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Gopinathan G, Zhang X, Luan X, Diekwisch TGH. Changes in Hox Gene Chromatin Organization during Odontogenic Lineage Specification. Genes (Basel) 2023; 14:198. [PMID: 36672939 PMCID: PMC9859321 DOI: 10.3390/genes14010198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Craniofacial tissues comprise highly evolved organs characterized by a relative lack of expression in the HOX family transcription factors. In the present study, we sought to define the epigenetic events that limit HOX gene expression from undifferentiated neural crest cells to semi-differentiated odontogenic progenitors and to explore the effects of elevated levels of HOX. The ChIP-chip data demonstrated high levels of repressive H3K27me3 marks on the HOX gene promoters in ES and cranial neural crest cells when compared to the H3K4me3 marks, while the K4/K27 ratio was less repressive in the odontogenic progenitors, dental follicle, dental pulp, periodontal ligament fibroblasts, alveolar bone osteoblasts, and cementoblasts. The gene expression of multiple HOX genes, especially those from the HOXA and HOXB clusters, was significantly elevated and many times higher in alveolar bone cells than in the dental follicle cells. In addition, the HOX levels in the skeletal osteoblasts were many times higher in the trunk osteoblasts compared to the alveolar bone osteoblasts, and the repressive mark H3K27me3 promoter occupancy was substantially and significantly elevated in the alveolar bone osteoblasts when compared to the trunk osteoblasts. To explore the effect of elevated HOX levels in craniofacial neural crest cells, HOX expression was induced by transfecting cells with the Cdx4 transcription factor, resulting in a significant decrease in the mineralization markers, RUNX2, OSX, and OCN upon HOX elevation. Promoting HOX gene expression in developing teeth using the small molecule EZH2 inhibitor GSK126 resulted in an increased number of patterning events, supernumerary cusp formation, and increased Hoxa4 and Hoxb6 gene expression when compared to the controls. Together, these studies illustrate the profound effects of epigenetic regulatory events at all stages of the differentiation of craniofacial peripheral tissues from the neural crest, including lineage specification, tissue differentiation, and patterning.
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Affiliation(s)
- Gokul Gopinathan
- Center for Craniofacial Research and Diagnosis, Texas A&M University, Dallas, TX 75246, USA
| | - Xinmin Zhang
- Bioinforx Inc., 510 Charmany Dr#275a, Madison, WI 53719, USA
| | - Xianghong Luan
- Center for Craniofacial Research and Diagnosis, Texas A&M University, Dallas, TX 75246, USA
| | - Thomas G. H. Diekwisch
- Center for Craniofacial Research and Diagnosis, Texas A&M University, Dallas, TX 75246, USA
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Bondhus L, Wei A, Arboleda VA. DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features. BMC Bioinformatics 2022; 23:364. [PMID: 36064314 PMCID: PMC9447346 DOI: 10.1186/s12859-022-04899-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/22/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Pathogenic mutations in genes that control chromatin function have been implicated in rare genetic syndromes. These chromatin modifiers exhibit extraordinary diversity in the scale of the epigenetic changes they affect, from single basepair modifications by DNMT1 to whole genome structural changes by PRM1/2. Patterns of DNA methylation are related to a diverse set of epigenetic features across this full range of epigenetic scale, making DNA methylation valuable for mapping regions of general epigenetic dysregulation. However, existing methods are unable to accurately identify regions of differential methylation across this full range of epigenetic scale directly from DNA methylation data. RESULTS To address this, we developed DMRscaler, a novel method that uses an iterative windowing procedure to capture regions of differential DNA methylation (DMRs) ranging in size from single basepairs to whole chromosomes. We benchmarked DMRscaler against several DMR callers in simulated and natural data comparing XX and XY peripheral blood samples. DMRscaler was the only method that accurately called DMRs ranging in size from 100 bp to 1 Mb (pearson's r = 0.94) and up to 152 Mb on the X-chromosome. We then analyzed methylation data from rare-disease cohorts that harbor chromatin modifier gene mutations in NSD1, EZH2, and KAT6A where DMRscaler identified novel DMRs spanning gene clusters involved in development. CONCLUSION Taken together, our results show DMRscaler is uniquely able to capture the size of DMR features across the full range of epigenetic scale and identify novel, co-regulated regions that drive epigenetic dysregulation in human disease.
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Affiliation(s)
- Leroy Bondhus
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA
| | - Angela Wei
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Bioinformatics Interdepartmental PhD Program, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA
| | - Valerie A. Arboleda
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Bioinformatics Interdepartmental PhD Program, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Molecular Biology Institute, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095 USA
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Chu S, Avery A, Yoshimoto J, Bryan JN. Genome wide exploration of the methylome in aggressive B-cell lymphoma in Golden Retrievers reveals a conserved hypermethylome. Epigenetics 2022; 17:2022-2038. [PMID: 35912844 PMCID: PMC9665123 DOI: 10.1080/15592294.2022.2105033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Few recurrent DNA mutations are seen in aggressive canine B cell lymphomas (cBCL), suggesting other frequent drivers. The methylated island recovery assay (MIRA-seq) or methylated CpG-binding domain sequencing (MBD-seq) was used to define the genome-wide methylation profiles in aggressive cBCL in Golden Retrievers to determine if cBCL can be better defined by epigenetic changes than by DNA mutations. DNA hypermethylation patterns were relatively homogenous within cBCL samples in Golden Retrievers, in different breeds and in geographical regions. Aberrant hypermethylation is thus suspected to be a central and early event in cBCL lymphomagenesis. Distinct subgroups within cBCL in Golden Retrievers were not identified with DNA methylation profiles. In comparison, the methylome profile of human DLBCL (hDLBCL) is relatively heterogeneous. Only moderate similarity between hDLBCL and cBCL was seen and cBCL likely cannot be accurately classified into the subtypes seen in hDLBCL. Genes with hypermethylated regions in the promoter-TSS-first exon of cBCL compared to normal B cells often also had additional hyper- and hypomethylated regions distributed throughout the gene suggesting non-randomized repeat targeting of key genes by epigenetic mechanisms. The prevalence of hypermethylation in transcription factor families in aggressive cBCL may represent a fundamental step in lymphomagenesis.
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Affiliation(s)
- Shirley Chu
- Department of Veterinary Medicine and Surgery, University of Missouri, 900 E. Campus Drive, Columbia, MO, USA
| | - Anne Avery
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Janna Yoshimoto
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jeffrey N Bryan
- Department of Veterinary Medicine and Surgery, University of Missouri, 900 E. Campus Drive, Columbia, MO, USA
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4
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Aberrant somatic hypermutation of CCND1 generates non-coding drivers of mantle cell lymphomagenesis. Cancer Gene Ther 2022; 29:484-493. [PMID: 35145272 PMCID: PMC9113931 DOI: 10.1038/s41417-022-00428-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/26/2021] [Accepted: 01/25/2022] [Indexed: 02/02/2023]
Abstract
Aberrant somatic hypermutation (aSHM) can target proto-oncogenes and drive oncogenesis. In mantle cell lymphoma (MCL), CCND1 is targeted by aSHM in the non-nodal subtype (nnMCL), giving rise to exon1 encoded mutant proteins like E36K, Y44D, and C47S that contribute to lymphomagenesis by virtue of their increased protein stability and nuclear localization. However, the vast majority of somatic variants generated by aSHM are found in the first intron of CCND1 but their significance for mantle cell lymphomagenesis is unknown. We performed whole-genome and whole-transcriptome sequencing in 84 MCL patients to explore the contribution of non-coding somatic variants created by aSHM to lymphomagenesis. We show that non-coding variants are enriched in a MCL specific manner in transcription factor-binding sites, that non-coding variants are associated with increased CCND1 mRNA expression, and that coding variants in the first exon of CCND1 are more often synonymous or cause benign amino acid changes than in other types of lymphomas carrying a t(11;14) translocation. Therefore, the increased frequency of somatic variants due to aSHM might be a consequence of selection pressure manifested at the transcriptional level rather than being a mere mechanistic consequence of misguided activation-induced cytidine deaminase (AID) activity.
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Martinez-Baquero D, Sakhdari A, Mo H, Kim DH, Kanagal-Shamanna R, Li S, Young KH, O'Malley DP, Dogan A, Jain P, Wang ML, McDonnell TJ, Miranda RN, Vega F, Medeiros LJ, Ok CY. EZH2 expression is associated with inferior overall survival in mantle cell lymphoma. Mod Pathol 2021; 34:2183-2191. [PMID: 34376807 PMCID: PMC10563799 DOI: 10.1038/s41379-021-00885-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 11/09/2022]
Abstract
Enhancer of zeste homolog 2 (EZH2) is a catalytic component of the polycomb repressive complex 2 (PRC2) which reduces gene expression via trimethylation of a lysine residue of histone 3 (H3K27me3). Expression of EZH2 has not been assessed systematically in mantle cell lymphoma (MCL). Expression of EZH2 was assessed by immunohistochemistry in 166 patients with MCL. We also assessed other PRC2 components and H3K27me3. Fifty-seven (38%) of MCL patients were positive for EZH2 using 40% cutoff. EZH2 expression was associated with aggressive histologic variants (65% vs. 29%, p < 0.001), high Ki-67 proliferation rate (median, 72% vs. 19%, p < 0.001), and p53 overexpression (43% vs. 2%, p < 0.001). EZH2 expression did not correlate with expression of other PRC2 components (EED and SUZ12), H3K27me3, MHC-I, and MHC-II. Patients with EZH2 expression (EZH2+) had a poorer overall survival (OS) compared with patients without EZH2 expression (EZH2-) (median OS: 3.9 years versus 9.4 years, respectively, p < 0.001). EZH2 expression also predicted a poorer prognosis in MCL patients with classic histology (median OS, 4.6 years for EZH2+ and 9.6 years for EZH2-negative, respectively, p < 0.001) as well as aggressive histology (median OS, 3.7 years for EZH2+ and 7.9 years for EZH2-negative, respectively, p = 0.046). However, EZH2 expression did not independently correlate with overall survival in a multivariate analysis. Gene expression analysis and pathway enrichment analysis demonstrated a significant enrichment in cell cycle and mitotic transition pathways in MCL with EZH2 expression. EZH2 expression detected by immunohistochemistry is present in 38% of MCL cases and it is associated with high proliferation rate, p53 overexpression, aggressive histologic variants, and poorer OS. Based on gene expression profiling data, EZH2 expression could potentiate cell cycle machinery in MCL. These data suggest that assessment of EZH2 expression could be useful to stratify MCL patients into low- and high-risk groups.
