1
|
Sahu RK, Tandon S, Singh S, Das BC, Hedau ST. Methyl CpG binding protein MBD2 has a regulatory role on the BRCA1 gene expression and its modulation by resveratrol in ER+, PR+ & triple-negative breast cancer cells. BMC Cancer 2024; 24:566. [PMID: 38711004 PMCID: PMC11071212 DOI: 10.1186/s12885-024-12274-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Resveratrol has demonstrated its ability to regulate BRCA1 gene expression in breast cancer cells, and previous studies have established the binding of MBD proteins to BRCA1 gene promoter regions. However, the molecular mechanism underlying these interactions remains to be elucidated. The aimed to evaluate the impact of MBD proteins on the regulation of BRCA1, BRCA2, and p16 genes and their consequential effects on breast cancer cells. METHODS Efficacy of resveratrol was assessed using the MTT assay. Binding interactions were investigated through EMSA, ChIP, & MeIP assay. Expression analyses of MBD genes and proteins were conducted using qRT-PCR and western blotting, respectively. Functional assays, including clonogenic, migratory, and sphere formation assays were used to assess cancer cells' colony-forming, metastatic, and tumor-forming abilities. The cytotoxicity of resveratrol on cancer cells was also tested using an apoptosis assay. RESULTS The study determined an IC50 of 30µM for resveratrol. MBD proteins were found to bind to the BRCA1 gene promoter. Resveratrol exhibited regulatory effects on MBD gene expression, subsequently impacting BRCA1 gene expression and protein levels. Higher concentrations of resveratrol resulted in reduced colony and sphere formation, decreases migration of cancer cells, and an increases number of apoptotic cells in breast cancer cells. Impact Identification of MBD2-BRCA1 axis indicates their significant role in the induction of apoptosis and reduction of metastasis and proliferation in breast cancer cells. Further therapy can be designed to target these MBD proteins and resveratrol could be used along with other anticancer drugs to target breast cancer. CONCLUSIONS In conclusion MBD2 protein interact to the BRCA1 gene promoter, and resveratrol modulates MBD2 gene expression, which in turn regulates BRCA1 gene expression, and inhibits cell proliferation, migration, and induces apoptosis in ER+, PR+ & Triple negative breast cancer cells.
Collapse
Affiliation(s)
- Ram Krishna Sahu
- Division of Molecular Oncology, ICMR-National Institute of Cancer Prevention and Research, I -7, Sector - 39, Noida, Uttar Pradesh, 201301, India
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida, Uttar Pradesh, 201313, India
| | | | - Shalini Singh
- Division of Clinical Oncology, ICMR-National Institute of Cancer Prevention and Research, I -7, Sector - 39, Noida, Uttar Pradesh, 201301, India
| | - Bhudev Chandra Das
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Suresh T Hedau
- Division of Molecular Oncology, ICMR-National Institute of Cancer Prevention and Research, I -7, Sector - 39, Noida, Uttar Pradesh, 201301, India.
| |
Collapse
|
2
|
Haidar L, Georgescu M, Drăghici GA, Bănățean-Dunea I, Nica DV, Șerb AF. DNA Methylation Machinery in Gastropod Mollusks. Life (Basel) 2024; 14:537. [PMID: 38672807 PMCID: PMC11050768 DOI: 10.3390/life14040537] [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: 03/11/2024] [Revised: 04/17/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024] Open
Abstract
The role of DNA methylation in mollusks is just beginning to be understood. This review synthesizes current knowledge on this potent molecular hallmark of epigenetic control in gastropods-the largest class of mollusks and ubiquitous inhabitants of diverse habitats. Their DNA methylation machinery shows a high degree of conservation in CG maintenance methylation mechanisms, driven mainly by DNMT1 homologues, and the presence of MBD2 and MBD2/3 proteins as DNA methylation readers. The mosaic-like DNA methylation landscape occurs mainly in a CG context and is primarily confined to gene bodies and housekeeping genes. DNA methylation emerges as a critical regulator of reproduction, development, and adaptation, with tissue-specific patterns being observed in gonadal structures. Its dynamics also serve as an important regulatory mechanism underlying learning and memory processes. DNA methylation can be affected by various environmental stimuli, including as pathogens and abiotic stresses, potentially impacting phenotypic variation and population diversity. Overall, the features of DNA methylation in gastropods are complex, being an essential part of their epigenome. However, comprehensive studies integrating developmental stages, tissues, and environmental conditions, functional annotation of methylated regions, and integrated genomic-epigenomic analyses are lacking. Addressing these knowledge gaps will advance our understanding of gastropod biology, ecology, and evolution.
Collapse
Affiliation(s)
- Laura Haidar
- Department of Functional Sciences, Physiology Discipline, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania;
- Center of Immuno-Physiology and Biotechnologies (CIFBIOTEH), “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
| | - Marius Georgescu
- Department of Functional Sciences, Physiology Discipline, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania;
- Center of Immuno-Physiology and Biotechnologies (CIFBIOTEH), “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
| | - George Andrei Drăghici
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania
| | - Ioan Bănățean-Dunea
- Biology and Plant Protection Department, Faculty of Agriculture, University of Life Sciences “King Mihai I” from Timișoara, Calea Aradului 119, 300645 Timișoara, Romania;
| | - Dragoș Vasile Nica
- The National Institute of Research—Development for Machines and Installations Designed for Agriculture and Food Industry (INMA), Bulevardul Ion Ionescu de la Brad 6, 077190 București, Romania
| | - Alina-Florina Șerb
- Department of Biochemistry and Pharmacology, Biochemistry Discipline, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
| |
Collapse
|
3
|
Papin C, Ibrahim A, Sabir JSM, Le Gras S, Stoll I, Albiheyri RS, Zari AT, Bahieldin A, Bellacosa A, Bronner C, Hamiche A. MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density. J Exp Clin Cancer Res 2023; 42:301. [PMID: 37957685 PMCID: PMC10644448 DOI: 10.1186/s13046-023-02882-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Inherited defects in the base-excision repair gene MBD4 predispose individuals to adenomatous polyposis and colorectal cancer, which is characterized by an accumulation of C > T transitions resulting from spontaneous deamination of 5'-methylcytosine. METHODS Here, we have investigated the potential role of MBD4 in regulating DNA methylation levels using genome-wide transcriptome and methylome analyses. Additionally, we have elucidated its function through a series of in vitro experiments. RESULTS Here we show that the protein MBD4 is required for DNA methylation maintenance and G/T mismatch repair. Transcriptome and methylome analyses reveal a genome-wide hypomethylation of promoters, gene bodies and repetitive elements in the absence of MBD4 in vivo. Methylation mark loss is accompanied by a broad transcriptional derepression phenotype affecting promoters and retroelements with low methylated CpG density. MBD4 in vivo forms a complex with the mismatch repair proteins (MMR), which exhibits high bi-functional glycosylase/AP-lyase endonuclease specific activity towards methylated DNA substrates containing a G/T mismatch. Experiments using recombinant proteins reveal that the association of MBD4 with the MMR protein MLH1 is required for this activity. CONCLUSIONS Our data identify MBD4 as an enzyme specifically designed to repair deaminated 5-methylcytosines and underscores its critical role in safeguarding against methylation damage. Furthermore, it illustrates how MBD4 functions in normal and pathological conditions.
Collapse
Affiliation(s)
- Christophe Papin
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Abdulkhaleg Ibrahim
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
- National Research Centre for Tropical and Transboundary Diseases (NRCTTD), Alzentan, 99316, Libya
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Stéphanie Le Gras
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Isabelle Stoll
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Raed S Albiheyri
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ali T Zari
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alfonso Bellacosa
- Cancer Biology Program, Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Christian Bronner
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France.
| | - Ali Hamiche
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France.
| |
Collapse
|
4
|
de Luna FCF, Ferreira WAS, Casseb SMM, de Oliveira EHC. Anticancer Potential of Flavonoids: An Overview with an Emphasis on Tangeretin. Pharmaceuticals (Basel) 2023; 16:1229. [PMID: 37765037 PMCID: PMC10537037 DOI: 10.3390/ph16091229] [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: 07/26/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Natural compounds with pharmacological activity, flavonoids have been the subject of an exponential increase in studies in the field of scientific research focused on therapeutic purposes due to their bioactive properties, such as antioxidant, anti-inflammatory, anti-aging, antibacterial, antiviral, neuroprotective, radioprotective, and antitumor activities. The biological potential of flavonoids, added to their bioavailability, cost-effectiveness, and minimal side effects, direct them as promising cytotoxic anticancer compounds in the optimization of therapies and the search for new drugs in the treatment of cancer, since some extensively antineoplastic therapeutic approaches have become less effective due to tumor resistance to drugs commonly used in chemotherapy. In this review, we emphasize the antitumor properties of tangeretin, a flavonoid found in citrus fruits that has shown activity against some hallmarks of cancer in several types of cancerous cell lines, such as antiproliferative, apoptotic, anti-inflammatory, anti-metastatic, anti-angiogenic, antioxidant, regulatory expression of tumor-suppressor genes, and epigenetic modulation.
