1
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Rezaie N, Bayati M, Hamidi M, Tahaei MS, Khorasani S, Lovell NH, Breen J, Rabiee HR, Alinejad-Rokny H. Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer. Commun Biol 2022; 5:556. [PMID: 35672401 PMCID: PMC9174258 DOI: 10.1038/s42003-022-03528-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/24/2022] [Indexed: 11/09/2022] Open
Abstract
Non-coding RNAs (ncRNAs) form a large portion of the mammalian genome. However, their biological functions are poorly characterized in cancers. In this study, using a newly developed tool, SomaGene, we analyze de novo somatic point mutations from the International Cancer Genome Consortium (ICGC) whole-genome sequencing data of 1,855 breast cancer samples. We identify 1030 candidates of ncRNAs that are significantly and explicitly mutated in breast cancer samples. By integrating data from the ENCODE regulatory features and FANTOM5 expression atlas, we show that the candidate ncRNAs significantly enrich active chromatin histone marks (1.9 times), CTCF binding sites (2.45 times), DNase accessibility (1.76 times), HMM predicted enhancers (2.26 times) and eQTL polymorphisms (1.77 times). Importantly, we show that the 1030 ncRNAs contain a much higher level (3.64 times) of breast cancer-associated genome-wide association (GWAS) single nucleotide polymorphisms (SNPs) than genome-wide expectation. Such enrichment has not been seen with GWAS SNPs from other cancers. Using breast cell line related Hi-C data, we then show that 82% of our candidate ncRNAs (1.9 times) significantly interact with the promoter of protein-coding genes, including previously known cancer-associated genes, suggesting the critical role of candidate ncRNA genes in the activation of essential regulators of development and differentiation in breast cancer. We provide an extensive web-based resource (https://www.ihealthe.unsw.edu.au/research) to communicate our results with the research community. Our list of breast cancer-specific ncRNA genes has the potential to provide a better understanding of the underlying genetic causes of breast cancer. Lastly, the tool developed in this study can be used to analyze somatic mutations in all cancers. The SomaGene tool is developed to identify non-coding RNAs (ncRNAs) mutated in breast cancer but can be used for other cancers. Candidate ncRNAs are shown to be enriched for regulatory features and to contain specific trait loci polymorphisms.
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Affiliation(s)
- Narges Rezaie
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA, 92697, USA
| | - Masroor Bayati
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, Tehran, 11365, Iran
| | - Mehrab Hamidi
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, Tehran, 11365, Iran
| | - Maedeh Sadat Tahaei
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, Tehran, 11365, Iran
| | - Sadegh Khorasani
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, Tehran, 11365, Iran
| | - Nigel H Lovell
- Tyree Institute of Health Engineering and The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - James Breen
- South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, SA, 5006, Australia.,Bioinformatics Hub, University of Adelaide, Adelaide, SA, 5006, Australia
| | - Hamid R Rabiee
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, Tehran, 11365, Iran.
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia. .,UNSW Data Science Hub, The University of New South Wales (UNSW Sydney), Sydney, NSW, 2052, Australia. .,Health Data Analytics Program, AI-enabled Processes (AIP) Research Centre, Macquarie University, Sydney, NSW, 2109, Australia.
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2
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Functional genomics data: privacy risk assessment and technological mitigation. Nat Rev Genet 2022; 23:245-258. [PMID: 34759381 DOI: 10.1038/s41576-021-00428-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2021] [Indexed: 12/15/2022]
Abstract
The generation of functional genomics data by next-generation sequencing has increased greatly in the past decade. Broad sharing of these data is essential for research advancement but poses notable privacy challenges, some of which are analogous to those that occur when sharing genetic variant data. However, there are also unique privacy challenges that arise from cryptic information leakage during the processing and summarization of functional genomics data from raw reads to derived quantities, such as gene expression values. Here, we review these challenges and present potential solutions for mitigating privacy risks while allowing broad data dissemination and analysis.
