51
|
Nguyen TTT, Zhang Y, Shang E, Shu C, Torrini C, Zhao J, Bianchetti E, Mela A, Humala N, Mahajan A, Harmanci AO, Lei Z, Maienschein-Cline M, Quinzii CM, Westhoff MA, Karpel-Massler G, Bruce JN, Canoll P, Siegelin MD. HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models. J Clin Invest 2020; 130:3699-3716. [PMID: 32315286 PMCID: PMC7324177 DOI: 10.1172/jci129049] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
The Warburg effect is a tumor-related phenomenon that could potentially be targeted therapeutically. Here, we showed that glioblastoma (GBM) cultures and patients' tumors harbored super-enhancers in several genes related to the Warburg effect. By conducting a transcriptome analysis followed by ChIP-Seq coupled with a comprehensive metabolite analysis in GBM models, we found that FDA-approved global (panobinostat, vorinostat) and selective (romidepsin) histone deacetylase (HDAC) inhibitors elicited metabolic reprogramming in concert with disruption of several Warburg effect-related super-enhancers. Extracellular flux and carbon-tracing analyses revealed that HDAC inhibitors blunted glycolysis in a c-Myc-dependent manner and lowered ATP levels. This resulted in the engagement of oxidative phosphorylation (OXPHOS) driven by elevated fatty acid oxidation (FAO), rendering GBM cells dependent on these pathways. Mechanistically, interference with HDAC1/-2 elicited a suppression of c-Myc protein levels and a concomitant increase in 2 transcriptional drivers of oxidative metabolism, PGC1α and PPARD, suggesting an inverse relationship. Rescue and ChIP experiments indicated that c-Myc bound to the promoter regions of PGC1α and PPARD to counteract their upregulation driven by HDAC1/-2 inhibition. Finally, we demonstrated that combination treatment with HDAC and FAO inhibitors extended animal survival in patient-derived xenograft model systems in vivo more potently than single treatments in the absence of toxicity.
Collapse
Affiliation(s)
- Trang Thi Thu Nguyen
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Yiru Zhang
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Enyuan Shang
- Department of Biological Sciences, Bronx Community College, City University of New York, Bronx, New York, USA
| | - Chang Shu
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Consuelo Torrini
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Junfei Zhao
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Elena Bianchetti
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Angeliki Mela
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Nelson Humala
- Department of Neurological Surgery, Columbia University Medical Center, New York, New York, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, Columbia University Medical Center, New York, New York, USA
| | - Arif O. Harmanci
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Zhengdeng Lei
- Core for Research Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Mark Maienschein-Cline
- Core for Research Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Catarina M. Quinzii
- Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | | | | | - Jeffrey N. Bruce
- Department of Neurological Surgery, Columbia University Medical Center, New York, New York, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Markus D. Siegelin
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| |
Collapse
|
52
|
Verza FA, Das U, Fachin AL, Dimmock JR, Marins M. Roles of Histone Deacetylases and Inhibitors in Anticancer Therapy. Cancers (Basel) 2020; 12:cancers12061664. [PMID: 32585896 PMCID: PMC7352721 DOI: 10.3390/cancers12061664] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022] Open
Abstract
Histones are the main structural proteins of eukaryotic chromatin. Histone acetylation/ deacetylation are the epigenetic mechanisms of the regulation of gene expression and are catalyzed by histone acetyltransferases (HAT) and histone deacetylases (HDAC). These epigenetic alterations of DNA structure influence the action of transcription factors which can induce or repress gene transcription. The HATs catalyze acetylation and the events related to gene transcription and are also responsible for transporting newly synthesized histones from the cytoplasm to the nucleus. The activity of HDACs is mainly involved in silencing gene expression and according to their specialized functions are divided into classes I, II, III and IV. The disturbance of the expression and mutations of HDAC genes causes the aberrant transcription of key genes regulating important cancer pathways such as cell proliferation, cell-cycle regulation and apoptosis. In view of their role in cancer pathways, HDACs are considered promising therapeutic targets and the development of HDAC inhibitors is a hot topic in the search for new anticancer drugs. The present review will focus on HDACs I, II and IV, the best known inhibitors and potential alternative inhibitors derived from natural and synthetic products which can be used to influence HDAC activity and the development of new cancer therapies.