Collapse
Affiliation(s)
- Francisco Canindé Ferreira de Luna
- Laboratory of Cytogenomics and Environmental Mutagenesis, Environment Section (SEAMB), Evandro Chagas Institute (IEC), BR 316, KM 7, s/n, Levilândia, Ananindeua 67030-000, Brazil; (W.A.S.F.); (E.H.C.d.O.)
| | - Wallax Augusto Silva Ferreira
- Laboratory of Cytogenomics and Environmental Mutagenesis, Environment Section (SEAMB), Evandro Chagas Institute (IEC), BR 316, KM 7, s/n, Levilândia, Ananindeua 67030-000, Brazil; (W.A.S.F.); (E.H.C.d.O.)
| | | | - Edivaldo Herculano Correa de Oliveira
- Laboratory of Cytogenomics and Environmental Mutagenesis, Environment Section (SEAMB), Evandro Chagas Institute (IEC), BR 316, KM 7, s/n, Levilândia, Ananindeua 67030-000, Brazil; (W.A.S.F.); (E.H.C.d.O.)
- Faculty of Natural Sciences, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Rua Augusto Correa, 01, Belém 66075-990, Brazil
| |
Collapse
|
5
|
Rubio K, Hernández-Cruz EY, Rogel-Ayala DG, Sarvari P, Isidoro C, Barreto G, Pedraza-Chaverri J. Nutriepigenomics in Environmental-Associated Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12030771. [PMID: 36979019 PMCID: PMC10045733 DOI: 10.3390/antiox12030771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Complex molecular mechanisms define our responses to environmental stimuli. Beyond the DNA sequence itself, epigenetic machinery orchestrates changes in gene expression induced by diet, physical activity, stress and pollution, among others. Importantly, nutrition has a strong impact on epigenetic players and, consequently, sustains a promising role in the regulation of cellular responses such as oxidative stress. As oxidative stress is a natural physiological process where the presence of reactive oxygen-derived species and nitrogen-derived species overcomes the uptake strategy of antioxidant defenses, it plays an essential role in epigenetic changes induced by environmental pollutants and culminates in signaling the disruption of redox control. In this review, we present an update on epigenetic mechanisms induced by environmental factors that lead to oxidative stress and potentially to pathogenesis and disease progression in humans. In addition, we introduce the microenvironment factors (physical contacts, nutrients, extracellular vesicle-mediated communication) that influence the epigenetic regulation of cellular responses. Understanding the mechanisms by which nutrients influence the epigenome, and thus global transcription, is crucial for future early diagnostic and therapeutic efforts in the field of environmental medicine.
Collapse
Affiliation(s)
- Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Estefani Y Hernández-Cruz
- Postgraduate in Biological Sciences, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
| | - Diana G Rogel-Ayala
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | | | - Ciro Isidoro
- Department of Health Sciences, Università del Piemonte Orientale, Via Paolo Solaroli 17, 28100 Novara, Italy
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
| |
Collapse
|
6
|
Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
Collapse
|
7
|
Lafont JE, Moustaghfir S, Durand AL, Mallein-Gerin F. The epigenetic players and the chromatin marks involved in the articular cartilage during osteoarthritis. Front Physiol 2023; 14:1070241. [PMID: 36733912 PMCID: PMC9887161 DOI: 10.3389/fphys.2023.1070241] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Epigenetics defines the modifications of the genome that do not involve a change in the nucleotide sequence of DNA. These modifications constitute a mechanism of gene regulation poorly explored in the context of cartilage physiology. They are now intensively studied by the scientific community working on articular cartilage and its related pathology such as osteoarthritis. Indeed, epigenetic regulations can control the expression of crucial gene in the chondrocytes, the only resident cells of cartilage. Some epigenetic changes are considered as a possible cause of the abnormal gene expression and the subsequent alteration of the chondrocyte phenotype (hypertrophy, proliferation, senescence…) as observed in osteoarthritic cartilage. Osteoarthritis is a joint pathology, which results in impaired extracellular matrix homeostasis and leads ultimately to the progressive destruction of cartilage. To date, there is no pharmacological treatment and the exact causes have yet to be defined. Given that the epigenetic modifying enzymes can be controlled by pharmacological inhibitors, it is thus crucial to describe the epigenetic marks that enable the normal expression of extracellular matrix encoding genes, and those associated with the abnormal gene expression such as degradative enzyme or inflammatory cytokines encoding genes. In this review, only the DNA methylation and histone modifications will be detailed with regard to normal and osteoarthritic cartilage. Although frequently referred as epigenetic mechanisms, the regulatory mechanisms involving microRNAs will not be discussed. Altogether, this review will show how this nascent field influences our understanding of the pathogenesis of OA in terms of diagnosis and how controlling the epigenetic marks can help defining epigenetic therapies.
Collapse
|
8
|
Chen R, Li J, Fujimoto J, Hong L, Hu X, Quek K, Tang M, Mitra A, Behrens C, Chow CW, Jiang P, Little LD, Gumbs C, Song X, Zhang J, Tan D, Heymach JV, Wistuba I, Futreal PA, Gibbons DL, Byers LA, Zhang J, Reuben A. Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma. J Exp Clin Cancer Res 2022; 41:172. [PMID: 35546239 PMCID: PMC9092788 DOI: 10.1186/s13046-022-02361-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Lung cancer is the leading cause of cancer death, partially owing to its extensive heterogeneity. The analysis of intertumor heterogeneity has been limited by an inability to concurrently obtain tissue from synchronous metastases unaltered by multiple prior lines of therapy.
Methods
In order to study the relationship between genomic, epigenomic and T cell repertoire heterogeneity in a rare autopsy case from a 32-year-old female never-smoker with left lung primary late-stage lung adenocarcinoma (LUAD), we did whole-exome sequencing (WES), DNA methylation and T cell receptor (TCR) sequencing to characterize the immunogenomic landscape of one primary and 19 synchronous metastatic tumors.
Results
We observed heterogeneous mutation, methylation, and T cell patterns across distinct metastases. Only TP53 mutation was detected in all tumors suggesting an early event while other cancer gene mutations were later events which may have followed subclonal diversification. A set of prevalent T cell clonotypes were completely excluded from left-side thoracic tumors indicating distinct T cell repertoire profiles between left-side and non left-side thoracic tumors. Though a limited number of predicted neoantigens were shared, these were associated with homology of the T cell repertoire across metastases. Lastly, ratio of methylated neoantigen coding mutations was negatively associated with T-cell density, richness and clonality, suggesting neoantigen methylation may partially drive immunosuppression.
Conclusions
Our study demonstrates heterogeneous genomic and T cell profiles across synchronous metastases and how restriction of unique T cell clonotypes within an individual may differentially shape the genomic and epigenomic landscapes of synchronous lung metastases.
Collapse
|
9
|
Antioxidative, Anti-Inflammatory, Anti-Obesogenic, and Antidiabetic Properties of Tea Polyphenols-The Positive Impact of Regular Tea Consumption as an Element of Prophylaxis and Pharmacotherapy Support in Endometrial Cancer. Int J Mol Sci 2022; 23:ijms23126703. [PMID: 35743146 PMCID: PMC9224362 DOI: 10.3390/ijms23126703] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
Endometrial cancer (EC) is second only to cervical carcinoma among the most commonly diagnosed malignant tumours of the female reproductive system. The available literature provides evidence for the involvement of 32 genes in the hereditary incidence of EC. The physiological markers of EC and coexisting diet-dependent maladies include antioxidative system disorders but also progressing inflammation; hence, the main forms of prophylaxis and pharmacotherapy ought to include a diet rich in substances aiding the organism’s response to this type of disorder, with a particular focus on ones suitable for lifelong consumption. Tea polyphenols satisfy those requirements due to their proven antioxidative, anti-inflammatory, anti-obesogenic, and antidiabetic properties. Practitioners ought to consider promoting tea consumption among individuals genetically predisposed for EC, particularly given its low cost, accessibility, confirmed health benefits, and above all, suitability for long-term consumption regardless of the patient’s age. The aim of this paper is to analyse the potential usability of tea as an element of prophylaxis and pharmacotherapy support in EC patients. The analysis is based on information available from worldwide literature published in the last 15 years.
Collapse
|
10
|
Duan J, Zhong B, Fan Z, Zhang H, Xu M, Zhang X, Sanders YY. DNA methylation in pulmonary fibrosis and lung cancer. Expert Rev Respir Med 2022; 16:519-528. [PMID: 35673969 DOI: 10.1080/17476348.2022.2085091] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Juan Duan
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Baiyun Zhong
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhihua Fan
- Xiangya Medical school of Central South University, Changsha, Hunan, China
| | - Hao Zhang
- Xiangya Medical school of Central South University, Changsha, Hunan, China
| | - Mengmeng Xu
- Xiangya Medical school of Central South University, Changsha, Hunan, China
| | - Xiangyu Zhang
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Y Sanders
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, 901 19 Street South, BMRII Room 408, Birmingham, AL 35294, USA
| |
Collapse
|
11
|
Du C, Liu X, Li M, Zhao Y, Li J, Wen Z, Liu M, Yang M, Fu B, Wei M. Analysis of 5-Methylcytosine Regulators and DNA Methylation-Driven Genes in Colon Cancer. Front Cell Dev Biol 2022; 9:657092. [PMID: 35174154 PMCID: PMC8842075 DOI: 10.3389/fcell.2021.657092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the methylation-driven gene expression. However, the effect of the 5mC regulators on the oncogenic pathways in colon cancer (CC) remains unclear. Also, the clinical value of such epigenetic-driven events needs further research. Methods: The transcriptome and matching epigenetic data were obtained from The Cancer Genome Atlas dataset. The gene set variation analysis identified the oncogenic pathways adjusted by 5mC regulators. The “edgeR” and “methylmix” package identified the differential expression genes of DNA methylation-driven genes. The correlation between 5mC regulators or transcription factors and shortlisted genes was investigated by calculating the Spearman's rank correlation coefficient. Among them, the genes related to diagnosis were screened out based on differential gene expression in extracellular vesicles (EVs) by the “limma” package and histology by immunohistochemistry. Then, a risk signature was constructed by fitting the generalized linear model and validated by the receiver operating characteristic curve. Results: MYC targets pathway and phosphatidylinositol-3-kinase–AKT–mammalian target of rapamycin signaling pathway were identified as the hallmark-related pathways associated with 5mC regulators. Also, the P53 pathway was subject to the influence of regulators' expression. A five methylation-driven gene signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) was developed as the biomarker for CC diagnosis. Meanwhile, those genes positively related to 5mC regulators and interacted with their relevant or transcription factors. Conclusion: In general, 5mC regulators are positively related to each other and DNA methylation-driven genes, with the relationship of multiple active and inhibitory pathways related to cancer. Meanwhile, the signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) can prefigure prospective diagnosis in CC.