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3
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Pei J, van den Dungen NAM, Asselbergs FW, Mokry M, Harakalova M. Chromatin Immunoprecipitation Sequencing (ChIP-seq) Protocol for Small Amounts of Frozen Biobanked Cardiac Tissue. Methods Mol Biol 2022; 2458:97-111. [PMID: 35103964 DOI: 10.1007/978-1-0716-2140-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chromatin immunoprecipitation and sequencing (ChIP-seq) is a well-established method to study the epigenetic profile at the genome-wide scale, including histone modifications and DNA-protein interactions. It provides valuable insights to better understand disease mechanisms. Here we present an optimized ChIP-seq protocol suitable for human cardiac tissues, especially the frozen biobanked small biopsy samples.
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Affiliation(s)
- Jiayi Pei
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, The Netherlands
- Regenerative Medicine Utrecht (RMU), UMC Utrecht, University of Utrecht, Utrecht, The Netherlands
| | | | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
| | - Michal Mokry
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, The Netherlands
- Laboratory of Clinical Chemistry and Hematology, UMC Utrecht, Utrecht, The Netherlands
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, The Netherlands.
- Regenerative Medicine Utrecht (RMU), UMC Utrecht, University of Utrecht, Utrecht, The Netherlands.
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4
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Abdulmawjood B, Costa B, Roma-Rodrigues C, Baptista PV, Fernandes AR. Genetic Biomarkers in Chronic Myeloid Leukemia: What Have We Learned So Far? Int J Mol Sci 2021; 22:12516. [PMID: 34830398 PMCID: PMC8626020 DOI: 10.3390/ijms222212516] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022] Open
Abstract
Chronic Myeloid Leukemia (CML) is a rare malignant proliferative disease of the hematopoietic system, whose molecular hallmark is the Philadelphia chromosome (Ph). The Ph chromosome originates an aberrant fusion gene with abnormal kinase activity, leading to the buildup of reactive oxygen species and genetic instability of relevance in disease progression. Several genetic abnormalities have been correlated with CML in the blast phase, including chromosomal aberrations and common altered genes. Some of these genes are involved in the regulation of cell apoptosis and proliferation, such as the epidermal growth factor receptor (EGFR), tumor protein p53 (TP53), or Schmidt-Ruppin A-2 proto-oncogene (SRC); cell adhesion, e.g., catenin beta 1 (CTNNB1); or genes associated to TGF-β, such as SKI like proto-oncogene (SKIL), transforming growth factor beta 1 (TGFB1) or transforming growth factor beta 2 (TGFB2); and TNF-α pathways, such as Tumor necrosis factor (TNFA) or Nuclear factor kappa B subunit 1 (NFKB1). The involvement of miRNAs in CML is also gaining momentum, where dysregulation of some critical miRNAs, such as miRNA-451 and miRNA-21, which have been associated to the molecular modulation of pathogenesis, progression of disease states, and response to therapeutics. In this review, the most relevant genomic alterations found in CML will be addressed.
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Affiliation(s)
- Bilal Abdulmawjood
- i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (B.A.); (B.C.); (C.R.-R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Beatriz Costa
- i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (B.A.); (B.C.); (C.R.-R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Catarina Roma-Rodrigues
- i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (B.A.); (B.C.); (C.R.-R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Pedro V. Baptista
- i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (B.A.); (B.C.); (C.R.-R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Alexandra R. Fernandes
- i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (B.A.); (B.C.); (C.R.-R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
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5
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Ptasinska A, Pickin A, Assi SA, Chin PS, Ames L, Avellino R, Gröschel S, Delwel R, Cockerill PN, Osborne CS, Bonifer C. RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction. Cell Rep 2020; 28:3022-3031.e7. [PMID: 31533028 PMCID: PMC6899442 DOI: 10.1016/j.celrep.2019.08.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 06/07/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is associated with mutations in transcriptional and epigenetic regulator genes impairing myeloid differentiation. The t(8;21)(q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoietic master regulator RUNX1. We previously showed that the maintenance of t(8;21) AML is dependent on RUNX1-ETO expression. Its depletion causes extensive changes in transcription factor binding, as well as gene expression, and initiates myeloid differentiation. However, how these processes are connected within a gene regulatory network is unclear. To address this question, we performed Promoter-Capture Hi-C assays, with or without RUNX1-ETO depletion and assigned interacting cis-regulatory elements to their respective genes. To construct a RUNX1-ETO-dependent gene regulatory network maintaining AML, we integrated cis-regulatory element interactions with gene expression and transcription factor binding data. This analysis shows that RUNX1-ETO participates in cis-regulatory element interactions. However, differential interactions following RUNX1-ETO depletion are driven by alterations in the binding of RUNX1-ETO-regulated transcription factors.
