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Zakari S, Niels NK, Olagunju GV, Nnaji PC, Ogunniyi O, Tebamifor M, Israel EN, Atawodi SE, Ogunlana OO. Emerging biomarkers for non-invasive diagnosis and treatment of cancer: a systematic review. Front Oncol 2024; 14:1405267. [PMID: 39132504 PMCID: PMC11313249 DOI: 10.3389/fonc.2024.1405267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
Cancer remains a global health challenge, necessitating continuous advancements in diagnostic and treatment strategies. This review focuses on the utility of non-invasive biomarkers in cancer diagnosis and treatment, their role in early detection, disease monitoring, and personalized therapeutic interventions. Through a systematic review of the literature, we identified 45 relevant studies that highlight the potential of these biomarkers across various cancer types, such as breast, prostate, lung, and colorectal cancers. The non-invasive biomarkers discussed include liquid biopsies, epigenetic markers, non-coding RNAs, exosomal cargo, and metabolites. Notably, liquid biopsies, particularly those based on circulating tumour DNA (ctDNA), have emerged as the most promising method for early, non-invasive cancer detection due to their ability to provide comprehensive genetic and epigenetic information from easily accessible blood samples. This review demonstrates how non-invasive biomarkers can facilitate early cancer detection, accurate subtyping, and tailored treatment strategies, thereby improving patient outcomes. It underscores the transformative potential of non-invasive biomarkers in oncology, highlighting their application for enhancing early detection, survival rates, and treatment precision in cancer care. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023474749 PROSPERO, identifier CRD42023474749.
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Affiliation(s)
- Suleiman Zakari
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication - Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, College of Medicine, Federal University of Health Sciences Otukpo, Otukpo, Benue State, Nigeria
| | - Nguedia K. Niels
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication - Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
- Biotechnology Centre, University of Yaounde I, Yaounde, Cameroon
| | - Grace V. Olagunju
- Department of Molecular Biology, New Mexico State University, Las Cruces, NM, United States
| | - Precious C. Nnaji
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
| | - Oluwabusayo Ogunniyi
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
| | - Mercy Tebamifor
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication - Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
| | - Emmanuel N. Israel
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication - Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
| | - Sunday E. Atawodi
- Department of Biochemistry, Federal University Lokoja, Lokoja, Kogi State, Nigeria
| | - Olubanke Olujoke Ogunlana
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication - Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
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2
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Manivannan V, Inamdar MM, Padinhateeri R. Role of diffusion and reaction of the constituents in spreading of histone modification marks. PLoS Comput Biol 2024; 20:e1012235. [PMID: 38991050 PMCID: PMC11265668 DOI: 10.1371/journal.pcbi.1012235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 07/23/2024] [Accepted: 06/06/2024] [Indexed: 07/13/2024] Open
Abstract
Cells switch genes ON or OFF by altering the state of chromatin via histone modifications at specific regulatory locations along the chromatin polymer. These gene regulation processes are carried out by a network of reactions in which the histone marks spread to neighboring regions with the help of enzymes. In the literature, this spreading has been studied as a purely kinetic, non-diffusive process considering the interactions between neighboring nucleosomes. In this work, we go beyond this framework and study the spreading of modifications using a reaction-diffusion (RD) model accounting for the diffusion of the constituents. We quantitatively segregate the modification profiles generated from kinetic and RD models. The diffusion and degradation of enzymes set a natural length scale for limiting the domain size of modification spreading, and the resulting enzyme limitation is inherent in our model. We also demonstrate the emergence of confined modification domains without the explicit requirement of a nucleation site. We explore polymer compaction effects on spreading and show that single-cell domains may differ from averaged profiles. We find that the modification profiles from our model are comparable with existing H3K9me3 data of S. pombe.
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Affiliation(s)
- Vinoth Manivannan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Mandar M. Inamdar
- Department of Civil Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Mumbai, India
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Vai A, Noberini R, Ghirardi C, Rodrigues de Paula D, Carminati M, Pallavi R, Araújo N, Varga-Weisz P, Bonaldi T. Improved Mass Spectrometry-Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles. Mol Cell Proteomics 2024; 23:100799. [PMID: 38866077 PMCID: PMC11277384 DOI: 10.1016/j.mcpro.2024.100799] [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] [Received: 08/03/2023] [Revised: 05/07/2024] [Accepted: 06/09/2024] [Indexed: 06/14/2024] Open
Abstract
Histone posttranslational modifications (PTMs) have crucial roles in a multitude of cellular processes, and their aberrant levels have been linked with numerous diseases, including cancer. Although histone PTM investigations have focused so far on methylations and acetylations, alternative long-chain acylations emerged as new dimension, as they are linked to cellular metabolic states and affect gene expression through mechanisms distinct from those regulated by acetylation. Mass spectrometry is the most powerful, comprehensive, and unbiased method to study histone PTMs. However, typical mass spectrometry-based protocols for histone PTM analysis do not allow the identification of naturally occurring propionylation and butyrylation. Here, we present improved state-of-the-art sample preparation and analysis protocols to quantitate these classes of modifications. After testing different derivatization methods coupled to protease digestion, we profiled common histone PTMs and histone acylations in seven mouse tissues and human normal and tumor breast clinical samples, obtaining a map of propionylations and butyrylations found in different tissue contexts. A quantitative histone PTM analysis also revealed a contribution of histone acylations in discriminating different tissues, also upon perturbation with antibiotics, and breast cancer samples from the normal counterpart. Our results show that profiling only classical modifications is limiting and highlight the importance of using sample preparation methods that allow the analysis of the widest possible spectrum of histone modifications, paving the way for deeper insights into their functional significance in cellular processes and disease states.
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Affiliation(s)
- Alessandro Vai
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy
| | - Chiara Ghirardi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy
| | - Dieggo Rodrigues de Paula
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Michele Carminati
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy
| | - Rani Pallavi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy
| | - Nathália Araújo
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Patrick Varga-Weisz
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; São Paulo Excellence Chair, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; School of Biological Sciences, University of Essex, Colchester, UK
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy; Department of Oncology and Hematology-Oncology (DIPO), University of Milan, Milan, Italy.
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4
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Chen K, Beeraka NM, Zhang X, Sinelnikov MY, Plotnikova M, Zhao C, Basavaraj V, Zhang J, Lu P. Recent Advances in Therapeutic Modalities Against Breast Cancer-Related Lymphedema: Future Epigenetic Landscape. Lymphat Res Biol 2023; 21:536-548. [PMID: 37267206 PMCID: PMC10753987 DOI: 10.1089/lrb.2022.0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
Background: Lymphedema is a significant postsurgical complication observed in the majority of breast cancer patients. These multifactorial etiopathogenesis have a significant role in the development of novel diagnostic/prognostic biomarkers and the development of novel therapies. This review aims to ascertain the epigenetic alterations that lead to breast cancer-related lymphedema (BCRL), multiple pathobiological events, and the underlying genetic predisposing factors, signaling cascades pertinent to the lapses in effective prognosis/diagnosis, and finally to develop a suitable therapeutic regimen. Methods and Results: We have performed a literature search in public databases such as PubMed, Medline, Google Scholar, National Library of Medicine and screened several published reports. Search words such as epigenetics to induce BCRL, prognosis/diagnosis, primary lymphedema, secondary lymphedema, genetic predisposing factors for BRCL, conventional therapies, and surgery were used in these databases. This review described several epigenetic-based predisposing factors and the pathophysiological consequences of BCRL, which affect the overall quality of life, and the interplay of these events could foster the progression of lymphedema in breast cancer survivors. Prognosis/diagnostic and therapy lapses for treating BCRL are highly challenging due to genetic and anatomical variations, alteration in the lymphatic vessel contractions, and variable expression of several factors such as vascular endothelial growth factor (VEGF)-E and vascular endothelial growth factor receptor (VEGFR) in breast cancer survivors. Conclusion: We compared the efficacy of various conventional therapies for treating BCRL as a multidisciplinary approach. Further substantial research is required to decipher underlying signaling epigenetic pathways to develop chromatin-modifying therapies pertinent to the multiple etiopathogenesis to explore the correlation between the disease pathophysiology and novel therapeutic modalities to treat BCRL.
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Affiliation(s)
- Kuo Chen
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Narasimha M. Beeraka
- Raghavendra Institute of Pharmaceutical Education and Research (RIPER), Anantapuramu, Andhra Pradesh, India
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Xinliang Zhang
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Mikhail Y. Sinelnikov
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Maria Plotnikova
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Cuiping Zhao
- The 80th Army Hospital of the Chinese People's Liberation Army, Weifang, China
| | - Vijaya Basavaraj
- Department of Pathology, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka, India
| | - Jin Zhang
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Pengwei Lu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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5
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Jiang H, Li G. Transcription factors direct epigenetic reprogramming at specific loci in human cancers. Front Genet 2023; 14:1234515. [PMID: 37876590 PMCID: PMC10591108 DOI: 10.3389/fgene.2023.1234515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
The characterization of epigenetic changes during cancer development and progression led to notable insights regarding the roles of cancer-specific epigenetic reprogramming. Recent studies showed that transcription factors (TFs) are capable to regulate epigenetic reprogramming at specific loci in different cancer types through their DNA-binding activities. However, the causal association of dynamic histone modification change mediated by TFs is still not well elucidated. Here we evaluated the impacts of 636 transcription factor binding activities on histone modification in 24 cancer types. We performed Instrumental Variables analysis by using genetic lesions of TFs as our instrumental proxies, which previously discovered to be associated with histone mark activities. As a result, we showed a total of 6 EpiTFs as strong directors of epigenetic reprogramming of histone modification in cancers, which alters the molecular and clinical phenotypes of cancer. Together our findings highlight a causal mechanism driven by the TFs and genome-wide histone modification, which is relevant to multiple status of oncogenesis.
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Affiliation(s)
| | - Guoxin Li
- Department of General Surgery, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
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Pierzynska-Mach A, Cainero I, Oneto M, Ferrando-May E, Lanzanò L, Diaspro A. Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model. Sci Rep 2023; 13:12749. [PMID: 37550322 PMCID: PMC10406876 DOI: 10.1038/s41598-023-38685-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 07/12/2023] [Indexed: 08/09/2023] Open
Abstract
Epigenetic dysregulation of chromatin is one of the hallmarks of cancer development and progression, and it is continuously investigated as a potential general bio-marker of this complex disease. One of the nuclear factors involved in gene regulation is the unique DEK protein-a histone chaperon modulating chromatin topology. DEK expression levels increase significantly from normal to cancer cells, hence raising the possibility of using DEK as a tumor marker. Although DEK is known to be implicated in epigenetic and transcriptional regulation, the details of these interactions and their relevance in cancer development remain largely elusive. In this work, we investigated the spatial correlation between the nuclear distribution of DEK and chromatin patterns-alongside breast cancer progression-leveraging image cross-correlation spectroscopy (ICCS) coupled with Proximity Ligation Assay (PLA) analysis. We performed our study on the model based on three well-established human breast cell lines to consider this tumor's heterogeneity (MCF10A, MCF7, and MDA-MB-231 cells). Our results show that overexpression of DEK correlates with the overall higher level of spatial proximity between DEK and histone marks corresponding to gene promoters regions (H3K9ac, H3K4me3), although it does not correlate with spatial proximity between DEK and gene enhancers (H3K27ac). Additionally, we observed that colocalizing fractions of DEK and histone marks are lower for the non-invasive cell subtype than for the highly invasive cell line (MDA-MB-231). Thus, this study suggests that the role of DEK on transcriptionally active chromatin regions varies depending on the subtype of the breast cancer cell line.
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Affiliation(s)
| | - Isotta Cainero
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Michele Oneto
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
| | - Elisa Ferrando-May
- Department of Biology, University of Konstanz, Konstanz, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Luca Lanzanò
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
- Department of Physics and Astronomy, University of Catania, Catania, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy.
- DIFILAB, Department of Physics, University of Genoa, Genoa, Italy.