Collapse
Affiliation(s)
- Cheng Du
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - XinLi Liu
- Department of Digestive Oncology, Cancer Hospital of China Medical University, Shenyang, China
| | - Mingwei Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Yi Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Jie Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Zhikang Wen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Min Liu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Meina Yang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Boshi Fu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| |
Collapse
|
12
|
Sahu RK, Verma VV, Kumar A, Tandon S, Chandra Das B, Hedau ST. In silico prediction and interaction of resveratrol on methyl-CpG binding proteins by molecular docking and MD simulations study. RSC Adv 2022; 12:11493-11504. [PMID: 35425086 PMCID: PMC9006347 DOI: 10.1039/d2ra00432a] [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] [Accepted: 03/31/2022] [Indexed: 11/26/2022] Open
Abstract
Resveratrol enhances the BRCA1 gene expression and the MBD family of proteins bind to the promoter region of the BRCA1 gene. However, the molecular interaction is not yet reported. Here we have analyzed the binding affinity of resveratrol with MBD proteins. Our results suggest that resveratrol binds to the MBD proteins with higher binding affinity toward MeCP2 protein (ΔG = −6.5) by sharing four hydrogen bonds as predicted by molecular docking studies. Further, the molecular dynamics simulations outcomes showed that the backbones of all three protein–ligand complexes are stabilized after the period of 75 ns, constantly fluctuating around the deviations of 0.4 Å, 0.5 Å and 0.7 Å for MBD1, MBD2 and MeCP2, respectively. The inter-molecular hydrogen bonding trajectory analysis for protein–ligand complexes also support the strong binding between MeCP2–resveratrol complex. Further, binding free energy calculations showed binding energy of −94.764 kJ mol−1, −53.826 kJ mol−1 and −36.735 kJ mol−1 for MeCP2–resveratrol, MBD2–resveratrol and MBD1–resveratrol complexes, respectively, which also supported our docking results. Our study also highlighted that the MBD family of proteins forms a binding interaction with other signaling proteins that are involved in various cancer initiation pathways. Resveratrol enhances the BRCA1 gene expression and the MBD family of proteins bind to the promoter region of the BRCA1 gene.![]()
Collapse
Affiliation(s)
- Ram Krishna Sahu
- Division of Molecular Oncology, National Institute of Cancer Prevention and Research, ICMR, I – 7, Sector – 39, Noida – 201 301, Utter Pradesh, India
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida – 201301, Utter Pradesh, India
| | - Ved Vrat Verma
- Information System for Research Management Division, ICMR, Aruna Asif Ali Marg, New Delhi – 110029, India
| | - Amit Kumar
- Information System for Research Management Division, ICMR, Aruna Asif Ali Marg, New Delhi – 110029, India
| | - Simran Tandon
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida – 201301, Utter Pradesh, India
| | - Bhudev Chandra Das
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida – 201301, Utter Pradesh, India
| | - Suresh T. Hedau
- Division of Molecular Oncology, National Institute of Cancer Prevention and Research, ICMR, I – 7, Sector – 39, Noida – 201 301, Utter Pradesh, India
| |
Collapse
|
13
|
Wu SC, Münger K. Role and Clinical Utility of Cancer/Testis Antigens in Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13225690. [PMID: 34830845 PMCID: PMC8616139 DOI: 10.3390/cancers13225690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer/testis (CT) antigens exhibit selective expression predominantly in immunoprivileged tissues in non-pathological contexts but are aberrantly expressed in diverse cancers. Due to their expression pattern, they have historically been attractive targets for immunotherapies. A growing number of studies implicate CT antigens in almost all hallmarks of cancer, suggesting that they may act as cancer drivers. CT antigens are expressed in head and neck squamous cell carcinomas. However, their role in the pathogenesis of these cancers remains poorly studied. Given that CT antigens hold intriguing potential as therapeutic targets and as biomarkers for prognosis and that they can provide novel insights into oncogenic mechanisms, their further study in the context of head and squamous cell carcinoma is warranted.
Collapse
Affiliation(s)
- Sharon Changshan Wu
- Molecular Microbiology Program, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA;
| | - Karl Münger
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
- Correspondence:
| |
Collapse
|
14
|
Wang Y, Imran A, Shami A, Chaudhary AA, Khan S. Decipher the Helicobacter pylori Protein Targeting in the Nucleus of Host Cell and their Implications in Gallbladder Cancer: An insilico approach. J Cancer 2021; 12:7214-7222. [PMID: 34729122 PMCID: PMC8558644 DOI: 10.7150/jca.63517] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/03/2021] [Indexed: 12/26/2022] Open
Abstract
Gallbladder cancer (GBC) is one of the leading causes of cancer-related mortality worldwide. Researchers have investigated that specific strains of bacteria are connected with growth of different types of cancers in human. Some reports show possible implication of Helicobacter pylori (H. pylori) in the etiology of gallbladder cancer (GBC). Their enigmatic mechanisms, nevertheless, are not still well clear. We sought to predict whether various proteins of H. pylori targeted to nucleus of host cells and their implication in growth of gallbladder cancer. GBC is one of the leading causes of cancer mortality worldwide. We applied bioinformatics approach to analyze the H. pylori proteins targeting into the nucleus of host cells using different bioinformatics predictors including nuclear localization signal (NLS) mapper Balanced Subcellular Localization (BaCelLo) and Hum-mPLoc 2.0. Various nuclear targeting proteins may have a potential role in GBC etiology during intracellular infection. We identified 46 H. pylori proteins targeted into nucleus of host cell through bioinformatics tools. These H. pylori nucleus-targeting proteins might alter the normal function of host cells by disturbing the different pathways including replication, transcription, translation etc. Various nucleus-targeted proteins can affect the normal growth and development of infected cells. We propose that H. pylori proteins targeting into the nucleus of host cells regulate GBC growth using different strategies. These integrative bioinformatics research demonstrated several H. pylori proteins that may serve as possible targets or biomarkers for early cure and treatment or diagnosis GBC.
Collapse
Affiliation(s)
- Yunjian Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou City, Henan Province, 450008, China
| | - Ahamad Imran
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ashwag Shami
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Shahanavaj Khan
- Department of Health Sciences, Novel Global Community Educational Foundation, Australia.,Department of Bioscience, Shri Ram Group of College (SRGC), Muzaffarnagar, UP, India.,Department of Pharmaceutics, College of Pharmacy, PO Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
| |
Collapse
|
15
|
Rotondo JC, Lanzillotti C, Mazziotta C, Tognon M, Martini F. Epigenetics of Male Infertility: The Role of DNA Methylation. Front Cell Dev Biol 2021; 9:689624. [PMID: 34368137 PMCID: PMC8339558 DOI: 10.3389/fcell.2021.689624] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/17/2021] [Indexed: 12/18/2022] Open
Abstract
In recent years, a number of studies focused on the role of epigenetics, including DNA methylation, in spermatogenesis and male infertility. We aimed to provide an overview of the knowledge concerning the gene and genome methylation and its regulation during spermatogenesis, specifically in the context of male infertility etiopathogenesis. Overall, the findings support the hypothesis that sperm DNA methylation is associated with sperm alterations and infertility. Several genes have been found to be differentially methylated in relation to impaired spermatogenesis and/or reproductive dysfunction. Particularly, DNA methylation defects of MEST and H19 within imprinted genes and MTHFR within non-imprinted genes have been repeatedly linked with male infertility. A deep knowledge of sperm DNA methylation status in association with reduced reproductive potential could improve the development of novel diagnostic tools for this disease. Further studies are needed to better elucidate the mechanisms affecting methylation in sperm and their impact on male infertility.
Collapse
Affiliation(s)
- John Charles Rotondo
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Carmen Lanzillotti
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Mazziotta
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Mauro Tognon
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Martini
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| |
Collapse
|
16
|
Yang X, Siddique A, Khan AA, Wang Q, Malik A, Jan AT, Rudayni HA, Chaudhary AA, Khan S. Chlamydia Trachomatis Infection: Their potential implication in the Etiology of Cervical Cancer. J Cancer 2021; 12:4891-4900. [PMID: 34234859 PMCID: PMC8247366 DOI: 10.7150/jca.58582] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Pathogenic bacterial strains can alter the normal function of cells and induce different levels of inflammatory responses that are connected to the development of different diseases, such as tuberculosis, diarrhea, cancer etc. Chlamydia trachomatis (C. trachomatis) is an intracellular obligate gram-negative bacterium which has been connected with the cervical cancer etiology. Nevertheless, establishment of causality and the underlying mechanisms of carcinogenesis of cervical cancer associated with C. trachomatis remain unclear. Studies reveal the existence of C. trachomatis in cervical cancer patients. The DNA repair pathways including mismatch repair, nucleotide excision, and base excision are vital in the abatement of accumulated mutations that can direct to the process of carcinogenesis. C. trachomatis recruits DDR proteins away from sites of DNA damage and, in this way, impedes the DDR. Therefore, by disturbing host cell-cycle control, chromatin and DDR repair, C. trachomatis makes a situation favorable for malignant transformation. Inflammation originated due to infection directs over production of reactive oxygen species (ROS) and consequent oxidative DNA damage. This review may aid our current understanding of the etiology of cervical cancer in C. trachomatis-infected patients.
