis as a pleiotropic positive regulator of many metastasis genes, including TNC. In addition, RBP2 loss suppresses tumor formation in MMTV-neu transgenic mice. These results suggest that therapeutic targeting of RBP2 is a potential strategy for inhibition of tumor progression and metastasis.
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Affiliation(s)
- Jian Cao
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zongzhi Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - William K C Cheung
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Minghui Zhao
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sophia Y Chen
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Siew Wee Chan
- Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Carmen J Booth
- Section of Comparative Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Don X Nguyen
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
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66
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Johansson C, Tumber A, Che K, Cain P, Nowak R, Gileadi C, Oppermann U. The roles of Jumonji-type oxygenases in human disease. Epigenomics 2014; 6:89-120. [PMID: 24579949 PMCID: PMC4233403 DOI: 10.2217/epi.13.79] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The iron- and 2-oxoglutarate-dependent oxygenases constitute a phylogenetically conserved class of enzymes that catalyze hydroxylation reactions in humans by acting on various types of substrates, including metabolic intermediates, amino acid residues in different proteins and various types of nucleic acids. The discovery of jumonji (Jmj), the founding member of a class of Jmj-type chromatin modifying enzymes and transcriptional regulators, has culminated in the discovery of several branches of histone lysine demethylases, with essential functions in regulating the epigenetic landscape of the chromatin environment. This work has now been considerably expanded into other aspects of epigenetic biology and includes the discovery of enzymatic steps required for methyl-cytosine demethylation as well as modification of RNA and ribosomal proteins. This overview aims to summarize the current knowledge on the human Jmj-type enzymes and their involvement in human pathological processes, including development, cancer, inflammation and metabolic diseases.
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Affiliation(s)
- Catrine Johansson
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - KaHing Che
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
| | - Peter Cain
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
| | - Radoslaw Nowak
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
- Systems Approaches to Biomedical Sciences, Industrial Doctorate Center (SABS IDC) Oxford, UK
| | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
- Systems Approaches to Biomedical Sciences, Industrial Doctorate Center (SABS IDC) Oxford, UK
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67
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Gong W, Wang J, Perrett S, Feng Y. Retinoblastoma-binding protein 1 has an interdigitated double Tudor domain with DNA binding activity. J Biol Chem 2013; 289:4882-95. [PMID: 24379399 DOI: 10.1074/jbc.m113.501940] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Retinoblastoma-binding protein 1 (RBBP1) is a tumor and leukemia suppressor that binds both methylated histone tails and DNA. Our previous studies indicated that RBBP1 possesses a Tudor domain, which cannot bind histone marks. In order to clarify the function of the Tudor domain, the solution structure of the RBBP1 Tudor domain was determined by NMR and is presented here. Although the proteins are unrelated, the RBBP1 Tudor domain forms an interdigitated double Tudor structure similar to the Tudor domain of JMJD2A, which is an epigenetic mark reader. This indicates the functional diversity of Tudor domains. The RBBP1 Tudor domain structure has a significant area of positively charged surface, which reveals a capability of the RBBP1 Tudor domain to bind nucleic acids. NMR titration and isothermal titration calorimetry experiments indicate that the RBBP1 Tudor domain binds both double- and single-stranded DNA with an affinity of 10-100 μM; no apparent DNA sequence specificity was detected. The DNA binding mode and key interaction residues were analyzed in detail based on a model structure of the Tudor domain-dsDNA complex, built by HADDOCK docking using the NMR data. Electrostatic interactions mediate the binding of the Tudor domain with DNA, which is consistent with NMR experiments performed at high salt concentration. The DNA-binding residues are conserved in Tudor domains of the RBBP1 protein family, resulting in conservation of the DNA-binding function in the RBBP1 Tudor domains. Our results provide further insights into the structure and function of RBBP1.
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Affiliation(s)
- Weibin Gong
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and
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68
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Wang S, Wang Y, Wu H, Hu L. RBP2 induces epithelial-mesenchymal transition in non-small cell lung cancer. PLoS One 2013; 8:e84735. [PMID: 24376841 PMCID: PMC3869927 DOI: 10.1371/journal.pone.0084735] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 11/19/2013] [Indexed: 12/11/2022] Open
Abstract
RBP2 has been found to actively participate in cancer progression. It inhibits the senescence of cancer cells, mediates cancer cell proliferation and promotes cancer metastasis. It is also essential to drug tolerance. However, the effects of RBP2 on epithelial-mesenchymal transition are still unknown. In this study, we analyzed the effects of RBP2 on epithelial-mesenchymal transition in non-small cell lung cancer. The results showed that RBP2 down-regulated the expression of E-cadherin by inhibiting the promoter activity of E-cadherin and up-regulated the expression of N-cadherin and snail via the activation of Akt signaling, and the overexpression of RBP2 induced epithelial-mesenchymal transition in non-small cell lung cancer cells. Our study further indicated that RBP2 may be a potential target for anti-lung cancer therapy.
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Affiliation(s)
- Shikun Wang
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Yang Wang
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Haijian Wu
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Likuan Hu
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
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69
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Abstract
Similar to genetic alterations, epigenetic aberrations contribute significantly to tumor initiation and progression. In many cases, these changes are caused by activation or inactivation of the regulators that maintain epigenetic states. Here we review our current knowledge on the KDM5/JARID1 family of histone demethylases. This family of enzymes contains a JmjC domain and is capable of removing tri- and di- methyl marks from lysine 4 on histone H3. Among these proteins, RBP2 mediates drug resistance while JARID1B is required for melanoma maintenance. Preclinical studies suggest inhibition of these enzymes can suppress tumorigenesis and provide strong rationale for development of their inhibitors for use in cancer therapy.
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70
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Gu B, Lee MG. Histone H3 lysine 4 methyltransferases and demethylases in self-renewal and differentiation of stem cells. Cell Biosci 2013; 3:39. [PMID: 24172249 PMCID: PMC3953348 DOI: 10.1186/2045-3701-3-39] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 07/27/2013] [Indexed: 12/22/2022] Open
Abstract
Epigenetic mechanisms are fundamental to understanding the regulatory networks of
gene expression that govern stem cell maintenance and differentiation.