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7
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Liu R, Wu J, Guo H, Yao W, Li S, Lu Y, Jia Y, Liang X, Tang J, Zhang H. Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e292. [PMID: 37220590 PMCID: PMC10200003 DOI: 10.1002/mco2.292] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Histones are DNA-binding basic proteins found in chromosomes. After the histone translation, its amino tail undergoes various modifications, such as methylation, acetylation, phosphorylation, ubiquitination, malonylation, propionylation, butyrylation, crotonylation, and lactylation, which together constitute the "histone code." The relationship between their combination and biological function can be used as an important epigenetic marker. Methylation and demethylation of the same histone residue, acetylation and deacetylation, phosphorylation and dephosphorylation, and even methylation and acetylation between different histone residues cooperate or antagonize with each other, forming a complex network. Histone-modifying enzymes, which cause numerous histone codes, have become a hot topic in the research on cancer therapeutic targets. Therefore, a thorough understanding of the role of histone post-translational modifications (PTMs) in cell life activities is very important for preventing and treating human diseases. In this review, several most thoroughly studied and newly discovered histone PTMs are introduced. Furthermore, we focus on the histone-modifying enzymes with carcinogenic potential, their abnormal modification sites in various tumors, and multiple essential molecular regulation mechanism. Finally, we summarize the missing areas of the current research and point out the direction of future research. We hope to provide a comprehensive understanding and promote further research in this field.
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Affiliation(s)
- Ruiqi Liu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jiajun Wu
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Haiwei Guo
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Weiping Yao
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Shuang Li
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentJinzhou Medical UniversityJinzhouLiaoningChina
| | - Yanwei Lu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Yongshi Jia
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiaodong Liang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jianming Tang
- Department of Radiation OncologyThe First Hospital of Lanzhou UniversityLanzhou UniversityLanzhouGansuChina
| | - Haibo Zhang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
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Ciaco S, Mazzoleni V, Javed A, Eiler S, Ruff M, Mousli M, Mori M, Mély Y. Inhibitors of UHRF1 base flipping activity showing cytotoxicity against cancer cells. Bioorg Chem 2023; 137:106616. [PMID: 37247564 DOI: 10.1016/j.bioorg.2023.106616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/28/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023]
Abstract
Ubiquitin-like containing PHD and RING finger domain 1 (UHRF1) is a nuclear multi-domain protein overexpressed in numerous human cancer types. We previously disclosed the anthraquinone derivative UM63 that inhibits UHRF1-SRA domain base-flipping activity, although having DNA intercalating properties. Herein, based on the UM63 structure, new UHRF1-SRA inhibitors were identified through a multidisciplinary approach, combining molecular modelling, biophysical assays, molecular and cell biology experiments. We identified AMSA2 and MPB7, that inhibit UHRF1-SRA mediated base flipping at low micromolar concentrations, but do not intercalate into DNA, which is a key advantage over UM63. These molecules prevent UHRF1/DNMT1 interaction at replication forks and decrease the overall DNA methylation in cells. Moreover, both compounds specifically induce cell death in numerous cancer cell lines, displaying marginal effect on non-cancer cells, as they preferentially affect cells with high level of UHRF1. Overall, these two compounds are promising leads for the development of anti-cancer drugs targeting UHRF1.
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Affiliation(s)
- Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France; Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Viola Mazzoleni
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Aqib Javed
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Sylvia Eiler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - Marc Mousli
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France.
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy.
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France.
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9
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Guo H, Cao W, Zhu Y, Li T, Hu B. A genome-wide cross-cancer meta-analysis highlights the shared genetic links of five solid cancers. Front Microbiol 2023; 14:1116592. [PMID: 36819030 PMCID: PMC9935838 DOI: 10.3389/fmicb.2023.1116592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023] Open
Abstract
Breast, ovarian, prostate, lung, and head/neck cancers are five solid cancers with complex interrelationships. However, the shared genetic factors of the five cancers were often revealed either by the combination of individual genome-wide association study (GWAS) approach or by the fixed-effect model-based meta-analysis approach with practically impossible assumptions. Here, we presented a random-effect model-based cross-cancer meta-analysis framework for identifying the genetic variants jointly influencing the five solid cancers. A comprehensive genetic correlation analysis (genome-wide, partitioned, and local) approach was performed by using GWAS summary statistics of the five cancers, and we observed three cancer pairs with significant genetic correlation: breast-ovarian cancer (r g = 0.221, p = 0.0003), breast-lung cancer (r g = 0.234, p = 7.6 × 10-6), and lung-head/neck cancer (r g = 0.652, p = 0.010). Furthermore, a random-effect model-based cross-trait meta-analysis was conducted for each significant cancer pair, and we found 27 shared genetic loci between breast and ovarian cancers, 18 loci between breast and lung cancers, and three loci between lung and head/neck cancers. Functional analysis indicates that the shared genes are enriched in human T-cell leukemia virus 1 infection (HTLV-1) and antigen processing and presentation (APP) pathways. Our study investigates the shared genetic links across five solid cancers and will help to reveal their potential molecular mechanisms.
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Affiliation(s)
- Hongping Guo
- School of Mathematics and Statistics, Hubei Normal University, Huangshi, China,*Correspondence: Hongping Guo ✉
| | - Wenhao Cao
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, United States
| | - Yiran Zhu
- School of Mathematics and Statistics, Hubei Normal University, Huangshi, China
| | - Tong Li
- School of Mathematics and Statistics, Hubei Normal University, Huangshi, China
| | - Boheng Hu
- School of Mathematics and Statistics, Hubei Normal University, Huangshi, China
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10
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Pierozan P, Kosnik M, Karlsson O. High-content analysis shows synergistic effects of low perfluorooctanoic acid (PFOS) and perfluorooctane sulfonic acid (PFOA) mixture concentrations on human breast epithelial cell carcinogenesis. ENVIRONMENT INTERNATIONAL 2023; 172:107746. [PMID: 36731186 DOI: 10.1016/j.envint.2023.107746] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Perfluoroalkyl substances (PFAS) have been associated with cancer, but the potential underlying mechanisms need to be further elucidated and include studies of PFAS mixtures. This mechanistic study revealed that very low concentrations (500 pM) of the binary PFOS and PFOA mixture induced synergistic effects on human epithelial breast cell (MCF-10A) proliferation. The cell proliferation was mediated by pregnane X receptor (PXR) activation, an increase in cyclin D1 and CDK6/4 levels, decrease in p21 and p53 levels, and by regulation of phosphor-Akt and β-catenin. The PFAS mixture also altered histone modifications, epigenetic mechanisms implicated in tumorigenesis, and promoted cell migration and invasion by reducing the levels of occludin. High-content screening using the cell painting assay, revealed that hundreds of cell features were affected by the PFAS mixture even at the lowest concentration tested (100 pM). The detailed phenotype profiling further demonstrated that the PFAS mixture altered cell morphology, mostly in parameters related to intensity and texture associated with mitochondria, endoplasmic reticulum, and nucleoli. Exposure to higher concentrations (≥50 µM) of the PFOS and PFOA mixture caused cell death through synergistic interactions that induced oxidative stress, DNA/RNA damage, and lipid peroxidation, illustrating the complexity of mixture toxicology. Increased knowledge about mixture-induced effects is important for better understanding of PFAS' possible role in cancer etiology, and may impact the risk assessment of these and other compounds. This study shows the potential of image-based multiplexed fluorescence assays and high-content screening for development of new approach methodologies in toxicology.
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Affiliation(s)
- Paula Pierozan
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm 114 18, Sweden
| | - Marissa Kosnik
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm 114 18, Sweden
| | - Oskar Karlsson
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm 114 18, Sweden.
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Kashyap D, Sharma R, Goel N, Buttar HS, Garg VK, Pal D, Rajab K, Shaikh A. Coding roles of long non-coding RNAs in breast cancer: Emerging molecular diagnostic biomarkers and potential therapeutic targets with special reference to chemotherapy resistance. Front Genet 2023; 13:993687. [PMID: 36685962 PMCID: PMC9852779 DOI: 10.3389/fgene.2022.993687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/07/2022] [Indexed: 01/08/2023] Open
Abstract
Dysregulation of epigenetic mechanisms have been depicted in several pathological consequence such as cancer. Different modes of epigenetic regulation (DNA methylation (hypomethylation or hypermethylation of promotor), histone modifications, abnormal expression of microRNAs (miRNAs), long non-coding RNAs, and small nucleolar RNAs), are discovered. Particularly, lncRNAs are known to exert pivot roles in different types of cancer including breast cancer. LncRNAs with oncogenic and tumour suppressive potential are reported. Differentially expressed lncRNAs contribute a remarkable role in the development of primary and acquired resistance for radiotherapy, endocrine therapy, immunotherapy, and targeted therapy. A wide range of molecular subtype specific lncRNAs have been assessed in breast cancer research. A number of studies have also shown that lncRNAs may be clinically used as non-invasive diagnostic biomarkers for early detection of breast cancer. Such molecular biomarkers have also been found in cancer stem cells of breast tumours. The objectives of the present review are to summarize the important roles of oncogenic and tumour suppressive lncRNAs for the early diagnosis of breast cancer, metastatic potential, and chemotherapy resistance across the molecular subtypes.
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Affiliation(s)
- Dharambir Kashyap
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Riya Sharma
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelam Goel
- Department of Information Technology, University Institute of Engineering & Technology, Panjab University, Chandigarh, India
| | - Harpal S. Buttar
- Department of Pathology and Laboratory Medicine, University of Ottawa, Faculty of Medicine, Ottawa, ON, Canada
| | - Vivek Kumar Garg
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Gharuan, Mohali, India,*Correspondence: Vivek Kumar Garg, ; Asadullah Shaikh,
| | - Deeksha Pal
- Department of Translational and Regenerative Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Khairan Rajab
- College of Computer Science and Information Systems, Najran University, Najran, Saudi Arabia
| | - Asadullah Shaikh
- College of Computer Science and Information Systems, Najran University, Najran, Saudi Arabia,*Correspondence: Vivek Kumar Garg, ; Asadullah Shaikh,
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12
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Fouque KJD, Miller SA, Pham K, Bhanu NV, Cintron-Diaz YL, Leyva D, Kaplan D, Voinov VG, Ridgeway ME, Park MA, Garcia BA, Fernandez-Lima F. Top-"Double-Down" Mass Spectrometry of Histone H4 Proteoforms: Tandem Ultraviolet-Photon and Mobility/Mass-Selected Electron Capture Dissociations. Anal Chem 2022; 94:15377-15385. [PMID: 36282112 PMCID: PMC11037235 DOI: 10.1021/acs.analchem.2c03147] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Post-translational modifications (PTMs) on intact histones play a major role in regulating chromatin dynamics and influence biological processes such as DNA transcription, replication, and repair. The nature and position of each histone PTM is crucial to decipher how this information is translated into biological response. In the present work, the potential of a novel tandem top-"double-down" approach─ultraviolet photodissociation followed by mobility and mass-selected electron capture dissociation and mass spectrometry (UVPD-TIMS-q-ECD-ToF MS/MS)─is illustrated for the characterization of HeLa derived intact histone H4 proteoforms. The comparison between q-ECD-ToF MS/MS spectra and traditional Fourier-transform-ion cyclotron resonance-ECD MS/MS spectra of a H4 standard showed a similar sequence coverage (∼75%) with significant faster data acquisition in the ToF MS/MS platform (∼3 vs ∼15 min). Multiple mass shifts (e.g., 14 and 42 Da) were observed for the HeLa derived H4 proteoforms for which the top-down UVPD and ECD fragmentation analysis were consistent in detecting the presence of acetylated PTMs at the N-terminus and Lys5, Lys8, Lys12, and Lys16 residues, as well as methylated, dimethylated, and trimethylated PTMs at the Lys20 residue with a high sequence coverage (∼90%). The presented top-down results are in good agreement with bottom-up TIMS ToF MS/MS experiments and allowed for additional description of PTMs at the N-terminus. The integration of a 213 nm UV laser in the present platform allowed for UVPD events prior to the ion mobility-mass precursor separation for collision-induced dissociation (CID)/ECD-ToF MS. Selected c305+ UVPD fragments, from different H4 proteoforms (e.g., Ac + Me2, 2Ac + Me2 and 3Ac + Me2), exhibited multiple IMS bands for which similar CID/ECD fragmentation patterns per IMS band pointed toward the presence of conformers, adopting the same PTM distribution, with a clear assignment of the PTM localization for each of the c305+ UVPD fragment H4 proteoforms. These results were consistent with the biological "zip" model, where acetylation proceeds in the Lys16 to Lys5 direction. This novel platform further enhances the structural toolbox with alternative fragmentation mechanisms (UVPD, CID, and ECD) in tandem with fast, high-resolution mobility separations and shows great promise for global proteoform analysis.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Samuel A. Miller
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Khoa Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Natarajan V. Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Yarixa L. Cintron-Diaz
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Dennys Leyva
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | | | | | | | - Melvin A. Park
- Bruker Daltonics Inc., Billerica, MA 01821, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
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13
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Akhoundova D, Rubin MA. Clinical application of advanced multi-omics tumor profiling: Shaping precision oncology of the future. Cancer Cell 2022; 40:920-938. [PMID: 36055231 DOI: 10.1016/j.ccell.2022.08.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/22/2022] [Accepted: 08/11/2022] [Indexed: 12/17/2022]
Abstract
Next-generation DNA sequencing technology has dramatically advanced clinical oncology through the identification of therapeutic targets and molecular biomarkers, leading to the personalization of cancer treatment with significantly improved outcomes for many common and rare tumor entities. More recent developments in advanced tumor profiling now enable dissection of tumor molecular architecture and the functional phenotype at cellular and subcellular resolution. Clinical translation of high-resolution tumor profiling and integration of multi-omics data into precision treatment, however, pose significant challenges at the level of prospective validation and clinical implementation. In this review, we summarize the latest advances in multi-omics tumor profiling, focusing on spatial genomics and chromatin organization, spatial transcriptomics and proteomics, liquid biopsy, and ex vivo modeling of drug response. We analyze the current stages of translational validation of these technologies and discuss future perspectives for their integration into precision treatment.
