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Patel LR, Stratton SA, McLaughlin M, Krause P, Allton K, Rivas AL, Barbosa D, Hart T, Barton MC. Genome-wide CRISPR-Cas9 screen analyzed by SLIDER identifies network of repressor complexes that regulate TRIM24. iScience 2023; 26:107126. [PMID: 37426340 PMCID: PMC10329041 DOI: 10.1016/j.isci.2023.107126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 03/12/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
TRIM24 is an oncogenic chromatin reader that is frequently overexpressed in human tumors and associated with poor prognosis. However, TRIM24 is rarely mutated, duplicated, or rearranged in cancer. This raises questions about how TRIM24 is regulated and what changes in its regulation are responsible for its overexpression. Here, we perform a genome-wide CRISPR-Cas9 screen by fluorescence-activated cell sorting (FACS) that nominated 220 negative regulators and elucidated a regulatory network that includes the KAP1 corepressor, CNOT deadenylase, and GID/CTLH E3 ligase. Knocking out required components of these three complexes caused TRIM24 overexpression, confirming their negative regulation of TRIM24. Our findings identify regulators of TRIM24 that nominate previously unexplored contexts for this oncoprotein in biology and disease. These findings were enabled by SLIDER, a new scoring system designed and vetted in our study as a broadly applicable tool for analysis of CRISPR screens performed by FACS.
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Affiliation(s)
- Lalit R. Patel
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX, USA
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sabrina A. Stratton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Megan McLaughlin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Krause
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, US
| | - Kendra Allton
- The Neurodegeneration Consortium, Therapeutics Discovery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrés López Rivas
- School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA
| | - Daniela Barbosa
- Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michelle C. Barton
- Division of Oncological Sciences, Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, US
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2
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Shah VV, Miao S, Krause PM, Stratton SA, Patel LR, Barton MC. Abstract IA017: An oncogenic histone reader promotes metaplastic TNBC. Cancer Res 2023. [DOI: 10.1158/1538-7445.agca22-ia017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Abstract
Human carcinosarcomas or metaplastic breast cancers (MpBC) are a rare, chemorefractory subclass of triple-negative breast cancers (TNBC). Conditional overexpression of histone reader Tripartite motif containing protein 24 (TRIM24) in mouse mammary epithelia (Trim24COE) led to spontaneous development of mammary carcinosarcoma tumors, lacking ER, PR and HER2, comprising 70% of all mammary tumors that developed with 40% penetrance. We saw strong correlation of Trim24COE carcinosarcoma tumors with human MpBC tumors and derived a conserved Trim24COE gene signature of Glycolysis, EMT and mTORC1 signaling pathways. Global and single-cell tumor profiling revealed Met as a direct oncogenic target of TRIM24, leading to aberrant PI3K/mTOR activation. To assess TRIM24-dependent metabolic alterations, we developed Trim24COE carcinosarcoma spheroid cultures. Tumor-derived Trim24COE carcinosarcoma spheroids exhibit TRIM24-dependent EMT and repressed cellular and mitochondrial ROS levels. We found that TRIM24 expression increased c-myc, NADPH and NRF2 levels to drive ROS repression and TRIM24-dependent cell survival under oxidative stress. TRIM24 mediates NRF2 activation at the level of chromatin structure activation, as shown by ATAC-seq of Trim24COE and shTrim24 carcinosarcoma spheroids. These in vivo and ex vivo models of metaplastic TNBC offer a platform for mechanistic discovery and nomination of potential therapeutic avenues for this highly malignant TNBC subtype.
Citation Format: Vrutant V. Shah, Shucheng Miao, Patrick M. Krause, Sabrina A. Stratton, Lalit R. Patel, Michelle C. Barton. An oncogenic histone reader promotes metaplastic TNBC [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr IA017.
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3
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Abstract
Activation of p53 regulates a transcriptional program that can cause cell cycle arrest, senescence, apoptosis, and ferroptosis, which are potent tumor suppressive mechanisms. Unexpectedly, Makino and colleagues show in this issue of Cancer Research that the constitutive activation of p53 in murine hepatocytes leads to tumor development. Detailed analyses indicate that p53 activation leads to loss of hepatocytes, increased expression of chemokines and humoral factors, and expansion of the hepatic progenitor cell population. These progenitor cells are highly proliferative, show chromosomal instability, and eventually transform. In chronic liver disease in humans, activation of p53 is associated with increased liver cancer development. This study highlights the complexity and non-cell autonomous nature of the physiologic p53 response. See related article by Makino et al., p. 2860.
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Affiliation(s)
- Michelle C Barton
- Division of Oncological Sciences, Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Guillermina Lozano
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
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4
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Kim MP, Li X, Deng J, Zhang Y, Dai B, Allton KL, Hughes TG, Siangco C, Augustine JJ, Kang Y, McDaniel JM, Xiong S, Koay EJ, McAllister F, Bristow CA, Heffernan TP, Maitra A, Liu B, Barton MC, Wasylishen AR, Fleming JB, Lozano G. Oncogenic KRAS Recruits an Expansive Transcriptional Network through Mutant p53 to Drive Pancreatic Cancer Metastasis. Cancer Discov 2021; 11:2094-2111. [PMID: 33839689 DOI: 10.1158/2159-8290.cd-20-1228] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/19/2021] [Accepted: 03/26/2021] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is almost uniformly fatal and characterized by early metastasis. Oncogenic KRAS mutations prevail in 95% of PDAC tumors and co-occur with genetic alterations in the TP53 tumor suppressor in nearly 70% of patients. Most TP53 alterations are missense mutations that exhibit gain-of-function phenotypes that include increased invasiveness and metastasis, yet the extent of direct cooperation between KRAS effectors and mutant p53 remains largely undefined. We show that oncogenic KRAS effectors activate CREB1 to allow physical interactions with mutant p53 that hyperactivate multiple prometastatic transcriptional networks. Specifically, mutant p53 and CREB1 upregulate the prometastatic, pioneer transcription factor FOXA1, activating its transcriptional network while promoting WNT/β-catenin signaling, together driving PDAC metastasis. Pharmacologic CREB1 inhibition dramatically reduced FOXA1 and β-catenin expression and dampened PDAC metastasis, identifying a new therapeutic strategy to disrupt cooperation between oncogenic KRAS and mutant p53 to mitigate metastasis. SIGNIFICANCE: Oncogenic KRAS and mutant p53 are the most commonly mutated oncogene and tumor suppressor gene in human cancers, yet direct interactions between these genetic drivers remain undefined. We identified a cooperative node between oncogenic KRAS effectors and mutant p53 that can be therapeutically targeted to undermine cooperation and mitigate metastasis.This article is highlighted in the In This Issue feature, p. 1861.
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Affiliation(s)
- Michael P Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xinqun Li
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jenying Deng
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yun Zhang
- Department of Pharmaceutical Sciences, Texas Southern University, Houston, Texas
| | - Bingbing Dai
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kendra L Allton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tara G Hughes
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christian Siangco
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jithesh J Augustine
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ya'an Kang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joy M McDaniel
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shunbin Xiong
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eugene J Koay
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Florencia McAllister
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher A Bristow
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anirban Maitra
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michelle C Barton
- Division of Oncological Sciences, Oregon Health and Science University School of Medicine, Portland, Oregon
| | - Amanda R Wasylishen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason B Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Guillermina Lozano
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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5
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Yang DS, Saeedi A, Davtyan A, Fathi M, Sherman MB, Safari MS, Klindziuk A, Barton MC, Varadarajan N, Kolomeisky AB, Vekilov PG. Mesoscopic protein-rich clusters host the nucleation of mutant p53 amyloid fibrils. Proc Natl Acad Sci U S A 2021; 118:e2015618118. [PMID: 33653952 PMCID: PMC7958401 DOI: 10.1073/pnas.2015618118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The protein p53 is a crucial tumor suppressor, often called "the guardian of the genome"; however, mutations transform p53 into a powerful cancer promoter. The oncogenic capacity of mutant p53 has been ascribed to enhanced propensity to fibrillize and recruit other cancer fighting proteins in the fibrils, yet the pathways of fibril nucleation and growth remain obscure. Here, we combine immunofluorescence three-dimensional confocal microscopy of human breast cancer cells with light scattering and transmission electron microscopy of solutions of the purified protein and molecular simulations to illuminate the mechanisms of phase transformations across multiple length scales, from cellular to molecular. We report that the p53 mutant R248Q (R, arginine; Q, glutamine) forms, both in cancer cells and in solutions, a condensate with unique properties, mesoscopic protein-rich clusters. The clusters dramatically diverge from other protein condensates. The cluster sizes are decoupled from the total cluster population volume and independent of the p53 concentration and the solution concentration at equilibrium with the clusters varies. We demonstrate that the clusters carry out a crucial biological function: they host and facilitate the nucleation of amyloid fibrils. We demonstrate that the p53 clusters are driven by structural destabilization of the core domain and not by interactions of its extensive unstructured region, in contradistinction to the dense liquids typical of disordered and partially disordered proteins. Two-step nucleation of mutant p53 amyloids suggests means to control fibrillization and the associated pathologies through modifying the cluster characteristics. Our findings exemplify interactions between distinct protein phases that activate complex physicochemical mechanisms operating in biological systems.
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Affiliation(s)
- David S Yang
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Arash Saeedi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Aram Davtyan
- Department of Chemistry, Rice University, Houston, TX 77251
| | - Mohsen Fathi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
| | - Mohammad S Safari
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | | | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Navin Varadarajan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, TX 77251
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77251
| | - Peter G Vekilov
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204;
- Department of Chemistry, University of Houston, Houston, TX 77204
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6
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Jung YS, Stratton SA, Lee SH, Kim MJ, Jun S, Zhang J, Zheng B, Cervantes CL, Cha JH, Barton MC, Park JI. TMEM9-v-ATPase Activates Wnt/β-Catenin Signaling Via APC Lysosomal Degradation for Liver Regeneration and Tumorigenesis. Hepatology 2021; 73:776-794. [PMID: 32380568 PMCID: PMC7647947 DOI: 10.1002/hep.31305] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS How Wnt signaling is orchestrated in liver regeneration and tumorigenesis remains elusive. Recently, we identified transmembrane protein 9 (TMEM9) as a Wnt signaling amplifier. APPROACH AND RESULTS TMEM9 facilitates v-ATPase assembly for vesicular acidification and lysosomal protein degradation. TMEM9 is highly expressed in regenerating liver and hepatocellular carcinoma (HCC) cells. TMEM9 expression is enriched in the hepatocytes around the central vein and acutely induced by injury. In mice, Tmem9 knockout impairs hepatic regeneration with aberrantly increased adenomatosis polyposis coli (Apc) and reduced Wnt signaling. Mechanistically, TMEM9 down-regulates APC through lysosomal protein degradation through v-ATPase. In HCC, TMEM9 is overexpressed and necessary to maintain β-catenin hyperactivation. TMEM9-up-regulated APC binds to and inhibits nuclear translocation of β-catenin, independent of HCC-associated β-catenin mutations. Pharmacological blockade of TMEM9-v-ATPase or lysosomal degradation suppresses Wnt/β-catenin through APC stabilization and β-catenin cytosolic retention. CONCLUSIONS Our results reveal that TMEM9 hyperactivates Wnt signaling for liver regeneration and tumorigenesis through lysosomal degradation of APC.