Methylated histone H3 lysine 4 (H3K4) has emerged as a key epigenetic signal for
gene transcription; it is dynamically modulated by several specific H3K4
methyltransferases and demethylases. Recent studies have described new
epigenetic mechanisms by which H3K4 methylation modifiers control self-renewal
and lineage commitments of stem cells. Such advances in stem cell biology would
have a high impact on the research fields of cancer stem cell and regenerative
medicine. In this review, we discuss the recent progress in understanding the
roles of H3K4 methylation modifiers in regulating embryonic and adult stem
cells’ fates.
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71
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Chai W, Lian Z, Chen C, Liu J, Shi LL, Wang Y. JARID1A, JMY, and PTGER4 polymorphisms are related to ankylosing spondylitis in Chinese Han patients: a case-control study. PLoS One 2013; 8:e74794. [PMID: 24069348 PMCID: PMC3777963 DOI: 10.1371/journal.pone.0074794] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 08/07/2013] [Indexed: 12/20/2022] Open
Abstract
Susceptibility to ankylosing spondylitis (AS) is largely genetically determined. JARID1A, JMY and PTGER4 have recently been found to be associated with AS in patients of western European descent. We aim to examine the influence of JARID1A, JMY, and PTGER4 polymorphisms on the susceptibility to and the severity of ankylosing spondylitis in Chinese ethnic majority Han population. This work can lead the clinical doctors to intervene earlier. Blood samples were drawn from 396 AS patients and 404 unrelated healthy controls. Both the AS patients and the controls are Han Chinese. The AS patients are classified based on the severity of the disease. Thirteen tag single nucleotide polymorphisms (tagSNPs) in JARID1A, JMY and PTGER4 are selected and genotyped. Frequencies of different genotypes and alleles are analyzed among the different severity AS patients and the controls. The rs2284336 SNP in JARID1A, the rs16876619 and rs16876657 SNPs in JMY are associated with susceptibility of AS. The rs11062357 SNP in JARID1A, the rs2607142 SNP in JMY and rs10440635 in PTGER4 are related to severity of AS. Haplotype analyses indicate PTGER4 is related to susceptibility to AS; JARID1A and JMY are related to severity of AS.
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Affiliation(s)
- Wei Chai
- Department of Orthopaedics, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Zijian Lian
- Department of Orthopaedics, Tianjin Hospital, Tianjin, China
| | - Chao Chen
- Department of Orthopaedics, Tianjin Hospital, Tianjin, China
| | - Jingyi Liu
- Medical School of Nankai University, Tianjin, China
| | - Lewis L. Shi
- Department of Orthopaedics, University of Chicago Hospital, Chicago, Illinois, United States of America
| | - Yan Wang
- Department of Orthopaedics, Chinese People’s Liberation Army General Hospital, Beijing, China
- Medical School of Nankai University, Tianjin, China
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Abstract
E7 is an accessory protein that is not encoded by all papillomaviruses. The E7 amino terminus contains two regions of similarity to conserved regions 1 and 2 of the adenovirus E1A protein, which are also conserved in the simian vacuolating virus 40 large tumor antigen. The E7 carboxyl terminus consists of a zinc-binding motif, which is related to similar motifs in E6 proteins. E7 proteins play a central role in the human papillomavirus life cycle, reprogramming the cellular environment to be conducive to viral replication. E7 proteins encoded by the cancer-associated alpha human papillomaviruses have potent transforming activities, which together with E6, are necessary but not sufficient to render their host squamous epithelial cell tumorigenic. This article strives to provide a comprehensive summary of the published research studies on human papillomavirus E7 proteins.
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73
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Teng YC, Lee CF, Li YS, Chen YR, Hsiao PW, Chan MY, Lin FM, Huang HD, Chen YT, Jeng YM, Hsu CH, Yan Q, Tsai MD, Juan LJ. Histone demethylase RBP2 promotes lung tumorigenesis and cancer metastasis. Cancer Res 2013; 73:4711-21. [PMID: 23722541 DOI: 10.1158/0008-5472.can-12-3165] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The retinoblastoma binding protein RBP2 (KDM5A) is a histone demethylase that promotes gastric cancer cell growth and is enriched in drug-resistant lung cancer cells. In tumor-prone mice lacking the tumor suppressor gene RB or MEN1, genetic ablation of RBP2 can suppress tumor initiation, but the pathogenic breadth and mechanistic aspects of this effect relative to human tumors have not been defined. Here, we approached this question in the context of lung cancer. RBP2 was overexpressed in human lung cancer tissues where its depletion impaired cell proliferation, motility, migration, invasion, and metastasis. RBP2 oncogenicity relied on its demethylase and DNA-binding activities. RBP2 upregulated expression of cyclins D1 and E1 while suppressing the expression of cyclin-dependent kinase inhibitor p27 (CDKN1B), each contributing to RBP2-mediated cell proliferation. Expression microarray analyses revealed that RBP2 promoted expression of integrin-β1 (ITGB1), which is implicated in lung cancer metastasis. Mechanistic investigations established that RBP2 bound directly to the p27, cyclin D1, and ITGB1 promoters and that exogenous expression of cyclin D1, cyclin E1, or ITGB1 was sufficient to rescue proliferation or migration/invasion, respectively. Taken together, our results establish an oncogenic role for RBP2 in lung tumorigenesis and progression and uncover novel RBP2 targets mediating this role.