Collapse
Affiliation(s)
- Flávia Alves Verza
- Biotechnology Unit, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil; (F.A.V.); (A.L.F.)
| | - Umashankar Das
- College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada;
| | - Ana Lúcia Fachin
- Biotechnology Unit, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil; (F.A.V.); (A.L.F.)
- Medicine School, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil
| | - Jonathan R. Dimmock
- College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada;
- Correspondence: (J.R.D.); (M.M.); Tel.: +1-306-966-6331 (J.R.D.); +55-16-3603-6728 (M.M.)
| | - Mozart Marins
- Biotechnology Unit, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil; (F.A.V.); (A.L.F.)
- College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada;
- Medicine School, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil
- Pharmaceutical Sciences School, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil
- Correspondence: (J.R.D.); (M.M.); Tel.: +1-306-966-6331 (J.R.D.); +55-16-3603-6728 (M.M.)
| |
Collapse
|
53
|
Tan LT, Phyo MY. Marine Cyanobacteria: A Source of Lead Compounds and their Clinically-Relevant Molecular Targets. Molecules 2020; 25:E2197. [PMID: 32397127 PMCID: PMC7249205 DOI: 10.3390/molecules25092197] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
The prokaryotic filamentous marine cyanobacteria are photosynthetic microbes that are found in diverse marine habitats, ranging from epiphytic to endolithic communities. Their successful colonization in nature is largely attributed to genetic diversity as well as the production of ecologically important natural products. These cyanobacterial natural products are also a source of potential drug leads for the development of therapeutic agents used in the treatment of diseases, such as cancer, parasitic infections and inflammation. Major sources of these biomedically important natural compounds are found predominately from marine cyanobacterial orders Oscillatoriales, Nostocales, Chroococcales and Synechococcales. Moreover, technological advances in genomic and metabolomics approaches, such as mass spectrometry and NMR spectroscopy, revealed that marine cyanobacteria are a treasure trove of structurally unique natural products. The high potency of a number of natural products are due to their specific interference with validated drug targets, such as proteasomes, proteases, histone deacetylases, microtubules, actin filaments and membrane receptors/channels. In this review, the chemistry and biology of selected potent cyanobacterial compounds as well as their synthetic analogues are presented based on their molecular targets. These molecules are discussed to reflect current research trends in drug discovery from marine cyanobacterial natural products.
Collapse
Affiliation(s)
- Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore;
| | | |
Collapse
|
54
|
Inhibition of histone deacetylation rescues phenotype in a mouse model of Birk-Barel intellectual disability syndrome. Nat Commun 2020; 11:480. [PMID: 31980599 PMCID: PMC6981138 DOI: 10.1038/s41467-019-13918-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 12/05/2019] [Indexed: 01/10/2023] Open
Abstract
Mutations in the actively expressed, maternal allele of the imprinted KCNK9 gene cause Birk-Barel intellectual disability syndrome (BBIDS). Using a BBIDS mouse model, we identify here a partial rescue of the BBIDS-like behavioral and neuronal phenotypes mediated via residual expression from the paternal Kcnk9 (Kcnk9pat) allele. We further demonstrate that the second-generation HDAC inhibitor CI-994 induces enhanced expression from the paternally silenced Kcnk9 allele and leads to a full rescue of the behavioral phenotype suggesting CI-994 as a promising molecule for BBIDS therapy. Thus, these findings suggest a potential approach to improve cognitive dysfunction in a mouse model of an imprinting disorder. Birk-Barel intellectual disability is an imprinting syndrome due to maternally-only transmitted mutations of KCNK9/TASK3. Here authors are using a heterozygous deletion of the active maternal Kcnk9 allele to model the disease and show phenotypic rescue by HDAC inhibition.