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Affiliation(s)
- Diana Martinez-Baquero
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Ali Sakhdari
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
- Department of Laboratory Medicine and Pathobiology, University Health Network, The University of Toronto, Toronto, ON, Canada
| | - Huan Mo
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Do Hwan Kim
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Shaoying Li
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ken H Young
- Division of Hematopathology and Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Dennis P O'Malley
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
- NeoGenomics, Aliso Viejo, CA, USA
| | - Ahmet Dogan
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Preetesh Jain
- Department of Lymphoma and Myeloma, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Michael L Wang
- Department of Lymphoma and Myeloma, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Timothy J McDonnell
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Roberto N Miranda
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Francisco Vega
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Chi Young Ok
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
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6
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De Martino M, Esposito F, Fusco A. Critical role of the high mobility group A proteins in hematological malignancies. Hematol Oncol 2021; 40:2-10. [PMID: 34637548 PMCID: PMC9293314 DOI: 10.1002/hon.2934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 12/17/2022]
Abstract
The high mobility group A (HMGA) protein family is composed of three non‐histone chromatin remodeling proteins that act as architectural transcriptional factors. Indeed, although HMGA proteins lack transcriptional activity per se, they bind the minor groove of DNA at AT‐rich sequences, and, interacting with the transcription machinery, are able to modify chromatin modeling, thus regulating the expression of several genes. HMGA proteins have been deeply involved in embryogenesis process, and a large volume of studies has pointed out their key role in human cancer. Here, we review the studies on the role of the HMGA proteins in human hematological malignancies: they are overexpressed in most of the cases and their expression correlates with a reduced survival. In some cases, such as in acute lymphoblastic leukemia and acute myelogenous leukemia, HMGA2 gene rearrangements have been also described. Finally, recent studies evidence a synergism between HMGA and EZH2 in diffuse B‐cell lymphomas, suggesting an innovative therapy for this disease based on the inhibition of the function of both these proteins.
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Affiliation(s)
- Marco De Martino
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), National Research Council (CNR), Institute for Experimental Endocrinology and Oncology (IEOS) "G. Salvatore", University of Naples "Federico II", Naples, Italy.,Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Francesco Esposito
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), National Research Council (CNR), Institute for Experimental Endocrinology and Oncology (IEOS) "G. Salvatore", University of Naples "Federico II", Naples, Italy
| | - Alfredo Fusco
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), National Research Council (CNR), Institute for Experimental Endocrinology and Oncology (IEOS) "G. Salvatore", University of Naples "Federico II", Naples, Italy
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7
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Sadeghi L, Wright AP. Migration and Adhesion of B-Lymphocytes to Specific Microenvironments in Mantle Cell Lymphoma: Interplay between Signaling Pathways and the Epigenetic Landscape. Int J Mol Sci 2021; 22:ijms22126247. [PMID: 34200679 PMCID: PMC8228059 DOI: 10.3390/ijms22126247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Lymphocyte migration to and sequestration in specific microenvironments plays a crucial role in their differentiation and survival. Lymphocyte trafficking and homing are tightly regulated by signaling pathways and is mediated by cytokines, chemokines, cytokine/chemokine receptors and adhesion molecules. The production of cytokines and chemokines is largely controlled by transcription factors in the context of a specific epigenetic landscape. These regulatory factors are strongly interconnected, and they influence the gene expression pattern in lymphocytes, promoting processes such as cell survival. The epigenetic status of the genome plays a key role in regulating gene expression during many key biological processes, and it is becoming more evident that dysregulation of epigenetic mechanisms contributes to cancer initiation, progression and drug resistance. Here, we review the signaling pathways that regulate lymphoma cell migration and adhesion with a focus on Mantle cell lymphoma and highlight the fundamental role of epigenetic mechanisms in integrating signals at the level of gene expression throughout the genome.
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8
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De Martino M, Nicolau-Neto P, Ribeiro Pinto LF, Traverse-Glehen A, Bachy E, Gigantino V, De Cecio R, Bertoni F, Chieffi P, Fusco A, Esposito F. HMGA1 induces EZH2 overexpression in human B-cell lymphomas. Am J Cancer Res 2021; 11:2174-2187. [PMID: 34094676 PMCID: PMC8167683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/03/2021] [Indexed: 06/12/2023] Open
Abstract
EZH2 is an enzymatic subunit of PRC2, an epigenetic regulator that triggers the methylation of the histone H3 lysine 27 silencing the transcription of several genes. EZH2 has a critical role in cancer progression, since its overexpression has been associated with increased cancer cell invasiveness, drug resistance and poor patient survival. However, the mechanisms accounting for EZH2 overexpression in cancer remain still unclear. Intriguingly, also HMGA protein overexpression is a feature of many human malignancies and correlates with the presence of metastases and a poor outcome. The HMGA proteins, including HMGA1 and HMGA2, belong to the architectural transcription factors that play a key role in the organization of chromatin structure. Here, we report a statistically significant correlation between HMGA1 and EZH2 expression in human lymphomas. We demonstrate that HMGA1 is able to bind EZH2 promoter and induce its activity. Consistently, silencing of HMGA1 expression results in the downregulation of the EZH2 levels leading to a decreased proliferation and migration rate of human lymphoma cell lines. Therefore, these data identify HMGA1 as an EZH2 activator, suggesting a novel molecular mechanism contributing to EZH2 overexpression in human malignancies and a synergism of these proteins in cancer progression.
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Affiliation(s)
- Marco De Martino
- Institute of Endocrinology and Experimental Oncology-CNR c/o Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”Naples, Italy
| | - Pedro Nicolau-Neto
- Molecular Carcinogenesis Program, National Cancer Institute-INCARua Andre Cavalcanti 37, Rio de Janeiro 20231-050, Brazil
| | - Luis Felipe Ribeiro Pinto
- Molecular Carcinogenesis Program, National Cancer Institute-INCARua Andre Cavalcanti 37, Rio de Janeiro 20231-050, Brazil
- Department of Biochemistry, Roberto Alcantara Gomes Biology Institute, State University of Rio de JaneiroRio de Janeiro 20551-030, Brazil
| | - Alexandra Traverse-Glehen
- Hospices Civils de Lyon, Department of Pathological AnatomyLyon, France
- Claude Bernard Lyon 1 UniversityLyon, France
| | - Emmanuel Bachy
- Claude Bernard Lyon 1 UniversityLyon, France
- Department of Hematology, Hospices Civils de Lyon, Lyon Sud HospitalPierre-Bénite, France
| | - Vincenzo Gigantino
- Pathology Unit, National Cancer Institute, IRCCS, Pascale FoundationNaples, Italy
| | - Rossella De Cecio
- Pathology Unit, National Cancer Institute, IRCCS, Pascale FoundationNaples, Italy
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USIBellinzona, Switzerland
- Oncology Institute of Southern SwitzerlandBellinzona, Switzerland
| | - Paolo Chieffi
- Department of Psychology, University of Campania “L. Vanvitelli”Caserta, Italy
| | - Alfredo Fusco
- Institute of Endocrinology and Experimental Oncology-CNR c/o Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”Naples, Italy
| | - Francesco Esposito
- Institute of Endocrinology and Experimental Oncology-CNR c/o Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”Naples, Italy
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Kagiyama Y, Fujita S, Shima Y, Yamagata K, Katsumoto T, Nakagawa M, Honma D, Adachi N, Araki K, Kato A, Inaki K, Ono Y, Fukuhara S, Kobayashi Y, Tobinai K, Kitabayashi I. CDKN1C-mediated growth inhibition by an EZH1/2 dual inhibitor overcomes resistance of mantle cell lymphoma to ibrutinib. Cancer Sci 2021; 112:2314-2324. [PMID: 33792119 PMCID: PMC8177787 DOI: 10.1111/cas.14905] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 12/26/2022] Open
Abstract
Mantle cell lymphoma (MCL) is a rare subtype of non‐Hodgkin's lymphoma, which is characterized by overexpression of cyclin D1. Although novel drugs, such as ibrutinib, show promising clinical outcomes, relapsed MCL often acquires drug resistance. Therefore, alternative approaches for refractory and relapsed MCL are needed. Here, we examined whether a novel inhibitor of enhancer of zeste homologs 1 and 2 (EZH1/2), OR‐S1 (a close analog of the clinical‐stage compound valemetostat), had an antitumor effect on MCL cells. In an ibrutinib‐resistant MCL patient–derived xenograft (PDX) mouse model, OR‐S1 treatment by oral administration significantly inhibited MCL tumor growth, whereas ibrutinib did not. In vitro growth assays showed that compared with an established EZH2‐specific inhibitor GSK126, OR‐S1 had a marked antitumor effect on MCL cell lines. Furthermore, comprehensive gene expression analysis was performed using OR‐S1–sensitive or insensitive MCL cell lines and showed that OR‐S1 treatment modulated B‐cell activation, differentiation, and cell cycle. In addition, we identified Cyclin Dependent Kinase Inhibitor 1C (CDKN1C, also known as p57, KIP2), which contributes to cell cycle arrest, as a direct target of EZH1/2 and showed that its expression influenced MCL cell proliferation. These results suggest that EZH1/2 may be a potential novel target for the treatment of aggressive ibrutinib‐resistant MCL via CDKN1C‐mediated cell cycle arrest.