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Affiliation(s)
- Youn-Sang Jung
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX.,Department of Life ScienceChung-Ang UniversitySeoulSouth Korea
| | - Sabrina A Stratton
- Department of Epigenetics and Molecular CarcinogenesisThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Sung Ho Lee
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Moon-Jong Kim
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Sohee Jun
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Jie Zhang
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Biyun Zheng
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Christopher L Cervantes
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Jong-Ho Cha
- Department of Biomedical SciencesCollege of MedicineInha UniversityIncheonSouth Korea
| | - Michelle C Barton
- Department of Epigenetics and Molecular CarcinogenesisThe University of Texas MD Anderson Cancer CenterHoustonTX.,Graduate School of Biomedical SciencesThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Jae-Il Park
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX.,Graduate School of Biomedical SciencesThe University of Texas MD Anderson Cancer CenterHoustonTX.,Program in Genetics and EpigeneticsThe University of Texas MD Anderson Cancer CenterHoustonTX
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7
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Wasylishen AR, Sun C, Moyer SM, Qi Y, Chau GP, Aryal NK, McAllister F, Kim MP, Barton MC, Estrella JS, Su X, Lozano G. Daxx maintains endogenous retroviral silencing and restricts cellular plasticity in vivo. Sci Adv 2020; 6:eaba8415. [PMID: 32821827 PMCID: PMC7406367 DOI: 10.1126/sciadv.aba8415] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/18/2020] [Indexed: 05/26/2023]
Abstract
Tumor sequencing studies have emphasized the role of epigenetics and altered chromatin homeostasis in cancer. Mutations in DAXX, which encodes a chaperone for the histone 3.3 variant, occur in 25% of pancreatic neuroendocrine tumors (PanNETs). To advance our understanding of physiological functions of Daxx, we developed a conditional Daxx allele in mice. We demonstrate that Daxx loss is well tolerated in the pancreas but creates a permissive transcriptional state that cooperates with environmental stress (inflammation) and other genetic lesions (Men1 loss) to alter gene expression and cell state, impairing pancreas recovery from inflammatory stress in vivo. The transcriptional changes are associated with dysregulation of endogenous retroviral elements (ERVs), and dysregulation of endogenous genes near ERVs is also observed in human PanNETs with DAXX mutations. Our results reveal a physiologic function of DAXX, provide a mechanism associated with impaired tissue regeneration and tumorigenesis, and expand our understanding of ERV regulation in somatic cells.
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Affiliation(s)
- Amanda R. Wasylishen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chang Sun
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Sydney M. Moyer
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yuan Qi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gilda P. Chau
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Neeraj K. Aryal
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael P. Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michelle C. Barton
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeannelyn S. Estrella
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guillermina Lozano
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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8
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Kumar J, Kaur G, Ren R, Lu Y, Lin K, Li J, Huang Y, Patel A, Barton MC, Macfarlan T, Zhang X, Cheng X. KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells. NAR Cancer 2020; 2:zcaa007. [PMID: 32743551 PMCID: PMC7380489 DOI: 10.1093/narcan/zcaa007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/25/2020] [Accepted: 04/30/2020] [Indexed: 01/31/2023] Open
Abstract
Interactions of KRAB (Krüppel-associated box)-associated protein KAP1 [also known as TRIM28 (tripartite motif containing protein 28)] with DNA-binding KRAB zinc finger (KRAB-ZF) proteins silence many transposable elements during embryogenesis. However, in some cancers, TRIM28 is upregulated and interacts with different partners, many of which are transcription regulators such as EZH2 in MCF7 cells, to form abnormal repressive or activating complexes that lead to misregulation of genes. We ask whether a KRAB domain-the TRIM28 interaction domain present in native binding partners of TRIM28 that mediate repression of transposable elements-could be used as a tool molecule to disrupt aberrant TRIM28 complexes. Expression of KRAB domain containing fragments from a KRAB-ZF protein (ZFP568) in MCF7 cells, without the DNA-binding zinc fingers, inhibited TRIM28-EZH2 interactions and caused degradation of both TRIM28 and EZH2 proteins as well as other components of the EZH2-associated polycomb repressor 2 complex. In consequence, the product of EZH2 enzymatic activity, trimethylation of histone H3 lysine 27 level, was significantly reduced. The expression of a synthetic KRAB domain significantly inhibits the growth of breast cancer cells (MCF7) but has no effect on normal (immortalized) human mammary epithelial cells (MCF10a). Further, we found that TRIM28 is a positive regulator of TRIM24 protein levels, as observed previously in prostate cancer cells, and expression of the KRAB domain also lowered TRIM24 protein. Importantly, reduction of TRIM24 levels, by treatment with either the KRAB domain or a small-molecule degrader targeted to TRIM24, is accompanied by an elevated level of tumor suppressor p53. Taken together, this study reveals a novel mechanism for a TRIM28-associated protein stability network and establishes TRIM28 as a potential therapeutic target in cancers where TRIM28 is elevated. Finally, we discuss a potential mechanism of KRAB-ZF gene expression controlled by a regulatory feedback loop of TRIM28-KRAB.
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Affiliation(s)
- Janani Kumar
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Todd Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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9
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Liang J, Wang L, Wang C, Shen J, Su B, Marisetty AL, Fang D, Kassab C, Jeong KJ, Zhao W, Lu Y, Jain AK, Zhou Z, Liang H, Sun SC, Lu C, Xu ZX, Yu Q, Shao S, Chen X, Gao M, Claret FX, Ding Z, Chen J, Chen P, Barton MC, Peng G, Mills GB, Heimberger AB. Verteporfin Inhibits PD-L1 through Autophagy and the STAT1-IRF1-TRIM28 Signaling Axis, Exerting Antitumor Efficacy. Cancer Immunol Res 2020; 8:952-965. [PMID: 32265228 DOI: 10.1158/2326-6066.cir-19-0159] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 10/07/2019] [Accepted: 04/02/2020] [Indexed: 12/30/2022]
Abstract
Programmed cell death 1 ligand 1 (PD-L1) is a key driver of tumor-mediated immune suppression, and targeting it with antibodies can induce therapeutic responses. Given the costs and associated toxicity of PD-L1 blockade, alternative therapeutic strategies are needed. Using reverse-phase protein arrays to assess drugs in use or likely to enter trials, we performed a candidate drug screen for inhibitors of PD-L1 expression and identified verteporfin as a possible small-molecule inhibitor. Verteporfin suppressed basal and IFN-induced PD-L1 expression in vitro and in vivo through Golgi-related autophagy and disruption of the STAT1-IRF1-TRIM28 signaling cascade, but did not affect the proinflammatory CIITA-MHC II cascade. Within the tumor microenvironment, verteporfin inhibited PD-L1 expression, which associated with enhanced T-lymphocyte infiltration. Inhibition of chromatin-associated enzyme PARP1 induced PD-L1 expression in high endothelial venules (HEV) in tumors and, when combined with verteporfin, enhanced therapeutic efficacy. Thus, verteporfin effectively targets PD-L1 through transcriptional and posttranslational mechanisms, representing an alternative therapeutic strategy for targeting PD-L1.
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Affiliation(s)
- Jiyong Liang
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Lulu Wang
- Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chao Wang
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Obstetrics & Gynecology, Obstetrics & Gynecology Hospital of Fu Dan University, Shanghai, China
| | - Jianfeng Shen
- Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bojin Su
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anantha L Marisetty
- Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dexing Fang
- Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cynthia Kassab
- Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kang Jin Jeong
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei Zhao
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yiling Lu
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Abhinav K Jain
- Genes and Development Graduate Program, Department of Epigenetics and Molecular Carcinogenesis, and Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhicheng Zhou
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Han Liang
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shao-Cong Sun
- Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Changming Lu
- The Institute of Oral Health, School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhi-Xiang Xu
- Division of Hematology and Oncology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Qinghua Yu
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shan Shao
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - XiaoHua Chen
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Meng Gao
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Francois X Claret
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhiyong Ding
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jian Chen
- Department of General Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Province, Hangzhou, China
| | - Pingsheng Chen
- Department of Pathology, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Michelle C Barton
- Genes and Development Graduate Program, Department of Epigenetics and Molecular Carcinogenesis, and Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guang Peng
- Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gordon B Mills
- Cell, Developmental & Cancer Biology, Oregon Health and Sciences University, Portland, Oregon.
| | - Amy B Heimberger
- Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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10
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Gallardo M, Malaney P, Aitken MJL, Zhang X, Link TM, Shah V, Alybayev S, Wu MH, Pageon LR, Ma H, Jacamo R, Yu L, Xu-Monette ZY, Steinman H, Lee HJ, Sarbassov D, Rapado I, Barton MC, Martinez-Lopez J, Bueso-Ramos C, Young KH, Post SM. Uncovering the Role of RNA-Binding Protein hnRNP K in B-Cell Lymphomas. J Natl Cancer Inst 2020; 112:95-106. [PMID: 31077320 PMCID: PMC7489062 DOI: 10.1093/jnci/djz078] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 03/22/2019] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is an RNA-binding protein that is aberrantly expressed in cancers. We and others have previously shown that reduced hnRNP K expression downmodulates tumor-suppressive programs. However, overexpression of hnRNP K is the more commonly observed clinical phenomenon, yet its functional consequences and clinical significance remain unknown. METHODS Clinical implications of hnRNP K overexpression were examined through immunohistochemistry on samples from patients with diffuse large B-cell lymphoma who did not harbor MYC alterations (n = 75). A novel transgenic mouse model that overexpresses hnRNP K specifically in B cells was generated to directly examine the role of hnRNP K overexpression in mice (three transgenic lines). Molecular consequences of hnRNP K overexpression were determined through proteomics, formaldehyde-RNA-immunoprecipitation sequencing, and biochemical assays. Therapeutic response to BET-bromodomain inhibition in the context of hnRNP K overexpression was evaluated in vitro and in vivo (n = 3 per group). All statistical tests were two-sided. RESULTS hnRNP K is overexpressed in diffuse large B-cell lymphoma patients without MYC genomic alterations. This overexpression is associated with dismal overall survival and progression-free survival (P < .001). Overexpression of hnRNP K in transgenic mice resulted in the development of lymphomas and reduced survival (P < .001 for all transgenic lines; Line 171[n = 30]: hazard ratio [HR] = 64.23, 95% confidence interval [CI] = 26.1 to 158.0; Line 173 [n = 31]: HR = 25.27, 95% CI = 10.3 to 62.1; Line 177 [n = 25]: HR = 119.5, 95% CI = 42.7 to 334.2, compared with wild-type mice). Clinical samples, mouse models, global screening assays, and biochemical studies revealed that hnRNP K's oncogenic potential stems from its ability to posttranscriptionally and translationally regulate MYC. Consequently, Hnrnpk overexpression renders cells sensitive to BET-bromodomain-inhibition in both in vitro and transplantation models, which represents a strategy for mitigating hnRNP K-mediated c-Myc activation in patients. CONCLUSION Our findings indicate that hnRNP K is a bona fide oncogene when overexpressed and represents a novel mechanism for c-Myc activation in the absence of MYC lesions.