Collapse
|
55
|
Zhang H, Wang L, Bai J, Jiao W, Wang M. MIER3 suppresses the progression of non-small cell lung cancer by inhibiting Wnt/β-Catenin pathway and histone acetyltransferase activity. Transl Cancer Res 2020; 9:346-357. [PMID: 35117188 PMCID: PMC8798777 DOI: 10.21037/tcr.2020.01.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/06/2020] [Indexed: 11/06/2022]
Abstract
BACKGROUND The mesoderm induction early response 1, family member 3 (MIER3) gene has been recognized as potentially being associated with cancer. However, in relation to the development of non-small cell lung cancer (NSCLC), the expression pattern and the role of MIER3 are yet to be reported. The aim of this research was to investigate the rate of expression of MIER3 in NSCLC cells and tissues and to investigate the role of MIER3 in NSCLC. METHODS Seventeen patients received NSCLC tissues and corresponding healthy tissues. MTT assay was used to determine cell proliferation. For detecting mRNA and protein expression, we used both quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot method. To measure cell apoptosis and cell cycle distribution, we applied the flow cytometry technique. We used a wound-healing assay and a Transwell invasion assay to study cell migration and invasion. RESULTS In comparison with adjacent normal tissues, the expression of MIER3 was down-regulated in NSCLC tissues. In addition, the level of MIER3 in NSCLC cell lines was also lower than in pulmonary epithelial cell BEAS-2B. Moreover, when MIER3 was overexpressed, cell proliferation, migration, and invasion were significantly inhibited, apoptosis increased, and cell cycle arrest was induced in A549 and H460 cells. MIER3 overexpression also suppressed tumor growth in NSCLC xenograft mouse models. Furthermore, our study demonstrated that MIER3 down-regulated the Wnt/β-catenin signaling pathway in NSCLC cells. More importantly, MIER3 decreased the activity of histone acetyltransferase (HAT) p300, which may have contributed to its regulation on β-catenin and tumorigenesis. CONCLUSIONS The data suggests MIER3 takes on the tumor-suppressor role in the progression of NSCLC and, therefore, could prove to be a valuable clinical marker in the prognosis of the disease.
Collapse
Affiliation(s)
- Hongye Zhang
- Department of Oncology, Linyi Central Hospital, Linyi 276400, China
| | - Ling Wang
- Department of Nephrology, Yishui People’s Hospital, Linyi 276400, China
| | - Juan Bai
- Department of Oncology, Affiliated Hospital of Chengdu University, Chengdu 610081, China
| | - Wenyu Jiao
- Department of Respiratory and Critical Care Medicine, Xi’an Daxing Hospital, Xi’an 710016, China
| | - Mingxia Wang
- Department of Oncology, Linyi Central Hospital, Linyi 276400, China
| |
Collapse
|
56
|
Gryder BE, Pomella S, Sayers C, Wu XS, Song Y, Chiarella AM, Bagchi S, Chou HC, Sinniah RS, Walton A, Wen X, Rota R, Hathaway NA, Zhao K, Chen J, Vakoc CR, Shern JF, Stanton BZ, Khan J. Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma. Nat Genet 2019; 51:1714-1722. [PMID: 31784732 PMCID: PMC6886578 DOI: 10.1038/s41588-019-0534-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/23/2019] [Indexed: 12/31/2022]
Abstract
Core regulatory transcription factors (CR TFs) orchestrate the placement of super-enhancers (SEs) to activate transcription of cell-identity specifying gene networks, and are critical in promoting cancer. Here, we define the core regulatory circuitry of rhabdomyosarcoma and identify critical CR TF dependencies. These CR TFs build SEs that have the highest levels of histone acetylation, yet paradoxically the same SEs also harbor the greatest amounts of histone deacetylases. We find that hyperacetylation selectively halts CR TF transcription. To investigate the architectural determinants of this phenotype, we used absolute quantification of architecture (AQuA) HiChIP, which revealed erosion of native SE contacts, and aberrant spreading of contacts that involved histone acetylation. Hyperacetylation removes RNA polymerase II (RNA Pol II) from core regulatory genetic elements, and eliminates RNA Pol II but not BRD4 phase condensates. This study identifies an SE-specific requirement for balancing histone modification states to maintain SE architecture and CR TF transcription.