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Affiliation(s)
- Yuki Kagiyama
- Division of Haematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Shuhei Fujita
- Division of Haematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Yutaka Shima
- Division of Haematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazutsune Yamagata
- Division of Haematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Takuo Katsumoto
- Division of Haematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Makoto Nakagawa
- Division of Haematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Daisuke Honma
- Oncology Research Laboratories, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Nobuaki Adachi
- Oncology Research Laboratories, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Kazushi Araki
- Oncology Research Laboratories, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Ayako Kato
- Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co., Ltd, Tokyo, Japan
| | - Koichiro Inaki
- Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co., Ltd, Tokyo, Japan
| | - Yoshimasa Ono
- Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co., Ltd, Tokyo, Japan
| | - Suguru Fukuhara
- Department of Haematology, National Cancer Center Hospital, Tokyo, Japan
| | - Yukio Kobayashi
- Department of Haematology, National Cancer Center Hospital, Tokyo, Japan
| | - Kensei Tobinai
- Department of Haematology, National Cancer Center Hospital, Tokyo, Japan
| | - Issay Kitabayashi
- Division of Haematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
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Quentmeier H, Pommerenke C, Hauer V, Uphoff CC, Zaborski M, Drexler HG. EZH2-activating mutation: no reliable indicator for efficacy of methyltransferase inhibitors. Leuk Lymphoma 2020; 61:2885-2893. [PMID: 32715799 DOI: 10.1080/10428194.2020.1795155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
EZH2 gain of function mutations (EZH2GOFmu) has been implicated in the pathogenesis of B-non-Hodgkin lymphoma. The EZH2-specific inhibitor GSK126 inhibits trimethylation of histone H3K27 and induces target gene expression. However, in 3/4 EZH2 GOFmu B-NHL lymphoma cell lines, GSK126 (400 nM) did not induce growth arrest. Only at high doses (10 µM), the inhibitor was effective as antiproliferative agent, comparably in EZH2 GOFmu, wild-type, and EZH2-negative cell lines, suggesting that at high concentrations, the antiproliferative effects of GSK126 are off-target effects. In sum, we could not confirm that B-NHL cell lines with EZH2 GOFmu show a higher sensitivity to GSK126 than EZH2 wild-type cell lines do. Only 1/4 EZH2 GOFmu B-NHL cell lines tested (PFEIFFER) were sensitive to GSK126 (400 nM) inducing growth arrest. If these results can be translated to patients, they raise the question of whether the presence of EZH2 activating mutations alone allows selection for targeted therapy with EZH2 inhibitors.
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Affiliation(s)
- Hilmar Quentmeier
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Bioinformatics and Databases, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vivien Hauer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cord C Uphoff
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Margarete Zaborski
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Wang J, Li P, Xu X, Zhang B, Zhang J. MicroRNA-200a Inhibits Inflammation and Atherosclerotic Lesion Formation by Disrupting EZH2-Mediated Methylation of STAT3. Front Immunol 2020; 11:907. [PMID: 32655542 PMCID: PMC7324475 DOI: 10.3389/fimmu.2020.00907] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022] Open
Abstract
Endothelial inflammation and dysfunction are critical to the process of atherosclerosis. Emerging evidence demonstrates that upregulation of miR-200a reduces VCAM-1 expression and prevents monocytic cell adhesion onto the aortic endothelium. However, limited information is available about the role of microRNA-200a (miR-200a) in facilitating atherosclerotic lesion formation. We investigated the anti-inflammatory and anti-atherosclerotic actions of miR-200a. Human umbilical vein endothelial cells (HUVECs) were cultured in the presence of oxidized low-density lipoprotein (ox-LDL), and their viability and apoptosis were evaluated using CCK-8 assays and flow cytometric analysis. The enhancer of zeste homolog 2 (EZH2) promoter activity was evaluated in the presence of miR-200a by dual luciferase reporter gene assay. EZH2-mediated methylation of signal transducer and activator of transcription 3 (STAT3) was validated by ChIP and IP assays. ApoE-/- mice were given a 12-week high-fat diet and developed as in vivo atherosclerotic models. miR-200a was downregulated but EZH2 and HMGB1 were upregulated in ox-LDL-treated HUVECs and the aorta tissues of atherosclerotic mouse models. Elevated miR-200a was shown to protect HUVECs against ox-LDL-induced apoptosis and inflammation. EZH2 was verified as a target of miR-200a. The protective effects of miR-200a were abrogated upon an elevation of EZH2. EZH2 methylated STAT3 and enhanced STAT3 activity by increased tyrosine phosphorylation of STAT3, thereby increasing apoptosis and release of pro-inflammatory cytokines in ox-LDL-treated HUVECs. An anti-atherosclerotic role of miR-200a was also demonstrated in atherosclerotic mouse models. Our study demonstrates that miR-200a has anti-inflammatory and anti-atherosclerotic activities dependent on the EZH2/STAT3 signaling cascade.
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Affiliation(s)
- Jinpeng Wang
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, China
| | - Ping Li
- Department of Developmental Pediatrics, The Second Hospital of Jilin University, Changchun, China
| | - Xiaofei Xu
- Department of Radiology, The Second Hospital of Jilin University, Changchun, China
| | - Beilin Zhang
- Department of Physiology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Jing Zhang
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, China
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12
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Dong Z, Gao M, Li C, Xu M, Liu S. LncRNA UCA1 Antagonizes Arsenic-Induced Cell Cycle Arrest through Destabilizing EZH2 and Facilitating NFATc2 Expression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903630. [PMID: 32537408 PMCID: PMC7284218 DOI: 10.1002/advs.201903630] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/17/2020] [Accepted: 03/08/2020] [Indexed: 05/17/2023]
Abstract
Arsenic (As) is a widespread metalloid contaminant, and its internal exposure is demonstrated to cause serious detrimental health problems. Albeit considerable studies are performed to interrogate the molecular mechanisms responsible for As-induced toxicities, the exact mechanisms are not fully understood yet, especially at the epigenetic regulation level. In the present study, it is identified that long non-coding RNA (lncRNA) urothelial cancer associated 1 (UCA1) alleviates As-induced G2/M phase arrest in human liver cells. Intensive mechanistic investigations illustrate that UCA1 interacts with enhancer of zeste homolog 2 (EZH2) and accelerates the latter's protein turnover rate under normal and As-exposure conditions. The phosphorylation of EZH2 at the Thr-487 site by cyclin dependent kinase 1 (CDK1) is responsible for As-induced EZH2 protein degradation, and UCA1 enhances this process through increasing the interaction between CDK1 and EZH2. As a consequence, the cell cycle regulator nuclear factor of activated T cells 2 (NFATc2), a downstream target of EZH2, is upregulated to resist As-blocked cell cycle progress and cytotoxicity. In conclusion, the findings decipher a novel prosurvival signaling pathway underlying As toxicity from the perspective of epigenetic regulation: UCA1 facilitates the ubiquitination of EZH2 to upregulate NFATc2 and further antagonizes As-induced cell cycle arrest.
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Affiliation(s)
- Zheng Dong
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijing100049China
| | - Ming Gao
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijing100049China
| | - Changying Li
- Liver Research CenterBeijing Friendship HospitalCapital Medical UniversityBeijing100050China
| | - Ming Xu
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijing100049China
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijing100049China
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13
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Sadeghi L, Arvidsson G, Merrien M, Wasik AM, Görgens A, Smith CE, Sander B, P. Wright A. Differential B-Cell Receptor Signaling Requirement for Adhesion of Mantle Cell Lymphoma Cells to Stromal Cells. Cancers (Basel) 2020; 12:cancers12051143. [PMID: 32370190 PMCID: PMC7281289 DOI: 10.3390/cancers12051143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 01/01/2023] Open
Abstract
Interactions between lymphoma cells and stromal cells play a key role in promoting tumor survival and development of drug resistance. We identified differences in key signaling pathways between the JeKo-1 and REC-1 mantle cell lymphoma (MCL) cell lines, displaying different patterns of stromal cell adhesion and chemotaxis towards stroma-conditioned medium. The identified adhesion-regulated genes reciprocated important aspects of microenvironment-mediated gene modulation in MCL patients. Five-hundred and ninety genes were differently regulated between the cell lines upon adhesion to stromal cells, while 32 genes were similarly regulated in both cell lines. Regulation of B-cell Receptor (BCR) signature genes in adherent cells was specific for JeKo-1. Inhibition of BCR using siRNA or clinically approved inhibitors, Ibrutinib and Acalabrutinib, decreased adhesion of JeKo-1, but not REC-1 cells. Cell surface levels of chemokine receptor CXCR4 were higher in JeKo-1, facilitating migration and adhesion of JeKo-1 but not REC-1 cells. Surface levels of ICAM1 adhesion protein differ for REC-1 and JeKo-1. While ICAM1 played a positive role in adherence of both cell lines to stromal cells, S1PR1 had an inhibitory effect. Our results provide a model framework for further investigation of mechanistic differences in patient-response to new pathway-specific drugs.