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Affiliation(s)
- Dilara Akhoundova
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Department of Medical Oncology, Inselspital, University Hospital of Bern, 3010 Bern, Switzerland
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, 3008 Bern, Switzerland.
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14
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Kumari S, Sharma S, Advani D, Khosla A, Kumar P, Ambasta RK. Unboxing the molecular modalities of mutagens in cancer. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:62111-62159. [PMID: 34611806 PMCID: PMC8492102 DOI: 10.1007/s11356-021-16726-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/22/2021] [Indexed: 04/16/2023]
Abstract
The etiology of the majority of human cancers is associated with a myriad of environmental causes, including physical, chemical, and biological factors. DNA damage induced by such mutagens is the initial step in the process of carcinogenesis resulting in the accumulation of mutations. Mutational events are considered the major triggers for introducing genetic and epigenetic insults such as DNA crosslinks, single- and double-strand DNA breaks, formation of DNA adducts, mismatched bases, modification in histones, DNA methylation, and microRNA alterations. However, DNA repair mechanisms are devoted to protect the DNA to ensure genetic stability, any aberrations in these calibrated mechanisms provoke cancer occurrence. Comprehensive knowledge of the type of mutagens and carcinogens and the influence of these agents in DNA damage and cancer induction is crucial to develop rational anticancer strategies. This review delineated the molecular mechanism of DNA damage and the repair pathways to provide a deep understanding of the molecular basis of mutagenicity and carcinogenicity. A relationship between DNA adduct formation and cancer incidence has also been summarized. The mechanistic basis of inflammatory response and oxidative damage triggered by mutagens in tumorigenesis has also been highlighted. We elucidated the interesting interplay between DNA damage response and immune system mechanisms. We addressed the current understanding of DNA repair targeted therapies and DNA damaging chemotherapeutic agents for cancer treatment and discussed how antiviral agents, anti-inflammatory drugs, and immunotherapeutic agents combined with traditional approaches lay the foundations for future cancer therapies.
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Affiliation(s)
- Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Sudhanshu Sharma
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Dia Advani
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Akanksha Khosla
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
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15
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Rath S, Chakraborty D, Pradhan J, Imran Khan M, Dandapat J. Epigenomic interplay in tumor heterogeneity: Potential of epidrugs as adjunct therapy. Cytokine 2022; 157:155967. [PMID: 35905624 DOI: 10.1016/j.cyto.2022.155967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 11/28/2022]
Abstract
"Heterogeneity" in tumor mass has immense importance in cancer progression and therapy. The impact of tumor heterogeneity is an emerging field and not yet fully explored. Tumor heterogeneity is mainly considered as intra-tumor heterogeneity and inter-tumor heterogeneity based on their origin. Intra-tumor heterogeneity refers to the discrepancy within the same cancer mass while inter-tumor heterogeneity refers to the discrepancy between different patients having the same tumor type. Both of these heterogeneity types lead to variation in the histopathological as well as clinical properties of the cancer mass which drives disease resistance towards therapeutic approaches. Cancer stem cells (CSCs) act as pinnacle progenitors for heterogeneity development along with various other genetic and epigenetic parameters that are regulating this process. In recent times epigenetic factors are one of the most studied parameters that drive oxidative stress pathways essential during cancer progression. These epigenetic changes are modulated by various epidrugs and have an impact on tumor heterogeneity. The present review summarizes various aspects of epigenetic regulation in the tumor microenvironment, oxidative stress, and progression towards tumor heterogeneity that creates complications during cancer treatment. This review also explores the possible role of epidrugs in regulating tumor heterogeneity and personalized therapy against drug resistance.
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Affiliation(s)
- Suvasmita Rath
- Center of Environment, Climate Change and Public Health, Utkal University, Vani Vihar, Bhubaneswar 751004, Odisha, India
| | - Diptesh Chakraborty
- Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India
| | - Jyotsnarani Pradhan
- Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India
| | - Mohammad Imran Khan
- Department of Biochemistry, King Abdulaziz University (KAU), Jeddah 21577, Saudi Arabia; Centre of Artificial Intelligence for Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jagneshwar Dandapat
- Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India; Centre of Excellence in Integrated Omics and Computational Biology, Utkal University, Bhubaneswar 751004, Odisha, India.
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16
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Ferrer-Bonsoms JA, Gimeno M, Olaverri D, Sacristan P, Lobato C, Castilla C, Carazo F, Rubio A. EventPointer 3.0: flexible and accurate splicing analysis that includes studying the differential usage of protein-domains. NAR Genom Bioinform 2022; 4:lqac067. [PMID: 36128425 PMCID: PMC9477077 DOI: 10.1093/nargab/lqac067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/29/2022] [Accepted: 09/07/2022] [Indexed: 12/05/2022] Open
Abstract
Alternative splicing (AS) plays a key role in cancer: all its hallmarks have been associated with different mechanisms of abnormal AS. The improvement of the human transcriptome annotation and the availability of fast and accurate software to estimate isoform concentrations has boosted the analysis of transcriptome profiling from RNA-seq. The statistical analysis of AS is a challenging problem not yet fully solved. We have included in EventPointer (EP), a Bioconductor package, a novel statistical method that can use the bootstrap of the pseudoaligners. We compared it with other state-of-the-art algorithms to analyze AS. Its performance is outstanding for shallow sequencing conditions. The statistical framework is very flexible since it is based on design and contrast matrices. EP now includes a convenient tool to find the primers to validate the discoveries using PCR. We also added a statistical module to study alteration in protein domain related to AS. Applying it to 9514 patients from TCGA and TARGET in 19 different tumor types resulted in two conclusions: i) aberrant alternative splicing alters the relative presence of Protein domains and, ii) the number of enriched domains is strongly correlated with the age of the patients.
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Affiliation(s)
- Juan A Ferrer-Bonsoms
- Biomedical Engineering and Science Department, TECNUN, Universidad de Navarra , San Sebastián , Spain
| | - Marian Gimeno
- Biomedical Engineering and Science Department, TECNUN, Universidad de Navarra , San Sebastián , Spain
| | - Danel Olaverri
- Biomedical Engineering and Science Department, TECNUN, Universidad de Navarra , San Sebastián , Spain
| | - Pablo Sacristan
- Biomedical Engineering and Science Department, TECNUN, Universidad de Navarra , San Sebastián , Spain
| | - César Lobato
- Biomedical Engineering and Science Department, TECNUN, Universidad de Navarra , San Sebastián , Spain
| | - Carlos Castilla
- Biomedical Engineering and Science Department, TECNUN, Universidad de Navarra , San Sebastián , Spain
| | - Fernando Carazo
- Biomedical Engineering and Science Department, TECNUN, Universidad de Navarra , San Sebastián , Spain
| | - Angel Rubio
- Biomedical Engineering and Science Department, TECNUN, Universidad de Navarra , San Sebastián , Spain
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17
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Gupta P, Jindal A, Ahuja G, Jayadeva, Sengupta D. A new deep learning technique reveals the exclusive functional contributions of individual cancer mutations. J Biol Chem 2022; 298:102177. [PMID: 35753349 PMCID: PMC9304782 DOI: 10.1016/j.jbc.2022.102177] [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: 02/21/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 11/26/2022] Open
Abstract
Cancers are caused by genomic alterations that may be inherited, induced by environmental carcinogens, or caused due to random replication errors. Postinduction of carcinogenicity, mutations further propagate and drastically alter the cancer genomes. Although a subset of driver mutations has been identified and characterized to date, most cancer-related somatic mutations are indistinguishable from germline variants or other noncancerous somatic mutations. Thus, such overlap impedes appreciation of many deleterious but previously uncharacterized somatic mutations. The major bottleneck arises due to patient-to-patient variability in mutational profiles, making it difficult to associate specific mutations with a given disease outcome. Here, we describe a newly developed technique Continuous Representation of Codon Switches (CRCS), a deep learning-based method that allows us to generate numerical vector representations of mutations, thereby enabling numerous machine learning-based tasks. We demonstrate three major applications of CRCS; first, we show how CRCS can help detect cancer-related somatic mutations in the absence of matched normal samples, which has applications in cell-free DNA–based assessment of tumor mutation burden. Second, the proposed approach also enables identification and exploration of driver genes; our analyses implicate DMD, RSK4, OFD1, WDR44, and AFF2 as potential cancer drivers. Finally, we used CRCS to score individual mutations in a tumor sample, which was found to be predictive of patient survival in bladder urothelial carcinoma, hepatocellular carcinoma, and lung adenocarcinoma. Taken together, we propose CRCS as a valuable computational tool for analysis of the functional significance of individual cancer mutations.
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Affiliation(s)
- Prashant Gupta
- Department of Electrical Engineering, Indian Institute of Technology Delhi, Hauz Khas, Delhi 110016, India
| | - Aashi Jindal
- Department of Electrical Engineering, Indian Institute of Technology Delhi, Hauz Khas, Delhi 110016, India
| | - Gaurav Ahuja
- Center for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
| | - Jayadeva
- Department of Electrical Engineering, Indian Institute of Technology Delhi, Hauz Khas, Delhi 110016, India.
| | - Debarka Sengupta
- Center for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India; Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Delhi 110020, India; Center for Artificial Intelligence, Indraprastha Institute of Information Technology, Delhi 110020, India.
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18
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Seo J, Sim Y, Kim J, Kim H, Cho I, Nam H, Yoon YG, Chang JB. PICASSO allows ultra-multiplexed fluorescence imaging of spatially overlapping proteins without reference spectra measurements. Nat Commun 2022; 13:2475. [PMID: 35513404 PMCID: PMC9072354 DOI: 10.1038/s41467-022-30168-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 04/20/2022] [Indexed: 12/19/2022] Open
Abstract
Ultra-multiplexed fluorescence imaging requires the use of spectrally overlapping fluorophores to label proteins and then to unmix the images of the fluorophores. However, doing this remains a challenge, especially in highly heterogeneous specimens, such as the brain, owing to the high degree of variation in the emission spectra of fluorophores in such specimens. Here, we propose PICASSO, which enables more than 15-color imaging of spatially overlapping proteins in a single imaging round without using any reference emission spectra. PICASSO requires an equal number of images and fluorophores, which enables such advanced multiplexed imaging, even with bandpass filter-based microscopy. We show that PICASSO can be used to achieve strong multiplexing capability in diverse applications. By combining PICASSO with cyclic immunofluorescence staining, we achieve 45-color imaging of the mouse brain in three cycles. PICASSO provides a tool for multiplexed imaging with high accessibility and accuracy for a broad range of researchers.
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Affiliation(s)
- Junyoung Seo
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Yeonbo Sim
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Korea
| | - Jeewon Kim
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Hyunwoo Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - In Cho
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Hoyeon Nam
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Young-Gyu Yoon
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
| | - Jae-Byum Chang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
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19
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Suchanti S, Stephen BJ, Awasthi S, Awasthi SK, Singh G, Singh A, Mishra R. Harnessing the role of epigenetic histone modification in targeting head and neck squamous cell carcinoma. Epigenomics 2022; 14:279-293. [PMID: 35184601 DOI: 10.2217/epi-2020-0348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent form of cancer worldwide. Despite advancements made in treatment strategies, the fatality rate of HNSCC is very high. An accumulating body of evidence suggests that epigenetic modification of histones plays an influential role in the development and progression of the disease. In this review we discuss the role of epigenetic modifications in HNSCC and the inter-relationships of human papillomavirus oncoproteins and histone-modifying agents. Further, we explore the possibility of identifying these modifications as biomarkers for their use as drugs in treatment strategies.