Collapse
Affiliation(s)
- Xingju Yang
- Department of Nursing, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 271199, China
| | - Anam Siddique
- Department of Biosciences, Shri Ram Group of College (SRGC), Muzaffarnagar 251001, India
| | - Abdul Arif Khan
- Division of Microbiology, Indian Council of Medical Research-National AIDS Research Institute, Pune, Maharashtra, India
| | - Qian Wang
- Department of Obstetrics and Gynecology, Jinan Fifth People's Hospital, Jinan, Shandong, 250022, China
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185236, India
| | - Hassan Ahmed Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Shahanavaj Khan
- Department of Biosciences, Shri Ram Group of College (SRGC), Muzaffarnagar 251001, India
- Department of Pharmaceutics, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
- Department of Health Sciences, Novel Global Community Educational Foundation, Australia
| |
Collapse
|
17
|
The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments. Cancers (Basel) 2021; 13:cancers13092071. [PMID: 33922974 PMCID: PMC8123355 DOI: 10.3390/cancers13092071] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The accumulated evidence on the role of epigenetic markers of prognosis in clear cell renal cell carcinoma (ccRCC) is reviewed, as well as state of the art on epigenetic treatments for this malignancy. Several epigenetic markers are likely candidates for clinical use, but still have not passed the test of prospective validation. Development of epigenetic therapies, either alone or in combination with tyrosine-kinase inhibitors of immune-checkpoint inhibitors, are still in their infancy. Abstract Clear cell renal cell carcinoma (ccRCC) is curable when diagnosed at an early stage, but when disease is non-confined it is the urologic cancer with worst prognosis. Antiangiogenic treatment and immune checkpoint inhibition therapy constitute a very promising combined therapy for advanced and metastatic disease. Many exploratory studies have identified epigenetic markers based on DNA methylation, histone modification, and ncRNA expression that epigenetically regulate gene expression in ccRCC. Additionally, epigenetic modifiers genes have been proposed as promising biomarkers for ccRCC. We review and discuss the current understanding of how epigenetic changes determine the main molecular pathways of ccRCC initiation and progression, and also its clinical implications. Despite the extensive research performed, candidate epigenetic biomarkers are not used in clinical practice for several reasons. However, the accumulated body of evidence of developing epigenetically-based biomarkers will likely allow the identification of ccRCC at a higher risk of progression. That will facilitate the establishment of firmer therapeutic decisions in a changing landscape and also monitor active surveillance in the aging population. What is more, a better knowledge of the activities of chromatin modifiers may serve to develop new therapeutic opportunities. Interesting clinical trials on epigenetic treatments for ccRCC associated with well established antiangiogenic treatments and immune checkpoint inhibitors are revisited.
Collapse
|
18
|
Natural products in the reprogramming of cancer epigenetics. Toxicol Appl Pharmacol 2021; 417:115467. [PMID: 33631231 DOI: 10.1016/j.taap.2021.115467] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
Owing to the technological advancements, including next generation sequencing, the significance of deregulated epigenetic mechanisms in cancer initiation, progression and treatment has become evident. The accumulating knowledge relating to the epigenetic markers viz. DNA methylation, Histone modifications and non-coding RNAs make them one of the most interesting candidates for developing anti-cancer therapies. The reversibility of deregulated epigenetic mechanisms through environmental and dietary factors opens numerous avenues in the field of chemoprevention and drug development. Recent studies have proven that plant-derived natural products encompass a great potential in targeting epigenetic signatures in cancer and numerous natural products are being explored for their possibility to be considered as "epi-drug". This review intends to highlight the major aberrant epigenetic mechanisms and summarizes the essential functions of natural products like Resveratrol, Quercetin, Genistein, EGCG, Curcumin, Sulforaphane, Apigenin, Parthenolide and Berberine in modulating these aberrations. This knowledge along with the challenges and limitations in this field has potential and wider implications in developing novel and successful therapeutic strategies. The increased focus in the area will possibly provide a better understanding for the development of dietary supplements and/or drugs either alone or in combination. The interaction of epigenetics with different hallmarks of cancer and how natural products can be utilized to target them will also be interesting in the future therapeutic approaches.
Collapse
|
19
|
Athreya N, Sarathya A, Xiong M, Leburton JP. 2D Solid-State Nanopore Field-Effect Transistors: Comprehensive Computational Methodology for Biosensing Applications. IEEE NANOTECHNOLOGY MAGAZINE 2020. [DOI: 10.1109/mnano.2020.3024388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
20
|
Li L, Li N, Liu N, Huo F, Zheng J. MBD2 Correlates with a Poor Prognosis and Tumor Progression in Renal Cell Carcinoma. Onco Targets Ther 2020; 13:10001-10012. [PMID: 33116585 PMCID: PMC7548338 DOI: 10.2147/ott.s256226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/27/2020] [Indexed: 01/21/2023] Open
Abstract
Purpose DNA methylation plays an important role in regulating gene expression. Methyl-CpG-binding domain (MBD) proteins recognize and bind to methylated DNA, which mediate gene silencing by the interaction with deacetylases and histone methyltransferases. MBD2 has been reported in various human cancers; however, its clinical implication and potential regulatory role in renal cell carcinoma (RCC) have not been elaborated. Materials and Methods In the study, we estimated the expression and prognostic value of MBD2 in RCC cell lines and tissues by Western blotting and immunohistochemistry. The associations of MBD2 expression and pathological characters and survival in RCC patients were performed using χ2 and Kaplan-Meier survival analysis, respectively. Univariate and multivariable Cox regression analyses suggested the independent predictors in RCC prognosis. The functional role of MBD2 in RCC progression was assessed by in vitro cell experiments. In addition, we identified the MBD2-mediated alterations of protein-related proliferation and EMT markers in RCC cells after MBD2 overexpression and knockdown. Results We found that the protein levels of MBD2 were upregulated in RCC cells and tissues. High MBD2 expression was related to TNM stage and predicted poorer survival in RCC. Enforced expression of MBD2 significantly promoted the proliferation, cycle progress, invasion and migration of RCC cells in vitro. However, downregulating MBD2 remarkably weakened the above cell functions. Mechanistically, the promotive effect of MBD2 overexpression may be regulated by its effects onp21, p53 and Cyclin D1 expression and EMT process. Conclusion These results indicated that MBD2confers an oncogenic function in the malignant progression of RCC. MBD2 could be served as a meaningful prognostic biomarker and a latent therapeutic target in RCC patients.
Collapse
Affiliation(s)
- Liantao Li
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou 221000, People's Republic of China
| | - Na Li
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Nianli Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou 221000, People's Republic of China
| | - Fuchun Huo
- Department of Pathology, Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Junnian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| |
Collapse
|
21
|
Malousi A, Andreou AZ, Kouidou S. In silico structural analysis of sequences containing 5-hydroxymethylcytosine reveals its potential as binding regulator for development, ageing and cancer-related transcription factors. Epigenetics 2020; 16:503-518. [PMID: 32752914 DOI: 10.1080/15592294.2020.1805693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The presence of 5-hydroxymethyl cytosine in DNA has been previously associated with ageing. Using in silico analysis of normal liver samples we presently observed that in 5-hydroxymethyl cytosine sequences, DNA methylation is dependent on the co-presence of G-quadruplexes and palindromes. This association exhibits discrete patterns depending on G-quadruplex and palindrome densities. DNase-Seq data show that 5-hydroxymethyl cytosine sequences are common among liver nucleosomes (p < 2.2x10-16) and threefold more frequent than nucleosome sequences. Nucleosomes lacking palindromes and potential G-quadruplexes are rare in vivo (1%) and nucleosome occupancy potential decreases with increasing G-quadruplexes. Palindrome distribution is similar to that previously reported in nucleosomes. In low and mixed complexity sequences 5-hydroxymethyl cytosine is frequently located next to three elements: G-quadruplexes or imperfect G-quadruplexes with CpGs, or unstable hairpin loops (TCCCAY6TGGGA) mostly located in antisense strands or finally A-/T-rich segments near these motifs. The high frequencies and selective distribution of pentamer sequences (including TCCCA, TGGGA) probably indicate the positive contribution of 5-hydroxymethyl cytosine to stabilize the formation of structures unstable in the absence of this cytosine modification. Common motifs identified in all total 5-hydroxymethyl cytosine-containing sequences exhibit high homology to recognition sites of several transcription factor families: homeobox, factors involved in growth, mortality/ageing, cancer, neuronal function, vision, and reproduction. We conclude that cytosine hydroxymethylation could play a role in the recognition of sequences with G-quadruplexes/palindromes by forming epigenetically regulated DNA 'springs' and governing expansions or compressions recognized by different transcription factors or stabilizing nucleosomes. The balance of these epigenetic elements is lost in hepatocellular carcinoma.