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Affiliation(s)
- Laia Sadeghi
- Department of Laboratory Medicine, Division of Biomedical and Cellular Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden; (L.S.); (G.A.); (A.G.); (C.I.E.S.)
| | - Gustav Arvidsson
- Department of Laboratory Medicine, Division of Biomedical and Cellular Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden; (L.S.); (G.A.); (A.G.); (C.I.E.S.)
| | - Magali Merrien
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, 141 52 Stockholm, Sweden; (M.M.); (A.M.W.); (B.S.)
| | - Agata M. Wasik
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, 141 52 Stockholm, Sweden; (M.M.); (A.M.W.); (B.S.)
| | - André Görgens
- Department of Laboratory Medicine, Division of Biomedical and Cellular Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden; (L.S.); (G.A.); (A.G.); (C.I.E.S.)
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg, 45 147 Essen, Germany
| | - C.I. Edvard Smith
- Department of Laboratory Medicine, Division of Biomedical and Cellular Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden; (L.S.); (G.A.); (A.G.); (C.I.E.S.)
| | - Birgitta Sander
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, 141 52 Stockholm, Sweden; (M.M.); (A.M.W.); (B.S.)
| | - Anthony P. Wright
- Department of Laboratory Medicine, Division of Biomedical and Cellular Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden; (L.S.); (G.A.); (A.G.); (C.I.E.S.)
- Correspondence:
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14
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Liu Y, Niu Y, Li L, Timani KA, He VL, Sanburns C, Xie J, He JJ. Tat expression led to increased histone 3 tri-methylation at lysine 27 and contributed to HIV latency in astrocytes through regulation of MeCP2 and Ezh2 expression. J Neurovirol 2019; 25:508-519. [PMID: 31020497 PMCID: PMC6750972 DOI: 10.1007/s13365-019-00751-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/03/2019] [Accepted: 04/04/2019] [Indexed: 02/07/2023]
Abstract
Astrocytes are susceptible to HIV infection and potential latent HIV reservoirs. Tat is one of three abundantly expressed HIV early genes in HIV-infected astrocytes and has been shown to be a major pathogenic factor for HIV/neuroAIDS. In this study, we sought to determine if and how Tat expression would affect HIV infection and latency in astrocytes. Using the glycoprotein from vesicular stomatitis virus-pseudotyped red-green HIV (RGH) reporter viruses, we showed that HIV infection was capable of establishing HIV latency in astrocytes. We also found that Tat expression decreased the generation of latent HIV-infected cells. Activation of latent HIV-infected astrocytes showed that treatment of GSK126, a selective inhibitor of methyltransferase enhancer of zeste homolog 2 (Ezh2) that is specifically responsible for tri-methylation of histone 3 lysine 27 (H3K27me3), led to activation of significantly more latent HIV-infected Tat-expressing astrocytes. Molecular analysis showed that H3K27me3, Ezh2, MeCP2, and Tat all exhibited a similar bimodal expression kinetics in the course of HIV infection and latency in astrocytes, although H3K27me3, Ezh2, and MeCP2 were expressed higher in Tat-expressing astrocytes and their expression were peaked immediately preceding Tat expression. Subsequent studies showed that Tat expression alone was sufficient to induce H3K27me3 expression, likely through its regulation of Ezh2 and MeCP2 expression. Taken together, these results showed for the first time that Tat expression induced H3K27me3 expression and contributed to HIV latency in astrocytes and suggest a new role and novel mechanism for Tat in HIV latency.
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Affiliation(s)
- Ying Liu
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA.
| | - Yinghua Niu
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
| | - Lu Li
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
| | - Khalid A Timani
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
| | - Victor L He
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
| | - Chris Sanburns
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
| | - Jiafeng Xie
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA
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15
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Kosalai ST, Morsy MHA, Papakonstantinou N, Mansouri L, Stavroyianni N, Kanduri C, Stamatopoulos K, Rosenquist R, Kanduri M. EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia. Epigenetics 2019; 14:1125-1140. [PMID: 31216925 PMCID: PMC6773411 DOI: 10.1080/15592294.2019.1633867] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
EZH2 is overexpressed in poor-prognostic chronic lymphocytic leukaemia (CLL) cases, acting as an oncogene; however, thus far, the EZH2 target genes in CLL have not been disclosed. In this study, using ChIP-sequencing, we identified EZH2 and H3K27me3 target genes in two prognostic subgroups of CLL with distinct prognosis and outcome, i.e., cases with unmutated (U-CLL, n = 6) or mutated IGHV genes (M-CLL, n = 6). While the majority of oncogenic pathways were equally enriched for EZH2 target genes in both prognostic subgroups, PI3K pathway genes were differentially bound by EZH2 in U-CLL versus M-CLL. The occupancy of EZH2 for selected PI3K pathway target genes was validated in additional CLL samples (n = 16) and CLL cell lines using siRNA-mediated EZH2 downregulation and ChIP assays. Intriguingly, we found that EZH2 directly binds to the IGF1R promoter along with MYC and upregulates IGF1R expression in U-CLL, leading to downstream PI3K activation. By investigating an independent CLL cohort (n = 96), a positive correlation was observed between EZH2 and IGF1R expression with higher levels in U-CLL compared to M-CLL. Accordingly, siRNA-mediated downregulation of either EZH2, MYC or IGF1R and treatment with EZH2 and MYC pharmacological inhibitors in the HG3 CLL cell line induced a significant reduction in PI3K pathway activation. In conclusion, we characterize for the first time EZH2 target genes in CLL revealing a hitherto unknown implication of EZH2 in modulating the PI3K pathway in a non-canonical, PRC2-independent way, with potential therapeutic implications considering that PI3K inhibitors are effective therapeutic agents for CLL.
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Affiliation(s)
- Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | | | - Nikos Papakonstantinou
- Institute of Applied Biosciences, Center for Research and Technology Hellas , Thessaloniki , Greece
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet , Stockholm , Sweden
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital , Thessaloniki , Greece
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas , Thessaloniki , Greece
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet , Stockholm , Sweden
| | - Meena Kanduri
- Department of Clinical chemistry and Transfusion medicine, Sahlgrenska University Hospital , Gothenburg , Sweden
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16
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Li L, Zhang X, Liu Q, Yin H, Diao Y, Zhang Z, Wang Y, Gao Y, Ren X, Li J, Cui D, Lu Y, Liu H. Emerging role of HOX genes and their related long noncoding RNAs in lung cancer. Crit Rev Oncol Hematol 2019; 139:1-6. [PMID: 31112877 DOI: 10.1016/j.critrevonc.2019.04.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/12/2019] [Accepted: 04/19/2019] [Indexed: 01/02/2023] Open
Abstract
The transcription factor homeobox (Hox) proteins are the master regulator for the embryonic development. Studies have identified new functions for HOX in the regulation of metabolism and other primary cellular processes in humans. Their dysregulation has been observed in a variety of cancers and accumulating evidence has revealed the crucial role of HOX in cancer progression, metastasis, and resistance to therapy. HOX-related long non-coding RNAs (lncRNAs) became the most attracting lncRNAs recently that play critical role in gene regulation and chromatin dynamics in cancers. In this review, we explore the roles of HOX and their related lncRNAs in lung cancer, indicating HOX genes as potential therapeutic targets in lung cancer.
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Affiliation(s)
- Lianlian Li
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Xiaoyu Zhang
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Qian Liu
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China; School of Life Science, Ludong University, Yantai, 264025, Shandong, China
| | - Haipeng Yin
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Yutao Diao
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Zhiyong Zhang
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Yang Wang
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Yan Gao
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Xia Ren
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Juan Li
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Dayong Cui
- School of Life Sciences, Qilu Normal University, Jinan, 250200, Shandong, China
| | - Yanqin Lu
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China
| | - Hongyan Liu
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China.
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17
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Xu J, Wang Z, Lu W, Jiang H, Lu J, Qiu J, Ye G. EZH2 promotes gastric cancer cells proliferation by repressing p21 expression. Pathol Res Pract 2019; 215:152374. [PMID: 30952377 DOI: 10.1016/j.prp.2019.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/09/2019] [Accepted: 03/02/2019] [Indexed: 12/12/2022]
Abstract
EZH2 is a core component of the polycomb repressive complex 2 (PRC2), which catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) and promotes carcinogenesis by epigenetically silencing many tumor suppressor genes. Increased EZH2 expression is a marker of advanced and metastatic in many cancers, including lung, prostate and breast cancer, and it has been considered as a potential novel therapeutic target. However, the clinical significance and molecular mechanisms of EZH2 controlling gastric cancer cell proliferation and invasion are not well documented. In this study, immunohistochemical analysis was conducted to investigate the EZH2 expression in gastric cancer. We found that EZH2 levels were increased in gastric cancer tissues compared with adjacent normal tissues. Moreover, patients with high levels of EZH2 expression had a relatively poor prognosis. Furthermore, knockdown of EZH2 expression by siRNA could impair cell proliferation and invasion both in vitro and vivo. Finally, we found that EZH2 influences gastric cancer cells proliferation partly through regulating p21 expression. Our findings present that EZH2 over-expression can be identified as a poor prognostic biomarker in gastric cancer.