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Affiliation(s)
- Surabhi Suchanti
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, India
| | - Bjorn J Stephen
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, India
| | - Sonali Awasthi
- Department of Life Sciences, CSJM University, Kanpur, Uttar Pradesh, 208024, India
| | - Sudhir K Awasthi
- Department of Life Sciences, CSJM University, Kanpur, Uttar Pradesh, 208024, India
| | - Gyanendra Singh
- Toxicology Division, ICMR-National Institute of Occupational Health, Ahmedabad, Gujarat, 380016, India
| | - Abhijeet Singh
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, India
| | - Rajeev Mishra
- Department of Life Sciences, CSJM University, Kanpur, Uttar Pradesh, 208024, India
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20
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Epi-miRNAs: Regulators of the Histone Modification Machinery in Human Cancer. JOURNAL OF ONCOLOGY 2022; 2022:4889807. [PMID: 35087589 PMCID: PMC8789461 DOI: 10.1155/2022/4889807] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/14/2021] [Indexed: 12/18/2022]
Abstract
Cancer is a leading cause of death and disability worldwide. Epigenetic deregulation is one of the most critical mechanisms in carcinogenesis and can be classified into effects on DNA methylation and histone modification. MicroRNAs are small noncoding RNAs involved in fine-tuning their target genes after transcription. Various microRNAs control the expression of histone modifiers and are involved in a variety of cancers. Therefore, overexpression or downregulation of microRNAs can alter cell fate and cause malignancies. In this review, we discuss the role of microRNAs in regulating the histone modification machinery in various cancers, with a focus on the histone-modifying enzymes such as acetylases, deacetylases, methyltransferases, demethylases, kinases, phosphatases, desumoylases, ubiquitinases, and deubiquitinases. Understanding of microRNA-related aberrations underlying histone modifiers in pathogenesis of different cancers can help identify novel therapeutic targets or early detection approaches that allow better management of patients or monitoring of treatment response.
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21
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Hsieh WC, Sutter BM, Ruess H, Barnes SD, Malladi VS, Tu BP. Glucose starvation induces a switch in the histone acetylome for activation of gluconeogenic and fat metabolism genes. Mol Cell 2022; 82:60-74.e5. [PMID: 34995509 PMCID: PMC8794035 DOI: 10.1016/j.molcel.2021.12.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/31/2021] [Accepted: 12/13/2021] [Indexed: 01/09/2023]
Abstract
Acetyl-CoA is a key intermediate situated at the intersection of many metabolic pathways. The reliance of histone acetylation on acetyl-CoA enables the coordination of gene expression with metabolic state. Abundant acetyl-CoA has been linked to the activation of genes involved in cell growth or tumorigenesis through histone acetylation. However, the role of histone acetylation in transcription under low levels of acetyl-CoA remains poorly understood. Here, we use a yeast starvation model to observe the dramatic alteration in the global occupancy of histone acetylation following carbon starvation; the location of histone acetylation marks shifts from growth-promoting genes to gluconeogenic and fat metabolism genes. This reallocation is mediated by both the histone deacetylase Rpd3p and the acetyltransferase Gcn5p, a component of the SAGA transcriptional coactivator. Our findings reveal an unexpected switch in the specificity of histone acetylation to promote pathways that generate acetyl-CoA for oxidation when acetyl-CoA is limiting.
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Affiliation(s)
- Wen-Chuan Hsieh
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Benjamin M. Sutter
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Holly Ruess
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Spencer D. Barnes
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Venkat S. Malladi
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Benjamin P. Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA,Correspondence and Lead Contact:
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22
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Borkiewicz L. Histone 3 Lysine 27 Trimethylation Signature in Breast Cancer. Int J Mol Sci 2021; 22:12853. [PMID: 34884658 PMCID: PMC8657745 DOI: 10.3390/ijms222312853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer development and progression rely on complicated genetic and also epigenetic changes which regulate gene expression without altering the DNA sequence. Epigenetic mechanisms such as DNA methylation, histone modifications, and regulation by lncRNAs alter protein expression by either promoting gene transcription or repressing it. The presence of so-called chromatin modification marks at various gene promoters and gene bodies is associated with normal cell development but also with tumorigenesis and progression of different types of cancer, including the most frequently diagnosed breast cancer. This review is focused on the significance of one of the abundant post-translational modifications of histone 3- trimethylation of lysine 27 (H3K27me3), which was shown to participate in tumour suppressor genes' silencing. Unlike other reviews in the field, here the overview of existing evidence linking H3K27me3 status with breast cancer biology and the tumour outcome is presented especially in the context of diverse breast cancer subtypes. Moreover, the potential of agents that target H3K27me3 for the treatment of this complex disease as well as H3K27 methylation in cross-talk with other chromatin modifications and lncRNAs are discussed.
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Affiliation(s)
- Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-059 Lublin, Poland
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23
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Starks RR, Kaur H, Tuteja G. Mapping cis-regulatory elements in the midgestation mouse placenta. Sci Rep 2021; 11:22331. [PMID: 34785717 PMCID: PMC8595355 DOI: 10.1038/s41598-021-01664-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/01/2021] [Indexed: 12/22/2022] Open
Abstract
The placenta is a temporary organ that provides the developing fetus with nutrients, oxygen, and protection in utero. Defects in its development, which may be caused by misregulated gene expression, can lead to devastating outcomes for the mother and fetus. In mouse, placental defects during midgestation commonly lead to embryonic lethality. However, the regulatory mechanisms controlling expression of genes during this period have not been thoroughly investigated. Therefore, we generated and analyzed ChIP-seq data for multiple histone modifications known to mark cis-regulatory regions. We annotated active and poised promoters and enhancers, as well as regions generally associated with repressed gene expression. We found that poised promoters were associated with neuronal development genes, while active promoters were largely associated with housekeeping genes. Active and poised enhancers were associated with placental development genes, though only active enhancers were associated with genes that have placenta-specific expression. Motif analysis within active enhancers identified a large network of transcription factors, including those that have not been previously studied in the placenta and are candidates for future studies. The data generated and genomic regions annotated provide researchers with a foundation for future studies, aimed at understanding how specific genes in the midgestation mouse placenta are regulated.
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Affiliation(s)
- Rebekah R Starks
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA.,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA
| | - Haninder Kaur
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Geetu Tuteja
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA. .,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA.
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24
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Pham KN, Fernandez-Lima F. Structural Characterization of Human Histone H4.1 by Tandem Nonlinear and Linear Ion Mobility Spectrometry Complemented with Molecular Dynamics Simulations. ACS OMEGA 2021; 6:29567-29576. [PMID: 34778628 PMCID: PMC8582071 DOI: 10.1021/acsomega.1c03744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Extracellular histone H4 is an attractive drug target owing to its roles in organ failure in sepsis and other diseases. To identify inhibitors using in silico methods, information on histone H4 structural dynamics and three-dimensional (3D) structural coordinates is required. Here, DNA-free histone H4 type 1 (H4.1) was characterized by utilizing tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry (MS) complemented with molecular dynamics (MD) simulations. The gas-phase structures of H4.1 are dependent on the starting solution conditions, evidenced by differences in charge state distributions, mobility distributions, and collision-induced unfolding (CIU) pathways. The experimental results show that H4.1 adopts diverse conformational types from compact (C) to partially folded (P) and subsequently elongated (E) structures. Molecular dynamics simulations provided candidate structures for the histone H4.1 monomer in solution and for the gas-phase structures observed using FAIMS-IMS-TOF MS as a function of the charge state and mobility distribution. A combination of the FAIMS-TIMS experimental results with theoretical dipole calculations reveals the important role of charge distribution in the dipole alignment of H4.1 elongated structures at high electric fields. A comparison of the secondary and primary structures of DNA-free H2A.1 and H4.1 is made based on the experimental IMS-MS and MD findings.
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Affiliation(s)
- Khoa N. Pham
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United States
- Biomolecular
Science Institute, Florida International
University, Miami, Florida 33199, United
States
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25
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Balzerano A, Paccosi E, Proietti-De-Santis L. Evolutionary Mechanisms of Cancer Suggest Rational Therapeutic Approaches. Cytogenet Genome Res 2021; 161:362-371. [PMID: 34461614 DOI: 10.1159/000516530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/25/2021] [Indexed: 11/19/2022] Open
Abstract
The goal in personalized therapeutic approaches for cancer medicine is to identify specific mutations with prognostic and therapeutic value in order to tailor the therapy for the single patient. The most powerful obstacle for personalized medicine arises from intratumor heterogeneity and clonal evolution, which can promote drug resistance. In this scenario, new technologies, such as next-generation sequencing, have emerged as a central diagnostic tool to profile cancer (epi)genomic landscapes. Therefore, a better understanding of the biological mechanisms underlying cancer evolution is mandatory and represents the current challenge to accurately predict whether cancer will recur after chemotherapy with the aim to tailor rational therapeutic approaches.
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Affiliation(s)
- Alessio Balzerano
- Unit of Molecular Genetics of Aging, Department of Ecology and Biology, University of Tuscia, Viterbo, Italy
| | - Elena Paccosi
- Unit of Molecular Genetics of Aging, Department of Ecology and Biology, University of Tuscia, Viterbo, Italy
| | - Luca Proietti-De-Santis
- Unit of Molecular Genetics of Aging, Department of Ecology and Biology, University of Tuscia, Viterbo, Italy
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26
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Gutman T, Goren G, Efroni O, Tuller T. Estimating the predictive power of silent mutations on cancer classification and prognosis. NPJ Genom Med 2021; 6:67. [PMID: 34385450 PMCID: PMC8361094 DOI: 10.1038/s41525-021-00229-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
In recent years it has been shown that silent mutations, in and out of the coding region, can affect gene expression and may be related to tumorigenesis and cancer cell fitness. However, the predictive ability of these mutations for cancer type diagnosis and prognosis has not been evaluated yet. In the current study, based on the analysis of 9,915 cancer genomes and approximately three million mutations, we provide a comprehensive quantitative evaluation of the predictive power of various types of silent and non-silent mutations over cancer classification and prognosis. The results indicate that silent-mutation models outperform the equivalent null models in classifying all examined cancer types and in estimating the probability of survival 10 years after the initial diagnosis. Additionally, combining both non-silent and silent mutations achieved the best classification results for 68% of the cancer types and the best survival estimation results for up to nine years after the diagnosis. Thus, silent mutations hold considerable predictive power over both cancer classification and prognosis, most likely due to their effect on gene expression. It is highly advised that silent mutations are integrated in cancer research in order to unravel the full genomic landscape of cancer and its ramifications on cancer fitness.
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Affiliation(s)
- Tal Gutman
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Guy Goren
- Department of Electrical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Omri Efroni
- Department of Electrical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel.
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27
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Kim HG, Sung JY, Na K, Kim SW. Low H3K9me3 Expression Is Associated With Poor Prognosis in Patients With Distal Common Bile Duct Cancer. In Vivo 2021; 34:3619-3626. [PMID: 33144476 DOI: 10.21873/invivo.12207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND/AIM Histone modification is associated with tumorigenesis and cancer progression. Recent studies have revealed the prognostic value of histone modification; however, its prognostic role in distal bile duct cancer remains unclear. PATIENTS AND METHODS We analyzed the expression of H3K9me3, H4K20me3, and H3K36me3 and its correlation with survival outcomes in resected samples from 88 patients with distal bile duct cancer. RESULTS Low expression rates of H3K9me3, H4K20me3, and H3K36me3 were significantly associated with poor overall survival (p=0.003, 0.008, and 0.047, respectively) and event-free survival (p=0.03 for H3K9m3). Additionally, low-expression of H3K9me3 was an independent poor prognostic indicator (p<0.001; HR=7.85; 95% CI=2.693-22.883). CONCLUSION H3K9me3 was an independent poor prognostic factor in distal common bile duct cancer. Our results suggest that histone markers are potential prognostic markers and provide better management for patients at risk for an aggressive course of disease.