Collapse
Affiliation(s)
- Andigoni Malousi
- Lab. of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Sofia Kouidou
- Lab. of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| |
Collapse
|
22
|
Karimzadeh MR, Pourdavoud P, Ehtesham N, Qadbeigi M, Asl MM, Alani B, Mosallaei M, Pakzad B. Regulation of DNA methylation machinery by epi-miRNAs in human cancer: emerging new targets in cancer therapy. Cancer Gene Ther 2020; 28:157-174. [PMID: 32773776 DOI: 10.1038/s41417-020-00210-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022]
Abstract
Disruption in DNA methylation processes can lead to alteration in gene expression and function that would ultimately result in malignant transformation. In this way, studies have shown that, in cancers, methylation-associated silencing inactivates tumor suppressor genes, as effectively as mutations. DNA methylation machinery is composed of several genes, including those with DNA methyltransferases activity, proteins that bind to methylated cytosine in the promoter region, and enzymes with demethylase activity. Based on a prominent body of evidence, DNA methylation machinery could be regulated by microRNAs (miRNAs) called epi-miRNAs. Numerous studies demonstrated that dysregulation in DNA methylation regulators like upstream epi-miRNAs is indispensable for carcinogenesis; consequently, the malignant capacity of these cells could be reversed by restoring of this regulatory system in cancer. Conceivably, recognition of these epi-miRNAs in cancer cells could not only reveal novel molecular entities in carcinogenesis, but also render promising targets for cancer therapy. In this review, at first, we have an overview of the methylation alteration in cancers, and the effect of this phenomenon in miRNAs expression and after that, we conduct an in-depth discussion about the regulation of DNA methylation regulators by epi-miRNAs in cancer cells.
Collapse
Affiliation(s)
- Mohammad Reza Karimzadeh
- Department of medical Genetics, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | | | - Naeim Ehtesham
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Masood Movahedi Asl
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrang Alani
- Department of Applied Cell Sciences, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Meysam Mosallaei
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahram Pakzad
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran.
| |
Collapse
|
23
|
Li J, Zakariah M, Malik A, Ola MS, Syed R, Chaudhary AA, Khan S. Analysis of Salmonella typhimurium Protein-Targeting in the Nucleus of Host Cells and the Implications in Colon Cancer: An in-silico Approach. Infect Drug Resist 2020; 13:2433-2442. [PMID: 32765017 PMCID: PMC7381790 DOI: 10.2147/idr.s258037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/09/2020] [Indexed: 12/23/2022] Open
Abstract
Background Infections of Salmonella typhimurium (S. typhimurium) are major threats to health, threats include diarrhoea, fever, acute intestinal inflammation, and cancer. Nevertheless, little information is available about the involvement of S. typhimurium in colon cancer etiology. Methods The present study was designed to predict nuclear targeting of S. typhimurium proteins in the host cell through computational tools, including nuclear localization signal (NLS) mapper, Balanced Subcellular Localization predictor (BaCeILo), and Hum-mPLoc using next-generation sequencing data. Results Several gene expression-associated proteins of S. typhimurium have been predicted to target the host nucleus during intracellular infections. Nuclear targeting of S. typhimurium proteins can lead to competitive interactions between the host and pathogen proteins with similar cellular substrates, and it may have a possible involvement in colon cancer growth. Our results suggested that S. typhimurium releases its proteins within compartments of the host cell, where they act as a component of the host cell proteome. Protein targeting is possibly involved in colon cancer etiology during intracellular bacterial infection. Conclusion The results of current in-silico study showed the potential involvement of S. typhimurium infection with alteration in normal functioning of host cell which act as possible factor to connect with the growth and development of colon cancer.
Collapse
Affiliation(s)
- Jianhua Li
- Department of General Surgery Ⅰ, Xinxiang Central Hospital, Xinxiang City, Henan Province 453000, People's Republic of China
| | - Mohammed Zakariah
- Research Center, College of Computer and Information Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Shamsul Ola
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Rabbani Syed
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Shahanavaj Khan
- Bioinformatics and Biotechnology Unit, Department of Bioscience, Shri Ram Group of College (SRGC), Muzaffarnagar, UP, India.,Nano-Biotechnology Unit, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| |
Collapse
|
24
|
Gong W, Ni M, Chen Z, Zheng Z. Expression and clinical significance of methyl-CpG binding domain protein 2 in high-grade serous ovarian cancer. Oncol Lett 2020; 20:2749-2756. [PMID: 32782591 PMCID: PMC7400232 DOI: 10.3892/ol.2020.11836] [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: 02/06/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Platinum resistance is an important cause of clinical recurrence and mortality of patients with high-grade serous ovarian cancer (HGSOC). Methyl-CpG binding domain protein 2 (MBD2) serves an important role in tumor progression; however, its role in HGSOC remains unclear. The aim of the present study was to investigate the expression of MBD2 in HGSOC and its role in drug resistance and prognosis of HGSOC. MBD2 expression was analyzed by immunohistochemical staining and western blotting. The associations between MBD2 expression and clinical pathological features, platinum resistance and patient prognosis were analyzed using a χ2 test, Kaplan-Meier analysis and Cox regression analysis. Positive MBD2 expression was detected in 73 (63.5%) of the HGSOC tissue samples, whereas it was undetectable in all 16 normal tissue samples (100%) analyzed, indicating a significantly higher expression level in tumor tissues compared with normal tissues (P<0.001). Additionally, MBD2 expression was significantly higher in platinum-resistant cases compared with that in platinum-sensitive cases (P<0.05). In addition, high expression of MBD2 was negatively associated with relapse-free survival (P<0.05). In conclusion, MBD2 was demonstrated to be a potential drug target and a biomarker for poor prognosis in HGSOC.
Collapse
Affiliation(s)
- Wangang Gong
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China.,Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Cancer Hospital of The University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Maowei Ni
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Cancer Hospital of The University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Zhongbo Chen
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Cancer Hospital of The University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Zhiguo Zheng
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Cancer Hospital of The University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| |
Collapse
|
25
|
Jiang W, Liang YL, Liu Y, Chen YY, Yang ST, Li BR, Yu YX, Lyu Y, Wang R. MeCP2 inhibits proliferation and migration of breast cancer via suppression of epithelial-mesenchymal transition. J Cell Mol Med 2020; 24:7959-7967. [PMID: 32510753 PMCID: PMC7348137 DOI: 10.1111/jcmm.15428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/24/2020] [Accepted: 05/08/2020] [Indexed: 12/29/2022] Open
Abstract
Methyl‐CpG‐binding protein 2 (MeCP2) is an important epigenetic regulator for normal neuronal maturation and brain glial cell function. Additionally, MeCP2 is also involved in a variety of cancers, such as breast, prostate, lung, liver and colorectal. However, whether MeCP2 contributes to the progression of breast cancer remains unknown. In the present study, we investigated the role of MeCP2 in cell proliferation, migration and invasion in vitro. We found that knockdown of MeCP2 inhibited expression of epithelial‐mesenchymal transition (EMT)‐related markers in breast cancer cell lines. In conclusion, our study suggests that MeCP2 inhibits proliferation and invasion through suppression of the EMT pathway in breast cancer.
Collapse
Affiliation(s)
- Wei Jiang
- Department of Anatomy & Histology, School of Basic Medical Sciences, Shenzhen University Health Science Centre, Shenzhen, China
| | - Yan-Ling Liang
- Guangdong Provincial People's Hospital's Nanhai Hospital, Foshan, China
| | - Yang Liu
- Department of Anatomy & Histology, School of Basic Medical Sciences, Shenzhen University Health Science Centre, Shenzhen, China
| | - Yu-Yan Chen
- Department of Anatomy & Histology, School of Basic Medical Sciences, Shenzhen University Health Science Centre, Shenzhen, China
| | - Shu-Ting Yang
- Department of Anatomy & Histology, School of Basic Medical Sciences, Shenzhen University Health Science Centre, Shenzhen, China
| | - Bi-Rong Li
- Department of Anatomy & Histology, School of Basic Medical Sciences, Shenzhen University Health Science Centre, Shenzhen, China
| | - Ying-Xian Yu
- Department of Anatomy & Histology, School of Basic Medical Sciences, Shenzhen University Health Science Centre, Shenzhen, China
| | - Yansi Lyu
- Department of Dermatology, Shenzhen University General Hospital, Shenzhen, China
| | - Rikang Wang
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| |
Collapse
|
26
|
Ghaedamini S, Nikbakht M, Soleimani M. Assessment of Immuno-Histochemical Expression of MBD1 in Colorectal Adenocarcinoma and Its Correlations with Prognostic Factors. Middle East J Dig Dis 2020; 12:39-44. [PMID: 32082520 PMCID: PMC7023652 DOI: 10.15171/mejdd.2020.162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND
MBD1, the largest member of methyl binding domain family, has the most downregulated
mRNA expression and upregulated methylation levels in advanced colorectal cancer (CRC). In this
study, we evaluated the immune-histochemical expression of MBD1 in CRC and assessed its correlation
with clinicopathological features to study its prognostic value in CRC.
METHODS
A total of 60 samples of CRC, from patients who underwent surgical gastroenterology operations,
were randomly selected. The samples included one tumor-rich section per case and one adjacent
tumor-free section as a normal control for that case. Then, immunohistochemistry (ICH) was performed
for MBD1 protein on all samples and the expression of MBD1 was analyzed in cancerous and
normal samples. In the next step, the correlation between MBD1 and clinicopathological features
including age, sex, location of the tumor, grade, and stage were evaluated.