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Affiliation(s)
- Jiewei Xu
- Department of General Surgery, Huzhou Central Hospital, Huzhou, People's Republic of China
| | - Zhong Wang
- Department of General Surgery, Huzhou Central Hospital, Huzhou, People's Republic of China
| | - Wei Lu
- Department of General Surgery, Huzhou Central Hospital, Huzhou, People's Republic of China
| | - Hao Jiang
- Department of General Surgery, Huzhou Central Hospital, Huzhou, People's Republic of China
| | - Jun Lu
- Department of General Surgery, Huzhou Central Hospital, Huzhou, People's Republic of China
| | - Jian Qiu
- Department of Obstetrics and Gynecology, Huzhou Central Hospital, Huzhou, 313000, People's Republic of China.
| | - Guochao Ye
- Department of General Surgery, Huzhou Central Hospital, Huzhou, People's Republic of China.
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18
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Jiang F, Li Y, Si L, Zhang Z, Li Z. Interaction of EZH2 and P65 is involved in the arsenic trioxide-induced anti-angiogenesis in human triple-negative breast cancer cells. Cell Biol Toxicol 2019; 35:361-371. [DOI: 10.1007/s10565-018-09458-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023]
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19
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Szurián K, Csala I, Marosvári D, Rajnai H, Dezső K, Bödör C, Piurkó V, Matolcsy A, Reiniger L. EZH2 is upregulated in the proliferation centers of CLL/SLL lymph nodes. Exp Mol Pathol 2018; 105:161-165. [PMID: 30031020 DOI: 10.1016/j.yexmp.2018.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 01/08/2023]
Abstract
Lymph node involvement of chronic lymphocytic leukaemia/small lymphocytic lymphoma (CLL/SLL) is characterised by the diffuse infiltration of small neoplastic lymphocytes, which is accompanied by the presence of proliferation centres (PCs) comprising prolymphocytes and paraimmunoblasts. There is increasing evidence of accumulation of various molecular alterations in the tumour cells of PCs, which may explain why extended PCs are related to a less favourable prognosis. To further characterize PCs, we compared the expression level of EZH2 protein, the overexpression of which has recently been recognized as poor prognostic factor in CLL/SLL, in the PCs and the intervening small cell areas in lymph nodes of 15 patients with CLL/SLL. We also investigated the mutational profile of EZH2 and the expression of its upstream regulators c-Myc, E2F1, pRB and miR-26a. Our results showed a significantly increased expression of EZH2 in the PCs. No EZH2 mutations were detected, however, overexpression of c-Myc, E2F1 and pRb proteins as well as reduced expression of the tumor suppressor miR-26a were demonstrated in the PCs. In summary our findings indicate that EZH2 pathway is significantly upregulated in the PCs of CLL/SLL lymph nodes, providing further evidence for the distinguished biological features of the PCs.
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Affiliation(s)
- Kinga Szurián
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Irén Csala
- Institute of Behavioural Sciences, Semmelweis University, Budapest, Hungary
| | - Dóra Marosvári
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Hajnalka Rajnai
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Katalin Dezső
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Csaba Bödör
- MTA-SE Lendulet Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Violetta Piurkó
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - András Matolcsy
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Lilla Reiniger
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary; MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, 2nd Department of Pathology, Semmelweis University, Budapest, Hungary.
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20
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Papakonstantinou N, Ntoufa S, Chartomatsidou E, Kotta K, Agathangelidis A, Giassafaki L, Karamanli T, Bele P, Moysiadis T, Baliakas P, Sutton LA, Stavroyianni N, Anagnostopoulos A, Makris AM, Ghia P, Rosenquist R, Stamatopoulos K. The histone methyltransferase EZH2 as a novel prosurvival factor in clinically aggressive chronic lymphocytic leukemia. Oncotarget 2017; 7:35946-35959. [PMID: 27191993 PMCID: PMC5094974 DOI: 10.18632/oncotarget.9371] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/24/2016] [Indexed: 12/19/2022] Open
Abstract
The histone methyltransferase EZH2 induces gene repression through trimethylation of histone H3 at lysine 27 (H3K27me3). EZH2 overexpression has been reported in many types of cancer and associated with poor prognosis. Here we investigated the expression and functionality of EZH2 in chronic lymphocytic leukemia (CLL). Aggressive cases with unmutated IGHV genes (U-CLL) displayed significantly higher EZH2 expression compared to indolent CLL cases with mutated IGHV genes (M-CLL); furthermore, in U-CLL EZH2 expression was upregulated with disease progression. Within U-CLL, EZH2high cases harbored significantly fewer (p = 0.033) TP53 gene abnormalities compared to EZH2low cases. EZH2high cases displayed high H3K27me3 levels and increased viability suggesting that EZH2 is functional and likely confers a survival advantage to CLL cells. This argument was further supported by siRNA-mediated downmodulation of EZH2 which resulted in increased apoptosis. Notably, at the intraclonal level, cell proliferation was significantly associated with EZH2 expression. Treatment of primary CLL cells with EZH2 inhibitors induced downregulation of H3K27me3 levels leading to increased cell apoptosis. In conclusion, EZH2 is overexpressed in adverse-prognosis CLL and associated with increased cell survival and proliferation. Pharmacologic inhibition of EZH2 catalytic activity promotes apoptosis, highlighting EZH2 as a novel potential therapeutic target for specific subgroups of patients with CLL.
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Affiliation(s)
- Nikos Papakonstantinou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stavroula Ntoufa
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elisavet Chartomatsidou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Konstantia Kotta
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Andreas Agathangelidis
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Lefki Giassafaki
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Tzeni Karamanli
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Panagiota Bele
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lesley Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | | | - Antonios M Makris
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Paolo Ghia
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
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Tsou PS, Coit P, Kilian NC, Sawalha AH. EZH2 Modulates the DNA Methylome and Controls T Cell Adhesion Through Junctional Adhesion Molecule A in Lupus Patients. Arthritis Rheumatol 2017; 70:98-108. [PMID: 28973837 DOI: 10.1002/art.40338] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/26/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE EZH2 is an epigenetic regulator that mediates H3K27 trimethylation (H3K27me3) and modulates DNA methylation. The aim of this study was to characterize the role of EZH2 in CD4+ T cells in the pathogenesis of systemic lupus erythematosus. METHODS EZH2 expression levels were determined in CD4+ T cells isolated from lupus patients and healthy controls. The epigenetic effects of EZH2 overexpression in CD4+ T cells were evaluated using a genome-wide DNA methylation approach. Gene expression profiles and microRNAs (miRNAs) were assessed by quantitative polymerase chain reaction, while protein expression was examined by Western blotting. A cell adhesion assay was used to assess adhesion of CD4+ T cells to human microvascular endothelial cells. RESULTS EZH2 and H3K27me3 levels were increased in CD4+ T cells from lupus patients compared to healthy controls. T cell production of EZH2 was down-regulated in the presence of miR-26a and miR-101, and levels of both miRNAs were reduced in lupus CD4+ T cells. Overexpression of EZH2 induced in CD4+ T cells resulted in significant DNA methylation changes. Genes involved in leukocyte adhesion and migration, including F11R (which encodes junctional adhesion molecule A [JAM-A]), became hypomethylated in CD4+ T cells when EZH2 was overexpressed. Overexpression of EZH2 resulted in increases in JAM-A expression and CD4+ T cell adhesion. Preincubation of EZH2-transfected CD4+ T cells with neutralizing antibodies against JAM-A significantly blunted cell adhesion. Similarly, CD4+ T cells from lupus patients overexpressed JAM-A and adhered significantly more to endothelial cells than to T cells from healthy controls. Blocking JAM-A or EZH2 significantly reduced the capacity of lupus CD4+ T cells to adhere to endothelial cells. CONCLUSION The results of this study identify a novel role of EZH2 in T cell adhesion mediated by epigenetic remodeling and up-regulation of JAM-A. Blockade of EZH2 or JAM-A might have therapeutic potential by acting to reduce T cell adhesion, migration, and extravasation in patients with lupus.