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Affiliation(s)
- Miguel Gallardo
- Department of Leukemia
- H12O-CNIO Haematological Malignancies Clinical Research Unit, Clinical Research Programme, CNIO, Madrid, Spain
| | | | - Marisa J L Aitken
- Department of Leukemia
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
| | | | | | - Vrutant Shah
- Department of Epigenetics and Molecular Carcinogenesis
| | | | | | | | | | | | - Li Yu
- Department of Hematopathology
| | | | | | - Hun Ju Lee
- Department of Lymphoma and Myeloma The University of Texas, MD Anderson Cancer Center, Houston, TX
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11
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Manshouri R, Coyaud E, Kundu ST, Peng DH, Stratton SA, Alton K, Bajaj R, Fradette JJ, Minelli R, Peoples MD, Carugo A, Chen F, Bristow C, Kovacs JJ, Barton MC, Heffernan T, Creighton CJ, Raught B, Gibbons DL. ZEB1/NuRD complex suppresses TBC1D2b to stimulate E-cadherin internalization and promote metastasis in lung cancer. Nat Commun 2019; 10:5125. [PMID: 31719531 PMCID: PMC6851102 DOI: 10.1038/s41467-019-12832-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/29/2019] [Indexed: 02/08/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death worldwide, due in part to the propensity of lung cancer to metastasize. Aberrant epithelial-to-mesenchymal transition (EMT) is a proposed model for the initiation of metastasis. During EMT cell-cell adhesion is reduced allowing cells to dissociate and invade. Of the EMT-associated transcription factors, ZEB1 uniquely promotes NSCLC disease progression. Here we apply two independent screens, BioID and an Epigenome shRNA dropout screen, to define ZEB1 interactors that are critical to metastatic NSCLC. We identify the NuRD complex as a ZEB1 co-repressor and the Rab22 GTPase-activating protein TBC1D2b as a ZEB1/NuRD complex target. We find that TBC1D2b suppresses E-cadherin internalization, thus hindering cancer cell invasion and metastasis. Non-small cell lung cancer (NSCLC) is often associated with metastasis to the lungs. Here, the authors perform independent screens and identify NuRD as a co-repressor of ZEB1, and demonstrate TBC1D2b as a downstream target of ZEB1/NuRD complex regulating NSCLC metastasis.
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Affiliation(s)
- Roxsan Manshouri
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Etienne Coyaud
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Samrat T Kundu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David H Peng
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sabrina A Stratton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kendra Alton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Rakhee Bajaj
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jared J Fradette
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Rosalba Minelli
- Department of Cancer Genomics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Michael D Peoples
- Department of Cancer Genomics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alessandro Carugo
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Fengju Chen
- Department of Medicine and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Christopher Bristow
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jeffrey J Kovacs
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Tim Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chad J Creighton
- Department of Medicine and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Brian Raught
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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12
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Patel LR, Mitsch J, Figueredo GP, Quinlan P, Jordan LB, Purdie CA, Krishnamurthy S, Barton MC, Thompson AM. Abstract 787: Cytosolic TRIM24 characterizes an aggressive subset of ER- PR- and TP53 mutant breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Tripartite Motif Containing 24 (TRIM24) is a PhD/Bromodomain containing steroid receptor co-activator that targets p53 for proteosomal degradation, transforms human mammary epithelial cells, and promotes treatment resistance in preclinical models. While bromodomain inhibitors and proteolysis targeting chimeras have been developed against TRIM24, the disease subtype it is most relevant to remains under explored. In this study, we characterize a uniquely annotated cohort of invasive ductal carcinomas for tumor expression of TRIM24 protein by immunohistochemistry (IHC) to assess its relationship with molecular and clinicopathological features.
Methods: Tissue microarrays (TMAs) representing 198 tumors with 6 cores/tumor were obtained from the Tayside Biospecimen Repository and stained by IHC for TRIM24. TMAs were scored for nuclear and cytosolic intensity and the proportion of tumor cells with staining. These values were combined into Histo-scores (H-Scores) and averaged as a semi-quantitative metric for tumor TRIM24 expression. Statistical associations between TRIM24 H-Scores, clinicopathological annotations, and existing molecular profiles generated from the same TMA were determined using SciPy and SPSS.
Results: TRIM24 has four distinct expression patterns in the 170 tumors with scorable cores on the TMA: nuclear (55), cytosolic (38), nuclear and cytosolic (35), and negative (42). Non-parametric analysis revealed associations between TRIM24 expression pattern and ER (χ2=21.3, p=0.000), PR (χ2=14.8, p=0.002), invasive grade (χ2=14.9, p=0.021), and TP53 mutation (χ2=9.55, p=0.023). No significant association was found with HER2 (χ2=1.51, p=0.68). Higher nuclear H-scores are observed in ER+ (p=0.0008) and PR+ (p=0.001) tumors. Higher cytosolic but not nuclear H-scores are observed in Grade 3 (p=0.003), triple negative (TNBC, p=0.004), and TP53 mutant (p=0.0289) cases. Kaplan-Meier analysis revealed high cytosolic (p=0.037) but not nuclear (p=0.601) H-scores associated with poor survival in ER- patients. No significant survival difference was found in ER+ patients stratified by nuclear (p=0.781) or cytosolic (p=0.683) H-scores. Similar analysis of TNBC was underpowered. TP53 mutant (p=0.142) but not TP53 wild type (p=0.378) disease with high cytosolic H-scores trend toward diminished survival. No such trend is observed in cases stratified by nuclear H-scores and TP53 status.
Conclusions: TRIM24 is overexpressed in most human breast cancers. Nuclear expression is more common in ER+/PR+ tumors but does not stratify outcome. Cytosolic expression occurs in Grade 3, ER-, and TP53 mutant tumors and associates with poor clinical outcome in ER- disease. This suggests TRIM24 may be a more relevant drug target in ER-/PR- than luminal breast cancer and emphasizes the need for studies investigating the cytosolic functions of TRIM24 in ER-/PR- and TP53-mutant breast cancer.
Citation Format: Lalit R. Patel, Jurgen Mitsch, Grazziela P. Figueredo, Philip Quinlan, Lee B. Jordan, Colin A. Purdie, Savitri Krishnamurthy, Michelle C. Barton, Alastair M. Thompson. Cytosolic TRIM24 characterizes an aggressive subset of ER- PR- and TP53 mutant breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 787.
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Affiliation(s)
- Lalit R. Patel
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jurgen Mitsch
- 2University of Nottingham, Nottingham, United Kingdom
| | | | | | - Lee B. Jordan
- 3Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Colin A. Purdie
- 3Ninewells Hospital and Medical School, Dundee, United Kingdom
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13
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Appikonda S, Thakkar KN, Shah PK, Dent SYR, Andersen JN, Barton MC. Cross-talk between chromatin acetylation and SUMOylation of tripartite motif-containing protein 24 (TRIM24) impacts cell adhesion. J Biol Chem 2018. [PMID: 29523690 DOI: 10.1074/jbc.ra118.002233] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Proteins with domains that recognize and bind post-translational modifications (PTMs) of histones are collectively termed epigenetic readers. Numerous interactions between specific reader protein domains and histone PTMs and their regulatory outcomes have been reported, but little is known about how reader proteins may in turn be modulated by these interactions. Tripartite motif-containing protein 24 (TRIM24) is a histone reader aberrantly expressed in multiple cancers. Here, our investigation revealed functional cross-talk between histone acetylation and TRIM24 SUMOylation. Binding of TRIM24 to chromatin via its tandem PHD-bromodomain, which recognizes unmethylated lysine 4 and acetylated lysine 23 of histone H3 (H3K4me0/K23ac), led to TRIM24 SUMOylation at lysine residues 723 and 741. Inactivation of the bromodomain, either by mutation or with a small-molecule inhibitor, IACS-9571, abolished TRIM24 SUMOylation. Conversely, inhibition of histone deacetylation markedly increased TRIM24's interaction with chromatin and its SUMOylation. Of note, gene expression profiling of MCF7 cells expressing WT versus SUMO-deficient TRIM24 identified cell adhesion as the major pathway regulated by the cross-talk between chromatin acetylation and TRIM24 SUMOylation. In conclusion, our findings establish a new link between histone H3 acetylation and SUMOylation of the reader protein TRIM24, a functional connection that may bear on TRIM24's oncogenic function and may inform future studies of PTM cross-talk between histones and epigenetic regulators.
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Affiliation(s)
- Srikanth Appikonda
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, Houston, Texas 77030
| | - Kaushik N Thakkar
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, Houston, Texas 77030; University of Texas M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030
| | - Parantu K Shah
- Institute for Applied Cancer Science, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, Houston, Texas 77030; University of Texas M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030
| | - Jannik N Andersen
- Institute for Applied Cancer Science, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, Houston, Texas 77030; University of Texas M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030.
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14
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Xi Y, Shi J, Li W, Tanaka K, Allton KL, Richardson D, Li J, Franco HL, Nagari A, Malladi VS, Coletta LD, Simper MS, Keyomarsi K, Shen J, Bedford MT, Shi X, Barton MC, Kraus WL, Li W, Dent SYR. Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. BMC Genomics 2018; 19:150. [PMID: 29458327 PMCID: PMC5819162 DOI: 10.1186/s12864-018-4533-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 02/05/2018] [Indexed: 12/19/2022] Open
Abstract
Background Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy. Results To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells. Discussion Using combinatorial patterns of distinct histone modification signals, we defined subtype-specific chromatin signatures to nominate potential biomarkers. This approach identified AFAP1-AS1 as a triple negative breast cancer-specific gene associated with cell proliferation and epithelial-mesenchymal-transition. In addition, our chromatin mapping data in basal TNBC cell lines are consistent with gene expression patterns in TCGA that indicate decreased activity of the androgen receptor pathway but increased activity of the vitamin D biosynthesis pathway. Conclusions Together, these datasets provide a comprehensive resource for histone modification profiles that define epigenetic landscapes and reveal key chromatin signatures in breast cancer cell line subtypes with potential to identify novel and actionable targets for treatment. Electronic supplementary material The online version of this article (10.1186/s12864-018-4533-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanxin Xi
- Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jiejun Shi
- Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Wenqian Li
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Kaori Tanaka
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Kendra L Allton
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Dana Richardson
- The Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Jing Li
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Hector L Franco
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Venkat S Malladi
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Luis Della Coletta
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Melissa S Simper
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Khandan Keyomarsi
- The Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Jianjun Shen
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Mark T Bedford
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Xiaobing Shi
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Michelle C Barton
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Wei Li
- Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Sharon Y R Dent
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
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15
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Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell Rep 2018; 19:875-889. [PMID: 28445736 DOI: 10.1016/j.celrep.2017.03.078] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/18/2017] [Accepted: 03/27/2017] [Indexed: 11/19/2022] Open
Abstract
The extent and nature of epigenomic changes associated with melanoma progression is poorly understood. Through systematic epigenomic profiling of 35 epigenetic modifications and transcriptomic analysis, we define chromatin state changes associated with melanomagenesis by using a cell phenotypic model of non-tumorigenic and tumorigenic states. Computation of specific chromatin state transitions showed loss of histone acetylations and H3K4me2/3 on regulatory regions proximal to specific cancer-regulatory genes in important melanoma-driving cell signaling pathways. Importantly, such acetylation changes were also observed between benign nevi and malignant melanoma human tissues. Intriguingly, only a small fraction of chromatin state transitions correlated with expected changes in gene expression patterns. Restoration of acetylation levels on deacetylated loci by histone deacetylase (HDAC) inhibitors selectively blocked excessive proliferation in tumorigenic cells and human melanoma cells, suggesting functional roles of observed chromatin state transitions in driving hyperproliferative phenotype. Through these results, we define functionally relevant chromatin states associated with melanoma progression.
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Affiliation(s)
- Petko Fiziev
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Kadir C Akdemir
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - John P Miller
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Emily Z Keung
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Neha S Samant
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Sneha Sharma
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Christopher A Natale
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher J Terranova
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Mayinuer Maitituoheti
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Samirkumar B Amin
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emmanuel Martinez-Ledesma
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Mayura Dhamdhere
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jacob B Axelrad
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Amiksha Shah
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Christine S Cheng
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Boston University, Boston, MA 02215, USA
| | - Harshad Mahadeshwar
- Division of Cancer Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Sahil Seth
- Division of Cancer Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexei Protopopov
- Division of Cancer Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Kenneth Y Tsai
- Division of Internal Medicine, Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael A Davies
- Division of Cancer Medicine, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ido Amit
- Weizmann Institute of Science, Rehovot 761001, Israel
| | - Lynda Chin
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Division of Cancer Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Institute for Health Transformation, The University of Texas System, Austin, TX 78701, USA.