RESULTS
The expression of MBD1 protein had a significant downregulation in cancerous samples compared
with normal control samples. This downregulation increased corresponding to both grade and stage
of cancer. However, no correlation was seen between the expression of MBD1 and sex, age and
location of the tumor.
CONCLUSION
MBD1 protein may be considered as a protein marker in the detection of CRC and its progression.
Collapse
Affiliation(s)
- Sholeh Ghaedamini
- Department of Anatomical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehdi Nikbakht
- Department of Anatomical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mitra Soleimani
- Department of Anatomical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
27
|
Li LT, Wang X, Zhu WT, Qian GW, Pei DS, Zheng JN. Reciprocal Role Of DNA Methylation And Sp1 Binding In Ki-67 Gene Transcription. Cancer Manag Res 2019; 11:9749-9759. [PMID: 31819613 PMCID: PMC6874502 DOI: 10.2147/cmar.s213769] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 10/16/2019] [Indexed: 01/26/2023] Open
Abstract
Purpose DNA methylation plays major regulatory roles in gene transcription. Our previous studies confirmed that Ki-67 promoter is hypomethylated and Sp1 is a transcriptional activator of Ki-67 gene in cancer cells. However, whether Sp1-mediated transcriptional activation of Ki-67 is related to its methylation has not been studied yet. Materials and methods In this study, we confirmed that methylated CpG binding protein 2 (MBD2) binding to methylated DNA hindered the binding of Sp1 to Ki-67 promoter and then repressed Ki-67 transcription through chromatin immunoprecipitation (ChIP) and quantitative real-time PCR (qRT-PCR). Co-immunoprecipitation (Co-IP), ChIP, methylation-specific PCR (MS-PCR) and Western blot were utilized to analyze the effects of Sp1 binding to Ki-67 promoter on its methylation status. Results Less DNA methyltransferase 1 (DNMT1) bound to the Ki-67 promoter in MKN45 cells than in HK-2 cells. Histone acetyltransferase p300 that was recruited by Sp1 to Ki-67 promoter could attenuate the methylation level of Ki-67 promoter. Furthermore, higher expression of Sp1 and Ki-67 was related to the overall survival (OS), first progression (FP) and post-progression survival (PPS) in gastric cancer by scrutinizing bioinformatics datasets. Conclusion Taken together, our findings suggested that hypomethylation of Ki-67 promoter enhanced the binding of Sp1, which in turn maintained hypomethylation of promoter, leading to increase Ki-67 expression in cancer cells. Sp1 and Ki-67 could act promising prognostic biomarkers for clinical diagnosis and treatment of cancer.
Collapse
Affiliation(s)
- Lian-Tao Li
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Xun Wang
- Department of Interventional Radiology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Wen-Tao Zhu
- Department of Pathology, Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Guo-Wei Qian
- Department of Medical Oncology, Shanghai Sixth People's Hospital, Shanghai 200000, People's Republic of China
| | - Dong-Sheng Pei
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Department of Pathology, Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Jun-Nian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| |
Collapse
|
28
|
Giudice-Nairn P, Downs J, Wong K, Wilson D, Ta D, Gattas M, Amor D, Thompson E, Kirrali-Borri C, Ellaway C, Leonard H. The incidence, prevalence and clinical features of MECP2 duplication syndrome in Australian children. J Paediatr Child Health 2019; 55:1315-1322. [PMID: 30756435 DOI: 10.1111/jpc.14399] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 01/20/2019] [Indexed: 12/22/2022]
Abstract
AIM The aim of this study was to assess the incidence and prevalence of MECP2 duplication syndrome in Australian children and further define its phenotype. METHODS The Australian Paediatric Surveillance Unit was used to identify children with MECP2 duplication syndrome between June 2014 and November 2017. Reporting clinicians were invited to complete a questionnaire. Clinician data (n = 20) were supplemented with information from the International Rett Syndrome Phenotype Database and from caregivers (n = 7). Birth prevalence and diagnostic incidence were calculated. RESULTS The birth prevalence of MECP2 duplication syndrome in Australia was 0.65/100 000 for all live births and 1/100 000 for males. Diagnostic incidence was 0.07/100 000 person-years overall and 0.12/100 000 person-years for males. The median age at diagnosis was 23.5 months (range 0 months-13 years). A history of pneumonia was documented in three quarters of the clinical cases, half of whom had more than nine episodes. Cardiovascular abnormalities were reported in three cases. A clinical vignette is presented for one child who died due to severe idiopathic pulmonary hypertension. The majority (13/15) of males had inherited the duplication from their mothers, and two had an unbalanced translocation. CONCLUSIONS MECP2 duplication syndrome is a rare but important diagnosis in children because of the burden of respiratory illness and recurrence risk. Pulmonary hypertension is a rare life-threatening complication. Array comparative genomic hybridisation testing is recommended for children with undiagnosed intellectual disability or global developmental delay. Early cardiac assessment and ongoing monitoring is recommended for MECP2 duplication syndrome.
Collapse
Affiliation(s)
- Peter Giudice-Nairn
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Jenny Downs
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia.,School of Physiotherapy and Exercise Science, Curtin University, Perth, Western Australia, Australia
| | - Kingsley Wong
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Dylan Wilson
- Leading Steps Paediatric Clinic, Gold Coast, Queensland, Australia
| | - Daniel Ta
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | | | - David Amor
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth Thompson
- SA Clinical Genetics Service, Women's and Children's Hospital, Adelaide, South Australia, Australia.,Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Cathy Kirrali-Borri
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, Sydney, New South Wales, Australia
| | - Carolyn Ellaway
- Genetic Medicine, and Child and Adolescent Health, University of Sydney, Sydney, New South Wales, Australia
| | - Helen Leonard
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| |
Collapse
|
29
|
Bian E, Chen X, Xu Y, Ji X, Cheng M, Wang H, Fang Z, Zhao B. A central role for MeCP2 in the epigenetic repression of miR-200c during epithelial-to-mesenchymal transition of glioma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:366. [PMID: 31429770 PMCID: PMC6702741 DOI: 10.1186/s13046-019-1341-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023]
Abstract
Background The epithelial-to-mesenchymal transition (EMT) has been linked to the regulation of glioma progression. However, the underlying signaling mechanisms that regulate EMT are poorly understood. Methods Quantitative real-time PCR (RT-qPCR) and western blot were performed to detect the expression of MeCP2 in glioma tissues and cell lines. MeCP2 functions were tested with cell immunofluorescence staining and western blot. For in vivo experiments, mouse xenograft model was used to investigate the effects of MeCP2 on glioma. ChIP and Co-IP were used to detect the relationships among MeCP2, miR-200c and Suv39H1. Results In this study, we found that MeCP2 was frequently up-regulated in human glioma tissues and cell lines. MeCP2 knockdown remarkably induced cell epithelial phenotype and inhibited mesenchymal marker ZEB1 and ZEB2 in vitro and in vivo. In addition, MeCP2 in glioma tissues was negatively correlated with miR-200c expression, and miR-200c overexpression partially abrogated mesenchymal phenotype induced by MeCP2. More importantly, we showed that MeCP2 recruited H3K9 to the promoter of miR-200c by interacting with SUV39H1, resulting in EMT of glioma cells. Conclusions This study for the first time reveals MeCP2 as a novel regulator of EMT in glioma and suggest that MeCP2 inhibition may represent a promising therapeutic option for suppressing EMT in glioma. Electronic supplementary material The online version of this article (10.1186/s13046-019-1341-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Xueran Chen
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China
| | - Yadi Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Xinghu Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Meng Cheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Hongliang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Zhiyou Fang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China.
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China. .,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China.
| |
Collapse
|
30
|
Mahmood N, Rabbani SA. DNA Methylation Readers and Cancer: Mechanistic and Therapeutic Applications. Front Oncol 2019; 9:489. [PMID: 31245293 PMCID: PMC6579900 DOI: 10.3389/fonc.2019.00489] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/23/2019] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is a major epigenetic process that regulates chromatin structure which causes transcriptional activation or repression of genes in a context-dependent manner. In general, DNA methylation takes place when methyl groups are added to the appropriate bases on the genome by the action of "writer" molecules known as DNA methyltransferases. How these methylation marks are read and interpreted into different functionalities represents one of the main mechanisms through which the genes are switched "ON" or "OFF" and typically involves different types of "reader" proteins that can recognize and bind to the methylated regions. A tightly balanced regulation exists between the "writers" and "readers" in order to mediate normal cellular functions. However, alterations in normal methylation pattern is a typical hallmark of cancer which alters the way methylation marks are written, read and interpreted in different disease states. This unique characteristic of DNA methylation "readers" has identified them as attractive therapeutic targets. In this review, we describe the current state of knowledge on the different classes of DNA methylation "readers" identified thus far along with their normal biological functions, describe how they are dysregulated in cancer, and discuss the various anti-cancer therapies that are currently being developed and evaluated for targeting these proteins.