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22
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Kopparapu PK, Abdelrazak Morsy MH, Kanduri C, Kanduri M. Gene-body hypermethylation controlled cryptic promoter and miR26A1-dependent EZH2 regulation of TET1 gene activity in chronic lymphocytic leukemia. Oncotarget 2017; 8:77595-77608. [PMID: 29100411 PMCID: PMC5652802 DOI: 10.18632/oncotarget.20668] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/29/2017] [Indexed: 12/18/2022] Open
Abstract
The Ten-eleven-translocation 1 (TET1) protein is a member of dioxygenase protein family that catalyzes the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine. TET1 is differentially expressed in many cancers, including leukemia. However, very little is known about mechanism behind TET1 deregulation. Previously, by characterizing global methylation patterns in CLL patients using MBD-seq, we found TET1 as one of the differentially methylated regions with gene-body hypermethylation. Herein, we characterize mechanisms that control TET1 gene activity at the transcriptional level. We show that treatment of CLL cell lines with 5-aza 2´-deoxycytidine (DAC) results in the activation of miR26A1, which causes decrease in both mRNA and protein levels of EZH2, which in turn results in the decreased occupancy of EZH2 over the TET1 promoter and consequently the loss of TET1 expression. In addition, DAC treatment also leads to the activation of antisense transcription overlapping the TET1 gene from a cryptic promoter, located in the hypermethylated intronic region. Increased expression of intronic transcripts correlates with decreased TET1 promoter activity through the loss of RNA Pol II occupancy. Thus, our data demonstrate that TET1 gene activation in CLL depends on miR26A1 regulated EZH2 binding at the TET1 promoter and silencing of novel cryptic promoter by gene-body hypermethylation.
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Affiliation(s)
- Pradeep Kumar Kopparapu
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Mohammad Hamdy Abdelrazak Morsy
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
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23
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Clancy KW, Russell AM, Subramanian V, Nguyen H, Qian Y, Campbell RM, Thompson PR. Citrullination/Methylation Crosstalk on Histone H3 Regulates ER-Target Gene Transcription. ACS Chem Biol 2017; 12:1691-1702. [PMID: 28485572 DOI: 10.1021/acschembio.7b00241] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Posttranslational modifications of histone tails are a key contributor to epigenetic regulation. Histone H3 Arg26 and Lys27 are both modified by multiple enzymes, and their modifications have profound effects on gene expression. Citrullination of H3R26 by PAD2 and methylation of H3K27 by PRC2 have opposing downstream impacts on gene regulation; H3R26 citrullination activates gene expression, and H3K27 methylation represses gene expression. Both of these modifications are drivers of a variety of cancers, and their writer enzymes, PAD2 and EZH2, are the targets of drug therapies. After biochemical and cell-based analysis of these modifications, a negative crosstalk interaction is observed. Methylation of H3K27 slows citrullination of H3R26 30-fold, whereas citrullination of H3R26 slows methylation 30,000-fold. Examination of the mechanism of this crosstalk interaction uncovered a change in structure of the histone tail upon citrullination which prevents methylation by the PRC2 complex. This mechanism of crosstalk is reiterated in cell lines using knockdowns and inhibitors of both enzymes. Based our data, we propose a model in which, after H3 Cit26 formation, H3K27 demethylases are recruited to the chromatin to activate transcription. In total, our studies support the existence of crosstalk between citrullination of H3R26 and methylation of H3K27.
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Affiliation(s)
- Kathleen W. Clancy
- Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, Indiana 46285, United States
- Department
of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Anna-Maria Russell
- Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, Indiana 46285, United States
| | - Venkataraman Subramanian
- Department
of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Hannah Nguyen
- Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, Indiana 46285, United States
| | - Yuewei Qian
- Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, Indiana 46285, United States
| | - Robert M. Campbell
- Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, Indiana 46285, United States
| | - Paul R. Thompson
- Department
of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Program
in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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24
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Wang J, Hua L, Guo M, Yang L, Liu X, Li Y, Shang X, Luo J. Notable roles of EZH2 and DNMT1 in epigenetic dormancy of the SHP1 gene during the progression of chronic myeloid leukaemia. Oncol Lett 2017; 13:4979-4985. [PMID: 28599500 DOI: 10.3892/ol.2017.6050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 12/20/2016] [Indexed: 12/17/2022] Open
Abstract
Tumor development is associated with the methylation of cytosine-guanine (CpG) islands. The occurrence of methylation requires several factors, such as DNA methylation systems and polycomb group (PcG) proteins. At present, novel drugs are needed for the treatment of chronic myeloid leukaemia (CML), particularly considering the current prognosis of CML. The methylation status of the Src homology 2 domain-containing tyrosine phosphatase 1 (SHP1) gene, a negative regulator of signal transduction, has been identified as being altered in numerous haematological malignancies. DNA methyltransferase 1 (DNMT1) and the PcG protein complex member enhancer of zeste homolog 2 (EZH2) participate in a number of gene methylation processes. The present study investigated the methylation status of the SHP1 gene in CML, and examined the association between DNMT1 and EZH2 activity and the SHP1 gene methylation status to develop novel strategies for the treatment of CML. The results revealed that SHP1 gene methylation status was altered during the progression of CML. These data indicated that SHP1 gene methylation is associated with the progression of this disease. The associations of DNMT1 and EZH2 activities with the methylation status of the SHP1 gene were additionally investigated via chromatin immunoprecipitation. DNMT1 and EZH2 were revealed to be bound to the promoter region of the SHP1 gene, and were involved in the process of SHP1 methylation. Furthermore, DNMT1 and EZH2 were associated with disease progression. Thus, the findings of the present study suggest a new target for the treatment of CML, particularly for future drug development.
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Affiliation(s)
- Jing Wang
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Luoming Hua
- Department of Hematology, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Ming Guo
- Department of Hematology, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Lin Yang
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Xiaojun Liu
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Yanmeng Li
- Clinical Medicine College of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Xiaoyan Shang
- Clinical Medicine College of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Jianmin Luo
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
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25
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Daer RM, Cutts JP, Brafman DA, Haynes KA. The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells. ACS Synth Biol 2017; 6:428-438. [PMID: 27783893 DOI: 10.1021/acssynbio.5b00299] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to efficiently edit eukaryotic genomes, it is critical to test the impact of chromatin dynamics on CRISPR/Cas9 function and develop strategies to adapt the system to eukaryotic contexts. So far, research has extensively characterized the relationship between the CRISPR endonuclease Cas9 and the composition of the RNA-DNA duplex that mediates the system's precision. Evidence suggests that chromatin modifications and DNA packaging can block eukaryotic genome editing by custom-built DNA endonucleases like Cas9; however, the underlying mechanism of Cas9 inhibition is unclear. Here, we demonstrate that closed, gene-silencing-associated chromatin is a mechanism for the interference of Cas9-mediated DNA editing. Our assays use a transgenic cell line with a drug-inducible switch to control chromatin states (open and closed) at a single genomic locus. We show that closed chromatin inhibits binding and editing at specific target sites and that artificial reversal of the silenced state restores editing efficiency. These results provide new insights to improve Cas9-mediated editing in human and other mammalian cells.
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Affiliation(s)
- René M. Daer
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - Josh P. Cutts
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - David A. Brafman
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - Karmella A. Haynes
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
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26
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Xu F, Liu L, Chang CK, He Q, Wu LY, Zhang Z, Shi WH, Guo J, Zhu Y, Zhao YS, Gu SC, Fei CM, Li X. Genomic loss of EZH2 leads to epigenetic modifications and overexpression of the HOX gene clusters in myelodysplastic syndrome. Oncotarget 2016; 7:8119-30. [PMID: 26812882 PMCID: PMC4884980 DOI: 10.18632/oncotarget.6992] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/01/2016] [Indexed: 12/11/2022] Open
Abstract
The role of EZH2 in cancer is complex and may vary depending on cancer type or stage. We examined the effect of altered EZH2 levels on H3K27 methylation, HOX gene expression, and malignant phenotype in myelodysplastic syndrome (MDS) cell lines and an in vivo xenograft model. We also studied links between EZH2 expression and prognosis in MDS patients. Patients with high-grade MDS exhibited lower levels of EZH2 expression than those with low-grade MDS. Low EZH2 expression was associated with high percentages of blasts, shorter survival, and increased transformation of MDS into acute myeloid leukemia (AML). MDS patients frequently had reductions in EZH2 copy number. EZH2 knockdown increased tumor growth capacity and reduced H3K27me3 levels in both MDS-derived leukemia cells and in a xenograft model. H3K27me3 levels were reduced and HOX gene cluster expression was increased in MDS patients. EZH2 knockdown also increased HOX gene cluster expression by reducing H3K27me3, and H3K27 demethylating agents increased HOX gene cluster expression in MDS-derived cell lines. These findings suggest genomic loss of EZH2 contributes to overexpression of the HOX gene clusters in MDS through epigenetic modifications.
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Affiliation(s)
- Feng Xu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Li Liu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chun-Kang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Qi He
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Ling-Yun Wu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zheng Zhang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Wen-Hui Shi
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Juan Guo
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yang Zhu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - You-Shan Zhao
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shu-Cheng Gu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Cheng-Ming Fei
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xiao Li
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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27
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Antigen receptor stereotypy in chronic lymphocytic leukemia. Leukemia 2016; 31:282-291. [PMID: 27811850 DOI: 10.1038/leu.2016.322] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/30/2016] [Accepted: 10/10/2016] [Indexed: 02/06/2023]
Abstract
The discovery of almost identical or 'stereotyped' B-cell receptor immunoglobulins (BcR IG) among unrelated patients with chronic lymphocytic leukemia (CLL) cemented the idea of antigen selection in disease ontogeny and evolution. The systematic analysis of the stereotypy phenomenon in CLL revealed that around one-third of CLL patients may be grouped into subsets based on shared sequence motifs within the variable heavy complementarity determining region 3. Stereotyped subsets display a strikingly similar biology of the leukemic clones, referring to many different levels, from the immunogenetic and genetic and extending to the epigenetic and functional levels. Even more importantly, the homogeneity of stereotyped subsets has clinical consequences as patients assigned to the same stereotyped subset generally exhibit an overall similar disease course and outcome. In other words, stereotypy-based patient classification of CLL has already provided a more compartmentalized view of this otherwise heterogeneous disease and can assist in refining prognostication models. While this is relevant only for the one-third of cases expressing stereotyped BcR IG; in principle, however, the findings from further analysis of the stereotyped subsets may also contribute towards improved understanding of the remaining non-stereotyped fraction of CLL patients.