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MESH Headings
- CCAAT-Enhancer-Binding Proteins/genetics
- CCAAT-Enhancer-Binding Proteins/metabolism
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 21/metabolism
- Chromosomes, Human, Pair 8/genetics
- Chromosomes, Human, Pair 8/metabolism
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Enhancer Elements, Genetic
- Gene Deletion
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic
- RUNX1 Translocation Partner 1 Protein/genetics
- RUNX1 Translocation Partner 1 Protein/metabolism
- Transcription Factor AP-1/genetics
- Transcription Factor AP-1/metabolism
- Translocation, Genetic
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Affiliation(s)
- Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Anna Pickin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Paulynn Suyin Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Roberto Avellino
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Stefan Gröschel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands; Oncode Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Cameron S Osborne
- Department of Medical & Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK.
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6
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Xiao L, Peng Z, Zhu A, Xue R, Lu R, Mi J, Xi S, Chen W, Jiang S. Inhibition of RUNX1 promotes cisplatin-induced apoptosis in ovarian cancer cells. Biochem Pharmacol 2020; 180:114116. [PMID: 32579960 DOI: 10.1016/j.bcp.2020.114116] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/13/2020] [Accepted: 06/18/2020] [Indexed: 02/07/2023]
Abstract
Runt-related transcription factor 1 (RUNX1), one subunit of core-binding factors in hematopoiesis and leukemia, was highly expressed in ovarian cancer (OC), but the role of RUNX1 in OC is largely unknown. Since we found that high expression of RUNX1 is correlated with poor survival in patients with OC through bioinformatic analysis of TCGA database, we developed RUNX1-knockout clones by CRISPR/Cas9 technique and discovered that RUNX1 depletion could promote cisplatin-induced apoptosis in OC cells, which was further confirmed by RUNX1 knockdown and overexpression. We also proved that RUNX1 could elevate the expression of BCL2. We then examined a total of 32 candidate miRNAs that might mediate the regulation between RUNX1 and BCL2, of which three miRNAs from the miR-17~92 cluster were found to be negatively regulated by RUNX1. Consistently, our analysis of data from TCGA database revealed the negative correlation between RUNX1 and the cluster. We further confirmed that miR-17~92 cluster could enhance cisplatin-induced apoptosis by directly targeting BCL2 3'UTR. Since rescue experiments proved that RUNX1 could repress cisplatin-induced apoptosis by up-regulating BCL2 via miR-17~92 cluster, combining RUNX1 inhibitor Ro5-3335 and cisplatin showed synergic effect in triggering OC cell apoptosis. Collectively, these findings show for the first time that combinational treatment of cisplatin and RUNX1 inhibitor could be used to potentiate apoptosis of ovarian cancer cells, and reveal the potential of targeting RUNX1 in ovarian cancer chemotherapy.
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Affiliation(s)
- Li Xiao
- Department of Biological Sciences & Technology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhennan Peng
- Department of Biological Sciences & Technology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anqi Zhu
- Department of Biological Sciences & Technology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Renxing Xue
- Department of Biological Sciences & Technology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Renming Lu
- Department of Biological Sciences & Technology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jing Mi
- Department of Biological Sciences & Technology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaowei Xi
- Department of Biological Sciences & Technology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Chen
- Department of Gynecology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Songshan Jiang
- Department of Biological Sciences & Technology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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7
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Zhang JG, Xu C, Zhang L, Zhu W, Shen H, Deng HW. Identify gene expression pattern change at transcriptional and post-transcriptional levels. Transcription 2019; 10:137-146. [PMID: 30696368 DOI: 10.1080/21541264.2019.1575159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Gene transcription is regulated with distinct sets of regulatory factors at multiple levels. Transcriptional and post-transcriptional regulation constitute two major regulation modes of gene expression to either activate or repress the initiation of transcription and thereby control the number of proteins synthesized during translation. Disruptions of the proper regulation patterns at transcriptional and post-transcriptional levels are increasingly recognized as causes of human diseases. Consequently, identifying the differential gene expression at transcriptional and post-transcriptional levels respectively is vital to identify potential disease-associated and/or causal genes and understand their roles in the disease development. Here, we proposed a novel method with a linear mixed model that can identify a set of differentially expressed genes at transcriptional and post-transcriptional levels. The simulation and real data analysis showed our method could provide an accurate way to identify genes subject to aberrant transcriptional and post-transcriptional regulation and reveal the potential causal genes that contributed to the diseases.