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Affiliation(s)
- Yu-Ching Teng
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang, Taipei, 115, Taiwan
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ARID4A and ARID4B regulate male fertility, a functional link to the AR and RB pathways. Proc Natl Acad Sci U S A 2013; 110:4616-21. [PMID: 23487765 DOI: 10.1073/pnas.1218318110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
ARID4A and ARID4B are homologous members of the ARID (AT-rich interaction domain) gene family. ARID4A and ARID4B physically interact with each other. ARID4A is a retinoblastoma (RB)-binding protein. Biological function of these interactions is still unknown. Here, we report that mice with complete deficiency of Arid4a, combined with haploinsufficiency of Arid4b (Arid4a(-/-)Arid4b(+/-)), showed progressive loss of male fertility, accompanied by hypogonadism and seminal vesicle agenesis/hypodysplasia. Arid4a and Arid4b are expressed mainly in Sertoli cells of testes, which implies that their roles in Sertoli cell function are to support spermatogenesis and create the impermeable blood-testis barrier. In fact, evaluation of germ cell development in the Arid4a(-/-)Arid4b(+/-) mice showed spermatogenic arrest at the stages of meiotic spermatocytes and postmeiotic haploid spermatids. Analysis of the integrity of the blood-testis barrier showed increased permeability of seminiferous tubules in the Arid4a(-/-)Arid4b(+/-) testes. Interestingly, phenotypic Sertoli cell dysfunction in the Arid4a(-/-)Arid4b(+/-) mice, including spermatogenic failures and the impaired blood-testis barrier, recapitulated the defects found in the Sertoli cell-specific androgen receptor (AR) knockout mice and the Sertoli cell-specific RB knockout mice. Investigation of the molecular mechanism identified several AR- and RB-responsive genes as downstream targets of ARID4A and ARID4B. Our results thus indicate that ARID4A and ARID4B function as transcriptional coactivators for AR and RB and play an integral part in the AR and RB regulatory pathways involved in the regulation of Sertoli cell function and male fertility.
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75
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Winter SF, Lukes L, Walker RC, Welch DR, Hunter KW. Allelic variation and differential expression of the mSIN3A histone deacetylase complex gene Arid4b promote mammary tumor growth and metastasis. PLoS Genet 2012; 8:e1002735. [PMID: 22693453 PMCID: PMC3364935 DOI: 10.1371/journal.pgen.1002735] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/12/2012] [Indexed: 12/26/2022] Open
Abstract
Accumulating evidence suggests that breast cancer metastatic progression is modified by germline polymorphism, although specific modifier genes have remained largely undefined. In the current study, we employ the MMTV-PyMT transgenic mouse model and the AKXD panel of recombinant inbred mice to identify AT-rich interactive domain 4B (Arid4b; NM_194262) as a breast cancer progression modifier gene. Ectopic expression of Arid4b promoted primary tumor growth in vivo as well as increased migration and invasion in vitro, and the phenotype was associated with polymorphisms identified between the AKR/J and DBA/2J alleles as predicted by our genetic analyses. Stable shRNA-mediated knockdown of Arid4b caused a significant reduction in pulmonary metastases, validating a role for Arid4b as a metastasis modifier gene. ARID4B physically interacts with the breast cancer metastasis suppressor BRMS1, and we detected differential binding of the Arid4b alleles to histone deacetylase complex members mSIN3A and mSDS3, suggesting that the mechanism of Arid4b action likely involves interactions with chromatin modifying complexes. Downregulation of the conserved Tpx2 gene network, which is comprised of many factors regulating cell cycle and mitotic spindle biology, was observed concomitant with loss of metastatic efficiency in Arid4b knockdown cells. Consistent with our genetic analysis and in vivo experiments in our mouse model system, ARID4B expression was also an independent predictor of distant metastasis-free survival in breast cancer patients with ER+ tumors. These studies support a causative role of ARID4B in metastatic progression of breast cancer.
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Affiliation(s)
- Scott F Winter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Lee CH, Alpert BO, Sankaranarayanan P, Alter O. GSVD comparison of patient-matched normal and tumor aCGH profiles reveals global copy-number alterations predicting glioblastoma multiforme survival. PLoS One 2012; 7:e30098. [PMID: 22291905 PMCID: PMC3264559 DOI: 10.1371/journal.pone.0030098] [Citation(s) in RCA: 30] [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: 09/06/2011] [Accepted: 12/09/2011] [Indexed: 11/18/2022] Open
Abstract
Despite recent large-scale profiling efforts, the best prognostic predictor of glioblastoma multiforme (GBM) remains the patient's age at diagnosis. We describe a global pattern of tumor-exclusive co-occurring copy-number alterations (CNAs) that is correlated, possibly coordinated with GBM patients' survival and response to chemotherapy. The pattern is revealed by GSVD comparison of patient-matched but probe-independent GBM and normal aCGH datasets from The Cancer Genome Atlas (TCGA). We find that, first, the GSVD, formulated as a framework for comparatively modeling two composite datasets, removes from the pattern copy-number variations (CNVs) that occur in the normal human genome (e.g., female-specific X chromosome amplification) and experimental variations (e.g., in tissue batch, genomic center, hybridization date and scanner), without a-priori knowledge of these variations. Second, the pattern includes most known GBM-associated changes in chromosome numbers and focal CNAs, as well as several previously unreported CNAs in >3% of the patients. These include the biochemically putative drug target, cell cycle-regulated serine/threonine kinase-encoding TLK2, the cyclin E1-encoding CCNE1, and the Rb-binding histone demethylase-encoding KDM5A. Third, the pattern provides a better prognostic predictor than the chromosome numbers or any one focal CNA that it identifies, suggesting that the GBM survival phenotype is an outcome of its global genotype. The pattern is independent of age, and combined with age, makes a better predictor than age alone. GSVD comparison of matched profiles of a larger set of TCGA patients, inclusive of the initial set, confirms the global pattern. GSVD classification of the GBM profiles of an independent set of patients validates the prognostic contribution of the pattern.