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Affiliation(s)
- Han Gyeol Kim
- Department of Medicine, Graduate School, Kyung Hee University, Seoul, Republic of Korea.,Department of Pathology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Republic of Korea
| | - Ji-Youn Sung
- Department of Pathology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Republic of Korea
| | - Kiyong Na
- Department of Pathology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Republic of Korea
| | - So-Woon Kim
- Department of Pathology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Republic of Korea
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28
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Pham KN, Mamun Y, Fernandez-Lima F. Structural Heterogeneity of Human Histone H2A.1. J Phys Chem B 2021; 125:4977-4986. [PMID: 33974801 PMCID: PMC8568062 DOI: 10.1021/acs.jpcb.1c00335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Histones are highly basic chromatin proteins that tightly package and order eukaryotic DNA into nucleosomes. While the atomic structure of the nucleosomes has been determined, the three-dimensional structure of DNA-free histones remains unresolved. Here, we combine tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry in parallel with molecular modeling to study the conformational space of a DNA-free histone H2A type 1 (H2A.1). Experimental results showed the dependence of the gas-phase structures on the starting solution conditions, characterized by charge state distributions, mobility distributions, and collision-induced-unfolding pathways. The measured H2A.1 gas-phase structures showed a high diversity of structural features ranging from compact (C) to partially folded (P) and then highly elongated (E) conformations. Molecular dynamics simulations provided candidate structures for the solution H2A.1 native conformation with folded N- and C-terminal tails, as well as gas-phase candidate structures associated with the mobility trends. Complementary collision cross section and dipole calculations showed that the charge distribution in the case of elongated gas-phase structures, where basic and acidic residues are mostly exposed (e.g., z > 15+), is sufficient to induce differences in the dipole alignment at high electric fields, in good agreement with the trends observed during the FAIMS-TIMS experiments.
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Affiliation(s)
- Khoa N Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Yasir Mamun
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States.,Biomolecular Science Institute, Florida International University, Miami, Florida 33199, United States
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29
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Oh JM, Ahn BC. Molecular mechanisms of radioactive iodine refractoriness in differentiated thyroid cancer: Impaired sodium iodide symporter (NIS) expression owing to altered signaling pathway activity and intracellular localization of NIS. Theranostics 2021; 11:6251-6277. [PMID: 33995657 PMCID: PMC8120202 DOI: 10.7150/thno.57689] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
The advanced, metastatic differentiated thyroid cancers (DTCs) have a poor prognosis mainly owing to radioactive iodine (RAI) refractoriness caused by decreased expression of sodium iodide symporter (NIS), diminished targeting of NIS to the cell membrane, or both, thereby decreasing the efficacy of RAI therapy. Genetic aberrations (such as BRAF, RAS, and RET/PTC rearrangements) have been reported to be prominently responsible for the onset, progression, and dedifferentiation of DTCs, mainly through the activation of mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K)/AKT signaling pathways. Eventually, these alterations result in a lack of NIS and disabling of RAI uptake, leading to the development of resistance to RAI therapy. Over the past decade, promising approaches with various targets have been reported to restore NIS expression and RAI uptake in preclinical studies. In this review, we summarized comprehensive molecular mechanisms underlying the dedifferentiation in RAI-refractory DTCs and reviews strategies for restoring RAI avidity by tackling the mechanisms.
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30
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Byun WS, Lee GH, Park HG, Lee SK. Inhibition of DOT1L by Half-Selenopsammaplin A Analogs Suppresses Tumor Growth and EMT-Mediated Metastasis in Triple-Negative Breast Cancer. Pharmaceuticals (Basel) 2020; 14:ph14010018. [PMID: 33379275 PMCID: PMC7824081 DOI: 10.3390/ph14010018] [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: 11/25/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 12/26/2022] Open
Abstract
Due to a lack of hormone receptors, current treatment strategies for triple-negative breast cancer (TNBC) are limited with frequent disease recurrence and metastasis. Recent findings have suggested that aberrant methylation of histone H3 lysine 79 residue (H3K79me) by the histone methyltransferase disruptor of telomeric silencing 1-like (DOT1L) is a potential therapeutic target for TNBC clinical management. Therefore, we developed DOT1L inhibitors as potential antitumor agents against TNBC cells. We reveal that a synthetic half-selenopsammaplin A analog 9l (subsequently known as 9l) exhibited inhibitory activity against DOT1L-mediated H3K79 methylation, and showed antitumor activity in TNBC cells. The analog 9l also significantly inhibited TNBC invasion and migration via the modulation of epithelial-mesenchymal transition (EMT) markers, including N-cadherin and vimentin downregulation and E-cadherin upregulation. In an MDA-MB-231/Luc-implanted orthotopic mouse metastasis model, treatment with 9l effectively inhibited tumor growth and lung metastasis via DOT1L regulatory activity and EMT processes. Taken together, these findings highlight the potential of 9l as a novel therapeutic candidate for treating metastatic TNBC via DOT1L modulation.
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Affiliation(s)
- Woong Sub Byun
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Korea;
| | - Gyu Ho Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea;
| | - Hyeung-geun Park
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea;
- Correspondence: (H.-g.P.); (S.K.L.)
| | - Sang Kook Lee
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Korea;
- Correspondence: (H.-g.P.); (S.K.L.)
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31
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Liang C, Niu J, Wang X, Zhang ZS, Yang RH, Yao X, Liu FY, Li WQ, Pei SH, Sun H, Wang CJ, Fang D, Xie SQ. P300-dependent acetylation of histone H3 is required for epidermal growth factor receptor-mediated high-mobility group protein A2 transcription in hepatocellular carcinoma. Cancer Sci 2020; 112:679-690. [PMID: 33164305 PMCID: PMC7894021 DOI: 10.1111/cas.14729] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 12/24/2022] Open
Abstract
High‐mobility group protein A2 (HMGA2) is highly expressed in hepatocellular carcinoma (HCC) cells and contributes to tumor metastasis and poor patient survival. However, the molecular mechanism through which HMGA2 is transcriptionally regulated in HCC cells remains largely unclear. Here, we showed that the expression HMGA2 was upregulated in HCC, and that elevated HMGA2 could promote tumor metastasis. Incubation of HCC cells with epidermal growth factor (EGF) could promote the expression of HMGA2 mRNA and protein. Mechanistic studies suggested that EGF can phosphorylate p300 at Ser1834 residue through the PI3K/Akt signaling pathway in HCC cells. Knockdown of p300 can reverse EGF‐induced HMGA2 expression and histone H3‐K9 acetylation, whereas a phosphorylation‐mimic p300 S1834D mutant can stimulate HMGA2 expression as well as H3‐K9 acetylation in HCC cells. Furthermore, we identified that p300‐mediated H3‐K9 acetylation participates in EGF‐induced HMGA2 expression in HCC. In addition, the levels of H3‐K9 acetylation positively correlated with the expression levels of HMGA2 in a chemically induced HCC model in rats and human HCC specimens.
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Affiliation(s)
- Chao Liang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Jie Niu
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Xiao Wang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Zhan-Sheng Zhang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Ruo-Han Yang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Xin Yao
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Fan-Ye Liu
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Wen-Qi Li
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Shu-Hua Pei
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Hua Sun
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Chao-Jie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
| | - Dong Fang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Song-Qiang Xie
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China.,Institute of Chemical Biology, School of Pharmacy, Henan University, Kaifeng, China
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32
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Buocikova V, Rios-Mondragon I, Pilalis E, Chatziioannou A, Miklikova S, Mego M, Pajuste K, Rucins M, Yamani NE, Longhin EM, Sobolev A, Freixanet M, Puntes V, Plotniece A, Dusinska M, Cimpan MR, Gabelova A, Smolkova B. Epigenetics in Breast Cancer Therapy-New Strategies and Future Nanomedicine Perspectives. Cancers (Basel) 2020; 12:E3622. [PMID: 33287297 PMCID: PMC7761669 DOI: 10.3390/cancers12123622] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic dysregulation has been recognized as a critical factor contributing to the development of resistance against standard chemotherapy and to breast cancer progression via epithelial-to-mesenchymal transition. Although the efficacy of the first-generation epigenetic drugs (epi-drugs) in solid tumor management has been disappointing, there is an increasing body of evidence showing that epigenome modulation, in synergy with other therapeutic approaches, could play an important role in cancer treatment, reversing acquired therapy resistance. However, the epigenetic therapy of solid malignancies is not straightforward. The emergence of nanotechnologies applied to medicine has brought new opportunities to advance the targeted delivery of epi-drugs while improving their stability and solubility, and minimizing off-target effects. Furthermore, the omics technologies, as powerful molecular epidemiology screening tools, enable new diagnostic and prognostic epigenetic biomarker identification, allowing for patient stratification and tailored management. In combination with new-generation epi-drugs, nanomedicine can help to overcome low therapeutic efficacy in treatment-resistant tumors. This review provides an overview of ongoing clinical trials focusing on combination therapies employing epi-drugs for breast cancer treatment and summarizes the latest nano-based targeted delivery approaches for epi-drugs. Moreover, it highlights the current limitations and obstacles associated with applying these experimental strategies in the clinics.
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Affiliation(s)
- Verona Buocikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (V.B.); (S.M.); (A.G.)
| | - Ivan Rios-Mondragon
- Department of Clinical Dentistry, University of Bergen, Aarstadveien 19, 5009 Bergen, Norway; (I.R.-M.); (M.R.C.)
| | - Eleftherios Pilalis
- e-NIOS Applications Private Company, Alexandrou Pantou 25, 17671 Kallithea, Greece; (E.P.); (A.C.)
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Aristotelis Chatziioannou
- e-NIOS Applications Private Company, Alexandrou Pantou 25, 17671 Kallithea, Greece; (E.P.); (A.C.)
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Svetlana Miklikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (V.B.); (S.M.); (A.G.)
| | - Michal Mego
- 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, Klenova 1, 833 10 Bratislava, Slovakia;
| | - Karlis Pajuste
- Latvian Institute of Organic Synthesis, Aizkraukles str. 21, LV-1006 Riga, Latvia; (K.P.); (M.R.); (A.S.); (A.P.)
| | - Martins Rucins
- Latvian Institute of Organic Synthesis, Aizkraukles str. 21, LV-1006 Riga, Latvia; (K.P.); (M.R.); (A.S.); (A.P.)
| | - Naouale El Yamani
- Health Effects Laboratory, NILU-Norwegian Institute for Air Research, 2007 Kjeller, Norway; (N.E.Y.); (E.M.L.); (M.D.)
| | - Eleonora Marta Longhin
- Health Effects Laboratory, NILU-Norwegian Institute for Air Research, 2007 Kjeller, Norway; (N.E.Y.); (E.M.L.); (M.D.)
| | - Arkadij Sobolev
- Latvian Institute of Organic Synthesis, Aizkraukles str. 21, LV-1006 Riga, Latvia; (K.P.); (M.R.); (A.S.); (A.P.)
| | - Muriel Freixanet
- Vall d Hebron, Institut de Recerca (VHIR), 08035 Barcelona, Spain; (M.F.); (V.P.)
| | - Victor Puntes
- Vall d Hebron, Institut de Recerca (VHIR), 08035 Barcelona, Spain; (M.F.); (V.P.)
- Institut Català de Nanosciència i Nanotecnologia (ICN2), Bellaterra, 08193 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Aiva Plotniece
- Latvian Institute of Organic Synthesis, Aizkraukles str. 21, LV-1006 Riga, Latvia; (K.P.); (M.R.); (A.S.); (A.P.)
| | - Maria Dusinska
- Health Effects Laboratory, NILU-Norwegian Institute for Air Research, 2007 Kjeller, Norway; (N.E.Y.); (E.M.L.); (M.D.)
| | - Mihaela Roxana Cimpan
- Department of Clinical Dentistry, University of Bergen, Aarstadveien 19, 5009 Bergen, Norway; (I.R.-M.); (M.R.C.)
| | - Alena Gabelova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (V.B.); (S.M.); (A.G.)
| | - Bozena Smolkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (V.B.); (S.M.); (A.G.)
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33
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Leber MF, Neault S, Jirovec E, Barkley R, Said A, Bell JC, Ungerechts G. Engineering and combining oncolytic measles virus for cancer therapy. Cytokine Growth Factor Rev 2020; 56:39-48. [PMID: 32718830 PMCID: PMC7333629 DOI: 10.1016/j.cytogfr.2020.07.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/02/2020] [Indexed: 12/18/2022]
Abstract
Cancer immunotherapy using tumor-selective, oncolytic viruses is an emerging therapeutic option for solid and hematologic malignancies. A considerable variety of viruses ranging from small picornaviruses to large poxviruses are currently being investigated as potential candidates. In the early days of virotherapy, non-engineered wild-type or vaccine-strain viruses were employed. However, these viruses often did not fully satisfy the major criteria of safety and efficacy. Since the advent of reverse genetics systems for manipulating various classes of viruses, the field has shifted to developing genetically engineered viruses with an improved therapeutic index. In this review, we will summarize the concepts and strategies of multi-level genetic engineering of oncolytic measles virus, a prime candidate for cancer immunovirotherapy. Furthermore, we will provide a brief overview of measles virus-based multimodal combination therapies for improved tumor control and clinical efficacy.