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA; Department of Computer Science, University of California, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Kunal Rai
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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16
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Franco HL, Nagari A, Malladi VS, Li W, Xi Y, Richardson D, Allton KL, Tanaka K, Li J, Murakami S, Keyomarsi K, Bedford MT, Shi X, Li W, Barton MC, Dent SYR, Kraus WL. Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. Genome Res 2017; 28:159-170. [PMID: 29273624 PMCID: PMC5793780 DOI: 10.1101/gr.226019.117] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 12/19/2017] [Indexed: 12/17/2022]
Abstract
Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 11 different human breast cancer cell lines representing five major molecular subtypes of breast cancer, as well as two immortalized (“normal”) human breast cell lines. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif P-values, and enrichment of H3K4me1 and H3K27ac. When applied across the 13 different cell lines noted above, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype-specific TFs that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes, including Forkhead TFs, FOSL1, and PLAG1. FOSL1, a Fos family TF, (1) is highly enriched at the enhancers of triple negative breast cancer (TNBC) cells, (2) acts as a key regulator of the proliferation and viability of TNBC cells, but not Luminal A cells, and (3) is associated with a poor prognosis in TNBC breast cancer patients. Taken together, our results validate our enhancer identification pipeline and reveal that enhancers transcribed in breast cancer cells direct critical gene regulatory networks that promote pathogenesis.
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Affiliation(s)
- Hector L Franco
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Venkat S Malladi
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Wenqian Li
- Department of Epigenetics and Molecular Carcinogenesis and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Yuanxin Xi
- Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Dana Richardson
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kendra L Allton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kaori Tanaka
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jing Li
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shino Murakami
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Khandan Keyomarsi
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Wei Li
- Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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17
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Wang L, Koutelou E, Hirsch C, McCarthy R, Schibler A, Lin K, Lu Y, Jeter C, Shen J, Barton MC, Dent SYR. GCN5 Regulates FGF Signaling and Activates Selective MYC Target Genes during Early Embryoid Body Differentiation. Stem Cell Reports 2017; 10:287-299. [PMID: 29249668 PMCID: PMC5768892 DOI: 10.1016/j.stemcr.2017.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022] Open
Abstract
Precise control of gene expression during development is orchestrated by transcription factors and co-regulators including chromatin modifiers. How particular chromatin-modifying enzymes affect specific developmental processes is not well defined. Here, we report that GCN5, a histone acetyltransferase essential for embryonic development, is required for proper expression of multiple genes encoding components of the fibroblast growth factor (FGF) signaling pathway in early embryoid bodies (EBs). Gcn5-/- EBs display deficient activation of ERK and p38, mislocalization of cytoskeletal components, and compromised capacity to differentiate toward mesodermal lineage. Genomic analyses identified seven genes as putative direct targets of GCN5 during early differentiation, four of which are cMYC targets. These findings established a link between GCN5 and the FGF signaling pathway and highlighted specific GCN5-MYC partnerships in gene regulation during early differentiation.
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Affiliation(s)
- Li Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Epigenetics and Molecular Carcinogenesis, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Calley Hirsch
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Ryan McCarthy
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Andria Schibler
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Genes and Development, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Collene Jeter
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Epigenetics and Molecular Carcinogenesis, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Program in Genes and Development, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Epigenetics and Molecular Carcinogenesis, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Program in Genes and Development, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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18
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Abstract
Evidence mounts, via two studies published in Molecular Cell (Riscal et al., 2016; Wienken et al., 2016), that chromatin-bound MDM2 impacts pluripotency and metabolism to promote survival and proliferation of cancer cells, independently of p53 degradation.
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Affiliation(s)
- Abhinav K Jain
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Stem Cell & Development Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michelle C Barton
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Stem Cell & Development Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA.
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19
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Jain AK, Xi Y, McCarthy R, Allton K, Akdemir KC, Patel LR, Aronow B, Lin C, Li W, Yang L, Barton MC. LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56. Mol Cell 2017; 64:967-981. [PMID: 27912097 DOI: 10.1016/j.molcel.2016.10.039] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/07/2016] [Accepted: 10/28/2016] [Indexed: 12/12/2022]
Abstract
Recent evidence suggests that lncRNAs play an integral regulatory role in numerous functions, including determination of cellular identity. We determined global expression (RNA-seq) and genome-wide profiles (ChIP-seq) of histone post-translational modifications and p53 binding in human embryonic stem cells (hESCs) undergoing differentiation to define a high-confidence set of 40 lncRNAs, which are p53 transcriptional targets. We focused on lncRNAs highly expressed in pluripotent hESCs and repressed by p53 during differentiation to identify lncPRESS1 as a p53-regulated transcript that maintains hESC pluripotency in concert with core pluripotency factors. RNA-seq of hESCs depleted of lncPRESS1 revealed that lncPRESS1 controls a gene network that promotes pluripotency. Further, we found that lncPRESS1 physically interacts with SIRT6 and prevents SIRT6 chromatin localization, which maintains high levels of histone H3K56 and H3K9 acetylation at promoters of pluripotency genes. In summary, we describe a p53-regulated, pluripotency-specific lncRNA that safeguards the hESC state by disrupting SIRT6 activity.
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Affiliation(s)
- Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Stem Cell and Development Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Yuanxin Xi
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan McCarthy
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Stem Cell and Development Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kendra Allton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Stem Cell and Development Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kadir C Akdemir
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lalit R Patel
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Li
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Stem Cell and Development Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA.
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20
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Bosnakovski D, Gearhart MD, Toso EA, Recht OO, Cucak A, Jain AK, Barton MC, Kyba M. p53-independent DUX4 pathology in cell and animal models of facioscapulohumeral muscular dystrophy. Dis Model Mech 2017; 10:1211-1216. [PMID: 28754837 PMCID: PMC5665455 DOI: 10.1242/dmm.030064] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 07/26/2017] [Indexed: 12/25/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a genetically dominant myopathy caused by mutations that disrupt repression of the normally silent DUX4 gene, which encodes a transcription factor that has been shown to interfere with myogenesis when misexpressed at very low levels in myoblasts and to cause cell death when overexpressed at high levels. A previous report using adeno-associated virus to deliver high levels of DUX4 to mouse skeletal muscle demonstrated severe pathology that was suppressed on a p53-knockout background, implying that DUX4 acted through the p53 pathway. Here, we investigate the p53 dependence of DUX4 using various in vitro and in vivo models. We find that inhibiting p53 has no effect on the cytoxicity of DUX4 on C2C12 myoblasts, and that expression of DUX4 does not lead to activation of the p53 pathway. DUX4 does lead to expression of the classic p53 target gene Cdkn1a (p21) but in a p53-independent manner. Meta-analysis of 5 publicly available data sets of DUX4 transcriptional profiles in both human and mouse cells shows no evidence of p53 activation, and further reveals that Cdkn1a is a mouse-specific target of DUX4. When the inducible DUX4 mouse model is crossed onto the p53-null background, we find no suppression of the male-specific lethality or skin phenotypes that are characteristic of the DUX4 transgene, and find that primary myoblasts from this mouse are still killed by DUX4 expression. These data challenge the notion that the p53 pathway is central to the pathogenicity of DUX4. Summary: DUX4 is thought to mediate cytopathology through p53. Here, DUX4 is shown to kill primary myoblasts and promote pathological phenotypes in the iDUX4[2.7] mouse model on the p53-null background, calling into question this notion.
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Affiliation(s)
- Darko Bosnakovski
- Lillehei Heart Institute, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA.,Department of Pediatrics, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA.,University Goce Delcev - Stip, Faculty of Medical Sciences, Krste Misirkov b.b., 2000 Stip, Republic of Macedonia
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA
| | - Erik A Toso
- Lillehei Heart Institute, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA.,Department of Pediatrics, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA
| | - Olivia O Recht
- Lillehei Heart Institute, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA.,Department of Pediatrics, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA
| | - Anja Cucak
- Lillehei Heart Institute, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA.,Department of Pediatrics, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA .,Department of Pediatrics, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA
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21
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Abstract
Mass cytometry utilizes antibodies conjugated with heavy metal labels, an approach that has greatly increased the number of parameters and opportunities for deep analysis well beyond what is possible with conventional fluorescence-based flow cytometry. As with any new technology, there are critical steps that help ensure the reliable generation of high-quality data. Presented here is an optimized protocol that incorporates multiple techniques for the processing of cell samples for mass cytometry analysis. The methods described here will help the user avoid common pitfalls and achieve consistent results by minimizing variability, which can lead to inaccurate data. To inform experimental design, the rationale behind optional or alternative steps in the protocol and their efficacy in uncovering new findings in the biology of the system being investigated is covered. Lastly, representative data is presented to illustrate expected results from the techniques presented here.
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Affiliation(s)
- Ryan L McCarthy
- Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center;
| | - Aundrietta D Duncan
- Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center
| | - Michelle C Barton
- Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center
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22
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Barton MC. Acidic shield puts a chink in p53's armour. Nature 2016; 538:45-46. [DOI: 10.1038/nature19469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Abstract
Prostate cancer is lethal when tumors evolve to activate androgen receptor signaling, which circumvents ligand-deprivation therapy. In this issue of Cancer Cell, Groner et al. show that histone reader and transcription co-regulator TRIM24 occupies a central role in this evolution, nominating inhibitors of TRIM24's bromodomain as a new therapeutic avenue.
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Affiliation(s)
- Lalit R Patel
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA.
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24
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Jain AK, Akdemir KC, Xi Y, McCarthy RL, Allton K, Aronow B, Lin C, Li W, Yang L, Barton MC. Abstract A06: Characterization of a novel p53-regulated embryonic stem cell-specific lncRNA that safeguards pluripotency. Cancer Res 2016. [DOI: 10.1158/1538-7445.nonrna15-a06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent work shows that long non-coding RNAs (lncRNAs), transcribed from 80% of our genomes, play important roles in gene regulation and are associated with disease pathogenesis. However, there is a broad gap in our knowledge regarding any contributions of lncRNAs in mediating p53 response or regulating stem cell state. Here, we report our discovery of lncRNAs that fine-tune p53's transcriptional outcomes in differentiating human embryonic stem cells (hESCs). By integrating RNA-Seq with p53 ChIP-Seq analyses along with active or repressive histone marks of hESCs undergoing differentiation, we defined a high-confidence set of 40 lncRNAs that are p53 transcriptional targets. We found that p53 directly regulates nuclear lncRNAs, which are either activated (HOTAIRM1) or repressed (lncPRESS-1) during hESC differentiation. Single-cell gene expression analysis during lineage-specific hESC differentiation revealed that lncPRESS-1 is a novel pluripotency-specific, p53-regulated transcript with expression tightly correlated with OCT4, NANOG and PRDM14. Loss-of-function of lncPRESS-1 results in diminished pluripotency and spontaneous differentiation of hESCs. In addition, mass cytometry-based multi-parametric analysis at a single cell level revealed that depletion of lncPRESS-1 results in overall loss of hESC pluripotency with marked induction of an ectoderm specific gene-signature. Further, we show that lncPRESS-1 physically interacts with SIRT6 and restrains its chromatin localization to maintain high levels of histone H3 Lys-56 (H3K56) and Lys-9 (H3K9) acetylation at promoters of pluripotency genes to sustain a chromatin architecture that favors pluripotency. In summary, we describe a novel pluripotency-specific lncRNA that safeguards the hESC state by disrupting SIRT6 activity. Since lncPRESS-1 is repressed by p53, we believe that cancers that harbor mutant TP53 will have robust expression of this lncRNA. Further investigations are underway to determine the disease relevance of lncPRESS-1 and correlation with p53-mutations.