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Affiliation(s)
- Cheng H. Lee
- Scientific Computing and Imaging (SCI) Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Benjamin O. Alpert
- Scientific Computing and Imaging (SCI) Institute, University of Utah, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, United States of America
| | - Preethi Sankaranarayanan
- Scientific Computing and Imaging (SCI) Institute, University of Utah, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, United States of America
| | - Orly Alter
- Scientific Computing and Imaging (SCI) Institute, University of Utah, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
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77
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Gong W, Zhou T, Mo J, Perrett S, Wang J, Feng Y. Structural insight into recognition of methylated histone tails by retinoblastoma-binding protein 1. J Biol Chem 2012; 287:8531-40. [PMID: 22247551 DOI: 10.1074/jbc.m111.299149] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Retinoblastoma-binding protein 1 (RBBP1), also named AT-rich interaction domain containing 4A (ARID4A), is a tumor and leukemia suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. Although the involvement in epigenetic regulation is proposed to involve its chromobarrel and/or Tudor domains because of their potential binding to methylated histone tails, the structures of these domains and their interactions with methylated histone tails are still uncharacterized. In this work, we first found that RBBP1 contains five domains by bioinformatics analysis. Three of the five domains, i.e. chromobarrel, Tudor, and PWWP domains, are Royal Family domains, which potentially bind to methylated histone tails. We further purified these domains and characterized their interaction with methylated histone tails by NMR titration experiments. Among the three Royal Family domains, only the chromobarrel domain could recognize trimethylated H4K20 (with an affinity of ∼3 mm), as well as recognizing trimethylated H3K9, H3K27, and H3K36 (with lower affinities). The affinity could be further enhanced up to 15-fold by the presence of DNA. The structure of the chromobarrel domain of RBBP1 determined by NMR spectroscopy has an aromatic cage. Mutagenesis analysis identified four aromatic residues of the cage as the key residues for methylated lysine recognition. Our studies indicate that the chromobarrel domain of RBBP1 is responsible for recognizing methylated histone tails in chromatin remodeling and epigenetic regulation, which presents a significant advance in our understanding of the mechanism and relationship between RBBP1-related gene suppression and epigenetic regulation.
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Affiliation(s)
- Weibin Gong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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78
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Kaelin WG. Cancer and altered metabolism: potential importance of hypoxia-inducible factor and 2-oxoglutarate-dependent dioxygenases. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2011; 76:335-45. [PMID: 22089927 DOI: 10.1101/sqb.2011.76.010975] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Hypoxia-inducible factor (HIF) deregulation contributes to the Warburg effect. HIF consists of an unstable α subunit and a stable β subunit. In the presence of oxygen, HIFα becomes prolyl hydroxylated by members of the EglN (also called PHD) family, leading to its proteasomal degradation. Under hypoxic conditions, EglN activity is diminished and HIF levels rise. EglN1 is the primary HIF prolyl hydroxylase with EglN2 and EglN3 playing compensatory roles under certain conditions. EglN2 and EglN3 also appear to play HIF-independent roles in regulating cell proliferation and apoptosis, respectively. The EglNs belong to a large family of 2-oxoglutarate-dependent dioxygenases that includes the TET DNA hydroxymethylases and JmjC-containing histone demethylases. Members of this superfamily can be inhibited by endogenous metabolites, including fumarate and succinate, which accumulate in tumors that have fumarate hydratase (FH) or succinate dehydrogenase (SDH) mutations, respectively, as well as by the 2-hydroxyglutarate detected in isocitrate dehydrogenase (IDH) mutant tumors. 2-Oxoglutarate-dependent dioxygenases therefore provide a link between altered metabolism and cancer.
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Affiliation(s)
- W G Kaelin
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.
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79
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Rotili D, Mai A. Targeting Histone Demethylases: A New Avenue for the Fight against Cancer. Genes Cancer 2011; 2:663-79. [PMID: 21941621 DOI: 10.1177/1947601911417976] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In addition to genetic disorders, epigenetic alterations have been shown to be involved in cancer, through misregulation of histone modifications. Miswriting, misreading, and mis-erasing of histone acetylation as well as methylation marks can be actually associated with oncogenesis and tumor proliferation. Historically, methylation of Arg and Lys residues has been considered a stable, irreversible process due to the slow turnover of methyl groups in chromatin. The discovery in recent years of a large number of histone Lys demethylases (KDMs, belonging to either the amino oxidase or the JmjC family) totally changed this point of view and suggested a new role for dynamic histone methylation in biological processes. Since overexpression, alteration, or mutation of a number of KDMs has been found in many types of cancers, such enzymes could represent diagnostic tools as well as epigenetic targets to modulate for obtaining novel therapeutic weapons against cancer. The first little steps in this direction are described here.
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Affiliation(s)
- Dante Rotili
- Pasteur Institute-Cenci-Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
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80
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Cauchy P, Benoukraf T, Ferrier P. Processing ChIP-chip data: from the scanner to the browser. Methods Mol Biol 2011; 719:251-68. [PMID: 21370088 DOI: 10.1007/978-1-61779-027-0_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
High-density tiling microarrays are increasingly used in combination with chromatin immunoprecipitation (ChIP) assays to delineate the regulation of gene expression. Besides the technical challenges inherent to such complex biological assays, a critical, often daunting issue is the correct interpretation of the sheer amount of raw data generated by utilizing computational methods. Here, we go through the main steps of this intricate process, including optimized chromatin immunoprecipitation on chip (ChIP-chip) data normalization, peak detection, as well as quality control reports. We also describe convenient standalone software suites, including our own, CoCAS, which works on the latest generation of Agilent high-density arrays, allows dye-swap, replicate correlation, and easy connection with genome browsers for results interpretation, or with, e.g., other peak detection algorithms. Overall, the guidelines described herein provide an effective introduction to ChIP-chip technology and analysis.
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81
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Pointon JJ, Harvey D, Karaderi T, Appleton LH, Farrar C, Wordsworth BP. The histone demethylase JARID1A is associated with susceptibility to ankylosing spondylitis. Genes Immun 2011; 12:395-8. [DOI: 10.1038/gene.2011.23] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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82
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Abstract
The RB1 gene is the first tumor suppressor gene identified whose mutational inactivation is the cause of a human cancer, the pediatric cancer retinoblastoma. The 25 years of research since its discovery has not only illuminated a general role for RB1 in human cancer, but also its critical importance in normal development. Understanding the molecular function of the RB1 encoded protein, pRb, is a long-standing goal that promises to inform our understanding of cancer, its relationship to normal development, and possible therapeutic strategies to combat this disease. Achieving this goal has been difficult, complicated by the complexity of pRb and related proteins. The goal of this review is to explore the hypothesis that, at its core, the molecular function of pRb is to dynamically regulate the location-specific assembly or disassembly of protein complexes on the DNA in response to the output of various signaling pathways. These protein complexes participate in a variety of molecular processes relevant to DNA including gene transcription, DNA replication, DNA repair, and mitosis. Through regulation of these processes, RB1 plays a uniquely prominent role in normal development and cancer.