Collapse
Affiliation(s)
| | - Silvia Pomella
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù Research Institute, IRCCS, Rome, Italy
| | - Carly Sayers
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Genetics Program, Stony Brook University, Stony Brook, NY, USA
| | - Young Song
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | - Anna M Chiarella
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Sukriti Bagchi
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD, USA
| | | | | | | | - Xinyu Wen
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rossella Rota
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù Research Institute, IRCCS, Rome, Italy
| | - Nathaniel A Hathaway
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Keji Zhao
- Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, NIBIB, NIH, Bethesda, MD, USA
| | | | - Jack F Shern
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD, USA
| | - Benjamin Z Stanton
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- The Research Institute at Nationwide, Nationwide Children's Hospital, Columbus, OH, USA
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, MD, USA.
| |
Collapse
|
57
|
Caslini C, Hong S, Ban YJ, Chen XS, Ince TA. HDAC7 regulates histone 3 lysine 27 acetylation and transcriptional activity at super-enhancer-associated genes in breast cancer stem cells. Oncogene 2019; 38:6599-6614. [PMID: 31375747 DOI: 10.1038/s41388-019-0897-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/20/2022]
Abstract
Chromatin regulation through histone modifications plays an essential role in coordinated expression of multiple genes. Alterations in chromatin induced by histone modifiers and readers regulate critical transcriptional programs involved in both normal development and tumor differentiation. Recently, we identified that histone deacetylases HDAC1 and HDAC7 are necessary to maintain cancer stem cells (CSCs) in both breast and ovarian tumors. Here, we sought to investigate the CSC-specific function of HDAC1 and HDAC7 mechanistically by using a stem-like breast cancer (BrCa) cell model BPLER and matched nonstem tumor cell (nsTC)-like HMLER, along with conventional BrCa cell lines with different CSC enrichment levels. We found that HDAC1 and HDAC3 inhibition or knockdown results in HDAC7 downregulation, which is associated with a decrease in histone 3 lysine 27 acetylation (H3K27ac) at transcription start sites (TSS) and super-enhancers (SEs) prominently in stem-like BrCa cells. Importantly, these changes in chromatin landscape also correlate with the repression of many SE-associated oncogenes, including c-MYC, CD44, CDKN1B, SLUG, VDR, SMAD3, VEGFA, and XBP1. In stem-like BrCa cells, HDAC7 binds near TSS and to SEs of these oncogenes where it appears to contribute to both H3K27ac and transcriptional regulation. These results suggest that HDAC7 inactivation, directly or through inhibition of HDAC1 and HDAC3, can result in the inhibition of the CSC phenotype by downregulating multiple SE-associated oncogenes. The CSC selective nature of this mechanism and the prospect of inhibiting multiple oncogenes simultaneously makes development of HDAC7 specific inhibitors a compelling objective.
Collapse
Affiliation(s)
- Corrado Caslini
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, 33136, USA.
| | - Sunhwa Hong
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, 33136, USA
| | - Yuguang J Ban
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, 33136, USA.,Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Xi S Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, 33136, USA.,Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Tan A Ince
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, 33136, USA. .,Department of Pathology and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
| |
Collapse
|
58
|
Hamdan FH, Johnsen SA. Perturbing Enhancer Activity in Cancer Therapy. Cancers (Basel) 2019; 11:cancers11050634. [PMID: 31067678 PMCID: PMC6563029 DOI: 10.3390/cancers11050634] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/26/2019] [Accepted: 05/05/2019] [Indexed: 02/07/2023] Open
Abstract
Tight regulation of gene transcription is essential for normal development, tissue homeostasis, and disease-free survival. Enhancers are distal regulatory elements in the genome that provide specificity to gene expression programs and are frequently misregulated in cancer. Recent studies examined various enhancer-driven malignant dependencies and identified different approaches to specifically target these programs. In this review, we describe numerous features that make enhancers good transcriptional targets in cancer therapy and discuss different approaches to overcome enhancer perturbation. Interestingly, a number of approved therapeutic agents, such as cyclosporine, steroid hormones, and thiazolidinediones, actually function by affecting enhancer landscapes by directly targeting very specific transcription factor programs. More recently, a broader approach to targeting deregulated enhancer programs has been achieved via Bromodomain and Extraterminal (BET) inhibition or perturbation of transcription-related cyclin-dependent kinases (CDK). One challenge to enhancer-targeted therapy is proper patient stratification. We suggest that monitoring of enhancer RNA (eRNA) expression may serve as a unique biomarker of enhancer activity that can help to predict and monitor responsiveness to enhancer-targeted therapies. A more thorough investigation of cancer-specific enhancers and the underlying mechanisms of deregulation will pave the road for an effective utilization of enhancer modulators in a precision oncology approach to cancer treatment.