Citation Format: Abhinav K. Jain, Kadir C. Akdemir, Yuanxin Xi, Ryan L. McCarthy, Kendra Allton, Bruce Aronow, Chunru Lin, Wei Li, Liuqing Yang, Michelle C. Barton. Characterization of a novel p53-regulated embryonic stem cell-specific lncRNA that safeguards pluripotency. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A06.
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Affiliation(s)
- Abhinav K. Jain
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Kadir C. Akdemir
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Yuanxin Xi
- 2Baylor College of Medicine, Houston, TX,
| | - Ryan L. McCarthy
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Kendra Allton
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Bruce Aronow
- 3Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Chunru Lin
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Wei Li
- 2Baylor College of Medicine, Houston, TX,
| | - Liuqing Yang
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
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25
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Franco HL, Nagari A, Xi Y, Li W, Richardson D, Tanaka K, Li J, Barton MC, Shi X, Keyomarsi K, Bedford MT, Li W, Dent SY, Kraus WL. Abstract PR06: Analysis of enhancer transcription reveals novel gene regulatory networks in breast cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.chromepi15-pr06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Enhancer transcription is a defining feature of active enhancers. We and others have shown that enhancers that produce transcripts (so called “eRNAs”) are more likely to (1) be associated with active chromatin marks, such as H3K4me1 and K3K27ac, (2) loop to target gene promoters, and (3) be associated with target gene activation. Thus, enhancer transcription is a good predictor of active enhancers. In this regard, we have shown that enhancer transcription can be used in the absence of any other genomic information to predict enhancers. We have used Global Run-On coupled deep sequencing (GRO-seq) in 14 different breast cancer cell lines representing the five distinct molecular subtypes of breast cancer, coupled with a computational pipeline that we have developed, to predict enhancers based solely on enhancer transcription. We found both common and unique sites of enhancer transcription across the cell lines. In addition, we observed that enhancer transcription correlates with nearest gene transcription. Unsupervised hierarchical clustering of enhancer transcription was sufficient to segregate the breast cancer cell lines into their specific molecular subtypes. Transcription factor motif analysis performed at the sites of enhancer transcription identified transcription factors that may be important for the transcriptional programs of each cell type. Transcription factors whose motifs were uniquely enriched in a specific cell type were observed to be bound at the enhancers using locus-specific ChIP-qPCR assay. siRNA-mediated knockdown of the cognate transcription factors reduced enhancer transcription and cell proliferation in those cell types. The GRO-seq data were integrated with ChIP-seq data for several histone modifications typically enriched at promoters, gene bodies, enhancers, and repressive regions of the genome. The results from these analyses provide additional support for our enhancer identification pipeline. Taken together, our analyses have revealed novel gene regulatory networks that underlie breast cancer subtype-specific biology.
This work was supported by a postdoctoral fellowship from the American Cancer Society - Lee National Denim Day Fellowship to H.L.F., grants from the NIH/NIDDK and CPRIT to W.L.K. and a grant from CPRIT to the LONESTAR Consortium.
Citation Format: Hector L. Franco, Anusha Nagari, Yuanxin Xi, Wenqian Li, Dana Richardson, Kaori Tanaka, Jing Li, The CPRIT LONESTAR Consortium, Michelle C. Barton, Xiaobing Shi, Khandan Keyomarsi, Mark T. Bedford, Wei Li, Sharon Y.R. Dent, W. Lee Kraus. Analysis of enhancer transcription reveals novel gene regulatory networks in breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr PR06.
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Affiliation(s)
- Hector L. Franco
- 1The Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX,
| | - Anusha Nagari
- 1The Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX,
| | - Yuanxin Xi
- 2Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX,
| | - Wenqian Li
- 3Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer, Smithville, TX,
| | - Dana Richardson
- 4The Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Kaori Tanaka
- 5The Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer, Houston, TX
| | - Jing Li
- 5The Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer, Houston, TX
| | - Michelle C. Barton
- 5The Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer, Houston, TX
| | - Xiaobing Shi
- 5The Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer, Houston, TX
| | - Khandan Keyomarsi
- 4The Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Mark T. Bedford
- 3Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer, Smithville, TX,
| | - Wei Li
- 2Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX,
| | - Sharon Y.R. Dent
- 3Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer, Smithville, TX,
| | - W. Lee Kraus
- 1The Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX,
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Rai K, Akdemir KC, Kwong LN, Fiziev P, Wu CJ, Keung EZ, Sharma S, Samant NS, Williams M, Axelrad JB, Shah A, Yang D, Grimm EA, Barton MC, Milton DR, Heffernan TP, Horner JW, Ekmekcioglu S, Lazar AJ, Ernst J, Chin L. Dual Roles of RNF2 in Melanoma Progression. Cancer Discov 2015; 5:1314-27. [PMID: 26450788 DOI: 10.1158/2159-8290.cd-15-0493] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 10/06/2015] [Indexed: 12/28/2022]
Abstract
UNLABELLED Epigenetic regulators have emerged as critical factors governing the biology of cancer. Here, in the context of melanoma, we show that RNF2 is prognostic, exhibiting progression-correlated expression in human melanocytic neoplasms. Through a series of complementary gain-of-function and loss-of-function studies in mouse and human systems, we establish that RNF2 is oncogenic and prometastatic. Mechanistically, RNF2-mediated invasive behavior is dependent on its ability to monoubiquitinate H2AK119 at the promoter of LTBP2, resulting in silencing of this negative regulator of TGFβ signaling. In contrast, RNF2's oncogenic activity does not require its catalytic activity nor does it derive from its canonical gene repression function. Instead, RNF2 drives proliferation through direct transcriptional upregulation of the cell-cycle regulator CCND2. We further show that MEK1-mediated phosphorylation of RNF2 promotes recruitment of activating histone modifiers UTX and p300 to a subset of poised promoters, which activates gene expression. In summary, RNF2 regulates distinct biologic processes in the genesis and progression of melanoma via different molecular mechanisms. SIGNIFICANCE The role of epigenetic regulators in cancer progression is being increasingly appreciated. We show novel roles for RNF2 in melanoma tumorigenesis and metastasis, albeit via different mechanisms. Our findings support the notion that epigenetic regulators, such as RNF2, directly and functionally control powerful gene networks that are vital in multiple cancer processes.
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Affiliation(s)
- Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Kadir C Akdemir
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lawrence N Kwong
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Petko Fiziev
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, California. Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, California. Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
| | - Chang-Jiun Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emily Z Keung
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Sneha Sharma
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neha S Samant
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maura Williams
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jacob B Axelrad
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amiksha Shah
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dong Yang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth A Grimm
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Denai R Milton
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James W Horner
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Suhendan Ekmekcioglu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, California. Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, California. Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California. Departments of Biological Chemistry and Computer Science, University of California, Los Angeles, Los Angeles, California. Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California
| | - Lynda Chin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas. Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas. Institute for Health Transformation, The University of Texas System, Houston, Texas.
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27
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Palmer WS, Poncet-Montange G, Liu G, Petrocchi A, Reyna N, Subramanian G, Theroff J, Yau A, Kost-Alimova M, Bardenhagen JP, Leo E, Shepard HE, Tieu TN, Shi X, Zhan Y, Zhao S, Barton MC, Draetta G, Toniatti C, Jones P, Geck Do M, Andersen JN. Structure-Guided Design of IACS-9571, a Selective High-Affinity Dual TRIM24-BRPF1 Bromodomain Inhibitor. J Med Chem 2015; 59:1440-54. [PMID: 26061247 DOI: 10.1021/acs.jmedchem.5b00405] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The bromodomain containing proteins TRIM24 (tripartite motif containing protein 24) and BRPF1 (bromodomain and PHD finger containing protein 1) are involved in the epigenetic regulation of gene expression and have been implicated in human cancer. Overexpression of TRIM24 correlates with poor patient prognosis, and BRPF1 is a scaffolding protein required for the assembly of histone acetyltransferase complexes, where the gene of MOZ (monocytic leukemia zinc finger protein) was first identified as a recurrent fusion partner in leukemia patients (8p11 chromosomal rearrangements). Here, we present the structure guided development of a series of N,N-dimethylbenzimidazolone bromodomain inhibitors through the iterative use of X-ray cocrystal structures. A unique binding mode enabled the design of a potent and selective inhibitor 8i (IACS-9571) with low nanomolar affinities for TRIM24 and BRPF1 (ITC Kd = 31 nM and ITC Kd = 14 nM, respectively). With its excellent cellular potency (EC50 = 50 nM) and favorable pharmacokinetic properties (F = 29%), 8i is a high-quality chemical probe for the evaluation of TRIM24 and/or BRPF1 bromodomain function in vitro and in vivo.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center , 1515 Holcombe Boulevard , Houston, Texas 77030, United States
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28
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Hirsch CL, Akdemir ZC, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X, Xia Z, Salinger AP, Wilson M, Vizeacoumar F, Datti A, Li W, Cooney AJ, Barton MC, Blencowe BJ, Wrana JL, Dent SYR. Corrigendum: Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev 2015; 29:1341. [PMID: 26109054 DOI: 10.1101/gad.266601.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Hirsch CL, Coban Akdemir Z, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X, Xia Z, Salinger AP, Wilson M, Vizeacoumar F, Datti A, Li W, Cooney AJ, Barton MC, Blencowe BJ, Wrana JL, Dent SYR. Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev 2015; 29:803-16. [PMID: 25877919 PMCID: PMC4403257 DOI: 10.1101/gad.255109.114] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/20/2015] [Indexed: 11/29/2022]
Abstract
Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Hirsch et al. performed a functional RNAi screen and identified components of the SAGA histone acetyltransferase complex, in particular Gcn5, as critical regulators of reprogramming initiation. In mouse pluripotent stem cells, Gcn5 strongly associates with Myc, and, upon initiation of somatic reprogramming, Gcn5 and Myc form a positive feed-forward loop that activates a distinct alternative splicing network and the early acquisition of pluripotency-associated splicing events. Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Pluripotent-specific transcriptional networks are sequentially reactivated as somatic cells reprogram to achieve pluripotency. How epigenetic regulators modulate this process and contribute to somatic cell reprogramming is not clear. Here we performed a functional RNAi screen to identify the earliest epigenetic regulators required for reprogramming. We identified components of the SAGA histone acetyltransferase complex, in particular Gcn5, as critical regulators of reprogramming initiation. Furthermore, we showed in mouse pluripotent stem cells that Gcn5 strongly associates with Myc and that, upon initiation of somatic reprogramming, Gcn5 and Myc form a positive feed-forward loop that activates a distinct alternative splicing network and the early acquisition of pluripotency-associated splicing events. These studies expose a Myc–SAGA pathway that drives expression of an essential alternative splicing regulatory network during somatic cell reprogramming.