Collapse
Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| |
Collapse
|
31
|
Cofre J, Saalfeld K, Abdelhay E. Cancer as an Embryological Phenomenon and Its Developmental Pathways: A Hypothesis regarding the Contribution of the Noncanonical Wnt Pathway. ScientificWorldJournal 2019; 2019:4714781. [PMID: 30940992 PMCID: PMC6421044 DOI: 10.1155/2019/4714781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 12/18/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023] Open
Abstract
For gastrulation to occur in human embryos, a mechanism that simultaneously regulates many different processes, such as cell differentiation, proliferation, migration, and invasion, is required to consistently and effectively create a human being during embryonic morphogenesis. The striking similarities in the processes of cancer and gastrulation have prompted speculation regarding the developmental pathways involved in their regulation. One of the fundamental requirements for the developmental pathways in gastrulation and cancer is the ability to respond to environmental stimuli, and it has been proposed that the Kaiso and noncanonical Wnt pathways participate in the mechanisms regulating these developmental pathways. In particular, these pathways might also explain the notable differences in invasive capacity between cancers of endodermal and mesodermal origins and cancers of ectodermal origin. Nevertheless, the available information indicates that cancer is an abnormal state of adult human cells in which developmental pathways are reactivated in inappropriate temporal and spatial contexts.
Collapse
Affiliation(s)
- Jaime Cofre
- Laboratório de Embriologia Molecular e Câncer, Universidade Federal de Santa Catarina, Sala 313b, 88040-900 Florianópolis, SC, Brazil
| | - Kay Saalfeld
- Laboratório de Filogenia Animal, Universidade Federal de Santa Catarina, Brazil
| | - Eliana Abdelhay
- Divisão de Laboratórios do CEMO, Instituto Nacional do Câncer, Rio de Janeiro, Brazil
| |
Collapse
|
32
|
Young MA, May S, Damo A, Yoon YS, Hur MW, Swat W, Parry L. Epigenetic Regulation of Dlg1, via Kaiso, Alters Mitotic Spindle Polarity and Promotes Intestinal Tumorigenesis. Mol Cancer Res 2019; 17:686-696. [PMID: 30552232 DOI: 10.1158/1541-7786.mcr-18-0280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 11/16/2022]
Abstract
Both alterations to the epigenome and loss of polarity have been linked to cancer initiation, progression, and metastasis. It has previously been demonstrated that loss of the epigenetic reader protein Kaiso suppresses intestinal tumorigenesis in the Apc+/min mouse model, in which altered polarity plays a key role. Thus, we investigated the link between Kaiso deficiency, polarity, and suppression of intestinal tumorigenesis. We used Kaiso-deficient mice to conditionally delete Apc within the intestinal epithelia and demonstrated upregulation of the spindle polarity genes Dlg1 and Dlgap1. To understand the role of Dlg1, we generated Villin-creApc+/minDlg1flx/flx Kaiso-/y mice to analyze gene expression, survival, tumor burden, and spindle orientation. In vivo analysis of the Dlg1-deficient intestine revealed improper orientation of mitotic spindles and a decreased rate of cellular migration. Loss of Dlg1 decreased survival in Apc+/min mice, validating its role as a tumor suppressor in the intestine. Significantly, the increased survival of Apc+/minKaisoy/- mice was shown to be dependent on Dlg1 expression. Taken together, these data indicate that maintenance of spindle polarity in the intestinal crypt requires appropriate regulation of Dlg1 expression. As Dlg1 loss leads to incorrect spindle orientation and a delay in cells transiting the intestinal crypt. We propose that the delayed exit from the crypt increase the window in which spontaneous mutations can become fixed, producing a "tumor-permissive" environment, without an increase in mutation rate. IMPLICATIONS: Loss of mitotic spindle polarity delays the exit of cells from the intestinal crypt and promotes a tumorigenic environment.
Collapse
Affiliation(s)
- Madeleine A Young
- European Cancer Stem Cell Research Institute, Cardiff School of Biosciences, Cardiff University, Cathays, Cardiff, United Kingdom
| | - Stephanie May
- European Cancer Stem Cell Research Institute, Cardiff School of Biosciences, Cardiff University, Cathays, Cardiff, United Kingdom
| | - Angelos Damo
- European Cancer Stem Cell Research Institute, Cardiff School of Biosciences, Cardiff University, Cathays, Cardiff, United Kingdom
| | - Young So Yoon
- Department of Biochemistry and Molecular Biology, Yonsei University School of Medicine, Yonsei-Ro, Seodaemoon-Ku, Seoul, Republic of Korea
| | - Man-Wook Hur
- Department of Biochemistry and Molecular Biology, Yonsei University School of Medicine, Yonsei-Ro, Seodaemoon-Ku, Seoul, Republic of Korea
| | - Wojiech Swat
- Department of Pathology & Immunology, Washington University School of Medicine, Missouri
| | - Lee Parry
- European Cancer Stem Cell Research Institute, Cardiff School of Biosciences, Cardiff University, Cathays, Cardiff, United Kingdom.
| |
Collapse
|
33
|
de Melo FHM, Oliveira JS, Sartorelli VOB, Montor WR. Cancer Chemoprevention: Classic and Epigenetic Mechanisms Inhibiting Tumorigenesis. What Have We Learned So Far? Front Oncol 2018; 8:644. [PMID: 30627525 PMCID: PMC6309127 DOI: 10.3389/fonc.2018.00644] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/07/2018] [Indexed: 12/21/2022] Open
Abstract
Cancers derive from step by step processes which are differentiated by the progressively accumulated mutations. For some tumors there is a clear progressive advancement from benign lesions to malignancy and for these, preventive screening programs exist. In such cases having those benign lesions are a clear indicator of predisposition while for some other cases, familial patterns of cancer incidence and the identification of mutations are the main indicators of higher risk for having the disease. For patients identified as having predisposition, chemoprevention is a goal and in some cases a possibility. Chemoprevention is the use of any compound, either natural or synthetic that abrogates carcinogenesis or tumor progression, through different mechanisms, some of which have already been described. For example, the classic mechanisms may involve activation of free radical scavenging enzymes, control of chronic inflammation, and downregulation of specific signaling pathways. More recently, epigenetics allowed further understanding of the chemopreventive potential of several agents, such as sulforaphane, green tea derived compounds, resveratrol, isoflavones, and others which we exploit in this review article. Throughout the text we discuss the properties compounds should have in order to be classified as chemopreventive ones and the challenges in translational research in this area, as lots of the success achieved in vitro cannot be translated into the clinical settings, due to several different drawbacks, which include toxicity, cost, dose definition, patient adherence, and regimen of use.
Collapse
Affiliation(s)
| | - Julia Salles Oliveira
- Department of Physiological Sciences, Santa Casa de São Paulo School of Medical Sciences (FCMSCSP), São Paulo, Brazil
| | | | - Wagner Ricardo Montor
- Department of Physiological Sciences, Santa Casa de São Paulo School of Medical Sciences (FCMSCSP), São Paulo, Brazil
| |
Collapse
|
34
|
Hudson NO, Buck-Koehntop BA. Zinc Finger Readers of Methylated DNA. Molecules 2018; 23:E2555. [PMID: 30301273 PMCID: PMC6222495 DOI: 10.3390/molecules23102555] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/07/2023] Open
Abstract
DNA methylation is a prevalent epigenetic modification involved in regulating a number of essential cellular processes, including genomic accessibility and transcriptional outcomes. As such, aberrant alterations in global DNA methylation patterns have been associated with a growing number of disease conditions. Nevertheless, the full mechanisms by which DNA methylation information is interpreted and translated into genomic responses is not yet fully understood. Methyl-CpG binding proteins (MBPs) function as important mediators of this essential process by selectively reading DNA methylation signals and translating this information into down-stream cellular outcomes. The Cys₂His₂ zinc finger scaffold is one of the most abundant DNA binding motifs found within human transcription factors, yet only a few zinc finger containing proteins capable of conferring selectivity for mCpG over CpG sites have been characterized. This review summarizes our current structural understanding for the mechanisms by which the zinc finger MBPs evaluated to date read this essential epigenetic mark. Further, some of the biological implications for mCpG readout elicited by this family of MBPs are discussed.
Collapse
Affiliation(s)
- Nicholas O Hudson
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA.
| | | |
Collapse
|
35
|
Sarathy A, Athreya NB, Varshney LR, Leburton JP. Classification of Epigenetic Biomarkers with Atomically Thin Nanopores. J Phys Chem Lett 2018; 9:5718-5725. [PMID: 30226383 DOI: 10.1021/acs.jpclett.8b02200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We use the electronic properties of 2D solid-state nanopore materials to propose a versatile and generally applicable biosensor technology by using a combination of molecular dynamics, nanoscale device simulations, and statistical signal processing algorithms. As a case study, we explore the classification of three epigenetic biomarkers, the methyl-CpG binding domain 1 (MBD-1), MeCP2, and γ-cyclodextrin, attached to double-stranded DNA to identify regions of hyper- or hypomethylations by utilizing a matched filter. We assess the sensing ability of the nanopore device to identify the biomarkers based on their characteristic electronic current signatures. Such a matched filter-based classifier enables real-time identification of the biomarkers that can be easily implemented on chip. This integration of a sensor with signal processing architectures could pave the way toward the development of a multipurpose technology for early disease detection.