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Affiliation(s)
- Meenalakshmi Chinnam
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, USA
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83
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Duncan EM, Allis CD. Errors in erasure: links between histone lysine methylation removal and disease. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2011; 67:69-90. [PMID: 21141725 DOI: 10.1007/978-3-7643-8989-5_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Many studies have demonstrated that covalent histone modifications are dynamically regulated to cause both chemical and physical changes to the chromatin template. Such changes in the chromatin template lead to biologically significant consequences, including differential gene expression. Histone lysine methylation, in particular, has been shown to correlate with gene expression both positively and negatively, depending on the specific site and degree (i.e., mono-, di-, or tri-) of methylation within the histone sequence. Although genetic alterations in the proteins that establish, or "write," methyl modifications and their effect in various human pathologies have been documented, connections between the misregulation of proteins that remove, or "erase," histone methylation and disease have emerged more recently. Here we discuss three mechanisms through which histone methylation can be removed from the chromatin template. We describe how these "erasure" mechanisms are linked to pathways that are known to be misregulated in diseases, such as cancer. We further describe how errors in the removal of histone methylation can and do lead to human pathologies, both directly and indirectly.
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Affiliation(s)
- Elizabeth M Duncan
- Department of Neurobiology and Anatomy, University of Utah, 20 North 1900 East, Salt Lake City, UT 84132, USA
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84
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Suryadinata R, Sadowski M, Steel R, Sarcevic B. Cyclin-dependent kinase-mediated phosphorylation of RBP1 and pRb promotes their dissociation to mediate release of the SAP30·mSin3·HDAC transcriptional repressor complex. J Biol Chem 2010; 286:5108-18. [PMID: 21148318 DOI: 10.1074/jbc.m110.198473] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic cell cycle progression is mediated by phosphorylation of protein substrates by cyclin-dependent kinases (CDKs). A critical substrate of CDKs is the product of the retinoblastoma tumor suppressor gene, pRb, which inhibits G(1)-S phase cell cycle progression by binding and repressing E2F transcription factors. CDK-mediated phosphorylation of pRb alleviates this inhibitory effect to promote G(1)-S phase cell cycle progression. pRb represses transcription by binding to the E2F transactivation domain and recruiting the mSin3·histone deacetylase (HDAC) transcriptional repressor complex via the retinoblastoma-binding protein 1 (RBP1). RBP1 binds to the pocket region of pRb via an LXCXE motif and to the SAP30 subunit of the mSin3·HDAC complex and, thus, acts as a bridging protein in this multisubunit complex. In the present study we identified RBP1 as a novel CDK substrate. RBP1 is phosphorylated by CDK2 on serines 864 and 1007, which are N- and C-terminal to the LXCXE motif, respectively. CDK2-mediated phosphorylation of RBP1 or pRb destabilizes their interaction in vitro, with concurrent phosphorylation of both proteins leading to their dissociation. Consistent with these findings, RBP1 phosphorylation is increased during progression from G(1) into S-phase, with a concurrent decrease in its association with pRb in MCF-7 breast cancer cells. These studies provide new mechanistic insights into CDK-mediated regulation of the pRb tumor suppressor during cell cycle progression, demonstrating that CDK-mediated phosphorylation of both RBP1 and pRb induces their dissociation to mediate release of the mSin3·HDAC transcriptional repressor complex from pRb to alleviate transcriptional repression of E2F.
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Affiliation(s)
- Randy Suryadinata
- Cell Cycle and Cancer, St Vincent’s Institute of Medical Research, The University of Melbourne, Fitzroy, Melbourne, Victoria 3065, Australia
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85
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Abstract
Inactivation of the von Hippel-Lindau tumor suppressor protein (pVHL) causes the most common form of kidney cancer. pVHL is part of a complex that polyubiquitinates the alpha subunit of the heterodimeric transcription factor HIF. In the presence of oxygen, HIF1α is prolyl hydroxylated by EglN1 (also called PHD2); this modification recruits pVHL, which then targets HIF1α for proteasomal degradation. In hypoxic or pVHL-defective cells, HIF1α accumulates, binds to HIF1β, and transcriptionally activates genes such as VEGF. VEGF inhibitors and mTOR inhibitors, which indirectly affect HIF, are now approved for the treatment of kidney cancer. EglN1 is a 2-oxoglutarate-dependent dioxygenase; such enzymes can be inhibited with drug-like small molecules and EglN1 inhibitors are currently being tested for the treatment of anemia. EglN2 (PHD1) and EglN3 (PHD3), which are EglN1 paralogs, appear to play HIF-independent roles in cell proliferation and apoptosis, respectively, and are garnering interest as potential cancer targets. A number of JmjC-containing proteins, including RBP2 and PLU-1, are 2-oxoglutarate-dependent dioxygenases that demethylate histones. Preclinical data suggest that inhibition of RBP2 or PLU-1 would suppress tumor growth.
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Affiliation(s)
- William G Kaelin
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
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86
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Pedersen MT, Helin K. Histone demethylases in development and disease. Trends Cell Biol 2010; 20:662-71. [PMID: 20863703 DOI: 10.1016/j.tcb.2010.08.011] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 08/09/2010] [Accepted: 08/23/2010] [Indexed: 01/21/2023]
Abstract
Histone modifications serve as regulatory marks that are instrumental for the control of transcription and chromatin architecture. Strict regulation of gene expression patterns is crucial during development and differentiation, where diverse cell types evolve from common predecessors. Since the first histone lysine demethylase was discovered in 2004, a number of demethylases have been identified and implicated in the control of gene expression programmes and cell fate decisions. Histone demethylases are now emerging as important players in developmental processes and have been linked to human diseases such as neurological disorders and cancer.