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Affiliation(s)
- Calley L Hirsch
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Zeynep Coban Akdemir
- Program in Genes and Development, Graduate School of Biomedical Sciences, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Li Wang
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA; Program in Molecular Carcinogenesis, Graduate School of Biomedical Sciences, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Gowtham Jayakumaran
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Dan Trcka
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Alexander Weiss
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - J Javier Hernandez
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Qun Pan
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Hong Han
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Xueping Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zheng Xia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Andrew P Salinger
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Marenda Wilson
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Frederick Vizeacoumar
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Alessandro Datti
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Wei Li
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Austin J Cooney
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michelle C Barton
- Program in Genes and Development, Graduate School of Biomedical Sciences, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Benjamin J Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Jeffrey L Wrana
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada;
| | - Sharon Y R Dent
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA;
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30
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Wen H, Li Y, Xi Y, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W, Li H, Shi X. ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature 2014; 508:263-8. [PMID: 24590075 DOI: 10.1038/nature13045] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 01/20/2014] [Indexed: 12/31/2022]
Abstract
Recognition of modified histones by 'reader' proteins plays a critical role in the regulation of chromatin. H3K36 trimethylation (H3K36me3) is deposited onto the nucleosomes in the transcribed regions after RNA polymerase II elongation. In yeast, this mark in turn recruits epigenetic regulators to reset the chromatin to a relatively repressive state, thus suppressing cryptic transcription. However, much less is known about the role of H3K36me3 in transcription regulation in mammals. This is further complicated by the transcription-coupled incorporation of the histone variant H3.3 in gene bodies. Here we show that the candidate tumour suppressor ZMYND11 specifically recognizes H3K36me3 on H3.3 (H3.3K36me3) and regulates RNA polymerase II elongation. Structural studies show that in addition to the trimethyl-lysine binding by an aromatic cage within the PWWP domain, the H3.3-dependent recognition is mediated by the encapsulation of the H3.3-specific 'Ser 31' residue in a composite pocket formed by the tandem bromo-PWWP domains of ZMYND11. Chromatin immunoprecipitation followed by sequencing shows a genome-wide co-localization of ZMYND11 with H3K36me3 and H3.3 in gene bodies, and its occupancy requires the pre-deposition of H3.3K36me3. Although ZMYND11 is associated with highly expressed genes, it functions as an unconventional transcription co-repressor by modulating RNA polymerase II at the elongation stage. ZMYND11 is critical for the repression of a transcriptional program that is essential for tumour cell growth; low expression levels of ZMYND11 in breast cancer patients correlate with worse prognosis. Consistently, overexpression of ZMYND11 suppresses cancer cell growth in vitro and tumour formation in mice. Together, this study identifies ZMYND11 as an H3.3-specific reader of H3K36me3 that links the histone-variant-mediated transcription elongation control to tumour suppression.
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Affiliation(s)
- Hong Wen
- 1] Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [2] Center for Cancer Epigenetics, Center for Genetics and Genomics, and Center for Stem Cell and Developmental Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [3]
| | - Yuanyuan Li
- 1] MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China [2] Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China [3]
| | - Yuanxin Xi
- 1] Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2]
| | - Shiming Jiang
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Sabrina Stratton
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Danni Peng
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kaori Tanaka
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yongfeng Ren
- 1] MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China [2] Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zheng Xia
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jun Wu
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Bing Li
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Michelle C Barton
- 1] Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [2] Center for Cancer Epigenetics, Center for Genetics and Genomics, and Center for Stem Cell and Developmental Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [3] Genes and Development Graduate Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Teaxs 77030, USA
| | - Wei Li
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Haitao Li
- 1] MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China [2] Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaobing Shi
- 1] Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [2] Center for Cancer Epigenetics, Center for Genetics and Genomics, and Center for Stem Cell and Developmental Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [3] Genes and Development Graduate Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Teaxs 77030, USA
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Jain AK, Akdemir KC, Allton K, Aronow B, Xu X, Cooney AJ, Li W, Barton MC. Abstract PR01: Genome wide profiling reveals stimulus-specific functions of p53 in human embryonic stem cells. Cancer Res 2013. [DOI: 10.1158/1538-7445.fbcr13-pr01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
p53 is a critical guardian of somatic cells in the face of cellular stress and genomic challenges. Recent work shows that functions of transcription factor p53 go beyond its well-studied roles in tumor suppression. In addition to functions in cell cycle arrest and apoptosis, p53 is a functional barrier to reprogramming adult cells into induced pluripotent (iPS) cells that are phenotypically similar to embryonic stem (ES) cells. How p53 is regulated and functions in stem cells, is poorly understood. Previously we have shown that p53 plays a significant role that depends on its transcriptional activity in early differentiation of human ES cells (hESCs), as induced in vitro by retinoic acid (RA). In order to delineate p53 transcriptional functions during differentiation and how p53 selectively responds to specific signals in hESCs we performed genome wide profiling of p53 chromatin interactions and target gene expression in hESCs in response to early differentiation or DNA damage. The majority of p53 binding sites is unique to each state and defines stimulus-specific p53 response in hESCs. p53 binding regions specific to differentiation significantly overlap with those of core-pluripotency factors OCT4 and NANOG. Differentiation-specific p53 targets are highly expressed, and include many developmental transcription factors, poised by OCT4/NANOG and bivalent histone marks (H3K4me3 and H3K27me3) in pluripotent hESCs. Activation of poised genes during differentiation is associated with elimination of H3K27me3 marks, which is largely dependent on p53. During hESC differentiation, p53 interacts with H3K37me3 specific de-methylases (JMJD3 and UTX) that are enriched at the upstream regions of poised genes resulting in alteration of bivalent histone status and subsequent gene activation. These studies suggest that p53 plays essential roles in regulating epigenetic bivalency in ES cells. In contrast, genes associated with cell migration and motility are bound by p53 specifically after DNA damage. Surveillance functions of p53 in cell death and cell cycle regulation are conserved in both DNA damage and differentiation. Thus, our findings expand the registry of p53-regulated genes to define p53-mediated opposition to pluripotency during early differentiation, a process highly distinct from stress-induced p53 response in hESCs.
This abstract is also presented as poster A68.
Citation Format: Abhinav K. Jain, Kadir C. Akdemir, Kendra Allton, Bruce Aronow, Xueping Xu, Austin J. Cooney, Wei Li, Michelle C. Barton. Genome wide profiling reveals stimulus-specific functions of p53 in human embryonic stem cells. [abstract]. In: Proceedings of the Third AACR International Conference on Frontiers in Basic Cancer Research; Sep 18-22, 2013; National Harbor, MD. Philadelphia (PA): AACR; Cancer Res 2013;73(19 Suppl):Abstract nr PR01.
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Affiliation(s)
- Abhinav K. Jain
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Kadir C. Akdemir
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Kendra Allton
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Bruce Aronow
- 2Cincinnati Children's Hospital Medical Center, Cincinnati,
| | - Xueping Xu
- 3Baylor College of Medicine, Houston, TX
| | | | - Wei Li
- 3Baylor College of Medicine, Houston, TX
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Bochkis IM, Schug J, Ye DZ, Kurinna S, Stratton SA, Barton MC, Kaestner KH. Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2. PLoS Genet 2012; 8:e1002770. [PMID: 22737085 PMCID: PMC3380847 DOI: 10.1371/journal.pgen.1002770] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/02/2012] [Indexed: 01/04/2023] Open
Abstract
Gene duplication is a powerful driver of evolution. Newly duplicated genes acquire new roles that are relevant to fitness, or they will be lost over time. A potential path to functional relevance is mutation of the coding sequence leading to the acquisition of novel biochemical properties, as analyzed here for the highly homologous paralogs Foxa1 and Foxa2 transcriptional regulators. We determine by genome-wide location analysis (ChIP-Seq) that, although Foxa1 and Foxa2 share a large fraction of binding sites in the liver, each protein also occupies distinct regulatory elements in vivo. Foxa1-only sites are enriched for p53 binding sites and are frequently found near genes important to cell cycle regulation, while Foxa2-restricted sites show only a limited match to the forkhead consensus and are found in genes involved in steroid and lipid metabolism. Thus, Foxa1 and Foxa2, while redundant during development, have evolved divergent roles in the adult liver, ensuring the maintenance of both genes during evolution. The duplication of a gene from a common ancestor, resulting in two copies known as paralogs, plays an important role in evolution. Newly duplicated genes must acquire new functions in order to remain relevant, otherwise they are lost via mutation over time. We have performed genome-wide location analysis (ChIP–Seq) in adult liver to examine the differences between two paralogous DNA binding proteins, Foxa1 and Foxa2. While Foxa1 and Foxa2 bind a number of common genomic locations, each protein also localizes to distinct regulatory regions. Sites specific for Foxa1 also contain a DNA motif bound by tumor suppressor p53 and are found near genes important to cell cycle regulation, while Foxa2-only sites are found near genes essential to steroid and lipid metabolism. Hence, Foxa1 and Foxa2 have developed unique functions in adult liver, contributing to the maintenance of both genes during evolution.
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Affiliation(s)
- Irina M. Bochkis
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jonathan Schug
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Diana Z. Ye
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Svitlana Kurinna
- Center for Stem Cell and Developmental Biology, Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Sabrina A. Stratton
- Center for Stem Cell and Developmental Biology, Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Michelle C. Barton
- Center for Stem Cell and Developmental Biology, Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Klaus H. Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Yiu TT, Barton MC. Abstract 3137: Epigenetic regulators influencing dual histone reader TRIM24 in estrogen receptor-mediated transcription in breast cancer. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-3137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Nuclear receptor-mediated regulation of gene expression, including estrogen-receptor-alpha (ERα), relies on a complex network of proteins that impose either repression or activation of gene expression. Among these, epigenetic “reader” proteins recognize combinatorial PTMs on histones, through distinct structure domains such as tandem plant homeodomains (PHD) and bromodomains (Bromo). We recently reported that tripartite motif-containing 24 (TRIM24), by means of its C-terminal tandem PHD finger and Bromo domains, recognizes unmethylated histone H3 lysine K4 (H3K4me0) and acetylated histone H3 lysine K23 (H3K23ac) within the same histone tail. In the presence of estrogen, dual chromatin reader TRIM24 preferentially recognizes these two histone marks, binds to ERα and regulates estrogen-dependent target genes. Depletion of TRIM24 inhibits breast cancer cell growth and enhances tamoxifen-induced growth inhibition. In addition, overexpression of TRIM24 correlates with decreased overall survival in breast cancer patients. We believe that TRIM24 can be a potential biomarker for breast cancer development, as well as a target for therapeutic treatment. The goal of my research is to target TRIM24 in breast cancer by identifying upstream epigenetic regulators that may influence TRIM24's function in ERα-regulated transcriptional activation. For TRIM24-regulated ERα target genes, estrogen stimulation results in a global loss of H3K4me2 at estrogen-responsive elements (EREs), where TRIM24 and ERα are recruited. Global binding profile of TRIM24 by ChIP-seq also shows that TRIM24 preferentially binds to regions depleted of H3K4me2, suggesting that upstream regulators may determine TRIM24 binding to chromatin. Demethylation of histones is mediated by specific enzymes called histone demethylases (HDMs). When we increase H3K4me2 at EREs by inhibiting the enzymatic activity of HDM, recruitment of both TRIM24 and ERα to target genes is diminished. As a result, activation of TRIM24-regulated estrogen-responsive genes is impaired. Previous work has suggested that the presence of threonine T6 phosphorylation on histone H3 (H3T6ph) prevents HDMs from demethylating H3K4me2. H3T6ph may therefore impose an inhibitory mark for LSD1-mediated demethylation of H3K4me2, and serves as an added layer of regulation for TRIM24 binding to histones, affecting subsequent function of TRIM24 as an ERα coactivator. These results may give insights into future therapeutic studies of targeting TRIM24 in breast cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3137. doi:1538-7445.AM2012-3137