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28
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NBAT1 suppresses breast cancer metastasis by regulating DKK1 via PRC2. Oncotarget 2016; 6:32410-25. [PMID: 26378045 PMCID: PMC4741702 DOI: 10.18632/oncotarget.5609] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/26/2015] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNA NBAT1 (neuroblastoma associated transcript 1) regulates cell proliferation and invasion by interacting with PRC2 (polycomb repressive complex 2) member EZH2 (enhancer of zeste 2). Decreased expression of NBAT1 is associated with poor clinical outcome in neuroblastomas. However, the roles of NBAT1 in other cancers remain unknown. Here, we report that NBAT1 is down-regulated in various types of cancer. Particularly, reduced NBAT1 in breast cancer is associated with tumor metastasis and poor patient prognosis. In vitro, ectopic NBAT1 inhibits migration and invasion of breast cancer cells. Mechanistic study shows that NBAT1 is associated with PRC2 member EZH2 and regulates global gene expression profile. Among them, DKK1 (dickkopf WNT signaling pathway inhibitor 1) is found to be regulated by NBAT1 in a PRC2 dependent manner, and is responsible for NBAT1's effects in inhibiting migration and invasion of breast cancer cells. Taken together, our study demonstrates that long noncoding RNA NBAT1 is a potential breast cancer prognostic marker, as well as a potential therapeutic target to inhibit breast cancer metastasis.
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29
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Lv YC, Tang YY, Zhang P, Wan W, Yao F, He PP, Xie W, Mo ZC, Shi JF, Wu JF, Peng J, Liu D, Cayabyab FS, Zheng XL, Tang XY, Ouyang XP, Tang CK. Histone Methyltransferase Enhancer of Zeste Homolog 2-Mediated ABCA1 Promoter DNA Methylation Contributes to the Progression of Atherosclerosis. PLoS One 2016; 11:e0157265. [PMID: 27295295 PMCID: PMC4905646 DOI: 10.1371/journal.pone.0157265] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 05/26/2016] [Indexed: 01/08/2023] Open
Abstract
ATP-binding cassette transporter A1 (ABCA1) plays a critical role in maintaining cellular cholesterol homeostasis. The purpose of this study is to identify the molecular mechanism(s) underlying ABCA1 epigenetic modification and determine its potential impact on ABCA1 expression in macrophage-derived foam cell formation and atherosclerosis development. DNA methylation induced foam cell formation from macrophages and promoted atherosclerosis in apolipoprotein E-deficient (apoE−/−) mice. Bioinformatics analyses revealed a large CpG island (CGI) located in the promoter region of ABCA1. Histone methyltransferase enhancer of zeste homolog 2 (EZH2) downregulated ABCA1 mRNA and protein expression in THP-1 and RAW264.7 macrophage-derived foam cells. Pharmacological inhibition of DNA methyltransferase 1 (DNMT1) with 5-Aza-dC or knockdown of DNMT1 prevented the downregulation of macrophage ABCA1 expression, suggesting a role of DNA methylation in ABCA1 expression. Polycomb protein EZH2 induced DNMT1 expression and methyl-CpG-binding protein-2 (MeCP2) recruitment, and stimulated the binding of DNMT1 and MeCP2 to ABCA1 promoter, thereby promoting ABCA1 gene DNA methylation and atherosclerosis. Knockdown of DNMT1 inhibited EZH2-induced downregulation of ABCA1 in macrophages. Conversely, EZH2 overexpression stimulated DNMT1-induced ABCA1 gene promoter methylation and atherosclerosis. EZH2-induced downregulation of ABCA1 gene expression promotes foam cell formation and the development of atherosclerosis by DNA methylation of ABCA1 gene promoter.
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Affiliation(s)
- Yun-Cheng Lv
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
- Laboratory of Clinical Anatomy, University of South China, Hengyang, 421001, China
| | - Yan-Yan Tang
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, 410013, China
| | - Ping Zhang
- School of Electronics and Information Engineering, Hunan University of Science and Engineering, Yongzhou, Hunan, 425100, China
- School of Information Science and Engineering, Central South University, Changsha, Hunan, 410000, China
| | - Wei Wan
- Laboratory of Clinical Anatomy, University of South China, Hengyang, 421001, China
| | - Feng Yao
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Ping-Ping He
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Wei Xie
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Zhong-Cheng Mo
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Jin-Feng Shi
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Jian-Feng Wu
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Juan Peng
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Dan Liu
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
| | - Francisco S. Cayabyab
- Department of Surgery, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Xi-Long Zheng
- Department of Biochemistry and Molecular Biology, The Libin Cardiovascular Institute of Alberta, The University of Calgary, Health Sciences Center, 3330 Hospital Dr NW, Calgary, Alberta, T2N 4N1, Canada
| | - Xiang-Yang Tang
- Laboratory of Clinical Anatomy, University of South China, Hengyang, 421001, China
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, WCI Suite C5018, 1701 Uppergate Drive, Atlanta, GA, 30322, United States of America
| | - Xin-Ping Ouyang
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
- * E-mail: (CKT); (XPOY)
| | - Chao-Ke Tang
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, 421001, China
- * E-mail: (CKT); (XPOY)
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30
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Kopparapu PK, Bhoi S, Mansouri L, Arabanian LS, Plevova K, Pospisilova S, Wasik AM, Croci GA, Sander B, Paulli M, Rosenquist R, Kanduri M. Epigenetic silencing of miR-26A1 in chronic lymphocytic leukemia and mantle cell lymphoma: Impact on EZH2 expression. Epigenetics 2016; 11:335-43. [PMID: 27052808 DOI: 10.1080/15592294.2016.1164375] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Downregulation of miR26A1 has been reported in various B-cell malignancies; however, the mechanism behind its deregulation remains largely unknown. We investigated miR26A1 methylation and expression levels in a well-characterized series of chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL). From 450K methylation arrays, we first observed miR26A1 (cg26054057) as uniformly hypermethylated in MCL (n = 24) (all >75%), while CLL (n = 18) showed differential methylation between prognostic subgroups. Extended analysis using pyrosequencing confirmed our findings and real-time quantitative PCR verified low miR26A1 expression in both CLL (n = 70) and MCL (n = 38) compared to normal B-cells. Notably, the level of miR26A1 methylation predicted outcome in CLL, with higher levels seen in poor-prognostic, IGHV-unmutated CLL. Since EZH2 was recently reported as a target for miR26A1, we analyzed the expression levels of both miR26A1 and EZH2 in primary CLL samples and observed an inverse correlation. By overexpression of miR26A1 in CLL and MCL cell lines, reduced EZH2 protein levels were observed using both Western blot and flow cytometry. In contrast, methyl-inhibitor treatment led to upregulated miR26A1 expression with a parallel decrease of EZH2 expression. Finally, increased levels of apoptosis were observed in miR26A1-overexpressing cell lines, further underscoring the functional relevance of miR26A1. In summary, we propose that epigenetic silencing of miR26A1 is required for the maintenance of increased levels of EZH2, which in turn translate into a worse outcome, as shown in CLL, highlighting miR26A1 as a tumor suppressor miRNA.
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Affiliation(s)
- Pradeep Kumar Kopparapu
- a Department of Clinical Chemistry and Transfusion Medicine , Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University , Sweden
| | - Sujata Bhoi
- b Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala , Sweden
| | - Larry Mansouri
- b Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala , Sweden
| | - Laleh S Arabanian
- a Department of Clinical Chemistry and Transfusion Medicine , Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University , Sweden
| | - Karla Plevova
- c Central European Institute of Technology, Masaryk University and University Hospital Brno , Czech Republic
| | - Sarka Pospisilova
- c Central European Institute of Technology, Masaryk University and University Hospital Brno , Czech Republic
| | - Agata M Wasik
- d Department of Laboratory Medicine , Division of Pathology, Karolinska University Hospital , Sweden
| | | | - Birgitta Sander
- d Department of Laboratory Medicine , Division of Pathology, Karolinska University Hospital , Sweden
| | - Marco Paulli
- e Department of Molecular Medicine , University of Pavia , Italy
| | - Richard Rosenquist
- b Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala , Sweden
| | - Meena Kanduri
- a Department of Clinical Chemistry and Transfusion Medicine , Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University , Sweden
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31
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Beltran H, Prandi D, Mosquera JM, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BV, Varambally S, Tomlins SA, Nanus DM, Tagawa ST, Van Allen EM, Elemento O, Sboner A, Garraway LA, Rubin MA, Demichelis F. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med 2016; 22:298-305. [PMID: 26855148 PMCID: PMC4777652 DOI: 10.1038/nm.4045] [Citation(s) in RCA: 1094] [Impact Index Per Article: 136.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/11/2016] [Indexed: 12/13/2022]
Abstract
An increasingly recognized resistance mechanism to androgen receptor (AR)-directed therapy in prostate cancer involves epithelial plasticity, in which tumor cells demonstrate low to absent AR expression and often have neuroendocrine features. The etiology and molecular basis for this 'alternative' treatment-resistant cell state remain incompletely understood. Here, by analyzing whole-exome sequencing data of metastatic biopsies from patients, we observed substantial genomic overlap between castration-resistant tumors that were histologically characterized as prostate adenocarcinomas (CRPC-Adeno) and neuroendocrine prostate cancer (CRPC-NE); analysis of biopsy samples from the same individuals over time points to a model most consistent with divergent clonal evolution. Genome-wide DNA methylation analysis revealed marked epigenetic differences between CRPC-NE tumors and CRPC-Adeno, and also designated samples of CRPC-Adeno with clinical features of AR independence as CRPC-NE, suggesting that epigenetic modifiers may play a role in the induction and/or maintenance of this treatment-resistant state. This study supports the emergence of an alternative, 'AR-indifferent' cell state through divergent clonal evolution as a mechanism of treatment resistance in advanced prostate cancer.