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Affiliation(s)
- Marianne Terndrup Pedersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmark
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87
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Macdonald AH, Rodríguez L, Aceña I, Martínez-Fernández ML, Sánchez-Izquierdo D, Zuazo E, Martínez-Frías ML. Subtelomeric deletion of 12p: Description of a third case and review. Am J Med Genet A 2010; 152A:1561-6. [PMID: 20503336 DOI: 10.1002/ajmg.a.33401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Only 12 cases with a cytogenetically visible deletion of the short arm of chromosome 12 (12p) have been reported so far. The difference in clinical features observed in these patients indicates that there is no distinct phenotype associated with this short arm deletion, although the existence of a del(12p) syndrome was previously suggested. Besides those 12 reports, only two patients have been described with a subtelomeric 12p deletion; both present in the same family in which the son showed a mild phenotype of moderate mental retardation and behavioral problems and his carrier mother had no apparent phenotype. In this article, we describe the third known patient with a subtelomeric 12p deletion in a young boy with mental retardation and microcephaly, and review the literature.
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Affiliation(s)
- A H Macdonald
- Estudio Colaborativo Español de Malformaciones Congénitas, Centro de Investigación sobre Anomalías Congénitas, Instituto de Salud Carlos III, Ministerio de Sanidad y Consumo, Madrid, Spain.
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88
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Sharma SV, Lee DY, Li B, Quinlan MP, Takahashi F, Maheswaran S, McDermott U, Azizian N, Zou L, Fischbach MA, Wong KK, Brandstetter K, Wittner B, Ramaswamy S, Classon M, Settleman J. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 2010; 141:69-80. [PMID: 20371346 DOI: 10.1016/j.cell.2010.02.027] [Citation(s) in RCA: 1786] [Impact Index Per Article: 127.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 11/26/2009] [Accepted: 02/08/2010] [Indexed: 12/26/2022]
Abstract
Accumulating evidence implicates heterogeneity within cancer cell populations in the response to stressful exposures, including drug treatments. While modeling the acute response to various anticancer agents in drug-sensitive human tumor cell lines, we consistently detected a small subpopulation of reversibly "drug-tolerant" cells. These cells demonstrate >100-fold reduced drug sensitivity and maintain viability via engagement of IGF-1 receptor signaling and an altered chromatin state that requires the histone demethylase RBP2/KDM5A/Jarid1A. This drug-tolerant phenotype is transiently acquired and relinquished at low frequency by individual cells within the population, implicating the dynamic regulation of phenotypic heterogeneity in drug tolerance. The drug-tolerant subpopulation can be selectively ablated by treatment with IGF-1 receptor inhibitors or chromatin-modifying agents, potentially yielding a therapeutic opportunity. Together, these findings suggest that cancer cell populations employ a dynamic survival strategy in which individual cells transiently assume a reversibly drug-tolerant state to protect the population from eradication by potentially lethal exposures.
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Affiliation(s)
- Sreenath V Sharma
- Massachusetts General Hospital Cancer Center, 149 13th Street, Charlestown, MA 02129, USA
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89
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Zhou X, Sun H, Chen H, Zavadil J, Kluz T, Arita A, Costa M. Hypoxia induces trimethylated H3 lysine 4 by inhibition of JARID1A demethylase. Cancer Res 2010; 70:4214-21. [PMID: 20406991 DOI: 10.1158/0008-5472.can-09-2942] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Histone H3 lysine 4 (H3K4) trimethylation (H3K4me3) at the promoter region of genes has been linked to transcriptional activation. In the present study, we found that hypoxia (1% oxygen) increased H3K4me3 in both normal human bronchial epithelial Beas-2B cells and human lung carcinoma A549 cells. The increase of H3K4me3 from hypoxia was likely caused by the inhibition of H3K4 demethylating activity, as hypoxia still increased H3K4me3 in methionine-deficient medium. Furthermore, an in vitro histone demethylation assay showed that 1% oxygen decreased the activity of H3K4 demethylases in Beas-2B nuclear extracts because ambient oxygen tensions were required for the demethylation reaction to proceed. Hypoxia only minimally increased H3K4me3 in the BEAS-2B cells with knockdown of JARID1A, which is the major histone H3K4 demethylase in this cell line. However, the mRNA and protein levels of JARID1A were not affected by hypoxia. GeneChip and pathway analysis in JARID1A knockdown Beas-2B cells revealed that JARID1A regulates the expression of hundreds of genes involved in different cellular functions, including tumorigenesis. Knocking down of JARID1A increased H3K4me3 at the promoters of HMOX1 and DAF genes. Thus, these results indicate that hypoxia might target JARID1A activity, which in turn increases H3K4me3 at both the global and gene-specific levels, leading to the altered programs of gene expression and tumor progression.
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Affiliation(s)
- Xue Zhou
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York 10987, USA
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90
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Lei X, Gao XC, Zhang FC. [Progress on X-linked mental retardation related gene JARID1C]. YI CHUAN = HEREDITAS 2010; 32:205-10. [PMID: 20233696 DOI: 10.3724/sp.j.1005.2010.00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
JARID1C is one of the genes related to X-linked mental retardation. Its express product influences transcription and expression of the related genes in brain nervous system, and may be associated with human cognitive ability. Study on the functions of JARID1C not only helps to understand its molecular role in mental retardation and human cognitive ability, but also provides references for clinical diagnosis and prevention of mental retardation. This article reviews the progresses on JARID1C in location, isolation, physiological functions, and cognitive functions of its encoding product. The future re-search work of JARID1C is also discussed.
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Affiliation(s)
- Xu Lei
- Institute of Population and Health, College of Life Science, Northwest University, Xi'an 710069, China.
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91
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92
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Abstract
Epigenetic modifications are heritable chromatin alterations that contribute to the temporal and spatial interpretation of the genome. The epigenetic information is conveyed through a multitude of chemical modifications, including DNA methylation, reversible modifications of histones, and ATP-dependent nucleosomal remodeling. Deregulation of the epigenetic machinery contributes to the development of several pathologies, including cancer. Chromatin modifications are multiple and interdependent and they are dynamically modulated in the course of various biological processes. Combinations of chromatin modifications give rise to a complex code that is superimposed on the genetic code embedded into the DNA sequence to regulate cell function. This review addresses the role of epigenetic modifications in cancer, focusing primarily on histone methylation marks and the enzymes catalyzing their removal.