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Affiliation(s)
- Teresa T. Yiu
- 1Department of Biochemistry and Molecular Biology, Program in Genes and Development, Graduate School of Biomedical Sciences, Centers for Cancer Epigenetics and Stem Cell and Developmental Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Michelle C. Barton
- 1Department of Biochemistry and Molecular Biology, Program in Genes and Development, Graduate School of Biomedical Sciences, Centers for Cancer Epigenetics and Stem Cell and Developmental Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX
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Pathiraja TN, Thakkar KN, Stampfer MR, Barton MC. Abstract 2213: Aberrant expression of TRIM24 in breast cancer progression is linked to loss of repressive histone marks at the promoter. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-2213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We recently discovered that TRIM24 is an E3-ubiquitin ligase that targets p53 for degradation in embryonic stem cells and breast cancer cell lines. TRIM24 functions in human cells as a reader of dual histone marks and binds chromatin and estrogen receptor (ER) to activate estrogen-dependent genes associated with cellular proliferation and tumor development. Intriguingly, we and others have shown that over-expression of TRIM24 is associated with poor prognosis and worse survival in breast cancer patients. Whether TRIM24 is causal in malignant transformation of breast epithelial cells during breast tumor development and progression is not known. Furthermore the mechanism that drives deregulated expression of TRIM24 in breast cancer is not understood. To develop a timeline of TRIM24 deregulation during malignant transformation, we used an isogenic human mammary epithelial cell (HMEC) model system that allows for assessment of molecular changes that occur at the earliest stages of multistep human breast carcinogenesis. Our analysis of TRIM24 expression in HMECs transitioning from finite lifespan, to immortality and to malignantly transformed HMECs showed gradual up-regulation of TRIM24 at both RNA and protein levels early in the transformation process. Consistent with these findings, Immunohistochemical (IHC) staining of TRIM24 in clinical breast tumor samples from a breast cancer progression array showed increased TRIM24 expression in hyperplasia, ductal carcinoma in situ (DCIS) and invasive carcinoma, compared to normal breast tissues. To understand the mechanism of TRIM24 deregulation in breast tumor progression, we studied the TRIM24 promoter region for aberrant DNA methylation changes by bisulfite genomic sequencing. There were no aberrant DNA methylation changes in HMEC transitioning from finite lifespan to malignant transformation suggesting that TRIM24 gene expression is regulated by mechanisms other than DNA methylation. Interestingly, Chromatin Immunoprecipitation (ChIP) studies in finite lifespan HMECs at the TRIM24 promoter showed an enrichment of repressive histone marks H3K9me2 and H3K9me3 which gradually decreased in immortal and malignantly transformed mammary epithelial cells. Further studies to see if TRIM24 is involved in transformation of normal mammary epithelial cells by stably overexpressing TRIM24 in HMECs are currently ongoing. Also more studies are ongoing to define additional levels of regulation of TRIM24, and which transcription factors are involved in its deregulated expression in breast cancer. Our studies suggest a unique role of TRIM24 in early steps of mammary carcinogenesis. Therefore, our study may provide valuable insights into the rational development of TRIM24-targeted therapeutic strategies against breast cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2213. doi:1538-7445.AM2012-2213
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Affiliation(s)
- Thushangi N. Pathiraja
- 1Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kaushik N. Thakkar
- 1Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Martha R. Stampfer
- 2Life Sciences Division, Lawrence Berkeley National laboratory, Berkeley, CA
| | - Michelle C. Barton
- 1Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
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Singh MM, Manton CA, Bhat KP, Tsai WW, Aldape K, Barton MC, Chandra J. Inhibition of LSD1 sensitizes glioblastoma cells to histone deacetylase inhibitors. Neuro Oncol 2011; 13:894-903. [PMID: 21653597 DOI: 10.1093/neuonc/nor049] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a particularly aggressive brain tumor and remains a clinically devastating disease. Despite innovative therapies for the treatment of GBM, there has been no significant increase in patient survival over the past decade. Enzymes that control epigenetic alterations are of considerable interest as targets for cancer therapy because of their critical roles in cellular processes that lead to oncogenesis. Several inhibitors of histone deacetylases (HDACs) have been developed and tested in GBM with moderate success. We found that treatment of GBM cells with HDAC inhibitors caused the accumulation of histone methylation, a modification removed by the lysine specific demethylase 1 (LSD1). This led us to examine the effects of simultaneously inhibiting HDACs and LSD1 as a potential combination therapy. We evaluated induction of apoptosis in GBM cell lines after combined inhibition of LSD1 and HDACs. LSD1 was inhibited by targeted short hairpin RNA or pharmacological means and inhibition of HDACs was achieved by treatment with either vorinostat or PCI-24781. Caspase-dependent apoptosis was significantly increased (>2-fold) in LSD1-knockdown GBM cells treated with HDAC inhibitors. Moreover, pharmacologically inhibiting LSD1 with the monoamine oxidase inhibitor tranylcypromine, in combination with HDAC inhibitors, led to synergistic apoptotic cell death in GBM cells; this did not occur in normal human astrocytes. Taken together, these results indicate that LSD1 and HDACs cooperate to regulate key pathways of cell death in GBM cell lines but not in normal counterparts, and they validate the combined use of LSD1 and HDAC inhibitors as a therapeutic approach for GBM.
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Affiliation(s)
- Melissa M Singh
- Department of Pediatrics Research, The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, Zwaka TP. Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells. Genes Dev 2010; 24:1479-84. [PMID: 20581084 DOI: 10.1101/gad.1935210] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Self-renewing embryonic stem (ES) cells have an exceptional need for timely biomass production, yet the transcriptional control mechanisms responsible for meeting this requirement are largely unknown. We report here that Ronin (Thap11), which is essential for the self-renewal of ES cells, binds with its transcriptional coregulator, Hcf-1, to a highly conserved enhancer element that previously lacked a recognized binding factor. The subset of genes bound by Ronin/Hcf-1 function primarily in transcription initiation, mRNA splicing, and cell metabolism; genes involved in cell signaling and cell development are conspicuously underrepresented in this target gene repertoire. Although Ronin/Hcf-1 represses the expression of some target genes, its activity at promoter sites more often leads to the up-regulation of genes essential to protein biosynthesis and energy production. We propose that Ronin/Hcf-1 controls a genetic program that contributes to the unimpeded growth of ES cells.
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Affiliation(s)
- Marion Dejosez
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030, USA
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Gu D, Sater AK, Ji H, Cho K, Clark M, Stratton SA, Barton MC, Lu Q, McCrea PD. Xenopus delta-catenin is essential in early embryogenesis and is functionally linked to cadherins and small GTPases. J Cell Sci 2009; 122:4049-61. [PMID: 19843587 DOI: 10.1242/jcs.031948] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Catenins of the p120 subclass display an array of intracellular localizations and functions. Although the genetic knockout of mouse delta-catenin results in mild cognitive dysfunction, we found severe effects of its depletion in Xenopus. delta-catenin in Xenopus is transcribed as a full-length mRNA, or as three (or more) alternatively spliced isoforms designated A, B and C. Further structural and functional complexity is suggested by three predicted and alternative translation initiation sites. Transcript analysis suggests that each splice isoform is expressed during embryogenesis, with the B and C transcript levels varying according to developmental stage. Unlike the primarily neural expression of delta-catenin reported in mammals, delta-catenin is detectable in most adult Xenopus tissues, although it is enriched in neural structures. delta-catenin associates with classical cadherins, with crude embryo fractionations further revealing non-plasma-membrane pools that might be involved in cytoplasmic and/or nuclear functions. Depletion of delta-catenin caused gastrulation defects, phenotypes that were further enhanced by co-depletion of the related p120-catenin. Depletion was significantly rescued by titrated p120-catenin expression, suggesting that these catenins have shared roles. Biochemical assays indicated that delta-catenin depletion results in reduced cadherin levels and cell adhesion, as well as perturbation of RhoA and Rac1. Titrated doses of C-cadherin, dominant-negative RhoA or constitutively active Rac1 significantly rescued delta-catenin depletion. Collectively, our experiments indicate that delta-catenin has an essential role in amphibian development, and has functional links to cadherins and Rho-family GTPases.
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Affiliation(s)
- Dongmin Gu
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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Lou CH, Alexander TB, Barton MC, Chu YH, Sater AK. The novel transcriptional co-repressor ashwin modulates beta-catenin dependent transcription during early Xenopus development. Dev Biol 2008. [DOI: 10.1016/j.ydbio.2008.05.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Gu D, Sater AK, Ji H, Clark M, Stratton SA, Barton MC, Lu Q, McCrea PD. δ-Catenin regulates Xenopus developmental morphogenesis. Dev Biol 2008. [DOI: 10.1016/j.ydbio.2008.05.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Qian J, Sarnaik AA, Bonney TM, Keirsey J, Combs KA, Steigerwald K, Acharya S, Behbehani GK, Barton MC, Lowy AM, Groden J. The APC tumor suppressor inhibits DNA replication by directly binding to DNA via its carboxyl terminus. Gastroenterology 2008; 135:152-62. [PMID: 18474248 PMCID: PMC2832605 DOI: 10.1053/j.gastro.2008.03.074] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 02/26/2008] [Accepted: 03/27/2008] [Indexed: 01/11/2023]
Abstract
BACKGROUND & AIMS The APC tumor suppressor is well known for its ability to regulate Wnt signaling through mediation of beta-catenin levels in the cell. Transient over expression of the tumor suppressor gene APC in colon cancer cells prevents entry into S phase of the cell cycle, a phenotype only partially restored by cotransfection of a transcriptionally active form of beta-catenin. In an attempt to define its transcription-independent tumor suppressor functions, we tested whether APC directly affects DNA replication. METHODS A transcriptionally quiescent in vitro DNA replication system, the polymerase chain reaction, DNA binding assays, and transient transfections in colon cancer cell lines were used to determine the effects of APC on DNA replication and the mechanism by which it works. RESULTS We report that exogenous full-length APC inhibits replication of template DNA through a function that maps to amino acids 2140-2421, a region of the protein commonly lost by somatic or germline mutation. This segment of APC directly interacts with DNA, while mutation of the DNA-binding S(T)PXX motifs within it abolishes DNA binding and reduces inhibition of DNA replication. Phosphorylation of this segment by cyclin-dependent kinases also reduces inhibition of DNA replication. Furthermore, transient transfection of an APC segment encoding amino acids 2140-2421 into a colon cancer cell line with mutant APC prevents cell cycle progression into or through S phase. CONCLUSIONS Our results suggest that APC can negatively regulate cell cycle progression through inhibition of DNA replication by direct interaction with DNA.
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Affiliation(s)
- Jiang Qian
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210-2207,Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Amod A. Sarnaik
- Division of Surgical Oncology in the Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Tera M. Bonney
- Division of Surgical Oncology in the Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Jeremy Keirsey
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210-2207
| | - Kelly A. Combs
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Kira Steigerwald
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Samir Acharya
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210-2207
| | - Gregory K. Behbehani
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Michelle C. Barton
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Andy M. Lowy
- Division of Surgical Oncology in the Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Joanna Groden
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210-2207,To whom reprint requests should be addressed:
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Qian J, Steigerwald K, Combs KA, Barton MC, Groden J. Caspase cleavage of the APC tumor suppressor and release of an amino-terminal domain is required for the transcription-independent function of APC in apoptosis. Oncogene 2007; 26:4872-6. [PMID: 17297457 DOI: 10.1038/sj.onc.1210265] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The adenomatous polyposis coli (APC) tumor suppressor is inactivated by mutation in most colorectal tumors. APC is a component of the Wnt signaling pathway and is best known for its ability to downregulate beta-catenin and consequent effects on transcriptional regulation. Previous work demonstrated that APC accelerates apoptosis-associated caspase activity independently of transcription, and suggested novel tumor suppressor functions of APC. In this work, we have mapped the APC apoptosis-accelerating region to amino acids (aa) 1-760 by testing a series of non-overlapping APC segments. Interestingly, this segment corresponds to a stable group II caspase cleavage product of APC released during apoptosis that includes the amino-terminal aa1-777. Mutation of the APC aspartic acid residue at position 777 to an alanine completely abolished in vitro cleavage of APC by a recombinant group II caspase and rendered the full-length protein unable to accelerate apoptosis in vitro. A truncated APC protein associated with familial and sporadic colorectal cancer, also unable to accelerate apoptosis in vitro and in vivo, is resistant to group II caspase cleavage. These results demonstrate that cleavage of APC and the subsequent release of an amino-terminal segment are necessary for the transcription-independent mechanism of APC-mediated apoptosis.