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Affiliation(s)
- Ji-Gang Zhang
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA.,b Computational Science , The Jackson Laboratory , Bar Harbor , ME , USA
| | - Chao Xu
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA.,c Department of Biostatistics and Epidemiology , University of Oklahoma Health Science Center , Oklahoma City , OK , USA
| | - Lan Zhang
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA
| | - Wei Zhu
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA
| | - Hui Shen
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA
| | - Hong-Wen Deng
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA.,d School of Basic Medical Science , Central South University , Changsha , China
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8
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Pentland I, Campos-León K, Cotic M, Davies KJ, Wood CD, Groves IJ, Burley M, Coleman N, Stockton JD, Noyvert B, Beggs AD, West MJ, Roberts S, Parish JL. Disruption of CTCF-YY1-dependent looping of the human papillomavirus genome activates differentiation-induced viral oncogene transcription. PLoS Biol 2018; 16:e2005752. [PMID: 30359362 PMCID: PMC6219814 DOI: 10.1371/journal.pbio.2005752] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 11/06/2018] [Accepted: 10/12/2018] [Indexed: 11/19/2022] Open
Abstract
The complex life cycle of oncogenic human papillomavirus (HPV) initiates in undifferentiated basal epithelial keratinocytes where expression of the E6 and E7 oncogenes is restricted. Upon epithelial differentiation, E6/E7 transcription is increased through unknown mechanisms to drive cellular proliferation required to support virus replication. We report that the chromatin-organising CCCTC-binding factor (CTCF) promotes the formation of a chromatin loop in the HPV genome that epigenetically represses viral enhancer activity controlling E6/E7 expression. CTCF-dependent looping is dependent on the expression of the CTCF-associated Yin Yang 1 (YY1) transcription factor and polycomb repressor complex (PRC) recruitment, resulting in trimethylation of histone H3 at lysine 27. We show that viral oncogene up-regulation during cellular differentiation results from YY1 down-regulation, disruption of viral genome looping, and a loss of epigenetic repression of viral enhancer activity. Our data therefore reveal a key role for CTCF-YY1-dependent looping in the HPV life cycle and identify a regulatory mechanism that could be disrupted in HPV carcinogenesis.
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Affiliation(s)
- Ieisha Pentland
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Karen Campos-León
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Marius Cotic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kelli-Jo Davies
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - C. David Wood
- School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Ian J. Groves
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Megan Burley
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Joanne D. Stockton
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Boris Noyvert
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Andrew D. Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Michelle J. West
- School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Sally Roberts
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Joanna L. Parish
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
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9
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Illendula A, Gilmour J, Grembecka J, Tirumala VSS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pulikkan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C, Bushweller JH. Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers. EBioMedicine 2016; 8:117-131. [PMID: 27428424 PMCID: PMC4919611 DOI: 10.1016/j.ebiom.2016.04.032] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/12/2016] [Accepted: 04/25/2016] [Indexed: 10/29/2022] Open
Abstract
Transcription factors have traditionally been viewed with skepticism as viable drug targets, but they offer the potential for completely novel mechanisms of action that could more effectively address the stem cell like properties, such as self-renewal and chemo-resistance, that lead to the failure of traditional chemotherapy approaches. Core binding factor is a heterodimeric transcription factor comprised of one of 3 RUNX proteins (RUNX1-3) and a CBFβ binding partner. CBFβ enhances DNA binding of RUNX subunits by relieving auto-inhibition. Both RUNX1 and CBFβ are frequently mutated in human leukemia. More recently, RUNX proteins have been shown to be key players in epithelial cancers, suggesting the targeting of this pathway could have broad utility. In order to test this, we developed small molecules which bind to CBFβ and inhibit its binding to RUNX. Treatment with these inhibitors reduces binding of RUNX1 to target genes, alters the expression of RUNX1 target genes, and impacts cell survival and differentiation. These inhibitors show efficacy against leukemia cells as well as basal-like (triple-negative) breast cancer cells. These inhibitors provide effective tools to probe the utility of targeting RUNX transcription factor function in other cancers.