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Affiliation(s)
- Mathias F Leber
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.
| | - Serge Neault
- Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada
| | - Elise Jirovec
- Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada
| | - Russell Barkley
- Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada
| | - Aida Said
- Children's Hospital of Eastern Ontario, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada; University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - John C Bell
- Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada
| | - Guy Ungerechts
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada
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34
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Dong Z, Cui H. The Emerging Roles of RNA Modifications in Glioblastoma. Cancers (Basel) 2020; 12:E736. [PMID: 32244981 PMCID: PMC7140112 DOI: 10.3390/cancers12030736] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma (GBM) is a grade IV glioma that is the most malignant brain tumor type. Currently, there are no effective and sufficient therapeutic strategies for its treatment because its pathological mechanism is not fully characterized. With the fast development of the Next Generation Sequencing (NGS) technology, more than 170 kinds of covalent ribonucleic acid (RNA) modifications are found to be extensively present in almost all living organisms and all kinds of RNAs, including ribosomal RNAs (rRNAs), transfer RNAs (tRNAs) and messenger RNAs (mRNAs). RNA modifications are also emerging as important modulators in the regulation of biological processes and pathological progression, and study of the epi-transcriptome has been a new area for researchers to explore their connections with the initiation and progression of cancers. Recently, RNA modifications, especially m6A, and their RNA-modifying proteins (RMPs) such as methyltransferase like 3 (METTL3) and α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5), have also emerged as important epigenetic mechanisms for the aggressiveness and malignancy of GBM, especially the pluripotency of glioma stem-like cells (GSCs). Although the current study is just the tip of an iceberg, these new evidences will provide new insights for possible GBM treatments. In this review, we summarize the recent studies about RNA modifications, such as N6-methyladenosine (m6A), N6,2'O-dimethyladenosine (m6Am), 5-methylcytosine (m5C), N1-methyladenosine (m1A), inosine (I) and pseudouridine (ψ) as well as the corresponding RMPs including the writers, erasers and readers that participate in the tumorigenesis and development of GBM, so as to provide some clues for GBM treatment.
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Affiliation(s)
- Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Biotechnology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Biotechnology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
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35
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Samec M, Liskova A, Koklesova L, Mestanova V, Franekova M, Kassayova M, Bojkova B, Uramova S, Zubor P, Janikova K, Danko J, Samuel SM, Büsselberg D, Kubatka P. Fluctuations of Histone Chemical Modifications in Breast, Prostate, and Colorectal Cancer: An Implication of Phytochemicals as Defenders of Chromatin Equilibrium. Biomolecules 2019; 9:E829. [PMID: 31817446 PMCID: PMC6995638 DOI: 10.3390/biom9120829] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
Natural substances of plant origin exert health beneficiary efficacy due to the content of various phytochemicals. Significant anticancer abilities of natural compounds are mediated via various processes such as regulation of a cell's epigenome. The potential antineoplastic activity of plant natural substances mediated by their action on posttranslational histone modifications (PHMs) is currently a highly evaluated area of cancer research. PHMs play an important role in maintaining chromatin structure and regulating gene expression. Aberrations in PHMs are directly linked to the process of carcinogenesis in cancer such as breast (BC), prostate (PC), and colorectal (CRC) cancer, common malignant diseases in terms of incidence and mortality among both men and women. This review summarizes the effects of plant phytochemicals (isolated or mixtures) on cancer-associated PHMs (mainly modulation of acetylation and methylation) resulting in alterations of chromatin structure that are related to the regulation of transcription activity of specific oncogenes, which are crucial in the development of BC, PC, and CRC. Significant effectiveness of natural compounds in the modulation of aberrant PHMs were confirmed by a number of in vitro or in vivo studies in preclinical cancer research. However, evidence concerning PHMs-modulating abilities of plant-based natural substances in clinical trials is insufficient.
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Affiliation(s)
- Marek Samec
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Alena Liskova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Lenka Koklesova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Veronika Mestanova
- Department of Histology and Embryology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Maria Franekova
- Department of Medical Biology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Monika Kassayova
- Department of Animal Physiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University, 04001 Kosice, Slovakia; (M.K.); (B.B.)
| | - Bianka Bojkova
- Department of Animal Physiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University, 04001 Kosice, Slovakia; (M.K.); (B.B.)
| | - Sona Uramova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Pavol Zubor
- OBGY Health & Care, Ltd., 01026 Zilina, Slovakia;
| | - Katarina Janikova
- Department of Pathological Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Jan Danko
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Samson Mathews Samuel
- Department of Physiology and Biophysics, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha 24144, Qatar;
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha 24144, Qatar;
| | - Peter Kubatka
- Department of Medical Biology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
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Yang Q, Jiang W, Hou P. Emerging role of PI3K/AKT in tumor-related epigenetic regulation. Semin Cancer Biol 2019; 59:112-124. [DOI: 10.1016/j.semcancer.2019.04.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/14/2019] [Accepted: 04/01/2019] [Indexed: 01/23/2023]
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37
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Paydar P, Asadikaram G, Nejad HZ, Akbari H, Abolhassani M, Moazed V, Nematollahi MH, Ebrahimi G, Fallah H. Epigenetic modulation of BRCA-1 and MGMT genes, and histones H4 and H3 are associated with breast tumors. J Cell Biochem 2019; 120:13726-13736. [PMID: 30938887 DOI: 10.1002/jcb.28645] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/03/2019] [Accepted: 02/14/2019] [Indexed: 12/11/2022]
Abstract
Aberrant patterns in promoter methylation of tumor-suppressor genes and posttranslational modifications of histone proteins are considered as major features of malignancy. In this study, we aimed to investigate promoter methylation of three tumor-suppressor genes (BRCA-1, MGMT, and P16) and three histone marks (H3K9ac, H3K18ac, and H4K20me3) in patients with breast tumors. This case-control study included 27 patients with malignant breast tumors (MBT) and 31 patients with benign breast tumors (BBT). The methylation-specific PCR was used for determining promoter methylation of BRCA-1, MGMT, and P16 genes. Western blot analysis was performed to detect histone lysine acetylation (H3K9ac and H3K18ac) and lysine methylation (H4K20me3). BRCA-1 promoter methylation was detected in 44.4% of the MBT whereas this alteration was found in 9.7% of BBT (P = 0.005). The Kaplan-Meier analysis indicated that hypermethylation in BRCA-1 promoter was significantly associated with poor overall survival of patients with breast cancer (P = 0.039). MGMT promoter methylation was identified in 18.5% of MBT and 0.0% of the BBT (P = 0.01). The frequency of P16 promoter methylation was 25.8% in BBT and 11.1% in MBT (P = 0.12). As compared with BBT, MBT samples displayed the aberrant patterns of histones marks with hypomethylation of H4K20 and hypoacetylation of H3K18 (P = 0.03 and P = 0.04, respectively). There was a negative significant correlation between H3K9ac levels and tumor size in MBT group (r = -0.672; P = 0.008). The present findings suggest that promoter hypermethylation of MGMT and BRCA-1 genes along with alterations in H3K18ac and H4K20me3 levels may have prognostic values in patients with breast cancer. Moreover, the detection of these epigenetic modifications in breast tumors could be helpful in finding new methods for breast cancer therapy.
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Affiliation(s)
- Parisa Paydar
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman, Iran.,Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Gholamreza Asadikaram
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Neuroscience Research Center, Institute of Neuropharmacology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Zeynali Nejad
- Department of Surgery, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamed Akbari
- Student Research Committee, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Moslem Abolhassani
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Vahid Moazed
- Department of Hematology and Oncology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hadi Nematollahi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Ghasem Ebrahimi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Fallah
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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38
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Cox MC, Deng C, Naler LB, Lu C, Verbridge SS. Effects of culture condition on epigenomic profiles of brain tumor cells. ACS Biomater Sci Eng 2019; 5:1544-1552. [PMID: 31799379 PMCID: PMC6886720 DOI: 10.1021/acsbiomaterials.9b00161] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Personalized cancer medicine offers the promise of more effective treatments that are tailored to an individual's own dynamic cancer phenotype. Meanwhile, tissue-engineering approaches to modeling tumors may complement these advances by providing a powerful new approach to understanding the adaptation dynamics occurring during treatment. However, in both of these areas new tools will be required to gain a full picture of the genetic and epigenetic regulators of phenotype dynamics occurring in the small populations of cells that drive resistance. In this study, we perform epigenomic analysis of brain tumor cells that are collected from micro-engineered three-dimensional tumor models, overcoming the challenges associated with the small numbers of cells contained within these micro-tissue niches, in this case collecting ~1,000 cells per sample. Specifically, we use a high-resolution epigenomic analysis method known as microfluidic-oscillatory-washing-based chromatin immunoprecipitation with sequencing (MOWChIP-seq) to analyze histone methylation patterns (H3K4me3). We identified gene loci that are associated with the H3K4me3 modification, which is generally a mark of active transcription. We compared methylation patterns in standard 2D cultures and 3D cultures based on type I collagen hydrogels, under both normoxic and hypoxic conditions. We found that culture dimensionality drastically impacted the H3k4me3 profile and resulted in differential modifications in response to hypoxic stress. Differentially H3K4me3-marked regions under the culture conditions used in this study have important implications for gene expression differences that have been previously observed. In total, our work illustrates a direct connection between cell culture or tissue niche condition and genome-wide alterations in histone modifications, providing the first steps towards analyzing the spatiotemporal variations in epigenetic regulation of cancer cell phenotypes. This study, to our knowledge, also represents the first time broad-spectrum epigenomic analysis has been applied to small cell samples collected from engineered micro-tissues.
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Affiliation(s)
- Megan C. Cox
- School of Biomedical Engineering and Mechanics, Virginia Tech-Wake Forest University
| | - Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Lynette B. Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Scott S. Verbridge
- School of Biomedical Engineering and Mechanics, Virginia Tech-Wake Forest University
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Kamińska K, Nalejska E, Kubiak M, Wojtysiak J, Żołna Ł, Kowalewski J, Lewandowska MA. Prognostic and Predictive Epigenetic Biomarkers in Oncology. Mol Diagn Ther 2019; 23:83-95. [PMID: 30523565 PMCID: PMC6394434 DOI: 10.1007/s40291-018-0371-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Epigenetic patterns, such as DNA methylation, histone modifications, and non-coding RNAs, can be both driver factors and characteristic features of certain malignancies. Aberrant DNA methylation can lead to silencing of crucial tumor suppressor genes or upregulation of oncogene expression. Histone modifications and chromatin spatial organization, which affect transcription, regulation of gene expression, DNA repair, and replication, have been associated with multiple tumors. Certain microRNAs (miRNAs), mainly those that silence tumor suppressor genes and occur in a greater number of copies, have also been shown to promote oncogenesis. Multiple patterns of these epigenetic factors occur specifically in certain malignancies, which allows their potential use as biomarkers. This review presents examples of tests for each group of epigenetic factors that are currently available or in development for use in early cancer detection, prediction, prognosis, and response to treatment. The availability of blood-based biomarkers is noted, as they allow sampling invasiveness to be reduced and the sampling procedure to be simplified. The article stresses the role of epigenetics as a crucial element of future cancer diagnostics and therapy.
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Affiliation(s)
- Katarzyna Kamińska
- Molecular Oncology and Genetics Department, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
- Department of Thoracic Surgery and Tumors, L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Ewelina Nalejska
- Molecular Oncology and Genetics Department, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
- Department of Thoracic Surgery and Tumors, L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Marta Kubiak
- Molecular Oncology and Genetics Department, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
- Department of Thoracic Surgery and Tumors, L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Joanna Wojtysiak
- Molecular Oncology and Genetics Department, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
- Department of Thoracic Surgery and Tumors, L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Łukasz Żołna
- Department of Thoracic Surgery and Tumors, L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Janusz Kowalewski
- Department of Thoracic Surgery and Tumors, L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Marzena Anna Lewandowska
- Molecular Oncology and Genetics Department, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland.
- Department of Thoracic Surgery and Tumors, L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland.
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40
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Han TS, Ban HS, Hur K, Cho HS. The Epigenetic Regulation of HCC Metastasis. Int J Mol Sci 2018; 19:ijms19123978. [PMID: 30544763 PMCID: PMC6321007 DOI: 10.3390/ijms19123978] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 12/22/2022] Open
Abstract
Epigenetic alterations, such as histone modification, DNA methylation, and miRNA-mediated processes, are critically associated with various mechanisms of proliferation and metastasis in several types of cancer. To overcome the side effects and limited effectiveness of drugs for cancer treatment, there is a continuous need for the identification of more effective drug targets and the execution of mechanism of action (MOA) studies. Recently, epigenetic modifiers have been recognized as important therapeutic targets for hepatocellular carcinoma (HCC) based on their reported abilities to suppress HCC metastasis and proliferation in both in vivo and in vitro studies. Therefore, here, we introduce epigenetic modifiers and alterations related to HCC metastasis and proliferation, and their molecular mechanisms in HCC metastasis. The existing data suggest that the study of epigenetic modifiers is important for the development of specific inhibitors and diagnostic targets for HCC treatment.