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Affiliation(s)
- Himisha Beltran
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine. New York, NY
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine. New York, NY
| | - Davide Prandi
- Centre for Integrative Biology, University of Trento. Trento, Italy
| | - Juan Miguel Mosquera
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Department of Pathology and Laboratory Medicine. Weill Cornell Medicine. New York, NY
| | - Matteo Benelli
- Centre for Integrative Biology, University of Trento. Trento, Italy
| | - Loredana Puca
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
| | - Joanna Cyrta
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
| | - Clarisse Marotz
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
| | | | | | | | | | - David M. Nanus
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine. New York, NY
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine. New York, NY
| | - Scott T. Tagawa
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine. New York, NY
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine. New York, NY
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- The Broad Institute of MIT and Harvard, Boston, MA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Department of Physiology and Biophysics. Weill Cornell Medicine. New York, NY
| | - Andrea Sboner
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine. New York, NY
| | - Levi A. Garraway
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- The Broad Institute of MIT and Harvard, Boston, MA
| | - Mark A. Rubin
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine. New York, NY
- Department of Pathology and Laboratory Medicine. Weill Cornell Medicine. New York, NY
| | - Francesca Demichelis
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine. New York, NY
- Centre for Integrative Biology, University of Trento. Trento, Italy
- Institute for Computational Biomedicine, Weill Cornell Medicine. New York, NY
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32
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Liu C, Li S, Dai X, Ma J, Wan J, Jiang H, Wang P, Liu Z, Zhang H. PRC2 regulates RNA polymerase III transcribed non-translated RNA gene transcription through EZH2 and SUZ12 interaction with TFIIIC complex. Nucleic Acids Res 2015; 43:6270-84. [PMID: 26038315 PMCID: PMC4513857 DOI: 10.1093/nar/gkv574] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 05/20/2015] [Indexed: 11/12/2022] Open
Abstract
Polycomb repression complex 2 (PRC2) component EZH2 tri-methylates H3K27 and exerts epigenetic repression on target gene expression. EZH2-mediated epigenetic control of RNA polymerase II (Pol II) transcribed coding gene transcription has been well established. However, little is known about EZH2-mediated epigenetic regulation of RNA polymerase III (Pol III) transcription. Here we present a paradigm that EZH2 is involved in the repression of Pol III transcription via interaction with transcriptional factor complex IIIC (TFIIIC). EZH2 and H3K27me3 co-occupy the promoter of tRNATyr, 5S rRNA and 7SL RNA genes. Depletion of EZH2 or inhibition of EZH2 methyltransferase activity led to upregulation of Pol III target gene transcription. EZH2-mediated repression of Pol III transcribed gene expression requires presence of SUZ12. SUZ12 was able to interact with TFIIIC complex and knockdown of SUZ12 decreased occupancy of EZH2 and H3K27me3 at the promoter of Pol III target genes. Our findings pointed out a previously unidentified role of PRC2 complex in suppressing transcription of Pol III transcribed non-translated RNA genes, putting Pol III on a new layer of epigenetic regulation.
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Affiliation(s)
- Chang Liu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Shuai Li
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Xiaoyan Dai
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Ji Ma
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Junhu Wan
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Hao Jiang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Peng Wang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Zhaoli Liu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Hongquan Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
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33
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Mosquera Orgueira A. Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways. Front Genet 2015; 6:163. [PMID: 26029238 PMCID: PMC4429616 DOI: 10.3389/fgene.2015.00163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 04/10/2015] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is a frequent epigenetic mechanism that participates in transcriptional repression. Variations in DNA methylation with respect to gene expression are constant, and, for unknown reasons, some genes with highly methylated promoters are sometimes overexpressed. In this study we have analyzed the expression and methylation patterns of thousands of genes in five groups of cancer and normal tissue samples in order to determine local and genome-wide differences. We observed significant changes in global methylation-expression correlation in all the neoplasms, which suggests that differential correlation events are frequent in cancer. A focused analysis in the breast cancer cohort identified 1662 genes whose correlation varies significantly between normal and cancerous breast, but whose DNA methylation and gene expression patterns do not change substantially. These genes were enriched in cancer-related pathways and repressive chromatin features across various model cell lines, such as PRC2 binding and H3K27me3 marks. Substantial changes in methylation-expression correlation indicate that these genes are subject to epigenetic remodeling, where the differential activity of other factors break the expected relationship between both variables. Our findings suggest a complex regulatory landscape where a redistribution of local and large-scale chromatin repressive domains at differentially correlated genes (DCGs) creates epigenetic hotspots that modulate cancer-specific gene expression.
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34
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DNA methylation profiling identifies two splenic marginal zone lymphoma subgroups with different clinical and genetic features. Blood 2015; 125:1922-31. [PMID: 25612624 DOI: 10.1182/blood-2014-08-596247] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Splenic marginal zone lymphoma is a rare lymphoma. Loss of 7q31 and somatic mutations affecting the NOTCH2 and KLF2 genes are the commonest genomic aberrations. Epigenetic changes can be pharmacologically reverted; therefore, identification of groups of patients with specific epigenomic alterations might have therapeutic relevance. Here we integrated genome-wide DNA-promoter methylation profiling with gene expression profiling, and clinical and biological variables. An unsupervised clustering analysis of a test series of 98 samples identified 2 clusters with different degrees of promoter methylation. The cluster comprising samples with higher-promoter methylation (High-M) had a poorer overall survival compared with the lower (Low-M) cluster. The prognostic relevance of the High-M phenotype was confirmed in an independent validation set of 36 patients. In the whole series, the High-M phenotype was associated with IGHV1-02 usage, mutations of NOTCH2 gene, 7q31-32 loss, and histologic transformation. In the High-M set, a number of tumor-suppressor genes were methylated and repressed. PRC2 subunit genes and several prosurvival lymphoma genes were unmethylated and overexpressed. A model based on the methylation of 3 genes (CACNB2, HTRA1, KLF4) identified a poorer-outcome patient subset. Exposure of splenic marginal zone lymphoma cell lines to a demethylating agent caused partial reversion of the High-M phenotype and inhibition of proliferation.
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35
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Kong KA, Lee JY, Oh JH, Lee Y, Kim MH. Akt1 mediates the posterior Hoxc gene expression through epigenetic modifications in mouse embryonic fibroblasts. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:793-9. [PMID: 24955524 DOI: 10.1016/j.bbagrm.2014.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 05/09/2014] [Accepted: 06/11/2014] [Indexed: 12/20/2022]
Abstract
The evolutionarily conserved Hox genes are organized in clusters and expressed colinearly to specify body patterning during embryonic development. Previously, Akt1 has been identified as a putative Hox gene regulator through in silico analysis. Substantial upregulation of consecutive 5' Hoxc genes has been observed when Akt1 is absent in mouse embryonic fibroblast (MEF) cells. In this study, we provide evidence that Akt1 regulates the 5' Hoxc gene expression by epigenetic modifications. Enrichment of histone H3K9 acetylation and a low level of the H3K27me3 mark were detected at the posterior 5' Hoxc loci when Akt1 is absent. A histone deacetylase (HDAC) inhibitor de-repressed 5' Hoxc gene expression when Akt1 is present, and a DNA demethylating reagent synergistically upregulated HDAC-induced 5' Hoxc gene expression. A knockdown study revealed that Hdac6 is mediated in the Hoxc12 repression through direct binding to the transcription start site (TSS) in the presence of Akt1. Co-immunoprecipitation analysis revealed that endogenous Akt1 directly interacted with Hdac6. Furthermore, exogenous Akt1 was enriched at the promoter region of the posterior Hoxc genes such as Hoxc11 and Hoxc12, not the Akt1-independent Hoxc5 and Hoxd10 loci. The regulation of the H3K27me3 mark by Ezh2 and Kdm6b at the 5' Hoxc gene promoter turned out to be Akt1 dependent. Taken together, these results suggest that Akt1 mediates the posterior 5' Hoxc gene expression through epigenetic modification such as histone methylation and acetylation, and partly through a direct binding to the promoter region of the 5' Hoxc genes and/or Hdac6 in mouse embryonic fibroblast cells.
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Affiliation(s)
- Kyoung-Ah Kong
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji Hoon Oh
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Youra Lee
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea.
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