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Affiliation(s)
- Sotirios C Kampranis
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts 02111, USA
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93
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How the Rb tumor suppressor structure and function was revealed by the study of Adenovirus and SV40. Virology 2009; 384:274-84. [PMID: 19150725 DOI: 10.1016/j.virol.2008.12.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Accepted: 12/08/2008] [Indexed: 12/14/2022]
Abstract
The review recounts the history of how the study of the DNA tumor viruses including polyoma, SV40 and Adenovirus brought key insights into the structure and function of the Retinoblastoma protein (Rb). Knudsen's model of the two-hit hypothesis to explain patterns of hereditary and sporadic retinoblastoma provided the foundation for the tumor suppressor hypothesis that ultimately led to the cloning of the Rb gene. The discovery that SV40 and Adenovirus could cause tumors when inoculated into animals was startling not only because SV40 had contaminated the poliovirus vaccine and Adenovirus was a common cause of viral induced pneumonia but also because they provided an opportunity to study the genetics and biochemistry of cancer. Studies of mutant forms of these viruses led to the identification of the E1A and Large T antigen (LT) oncogenes and their small transforming elements including the Adenovirus Conserved Regions (CR), the SV40 J domain and the LxCxE motif. The immunoprecipitation studies that initially revealed the size and ultimately the identity of cellular proteins that could bind to these transforming elements were enabled by the widespread development of highly specific monoclonal antibodies against E1A and LT. The identification of Rb as an E1A and LT interacting protein quickly led to the cloning of p107, p130, p300, CBP, p400 and TRRAP and the concept that viral transformation was due, at least in part, to the perturbation of the function of normal cellular proteins. In addition, studies on the ability of E1A to transactivate the Adenovirus E2 promoter led to the cloning of the heterodimeric E2F and DP transcription factor and recognition that Rb repressed transcription of cellular genes required for cell cycle entry and progression. More recent studies have revealed how E1A and LT combine the activity of Rb and the other cellular associated proteins to perturb expression of many genes during viral infection and tumor formation.
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94
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Wu MY, Eldin KW, Beaudet AL. Identification of chromatin remodeling genes Arid4a and Arid4b as leukemia suppressor genes. J Natl Cancer Inst 2008; 100:1247-59. [PMID: 18728284 PMCID: PMC2528019 DOI: 10.1093/jnci/djn253] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background Leukemia evolves through a multistep process from premalignancy to malignancy. Epigenetic alterations, including histone modifications, have been proposed to play an important role in tumorigenesis. The involvement of two chromatin remodeling genes, retinoblastoma-binding protein 1 (Rbbp1/Arid4a) and Rbbp1-like 1 (Rbbp1l1/Arid4b), in leukemogenesis was not characterized. Methods The leukemic phenotype of mice deficient for Arid4a with or without haploinsufficiency for Arid4b was investigated by serially monitoring complete blood counts together with microscopic histologic analysis and flow cytometric analysis of bone marrow and spleen from the Arid4a−/− mice or Arid4a−/−Arid4b+/− mice. Regulation in bone marrow cells of downstream genes important for normal hematopoiesis was analyzed by reverse transcription–polymerase chain reaction. Genotypic effects on histone modifications were examined by western blotting and immunofluorescence analysis. All statistical tests were two-sided. Results Young (2–5 months old) Arid4a-deficient mice had ineffective blood cell production in all hematopoietic lineages. Beyond 5 months of age, the Arid4a−/− mice manifested monocytosis, accompanied by severe anemia and thrombocytopenia. These sick Arid4a−/− mice showed bone marrow failure with myelofibrosis associated with splenomegaly and hepatomegaly. Five of 42 Arid4a−/− mice and 10 of 12 Arid4a−/−Arid4b+/− mice progressed to acute myeloid leukemia (AML) and had rapid further increases of leukocyte counts. Expression of Hox genes (Hoxb3, Hoxb5, Hoxb6, and Hoxb8) was decreased in Arid4a-deficient bone marrow cells with or without Arid4b haploinsufficiency, and FoxP3 expression was reduced in Arid4a−/−Arid4b+/− bone marrow. Increases of histone trimethylation of H3K4, H3K9, and H4K20 (fold increases in trimethylation = 32, 95% confidence interval [CI] = 27 to 32; 45, 95% CI = 41 to 49; and 2.2, 95% CI = 1.7 to 2.7, respectively) were observed in the bone marrow of Arid4a-deficient mice. Conclusions Arid4a-deficient mice initially display ineffective hematopoiesis, followed by transition to chronic myelomonocytic leukemia (CMML)–like myelodysplastic/myeloproliferative disorder, and then transformation to AML. The disease processes in the Arid4a-deficient mice are very similar to the course of events in humans with CMML and AML. This mouse model has the potential to furnish additional insights into the role of epigenetic alterations in leukemogenesis, and it may be useful in developing novel pharmacological approaches to treatment of preleukemic and leukemic states.
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Affiliation(s)
- Mei-Yi Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Cloos PAC, Christensen J, Agger K, Helin K. Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev 2008; 22:1115-40. [PMID: 18451103 DOI: 10.1101/gad.1652908] [Citation(s) in RCA: 506] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The enzymes catalyzing lysine and arginine methylation of histones are essential for maintaining transcriptional programs and determining cell fate and identity. Until recently, histone methylation was regarded irreversible. However, within the last few years, several families of histone demethylases erasing methyl marks associated with gene repression or activation have been identified, underscoring the plasticity and dynamic nature of histone methylation. Recent discoveries have revealed that histone demethylases take part in large multiprotein complexes synergizing with histone deacetylases, histone methyltransferases, and nuclear receptors to control developmental and transcriptional programs. Here we review the emerging biochemical and biological functions of the histone demethylases and discuss their potential involvement in human diseases, including cancer.