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Affiliation(s)
- Tae-Su Han
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
| | - Hyun Seung Ban
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
| | - Keun Hur
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu 41944, Korea.
| | - Hyun-Soo Cho
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
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41
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Huang MH, Chou YW, Li MH, Shih TE, Lin SZ, Chuang HM, Chiou TW, Su HL, Harn HJ. Epigenetic targeting DNMT1 of pancreatic ductal adenocarcinoma using interstitial control release biodegrading polymer reduced tumor growth through hedgehog pathway inhibition. Pharmacol Res 2018; 139:50-61. [PMID: 30385365 DOI: 10.1016/j.phrs.2018.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/28/2018] [Accepted: 10/15/2018] [Indexed: 12/18/2022]
Abstract
Annually, 48,000 people die from pancreatic ductal adenocarcinoma (PDAC), ranking it the fourth among cancer-related deaths in the United States. Currently, anti-cancer drugs are not effective against PDAC, and only extends survival by 3 months. Aberrant DNA methylation has been shown to play an important role during carcinogenesis in PDAC, with approximately 80% of tumor overexpressing the DNA methyltransferase 1 (DNMT1) protein. In the present study, we used DNMTs as a screening platform to find a new DNMT inhibitor, n-butylidenephthalide (n-BP), which is identified from a Chinese herbal drug. n-BP could inhibit DNMT1 expression in both dose-dependent and time-dependent manner. It also displays an effect in suppressing growth of PDAC cells and inducing cell cycle arrest at G0/G1 phase leading apoptosis. Growth suppression can be restored by the overexpression of DNMT1 in PDAC cells. Furthermore, we found n-BP-mediated DNMT1 suppression influenced the protein stability rather than changing the RNA expression. Through microarray studies, we found that the patched domain contained 4 (PTCHD4) is the potential downstream gene of DNMT1. Following silencing of PTCHD4 expression by siRNA, n-BP decreased tumor growth inhibition. Finally, in vivo, two animal models were used to evaluate the efficacy and survival after n-BP treatment by interstitial control release polymer delivery. The results show that n-BP could effectively inhibit PDAC tumor volume growth and extend animal survival. In summary, n-BP may inhibit the growth of human PDAC cells though reducing DNMT1 and increasing the expression of PTCHD4 both in vitro and in vivo.
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Affiliation(s)
- Mao-Hsuan Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Yi-Wen Chou
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Ming-Hsun Li
- Department of Pathology, Hualien Tzu Chi Hospital, Hualien, Taiwan
| | - Tina E Shih
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Shinn-Zong Lin
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan; Department of Neurosurgery, Hualien Tzu Chi Hospital, Hualien, Taiwan
| | - Hong-Meng Chuang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Tzyy-Wen Chiou
- Department of Life Science and Graduate Institute of Biotechnology, National Dong Hwa University, Hualien, Taiwan
| | - Hong-Lin Su
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
| | - Horng-Jyh Harn
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan; Department of Pathology, Hualien Tzu Chi Hospital, Hualien, Taiwan; Department of Pathology, Tzu Chi University, Hualien, Taiwan.
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42
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Rifaï K, Judes G, Idrissou M, Daures M, Bignon YJ, Penault-Llorca F, Bernard-Gallon D. SIRT1-dependent epigenetic regulation of H3 and H4 histone acetylation in human breast cancer. Oncotarget 2018; 9:30661-30678. [PMID: 30093977 PMCID: PMC6078139 DOI: 10.18632/oncotarget.25771] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the most frequently diagnosed malignancy in women worldwide. It is well established that the complexity of carcinogenesis involves profound epigenetic deregulations that contribute to the tumorigenesis process. Deregulated H3 and H4 acetylated histone marks are amongst those alterations. Sirtuin-1 (SIRT1) is a class-III histone deacetylase deeply involved in apoptosis, genomic stability, gene expression regulation and breast tumorigenesis. However, the underlying molecular mechanism by which SIRT1 regulates H3 and H4 acetylated marks, and consequently cancer-related gene expression in breast cancer, remains uncharacterized. In this study, we elucidated SIRT1 epigenetic role and analyzed the link between the latter and histones H3 and H4 epigenetic marks in all 5 molecular subtypes of breast cancer. Using a cohort of 135 human breast tumors and their matched normal tissues, as well as 5 human-derived cell lines, we identified H3k4ac as a new prime target of SIRT1 in breast cancer. We also uncovered an inverse correlation between SIRT1 and the 3 epigenetic marks H3k4ac, H3k9ac and H4k16ac expression patterns. We showed that SIRT1 modulates the acetylation patterns of histones H3 and H4 in breast cancer. Moreover, SIRT1 regulates its H3 acetylated targets in a subtype-specific manner. Furthermore, SIRT1 siRNA-mediated knockdown increases histone acetylation levels at 6 breast cancer-related gene promoters: AR, BRCA1, ERS1, ERS2, EZH2 and EP300. In summary, this report characterizes for the first time the epigenetic behavior of SIRT1 in human breast carcinoma. These novel findings point to a potential use of SIRT1 as an epigenetic therapeutic target in breast cancer.
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Affiliation(s)
- Khaldoun Rifaï
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
| | - Gaëlle Judes
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
| | - Mouhamed Idrissou
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
| | - Marine Daures
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
| | - Yves-Jean Bignon
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
| | - Frédérique Penault-Llorca
- INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France.,Department of Biopathology, Centre Jean Perrin, Clermont-Ferrand 63011, France
| | - Dominique Bernard-Gallon
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
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Yang T, Cao N, Zhang H, Wei J, Song X, Yi D, Chao S, Zhang L, Kong L, Han S, Yang Y, Ding S. Helicobacter pylori infection-induced H3Ser10 phosphorylation in stepwise gastric carcinogenesis and its clinical implications. Helicobacter 2018; 23:e12486. [PMID: 29656498 PMCID: PMC6001454 DOI: 10.1111/hel.12486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Our previous works have demonstrated that Helicobacter pylori (Hp) infection can alter histone H3 serine 10 phosphorylation status in gastric epithelial cells. However, whether Helicobacter pylori-induced histone H3 serine 10 phosphorylation participates in gastric carcinogenesis is unknown. We investigate the expression of histone H3 serine 10 phosphorylation in various stages of gastric disease and explore its clinical implication. MATERIALS AND METHODS Stomach biopsy samples from 129 patients were collected and stained with histone H3 serine 10 phosphorylation, Ki67, and Helicobacter pylori by immunohistochemistry staining, expressed as labeling index. They were categorized into nonatrophic gastritis, chronic atrophic gastritis, intestinal metaplasia, low-grade intraepithelial neoplasia, high-grade intraepithelial neoplasia, and intestinal-type gastric cancer groups. Helicobacter pylori infection was determined by either 13 C-urea breath test or immunohistochemistry staining. RESULTS In Helicobacter pylori-negative patients, labeling index of histone H3 serine 10 phosphorylation was gradually increased in nonatrophic gastritis, chronic atrophic gastritis, intestinal metaplasia groups, peaked at low-grade intraepithelial neoplasia, and declined in high-grade intraepithelial neoplasia and gastric cancer groups. In Helicobacter pylori-infected patients, labeling index of histone H3 serine 10 phosphorylation followed the similar pattern as above, with increased expression over the corresponding Helicobacter pylori-negative controls except in nonatrophic gastritis patient whose labeling index was decreased when compared with Helicobacter pylori-negative control. Labeling index of Ki67 in Helicobacter pylori-negative groups was higher in gastric cancer than chronic atrophic gastritis and low-grade intraepithelial neoplasia groups, and higher in intestinal metaplasia group compared with chronic atrophic gastritis group. In Helicobacter pylori-positive groups, Ki67 labeling index was increased stepwise from nonatrophic gastritis to gastric cancer except slightly decrease in chronic atrophic gastritis group. In addition, we noted that histone H3 serine 10 phosphorylation staining is accompanied with its location changes from gastric gland bottom expanded to whole gland as disease stage progress. CONCLUSIONS These results indicate that stepwise gastric carcinogenesis is associated with altered histone H3 serine 10 phosphorylation, Helicobacter pylori infection enhances histone H3 serine 10 phosphorylation expression in these processes; it is also accompanied with histone H3 serine 10 phosphorylation location change from gland bottom staining expand to whole gland expression. The results suggest that epigenetic dysregulation may play important roles in Helicobacter pylori-induced gastric cancer.
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Affiliation(s)
- Tao‐Tao Yang
- Department of Gastroenterology and HepatologyPeople's Hospital of Zhengzhou UniversityZhengzhouChina
| | - Na Cao
- Henan Police CollegeZhengzhouChina
| | - Hai‐Hui Zhang
- Department of Gastroenterology and HepatologyPeople's Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jian‐Bo Wei
- Department of Gastroenterology and HepatologyXinxiang Medical UniversityXinxiangChina
| | - Xiao‐Xia Song
- Department of PathologyPeople's Hospital of Zhengzhou UniversityZhengzhouChina
| | - Dong‐Min Yi
- Department of Gastroenterology and HepatologyPeople's Hospital of Zhengzhou UniversityZhengzhouChina
| | - Shuai‐Heng Chao
- Department of Gastroenterology and HepatologyPeople's Hospital of Zhengzhou UniversityZhengzhouChina
| | - Li‐Da Zhang
- Department of Gastroenterology and HepatologyPeople's Hospital of Zhengzhou UniversityZhengzhouChina
| | - Ling‐Fei Kong
- Department of PathologyPeople's Hospital of Zhengzhou UniversityZhengzhouChina
| | - Shuang‐Yin Han
- Department of Gastroenterology and HepatologyPeople's Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yu‐Xiu Yang
- Department of Gastroenterology and HepatologyPeople's Hospital of Zhengzhou UniversityZhengzhouChina
| | - Song‐Ze Ding
- Department of Gastroenterology and HepatologyPeople's Hospital of Zhengzhou UniversityZhengzhouChina
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Alves-Silva JC, de Carvalho JL, Rabello DA, Serejo TRT, Rego EM, Neves FAR, Lucena-Araujo AR, Pittella-Silva F, Saldanha-Araujo F. GLP overexpression is associated with poor prognosis in Chronic Lymphocytic Leukemia and its inhibition induces leukemic cell death. Invest New Drugs 2018; 36:955-960. [PMID: 29855824 DOI: 10.1007/s10637-018-0613-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/24/2018] [Indexed: 12/21/2022]
Abstract
Background Heterodimeric methyltransferases GLP (EHMT1/KMT1D) and G9a (EHMT2/KMT1C) are two closely related enzymes that promote the monomethylation and dimethylation of histone H3 lysine 9. Dysregulation of their activity has been implicated in several types of human cancer. Patients and methods Here, in order to investigate whether GLP/G9a exerts any impact on Chronic Lymphocytic Leukemia (CLL), GLP/G9a expression levels were assessed in a cohort of 50 patients and the effects of their inhibition were verified for the viability of CLL cells. Also, qRT-PCR was used to investigate the transcriptional levels of GLP/G9a in CLL patients. In addition, patient samples were classified according to ZAP-70 protein expression by flow cytometry and according to karyotype integrity by cytogenetics analysis. Finally, a selective small molecule inhibitor for GLP/G9a was used to ascertain whether these methyltransferases influenced the viability of MEC-1 CLL cell lineage. Results mRNA analysis revealed that CLL samples had higher levels of GLP, but not G9a, when compared to non-leukemic controls. Interestingly, patients with unfavorable cytogenetics showed higher expression levels of GLP compared to patients with favorable karyotypes. More importantly, GLP/G9a inhibition markedly induced cell death in CLL cells. Conclusion Taken together, these results indicate that GLP is associated with a worse prognosis in CLL, and that the inhibition of GLP/G9a influences CLL cell viability. Altogether, the present data demonstrate that these methyltransferases can be potential markers for disease progression, as well as a promising epigenetic target for CLL treatment and the prevention of disease evolution.