Collapse
Affiliation(s)
- Feda H Hamdan
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Steven A Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
| |
Collapse
|
59
|
Transcription shapes DNA replication initiation and termination in human cells. Nat Struct Mol Biol 2018; 26:67-77. [PMID: 30598550 PMCID: PMC6320713 DOI: 10.1038/s41594-018-0171-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/19/2018] [Indexed: 12/21/2022]
Abstract
Although DNA replication is a fundamental aspect of biology, it is not known what determines where DNA replication starts and stops in the human genome. Here we directly identify and quantitatively compare sites of replication initiation and termination in untransformed human cells. We report that replication preferentially initiates at the transcription start site of genes occupied by high levels of RNA polymerase II, and terminates at their polyadenylation sites, thus ensuring global co-directionality of transcription and replication, particularly at gene 5’ ends. During replication stress, replication initiation is stimulated downstream of genes and termination is redistributed to gene bodies; this globally re-orients replication relative to transcription around gene 3’ ends. These data suggest that replication initiation and termination are coupled to transcription in human cells, and propose a model for the impact of replication stress on genome integrity.
Collapse
|
60
|
Li ZY, Yang L, Liu XJ, Wang XZ, Pan YX, Luo JM. The Long Noncoding RNA MEG3 and its Target miR-147 Regulate JAK/STAT Pathway in Advanced Chronic Myeloid Leukemia. EBioMedicine 2018; 34:61-75. [PMID: 30072211 PMCID: PMC6117736 DOI: 10.1016/j.ebiom.2018.07.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 12/17/2022] Open
Abstract
Background Long non-coding (lnc) RNAs plays an important role in chronic myeloid leukemia (CML). In this study, we aimed to uncover the mechanism of the lncRNA maternally expressed 3 (MEG3) and its target microRNA-147 (miR-147) in CML. Methods Sixty CML patients and 10 healthy donors were included in the study. The methylation of MEG3 and miR-147 promoter was determined by methylation-specific PCR. The relationship of MEG3 and miR-147 was explored by luciferase assay. The interactions of proteins were studied by RNA pull-down assay, RNA immunoprecipitation and co-immunoprecipitation. Findings Patients in accelerated phase CML (CML-AP) and blast phase CML (CML-BP) showed lower expressions of MEG3 and miR-147 and higher expressions of DNMT1, DNMT3B, MBD2, MECP2 and HDAC1 compared to the controls. These patients also showed a higher degree of methylation of MEG3 and miR-147 while there was a reduction after chidamide treatment. Furthermore, the overexpression of MEG3 and miR-147 inhibited cell proliferation both in vivo and in vitro, promoted apoptosis and decreased the expressions of DNMT1, DNMT3A, DNMT3B, MBD2, HDAC1 and MECP2. We also found MEG3 interacted with DNMT1, JAK2, STAT3, HDAC1, and TYK2, and JAK2 was bound to STAT3, STAT5 and MYC. More interestingly, JAK2 was bound to TYK2 by the bridge of MEG3. Interpretation LncRNA MEG3 and its target miR-147 may serve as a novel therapeutic target for CML blast crisis, and chidamide might have a potential clinical application in treating CML blast crisis.
Collapse
Affiliation(s)
- Zi-Ye Li
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
| | - Lin Yang
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
| | - Xiao-Jun Liu
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
| | - Xing-Zhe Wang
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
| | - Yu-Xia Pan
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
| | - Jian-Min Luo
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China.
| |
Collapse
|
61
|
|