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Affiliation(s)
- Anuradha Illendula
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Jane Gilmour
- School of Cancer Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | | | | | - Adam Boulton
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Aravinda Kuntimaddi
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Charles Schmidt
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Lixin Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - John A Pulikkan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hongliang Zong
- Division of Hematology/Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY, USA
| | - Mahmut Parlak
- Department of Biochemistry, University of Virginia, Charlottesville, VA, USA
| | - Cem Kuscu
- Department of Biochemistry, University of Virginia, Charlottesville, VA, USA
| | - Anna Pickin
- School of Cancer Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - Yunpeng Zhou
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Yan Gao
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Lauren Mishra
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Mazhar Adli
- Department of Biochemistry, University of Virginia, Charlottesville, VA, USA
| | - Lucio H Castilla
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Roger A Rajewski
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Monica L Guzman
- Division of Hematology/Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY, USA
| | - Constanze Bonifer
- School of Cancer Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
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10
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Role of Epigenetics in Stem Cell Proliferation and Differentiation: Implications for Treating Neurodegenerative Diseases. Int J Mol Sci 2016; 17:ijms17020199. [PMID: 26848657 PMCID: PMC4783933 DOI: 10.3390/ijms17020199] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/17/2016] [Accepted: 01/27/2016] [Indexed: 12/15/2022] Open
Abstract
The main objectives of this review are to survey the current literature on the role of epigenetics in determining the fate of stem cells and to assess how this information can be used to enhance the treatment strategies for some neurodegenerative disorders, like Huntington’s disease, Parkinson’s disease and Alzheimer’s disease. Some of these epigenetic mechanisms include DNA methylation and histone modifications, which have a direct impact on the way that genes are expressed in stem cells and how they drive these cells into a mature lineage. Understanding how the stem cells are behaving and giving rise to mature cells can be used to inform researchers on effective ways to design stem cell-based treatments. In this review article, the way in which the basic understanding of how manipulating this process can be utilized to treat certain neurological diseases will be presented. Different genetic factors and their epigenetic changes during reprogramming of stem cells into induced pluripotent stem cells (iPSCs) have significant potential for enhancing the efficacy of cell replacement therapies.
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Tortorella SM, Hung A, Karagiannis TC. The implication of cancer progenitor cells and the role of epigenetics in the development of novel therapeutic strategies for chronic myeloid leukemia. Antioxid Redox Signal 2015; 22:1425-62. [PMID: 25366930 DOI: 10.1089/ars.2014.6096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SIGNIFICANCE Chronic myeloid leukemia (CML) involves the malignant transformation of hematopoietic stem cells, defined largely by the Philadelphia chromosome and expression of the breakpoint cluster region-Abelson (BCR-ABL) oncoprotein. Pharmacological tyrosine kinase inhibitors (TKIs), including imatinib mesylate, have overcome limitations in conventional treatment for the improved clinical management of CML. RECENT ADVANCES Accumulated evidence has led to the identification of a subpopulation of quiescent leukemia progenitor cells with stem-like self renewal properties that may initiate leukemogenesis, which are also shown to be present in residual disease due to their insensitivity to tyrosine kinase inhibition. CRITICAL ISSUES The characterization of quiescent leukemia progenitor cells as a unique cell population in CML pathogenesis has become critical with the complete elucidation of mechanisms involved in their survival independent of BCR-ABL that is important in the development of novel anticancer strategies. Understanding of these functional pathways in CML progenitor cells will allow for their selective therapeutic targeting. In addition, disease pathogenesis and drug responsiveness is also thought to be modulated by epigenetic regulatory mechanisms such as DNA methylation, histone acetylation, and microRNA expression, with a capacity to control CML-associated gene transcription. FUTURE DIRECTIONS A number of compounds in combination with TKIs are under preclinical and clinical investigation to assess their synergistic potential in targeting leukemic progenitor cells and/or the epigenome in CML. Despite the collective promise, further research is required in order to refine understanding, and, ultimately, advance antileukemic therapeutic strategies.