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Affiliation(s)
- J Qian
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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Park JI, Kim SW, Lyons JP, Ji H, Nguyen TT, Cho K, Barton MC, Deroo T, Vleminckx K, Moon RT, McCrea PD. Kaiso/p120-catenin and TCF/beta-catenin complexes coordinately regulate canonical Wnt gene targets. Dev Cell 2005; 8:843-54. [PMID: 15935774 DOI: 10.1016/j.devcel.2005.04.010] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 03/01/2005] [Accepted: 04/16/2005] [Indexed: 11/18/2022]
Abstract
Beta-catenin-dependent or canonical Wnt signals are fundamental in animal development and tumor progression. Using Xenopus laevis, we report that the BTB/POZ zinc finger family member Kaiso directly represses canonical Wnt gene targets (Siamois, c-Fos, Cyclin-D1, and c-Myc) in conjunction with TCF/LEF (TCF). Analogous to beta-catenin relief of TCF repressive activity, we show that p120-catenin relieves Kaiso-mediated repression of Siamois. Furthermore, Kaiso and TCF coassociate, and combined Kaiso and TCF derepression results in pronounced Siamois expression and increased beta-catenin coprecipitation with the Siamois promoter. The functional interdependency is underlined by Kaiso suppression of beta-catenin-induced axis duplication and by TCF-3 rescue of Kaiso depletion phenotypes. These studies point to convergence of parallel p120-catenin/Kaiso and beta-catenin/TCF signaling pathways to regulate gene expression in vertebrate development and possibly carcinogenesis.
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Affiliation(s)
- Jae-Il Park
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
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Park JI, Kim SW, Lyons JP, Ji H, Nguyen TT, Cho K, Barton MC, Deroo T, Vleminckx K, Moon RT, McCrea PD. Kaiso/p120-Catenin and TCF/β-Catenin Complexes Coordinately Regulate Canonical Wnt Gene Targets. Dev Cell 2005. [DOI: 10.1016/j.devcel.2005.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Ogden SK, Lee KC, Wernke-Dollries K, Stratton SA, Aronow B, Barton MC. p53 targets chromatin structure alteration to repress alpha-fetoprotein gene expression. J Biol Chem 2001; 276:42057-62. [PMID: 11572852 DOI: 10.1074/jbc.c100381200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Many of the functions ascribed to p53 tumor suppressor protein are mediated through transcription regulation. We have shown that p53 represses hepatic-specific alpha-fetoprotein (AFP) gene expression by direct interaction with a composite HNF-3/p53 DNA binding element. Using solid-phase, chromatin-assembled AFP DNA templates and analysis of chromatin structure and transcription in vitro, we find that p53 binds DNA and alters chromatin structure at the AFP core promoter to regulate transcription. Chromatin assembled in the presence of hepatoma extracts is activated for AFP transcription with an open, accessible core promoter structure. Distal (-850) binding of p53 during chromatin assembly, but not post-assembly, reverses transcription activation concomitant with promoter inaccessibility to restriction enzyme digestion. Inhibition of histone deacetylase activity by trichostatin-A (TSA) addition, prior to and during chromatin assembly, activated chromatin transcription in parallel with increased core promoter accessibility. Chromatin immunoprecipitation analyses showed increased H3 and H4 acetylated histones at the core promoter in the presence of TSA, while histone acetylation remained unchanged at the site of distal p53 binding. Our data reveal that p53 targets chromatin structure alteration at the core promoter, independently of effects on histone acetylation, to establish repressed AFP gene expression.
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Affiliation(s)
- S K Ogden
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati and Children's Hospital Research Foundation, Cincinnati, Ohio 45267, USA
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Abstract
Polymerase accessibility to chromatin is a limiting step in both RNA and DNA synthesis. Unwinding DNA and nucleosomes during polymerase complex binding and processing likely requires priming by chromatin restructuring. The initiating step in these processes remains an area of speculation. This review focuses on the physical handling of chromatin during transcription and replication, the fate of nucleosomes assembled on DNA during unwinding and processing the chromatin substrate, and how these alterations in chromatin structure may affect gene expression. Transcription or replication may alter chromatin structure during synthesis, enabling regulatory factor binding and, potentially, future rounds of transcription. As chromatin remodeling and transcription factor binding augment transcription and replication, and are themselves increased by these processes, a temporal model of structural alterations and gene activation is built that may be more circular than linear.
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Affiliation(s)
- M C Barton
- Department of Biochemistry and Molecular Biology, University of Texas, M.D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, Texas, TX 77030, USA
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Rockx DA, Mason R, van Hoffen A, Barton MC, Citterio E, Bregman DB, van Zeeland AA, Vrieling H, Mullenders LH. UV-induced inhibition of transcription involves repression of transcription initiation and phosphorylation of RNA polymerase II. Proc Natl Acad Sci U S A 2000; 97:10503-8. [PMID: 10973477 PMCID: PMC27054 DOI: 10.1073/pnas.180169797] [Citation(s) in RCA: 162] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cells from patients with Cockayne syndrome (CS) are hypersensitive to DNA-damaging agents and are unable to restore damage-inhibited RNA synthesis. On the basis of repair kinetics of different types of lesions in transcriptionally active genes, we hypothesized previously that impaired transcription in CS cells is a consequence of defective transcription initiation after DNA damage induction. Here, we investigated the effect of UV irradiation on transcription by using an in vitro transcription system that allowed uncoupling of initiation from elongation events. Nuclear extracts prepared from UV-irradiated or mock-treated normal human and CS cells were assayed for transcription activity on an undamaged beta-globin template. Transcription activity in nuclear extracts closely mimicked kinetics of transcription in intact cells: extracts from normal cells prepared 1 h after UV exposure showed a strongly reduced activity, whereas transcription activity was fully restored in extracts prepared 6 h after treatment. Extracts from CS cells exhibited reduced transcription activity at any time after UV exposure. Reduced transcription activity in extracts coincided with a strong reduction of RNA polymerase II (RNAPII) containing hypophosphorylated C-terminal domain, the form of RNAPII known to be recruited to the initiation complex. These results suggest that inhibition of transcription after UV irradiation is at least partially caused by repression of transcription initiation and not solely by blocked elongation at sites of lesions. Generation of hypophosphorylated RNAPII after DNA damage appears to play a crucial role in restoration of transcription. CS proteins may be required for this process in a yet unknown way.
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Affiliation(s)
- D A Rockx
- MGC-Department of Radiation Genetics and Chemical Mutagenesis, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
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47
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Abstract
Chronic infection with hepatitis B virus (HBV) is associated with development of hepatocellular carcinoma (HCC). The exact mechanism by which chronic infection with HBV contributes to onset of HCC is unknown. However, previous studies have implicated the HBV transactivator protein, HBx, in progression of HCC through its ability to bind the human tumor suppressor protein, p53. In this study, we have examined the ability of HBx to modify p53 regulation of the HCC tumor marker gene, alpha-fetoprotein (AFP). By utilizing in vitro chromatin assembly of DNA templates prior to transcription analysis, we have demonstrated that HBx functionally disrupts p53-mediated repression of AFP transcription through protein-protein interaction. HBx modification of p53 gene regulation is both tissue-specific and dependent upon the p53 binding element. Our data suggest that the mechanism by which HBx alleviates p53 repression of AFP transcription is through an association with DNA-bound p53, resulting in a loss of p53 interaction with liver-specific transcriptional co-repressors.
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Affiliation(s)
- S K Ogden
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio 45267, USA
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48
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Abstract
Aberrant expression of developmentally silenced genes, characteristic of tumor cells and regenerating tissue, is highly correlated with increased cell proliferation. By modeling this process in vitro in synthetic nuclei, we find that DNA replication leads to deregulation of established developmental expression patterns. Chromatin assembly in the presence of adult mouse liver nuclear extract mediates developmental stage-specific silencing of the tumor marker gene alpha-fetoprotein (AFP). Replication of silenced AFP chromatin in synthetic nuclei depletes sequence-specific transcription repressors, thereby disrupting developmentally regulated repression. Hepatoma-derived factors can target partial derepression of AFP, but full transcription activation requires DNA replication. Thus, unscheduled entry into S phase directly mediates activation of a developmentally silenced gene by (i) depleting developmental stage-specific transcription repressors and (ii) facilitating binding of transactivators.
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Affiliation(s)
- A J Crowe
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio 45267-0524, USA
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49
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Kroll SL, Paulding WR, Schnell PO, Barton MC, Conaway JW, Conaway RC, Czyzyk-Krzeska MF. von Hippel-Lindau protein induces hypoxia-regulated arrest of tyrosine hydroxylase transcript elongation in pheochromocytoma cells. J Biol Chem 1999; 274:30109-14. [PMID: 10514498 DOI: 10.1074/jbc.274.42.30109] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rat pheochromocytoma (PC12) cells were stably transfected with either wild type or mutated human von Hippel-Lindau tumor suppressor protein (hpVHL). These proteins have opposing effects on regulating expression of the gene encoding tyrosine hydroxylase (TH), the rate-limiting enzyme in catecholamine synthesis. Whereas wild type hpVHL represses levels of TH mRNA and protein 5-fold, a truncated pVHL mutant, pVHL(1-115), induces accumulation of TH mRNA and protein 3-fold. hpVHL-induced inhibition of TH gene expression does not involve either a decrease in TH mRNA stability or repression of TH promoter activity. However, repression results from inhibition of RNA elongation at a downstream region of the TH gene. This elongation pause is accompanied by hpVHL sequestration in the nuclear extracts of elongins B and C, regulatory components of the transcription elongation heterotrimer SIII (elongin A/B/C). Hypoxia, a physiological stimulus for TH gene expression, alleviates the elongation block. A truncated pVHL mutant, pVHL(1-115), stimulates TH gene expression by increasing the efficiency of TH transcript elongation. This is the first report showing pVHL-dependent regulation of specific transcript elongation in vivo, as well as dominant negative activity of pVHL mutants in pheochromocytoma cells.
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Affiliation(s)
- S L Kroll
- Department of Molecular Physiology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267-0576, USA
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50
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Crowe AJ, Sang L, Li KK, Lee KC, Spear BT, Barton MC. Hepatocyte nuclear factor 3 relieves chromatin-mediated repression of the alpha-fetoprotein gene. J Biol Chem 1999; 274:25113-20. [PMID: 10455192 DOI: 10.1074/jbc.274.35.25113] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The alpha-fetoprotein gene (AFP) is tightly regulated at the tissue-specific level, with expression confined to endoderm-derived cells. We have reconstituted AFP transcription on chromatin-assembled DNA templates in vitro. Our studies show that chromatin assembly is essential for hepatic-specific expression of the AFP gene. While nucleosome-free AFP DNA is robustly transcribed in vitro by both cervical (HeLa) and hepatocellular (HepG2) carcinoma extracts, the general transcription factors and transactivators present in HeLa extract cannot relieve chromatin-mediated repression of AFP. In contrast, preincubation with either HepG2 extract or HeLa extract supplemented with recombinant hepatocyte nuclear factor 3 alpha (HNF3alpha), a hepatic-enriched factor expressed very early during liver development, is sufficient to confer transcriptional activation on a chromatin-repressed AFP template. Transient transfection studies illustrate that HNF3alpha can activate AFP expression in a non-liver cellular environment, confirming a pivotal role for HNF3alpha in establishing hepatic-specific gene expression. Restriction enzyme accessibility assays reveal that HNF3alpha promotes the assembly of an open chromatin structure at the AFP promoter. Combined, these functional and structural data suggest that chromatin assembly establishes a barrier to block inappropriate expression of AFP in non-hepatic tissues and that tissue-specific factors, such as HNF3alpha, are required to alleviate the chromatin-mediated repression.
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Affiliation(s)
- A J Crowe
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio 45267-0524, USA
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