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Affiliation(s)
- Paul A C Cloos
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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96
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Agger K, Christensen J, Cloos PAC, Helin K. The emerging functions of histone demethylases. Curr Opin Genet Dev 2008; 18:159-68. [PMID: 18281209 DOI: 10.1016/j.gde.2007.12.003] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 12/18/2007] [Indexed: 01/05/2023]
Abstract
Epigenetic information refers to heritable changes in gene function that are stable between cell divisions but which is not a result of changes in the DNA sequence. Part of the epigenetic mechanism has been ascribed to modifications of histones or DNA that affects the transcription of specific genes. In this context, post-translational modifications of histone tails, in particular methylation of lysines, are regarded as important for the storage of epigenetic information. Regulation of this information plays an important role during cellular differentiation where cells with different characteristic features evolve from the same ancestor, despite identical genomic material. The characterization of several enzymes catalyzing histone lysine methylation have supported this concept by showing the requirement of these enzymes for normal development and their involvement in diseases such as cancer. The recent identification of proteins with histone demethylase activity has shown that the methylated mark is much more dynamic than previously anticipated, thereby potentially challenging the concept of histone-methylation in stable epigenetic programming.
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Affiliation(s)
- Karl Agger
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
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97
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Roesch A, Mueller AM, Stempfl T, Moehle C, Landthaler M, Vogt T. RBP2-H1/JARID1B is a transcriptional regulator with a tumor suppressive potential in melanoma cells. Int J Cancer 2008; 122:1047-57. [PMID: 17973255 DOI: 10.1002/ijc.23211] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The RBP2-H1/JARID1B nuclear protein belongs to the ARID family of DNA-binding proteins and is a potential tumor suppressor that is lost during melanoma development. As we have recently shown, one physiological function of RBP2-H1/JARID1B is to exert cell cycle control via maintenance of active retinoblastoma protein. We now add new evidence that RBP2-H1/JARID1B can also directly regulate gene transcription in a reporter assay system, either alone or as part of a multimolecular complex together with the developmental transcription factors FOXG1b and PAX9. In melanoma cells, chromatin immunoprecipitation combined with promoter chip analysis (ChIP-on-chip) suggests a direct binding of re-expressed RBP2-H1/JARID1B to a multitude of human regulatory chromosomal elements (promoters, enhancers and introns). Among those, a set of 23 genes, including the melanoma relevant genes CDK6 and JAG-1 could be confirmed by cDNA microarray analyses to be differentially expressed after RBP2-H1/JARID1B re-expression. In contrast, in nonmelanoma HEK 293 cells, RBP2-H1/JARID1B overexpression only evokes a minor transcriptional response in cDNA microarray analyses. Because the transcriptional regulation in melanoma cells is accompanied by an inhibition of proliferation, an increase in caspase activity and a partial cell cycle arrest in G1/0, our data support an anti-tumorigenic role of RBP2-H1/JARID1B in melanocytic cells.
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Affiliation(s)
- Alexander Roesch
- Department of Dermatology, Regensburg University Medical Center, D-93053 Regensburg, Germany.
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98
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Abstract
Chromatin-modifying proteins mold the genome into areas that are accessible for transcriptional activity and areas that are transcriptionally silent. This epigenetic gene regulation allows for different transcriptional programs to be conducted in different cell types at different timepoints-despite the fact that all cells in the organism contain the same genetic information. A large amount of data gathered over the last decades has demonstrated that deregulation of chromatin-modifying proteins is etiologically involved in the development and progression of cancer. Here we discuss how epigenetic alterations influence cancer development and review known cancer-associated alterations in chromatin-modifying proteins.
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Affiliation(s)
- Cathrine K Fog
- Biotech Research & Innovation Centre and Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, DK- 2200 Copenhagen Denmark
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99
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Dick FA. Structure-function analysis of the retinoblastoma tumor suppressor protein - is the whole a sum of its parts? Cell Div 2007; 2:26. [PMID: 17854503 PMCID: PMC2082274 DOI: 10.1186/1747-1028-2-26] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Accepted: 09/13/2007] [Indexed: 12/28/2022] Open
Abstract
Biochemical analysis of the retinoblastoma protein's function has received considerable attention since it was cloned just over 20 years ago. During this time pRB has emerged as a key regulator of the cell division cycle and its ability to block proliferation is disrupted in the vast majority of human cancers. Much has been learned about the regulation of E2F transcription factors by pRB in the cell cycle. However, many questions remain unresolved and researchers continue to explore this multifunctional protein. In particular, understanding how its biochemical functions contribute to its role as a tumor suppressor remains to be determined. Since pRB has been shown to function as an adaptor molecule that links different proteins together, or to particular promoters, analyzing pRB by disrupting individual protein interactions holds tremendous promise in unraveling the intricacies of its function. Recently, crystal structures have reported how pRB interacts with some of its molecular partners. This information has created the possibility of rationally separating pRB functions by studying mutants that disrupt individual binding sites. This review will focus on literature that investigates pRB by isolating functions based on binding sites within the pocket domain. This article will also discuss the prospects for using this approach to further explore the unknown functions of pRB.
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100
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Benevolenskaya EV. Histone H3K4 demethylases are essential in development and differentiationThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2007; 85:435-43. [PMID: 17713579 DOI: 10.1139/o07-057] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lysine histone methylation is one of the most robust epigenetic marks and is essential for the regulation of multiple cellular processes. The methylation of Lys4 of histone H3 seems to be of particular significance. It is associated with active regions of the genome, and in Drosophila it is catalyzed by trithorax-group proteins that have become paradigms of developmental regulators at the level of chromatin. Like other histone methylation events, H3K4 methylation was considered irreversible until the identification of a large number of histone demethylases indicated that demethylation events play an important role in histone modification dynamics. However, the described demethylases had no strictly assigned biological functions and the identity of the histone demethylases that would contribute to the epigenetic changes specifying certain biological processes was unknown. Recently, several groups presented evidence that a family of 4 JmjC domain proteins results in the global changes of histone demethylation, and in elegant studies using model organisms, they demonstrated the importance of this family of histone demethylases in cell fate determination. All 4 proteins possess the demethylase activity specific to H3K4 and belong to the poorly described JARID1 protein family.
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Affiliation(s)
- Elizaveta V Benevolenskaya
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA.
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