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Affiliation(s)
- Stephanie M Tortorella
- 1 Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct , Melbourne, Australia
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Jackson FLC, Niculescu MD, Jackson RT. Conceptual shifts needed to understand the dynamic interactions of genes, environment, epigenetics, social processes, and behavioral choices. Am J Public Health 2013; 103 Suppl 1:S33-42. [PMID: 23927503 DOI: 10.2105/ajph.2013.301221] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Social and behavioral research in public health is often intimately tied to profound, but frequently neglected, biological influences from underlying genetic, environmental, and epigenetic events. The dynamic interplay between the life, social, and behavioral sciences often remains underappreciated and underutilized in addressing complex diseases and disorders and in developing effective remediation strategies. Using a case-study format, we present examples as to how the inclusion of genetic, environmental, and epigenetic data can augment social and behavioral health research by expanding the parameters of such studies, adding specificity to phenotypic assessments, and providing additional internal control in comparative studies. We highlight the important roles of gene-environment interactions and epigenetics as sources of phenotypic change and as a bridge between the life and social and behavioral sciences in the development of robust interdisciplinary analyses.
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Affiliation(s)
- Fatimah L C Jackson
- Fatimah L. C. Jackson, and Mihai D. Niculescu are with the University of North Carolina at Chapel Hill. Robert T. Jackson is with the University of Maryland at College Park
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Abstract
The efficacy of therapeutic modalities in chronic myeloid leukemia (CML) depends on both genetic and epigenetic mechanisms. This review focuses on epigenetic mechanisms involved in the pathogenesis of CML and in resistance of tumor cells to tyrosine kinase inhibitors leading to the leukemic clone escape and propagation. Regulatory events at the levels of gene regulation by transcription factors and microRNAs are discussed in the context of CML pathogenesis and therapeutic modalities.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- DNA Methylation
- Drug Resistance, Neoplasm
- Epigenomics
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/therapeutic use
- Gene Expression Regulation, Leukemic/drug effects
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- MicroRNAs/physiology
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
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Affiliation(s)
| | - Jitka Koblihova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, Prague 2, 128 20 Czech Republic
| | - Tomas Stopka
- Institute of Pathophysiology, First Faculty of Medicine, Charles University in Prague, U Nemocnice 5, Prague 2, 128 53 Czech Republic
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Meier K, Mathieu EL, Finkernagel F, Reuter LM, Scharfe M, Doehlemann G, Jarek M, Brehm A. LINT, a novel dL(3)mbt-containing complex, represses malignant brain tumour signature genes. PLoS Genet 2012; 8:e1002676. [PMID: 22570633 PMCID: PMC3342951 DOI: 10.1371/journal.pgen.1002676] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 03/13/2012] [Indexed: 11/18/2022] Open
Abstract
Mutations in the l(3)mbt tumour suppressor result in overproliferation of Drosophila larval brains. Recently, the derepression of different gene classes in l(3)mbt mutants was shown to be causal for transformation. However, the molecular mechanisms of dL(3)mbt-mediated gene repression are not understood. Here, we identify LINT, the major dL(3)mbt complex of Drosophila. LINT has three core subunits—dL(3)mbt, dCoREST, and dLint-1—and is expressed in cell lines, embryos, and larval brain. Using genome-wide ChIP–Seq analysis, we show that dLint-1 binds close to the TSS of tumour-relevant target genes. Depletion of the LINT core subunits results in derepression of these genes. By contrast, histone deacetylase, histone methylase, and histone demethylase activities are not required to maintain repression. Our results support a direct role of LINT in the repression of brain tumour-relevant target genes by restricting promoter access. Mutations in the l(3)mbt result in the formation of brain tumours. The molecular basis underlying this phenotype has remained obscure. Here, we have isolated LINT, a novel protein complex containing dL(3)mbt, the corepressor dCoREST, and the uncharacterised protein dLint-1. We have used genome-wide ChIP–Seq analysis to map the binding sites of LINT. LINT occupies the promoters of many genes that are deregulated in l(3)mbt brain tumours, suggesting that these genes are repressed by LINT. Indeed, RNAi–mediated depletion of LINT subunits results in the derepression of these genes. Surprisingly, LINT-mediated repression is largely independent of histone modification status, arguing for a repression mechanism that operates by restricting promoter access.
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Affiliation(s)
- Karin Meier
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Eve-Lyne Mathieu
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Florian Finkernagel
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - L. Maximilian Reuter
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Maren Scharfe
- Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Michael Jarek
- Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Alexander Brehm
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
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