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Affiliation(s)
- Juliana Carvalho Alves-Silva
- Laboratório de Patologia Molecular do Câncer, Universidade de Brasília, Av. L2 Norte, Brasília, DF, 70.910-900, Brazil
- Laboratório de Farmacologia Molecular, Universidade de Brasília, Campus Darcy Ribeiro, Av. L2 Norte, Brasília, DF, 70.910-900, Brazil
| | - Juliana Lott de Carvalho
- Laboratório de Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B, Brasília, DF, 70790-160, Brazil
| | - Doralina Amaral Rabello
- Laboratório de Patologia Molecular do Câncer, Universidade de Brasília, Av. L2 Norte, Brasília, DF, 70.910-900, Brazil
| | - Teresa Raquel Tavares Serejo
- Laboratório de Farmacologia Molecular, Universidade de Brasília, Campus Darcy Ribeiro, Av. L2 Norte, Brasília, DF, 70.910-900, Brazil
| | - Eduardo Magalhaes Rego
- Laboratório de Hematologia, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP, 14.048-900, Brazil
| | - Francisco Assis Rocha Neves
- Laboratório de Farmacologia Molecular, Universidade de Brasília, Campus Darcy Ribeiro, Av. L2 Norte, Brasília, DF, 70.910-900, Brazil
| | - Antonio Roberto Lucena-Araujo
- Laboratório de Hematologia, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, Recife, PE, 50670-901, Brazil
| | - Fábio Pittella-Silva
- Laboratório de Patologia Molecular do Câncer, Universidade de Brasília, Av. L2 Norte, Brasília, DF, 70.910-900, Brazil
| | - Felipe Saldanha-Araujo
- Laboratório de Farmacologia Molecular, Universidade de Brasília, Campus Darcy Ribeiro, Av. L2 Norte, Brasília, DF, 70.910-900, Brazil.
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Han F, Ren J, Zhang J, Sun Y, Ma F, Liu Z, Yu H, Jia J, Li W. JMJD2B is required for Helicobacter pylori-induced gastric carcinogenesis via regulating COX-2 expression. Oncotarget 2018; 7:38626-38637. [PMID: 27232941 PMCID: PMC5122416 DOI: 10.18632/oncotarget.9573] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 05/05/2016] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori (H. pylori) infection is the strongest risk factor for the initiation and progression of gastric cancer. However, the mechanism of H. pylori-induced pathogenesis remains unclear. In this study, we investigate the role of H. pylori infection in JMJD2B upregulation and the mechanism underlying gastric carcinogenesis. We find that JMJD2B can be induced by H. pylori infection via β-catenin pathway. β-catenin directly binds to JMJD2B promoter and stimulates JMJD2B expression following H. pylori infection. Increased JMJD2B, together with NF-κB, binds to COX-2 promoter to enhance its transcription by demethylating H3K9me3 locally. JMJD2B and COX-2 expression is upregulated in H. pylori infected mice in vivo. Furthermore, JMJD2B and COX-2 expression is gradually increased in human gastric tissues from gastritis to gastric cancer. The level of JMJD2B and COX-2 in H. pylori-positive gastritis tissues is significantly higher than that in H. pylori-negative tissues. Moreover, a positive correlation between JMJD2B and COX-2 expression is found in both gastritis and gastric cancer tissues. Therefore, JMJD2B is a crucial factor in triggering H. pylori-induced chronic inflammation and progression of gastric carcinogenesis and it may serve as a novel target for the intervention of gastric cancer.
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Affiliation(s)
- Fengjuan Han
- Department of Microbiology, Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, PR China
| | - Juchao Ren
- Department of Microbiology, Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, PR China.,Department of Urology, Qilu Hospital, Shandong University, Jinan, PR China
| | - Jinjin Zhang
- Department of Microbiology, Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, PR China
| | - Yundong Sun
- Department of Microbiology, Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, PR China
| | - Fang Ma
- Department of Microbiology, Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, PR China
| | - Zhifang Liu
- Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, PR China
| | - Han Yu
- Department of Microbiology, Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, PR China
| | - Jihui Jia
- Department of Microbiology, Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, PR China
| | - Wenjuan Li
- Department of Microbiology, Key Laboratory for Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, PR China
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Carvalho Alves-Silva J, do Amaral Rabello D, Oliveira Bravo M, Lucena-Araujo A, Madureira de Oliveira D, Morato de Oliveira F, Magalhaes Rego E, Pittella-Silva F, Saldanha-Araujo F. Aberrant levels of SUV39H1 and SUV39H2 methyltransferase are associated with genomic instability in chronic lymphocytic leukemia. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:654-661. [PMID: 28833505 DOI: 10.1002/em.22128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/08/2017] [Accepted: 07/25/2017] [Indexed: 06/07/2023]
Abstract
Chromosomal alterations are commonly detected in patients with chronic lymphocytic leukemia (CLL) and impact disease pathogenesis, prognosis, and progression. Telomerase expression (hTERT), its activity and the telomere length are other important predictors of survival and multiple outcomes in CLL. SUV39H and SUV420H enzymes are histone methyltransferases (HMTases) involved in several cellular processes, including regulation of telomere length, heterochromatin organization, and genome stability. Here, we investigated whether SUV39H1, SUV39H2, SUV420H1, SUV420H2, and hTERT are associated with genomic instability of CLL. SUV39H (1/2), SUV420H (1/2), and hTERT expression was determined in 59 CLL samples by real time PCR. In addition, ZAP-70 protein expression was evaluated by Flow Cytometry and patients' karyotype was defined by Cytogenetic Analysis. Low expression of SUV39H1 was associated with the acquisition of altered and complex karyotypes. Conversely, high expression of SUV39H2 correlated with cytogenetic abnormalities in CLL patients. The pattern of karyotypic alterations differed in samples with detectable or undetectable hTERT expression. Furthermore, hTERT expression in CLL showed a correlation with transcript levels of SUV39H2, which, in part, can explain the association between SUV39H2 expression and cytogenetic abnormalities. Moreover, SUV39H1 correlated with SUV420H1 expression while SUV420H2 was associated with all other investigated HMTases. Our data show that the differential expression of SUV39H1 and SUV39H2 is associated with genomic instability and that the modulation of these HMTases can be an attractive approach to prevent CLL evolution. Environ. Mol. Mutagen. 58:654-661, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Juliana Carvalho Alves-Silva
- Laboratório de Patologia Molecular do Câncer, Universidade de Brasília, Av. L2 Norte, Brasília, DF, 70.910-900, Brasil
| | - Doralina do Amaral Rabello
- Laboratório de Patologia Molecular do Câncer, Universidade de Brasília, Av. L2 Norte, Brasília, DF, 70.910-900, Brasil
| | - Martha Oliveira Bravo
- Laboratório de Farmacologia Molecular, Universidade de Brasília, Av. L2 Norte, Brasília, DF, 70.910-900, Brasil
| | - Antônio Lucena-Araujo
- Laboratório de Hematologia, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, Recife, PE, 50670-901, Brasil
| | - Diego Madureira de Oliveira
- Laboratório de Patologia Molecular do Câncer, Universidade de Brasília, Av. L2 Norte, Brasília, DF, 70.910-900, Brasil
| | - Fábio Morato de Oliveira
- Laboratório de Hematologia, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP, 14.048-900, Brasil
| | - Eduardo Magalhaes Rego
- Laboratório de Hematologia, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP, 14.048-900, Brasil
| | - Fábio Pittella-Silva
- Laboratório de Patologia Molecular do Câncer, Universidade de Brasília, Av. L2 Norte, Brasília, DF, 70.910-900, Brasil
| | - Felipe Saldanha-Araujo
- Laboratório de Patologia Molecular do Câncer, Universidade de Brasília, Av. L2 Norte, Brasília, DF, 70.910-900, Brasil
- Laboratório de Farmacologia Molecular, Universidade de Brasília, Av. L2 Norte, Brasília, DF, 70.910-900, Brasil
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47
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Fernandes GFS, Silva GDB, Pavan AR, Chiba DE, Chin CM, Dos Santos JL. Epigenetic Regulatory Mechanisms Induced by Resveratrol. Nutrients 2017; 9:nu9111201. [PMID: 29104258 PMCID: PMC5707673 DOI: 10.3390/nu9111201] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/05/2017] [Accepted: 09/18/2017] [Indexed: 12/11/2022] Open
Abstract
Resveratrol (RVT) is one of the main natural compounds studied worldwide due to its potential therapeutic use in the treatment of many diseases, including cancer, diabetes, cardiovascular diseases, neurodegenerative diseases and metabolic disorders. Nevertheless, the mechanism of action of RVT in all of these conditions is not completely understood, as it can modify not only biochemical pathways but also epigenetic mechanisms. In this paper, we analyze the biological activities exhibited by RVT with a focus on the epigenetic mechanisms, especially those related to DNA methyltransferase (DNMT), histone deacetylase (HDAC) and lysine-specific demethylase-1 (LSD1).
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Affiliation(s)
- Guilherme Felipe Santos Fernandes
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800903 Araraquara, Brazil.
- Institute of Chemistry, São Paulo State University (UNESP), 14800060 Araraquara, Brazil.
| | | | - Aline Renata Pavan
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800903 Araraquara, Brazil.
| | - Diego Eidy Chiba
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800903 Araraquara, Brazil.
| | - Chung Man Chin
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800903 Araraquara, Brazil.
| | - Jean Leandro Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800903 Araraquara, Brazil.
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Spheroid growth in ovarian cancer alters transcriptome responses for stress pathways and epigenetic responses. PLoS One 2017; 12:e0182930. [PMID: 28793334 PMCID: PMC5549971 DOI: 10.1371/journal.pone.0182930] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 07/26/2017] [Indexed: 12/11/2022] Open
Abstract
Ovarian cancer is the most lethal gynecological cancer, with over 200,000 women diagnosed each year and over half of those cases leading to death. These poor statistics are related to a lack of early symptoms and inadequate screening techniques. This results in the cancer going undetected until later stages when the tumor has metastasized through a process that requires the epithelial to mesenchymal transition (EMT). In lieu of traditional monolayer cell culture, EMT and cancer progression in general is best characterized through the use of 3D spheroid models. In this study, we examine gene expression changes through microarray analysis in spheroid versus monolayer ovarian cancer cells treated with TGFβ to induce EMT. Transcripts that included Coiled-Coil Domain Containing 80 (CCDC80), Solute Carrier Family 6 (Neutral Amino Acid Transporter), Member 15 (SLC6A15), Semaphorin 3E (SEMA3E) and PIF1 5'-To-3' DNA Helicase (PIF1) were downregulated more than 10-fold in the 3D cells while Inhibitor Of DNA Binding 2, HLH Protein (ID2), Regulator Of Cell Cycle (RGCC), Protease, Serine 35 (PRSS35), and Aldo-Keto Reductase Family 1, Member C1 (AKR1C1) were increased more than 50-fold. Interestingly, EMT factors, stress responses and epigenetic processes were significantly affected by 3D growth. The heat shock response and the oxidative stress response were also identified as transcriptome responses that showed significant changes upon 3D growth. Subnetwork enrichment analysis revealed that DNA integrity (e.g. DNA damage, genetic instability, nucleotide excision repair, and the DNA damage checkpoint pathway) were altered in the 3D spheroid model. In addition, two epigenetic processes, DNA methylation and histone acetylation, were increased with 3D growth. These findings support the hypothesis that three dimensional ovarian cell culturing is physiologically different from its monolayer counterpart.
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49
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Attar N, Kurdistani SK. Exploitation of EP300 and CREBBP Lysine Acetyltransferases by Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026534. [PMID: 27881443 DOI: 10.1101/cshperspect.a026534] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
p300 and CREB-binding protein (CBP), two homologous lysine acetyltransferases in metazoans, have a myriad of cellular functions. They exert their influence mainly through their roles as transcriptional regulators but also via nontranscriptional effects inside and outside of the nucleus on processes such as DNA replication and metabolism. The versatility of p300/CBP as molecular tools has led to their exploitation by viral oncogenes for cellular transformation and by cancer cells to achieve and maintain an oncogenic phenotype. How cancer cells use p300/CBP in their favor varies depending on the cellular context and is evident by the growing list of loss- and gain-of-function genetic alterations in p300 and CBP in solid tumors and hematological malignancies. Here, we discuss the biological functions of p300/CBP and how disruption of these functions by mutations and alterations in expression or subcellular localization contributes to the cancer phenotype.
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Affiliation(s)
- Narsis Attar
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California 90095.,Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California 90095.,Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90095.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, California 90095
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50
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Morel D, Almouzni G, Soria JC, Postel-Vinay S. Targeting chromatin defects in selected solid tumors based on oncogene addiction, synthetic lethality and epigenetic antagonism. Ann Oncol 2017; 28:254-269. [DOI: 10.1093/annonc/mdw552] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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