Collapse
|
36
|
Chromatin dynamics at the core of kidney fibrosis. Matrix Biol 2018; 68-69:194-229. [DOI: 10.1016/j.matbio.2018.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/16/2018] [Accepted: 02/17/2018] [Indexed: 02/06/2023]
|
37
|
May S, Owen H, Phesse TJ, Greenow KR, Jones G, Blackwood A, Cook PC, Towers C, Gallimore AM, Williams GT, Stürzl M, Britzen‐Laurent N, Sansom OJ, MacDonald AS, Bird AP, Clarke AR, Parry L. Mbd2 enables tumourigenesis within the intestine while preventing tumour-promoting inflammation. J Pathol 2018; 245:270-282. [PMID: 29603746 PMCID: PMC6032908 DOI: 10.1002/path.5074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 02/22/2018] [Accepted: 03/08/2018] [Indexed: 01/14/2023]
Abstract
Epigenetic regulation plays a key role in the link between inflammation and cancer. Here we examine Mbd2, which mediates epigenetic transcriptional silencing by binding to methylated DNA. In separate studies the Mbd2-/- mouse has been shown (1) to be resistant to intestinal tumourigenesis and (2) to have an enhanced inflammatory/immune response, observations that are inconsistent with the links between inflammation and cancer. To clarify its role in tumourigenesis and inflammation, we used constitutive and conditional models of Mbd2 deletion to explore its epithelial and non-epithelial roles in the intestine. Using a conditional model, we found that suppression of intestinal tumourigenesis is due primarily to the absence of Mbd2 within the epithelia. Next, we demonstrated, using the DSS colitis model, that non-epithelial roles of Mbd2 are key in preventing the transition from acute to tumour-promoting chronic inflammation. Combining models revealed that prior to inflammation the altered Mbd2-/- immune response plays a role in intestinal tumour suppression. However, following inflammation the intestine converts from tumour suppressive to tumour promoting. To summarise, in the intestine the normal function of Mbd2 is exploited by cancer cells to enable tumourigenesis, while in the immune system it plays a key role in preventing tumour-enabling inflammation. Which role is dominant depends on the inflammation status of the intestine. As environmental interactions within the intestine can alter DNA methylation patterns, we propose that Mbd2 plays a key role in determining whether these interactions are anti- or pro-tumourigenic and this makes it a useful new epigenetic model for inflammation-associated carcinogenesis. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Stephanie May
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Heather Owen
- Wellcome Trust Centre for Cell BiologyUniversity of Edinburgh, Michael Swann BuildingEdinburghUK
| | - Toby J Phesse
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Kirsty R Greenow
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Gareth‐Rhys Jones
- Manchester Collaborative Centre for Inflammation ResearchManchesterUK
| | - Adam Blackwood
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Peter C Cook
- Manchester Collaborative Centre for Inflammation ResearchManchesterUK
| | - Christopher Towers
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Awen M Gallimore
- Cardiff Institute of Infection and Immunity, Henry Wellcome BuildingCardiffUK
| | - Geraint T Williams
- Institute of Cancer and GeneticsCardiff University School of MedicineCardiffUK
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Department of SurgeryFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg and Universitätsklinikum ErlangenErlangenGermany
| | - Nathalie Britzen‐Laurent
- Division of Molecular and Experimental Surgery, Department of SurgeryFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg and Universitätsklinikum ErlangenErlangenGermany
| | | | | | - Adrian P Bird
- Wellcome Trust Centre for Cell BiologyUniversity of Edinburgh, Michael Swann BuildingEdinburghUK
| | - Alan R Clarke
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Lee Parry
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| |
Collapse
|
38
|
Combined HAT/EZH2 modulation leads to cancer-selective cell death. Oncotarget 2018; 9:25630-25646. [PMID: 29876013 PMCID: PMC5986654 DOI: 10.18632/oncotarget.25428] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/02/2018] [Indexed: 12/20/2022] Open
Abstract
Epigenetic alterations have been associated with both pathogenesis and progression of cancer. By screening of library compounds, we identified a novel hybrid epi-drug MC2884, a HAT/EZH2 inhibitor, able to induce bona fide cancer-selective cell death in both solid and hematological cancers in vitro, ex vivo and in vivo xenograft models. Anticancer action was due to an epigenome modulation by H3K27me3, H3K27ac, H3K9/14ac decrease, and to caspase-dependent apoptosis induction. MC2884 triggered mitochondrial pathway apoptosis by up-regulation of cleaved-BID, and strong down-regulation of BCL2. Even aggressive models of cancer, such as p53-/- or TET2-/- cells, responded to MC2884, suggesting MC2884 therapeutic potential also for the therapy of TP53 or TET2-deficient human cancers. MC2884 induced massive apoptosis in ex vivo human primary leukemia blasts with poor prognosis in vivo, by targeting BCL2 expression. MC2884-treatment reduced acetylation of the BCL2 promoter at higher level than combined p300 and EZH2 inhibition. This suggests a key role for BCL-2 reduction in potentiating responsiveness, also in combination therapy with BCL2 inhibitors. Finally, we identified both the mechanism of MC2884 action as well as a potential therapeutic scheme of its use. Altogether, this provides proof of concept for the use of epi-drugs coupled with epigenome analyses to 'personalize' precision medicine.
Collapse
|
39
|
Sharma K, Singh J, Frost EE, Pillai PP. MeCP2 overexpression inhibits proliferation, migration and invasion of C6 glioma by modulating ERK signaling and gene expression. Neurosci Lett 2018. [DOI: 10.1016/j.neulet.2018.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
40
|
Hardwick JS, Lane AN, Brown T. Epigenetic Modifications of Cytosine: Biophysical Properties, Regulation, and Function in Mammalian DNA. Bioessays 2018; 40. [DOI: 10.1002/bies.201700199] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/13/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Jack S. Hardwick
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew N. Lane
- Department of Toxicology and Cancer Biology; University of Kentucky; 789 S. Limestone St. Lexington KY 40536 USA
| | - Tom Brown
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| |
Collapse
|
41
|
Abstract
The role of DNA methylation in brain development is an intense area of research because the brain has particularly high levels of CpG and mutations in many of the proteins involved in the establishment, maintenance, interpretation, and removal of DNA methylation impact brain development and/or function. These include DNA methyltransferase (DNMT), Ten-Eleven Translocation (TET), and Methyl-CpG binding proteins (MBPs). Recent advances in sequencing breadth and depth as well the detection of different forms of methylation have greatly expanded our understanding of the diversity of DNA methylation in the brain. The contributions of DNA methylation and associated proteins to embryonic and adult neurogenesis will be examined. Particular attention will be given to the impact on adult hippocampal neurogenesis (AHN), which is a key mechanism contributing to brain plasticity, learning, memory and mood regulation. DNA methylation influences multiple aspects of neurogenesis from stem cell maintenance and proliferation, fate specification, neuronal differentiation and maturation, and synaptogenesis. In addition, DNA methylation during neurogenesis has been shown to be responsive to many extrinsic signals, both under normal conditions and during disease and injury. Finally, crosstalk between DNA methylation, Methyl-DNA binding domain (MBD) proteins such as MeCP2 and MBD1 and histone modifying complexes is used as an example to illustrate the extensive interconnection between these epigenetic regulatory systems.
Collapse
Affiliation(s)
- Emily M Jobe
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Xinyu Zhao
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
42
|
Methyl-CpG-Binding Protein MBD1 Regulates Neuronal Lineage Commitment through Maintaining Adult Neural Stem Cell Identity. J Neurosci 2017; 37:523-536. [PMID: 28100736 DOI: 10.1523/jneurosci.1075-16.2016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 10/31/2016] [Accepted: 11/22/2016] [Indexed: 01/09/2023] Open
Abstract
Methyl-CpG-binding domain 1 (MBD1) belongs to a family of methyl-CpG-binding proteins that are epigenetic "readers" linking DNA methylation to transcriptional regulation. MBD1 is expressed in neural stem cells residing in the dentate gyrus of the adult hippocampus (aNSCs) and MBD1 deficiency leads to reduced neuronal differentiation, impaired neurogenesis, learning deficits, and autism-like behaviors in mice; however, the precise function of MBD1 in aNSCs remains unexplored. Here, we show that MBD1 is important for maintaining the integrity and stemness of NSCs, which is critical for their ability to generate neurons. MBD1 deficiency leads to the accumulation of undifferentiated NSCs and impaired transition into the neuronal lineage. Transcriptome analysis of neural stem and progenitor cells isolated directly from the dentate gyrus of MBD1 mutant (KO) and WT mice showed that gene sets related to cell differentiation, particularly astrocyte lineage genes, were upregulated in KO cells. We further demonstrated that, in NSCs, MBD1 binds and represses directly specific genes associated with differentiation. Our results suggest that MBD1 maintains the multipotency of NSCs by restraining the onset of differentiation genes and that untimely expression of these genes in MBD1-deficient stem cells may interfere with normal cell lineage commitment and cause the accumulation of undifferentiated cells. Our data reveal a novel role for MBD1 in stem cell maintenance and provide insight into how epigenetic regulation contributes to adult neurogenesis and the potential impact of its dysregulation. SIGNIFICANCE STATEMENT Adult neural stem cells (aNSCs) in the hippocampus self-renew and generate neurons throughout life. We show that methyl-CpG-binding domain 1 (MBD1), a DNA methylation "reader," is important for maintaining the integrity of NSCs, which is critical for their neurogenic potency. Our data reveal a novel role for MBD1 in stem cell maintenance and provide insight into how epigenetic regulation preserves the multipotency of stem cells for subsequent differentiation.
Collapse
|
43
|
Zhao J, Fan YC, Chen LY, Gao S, Li F, Wang K. Alteration of methyl-CpG binding domain family in patients with chronic hepatitis B. Clin Res Hepatol Gastroenterol 2017; 41:272-283. [PMID: 28065745 DOI: 10.1016/j.clinre.2016.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/25/2016] [Accepted: 11/30/2016] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND OBJECTIVE Epigenetics contributes to the outcome of chronic hepatitis B virus (HBV) infection. However, the role of methyl-CpG binding domain (MBD) family in the natural history of chronic hepatitis B (CHB) has not been demonstrated. It is aimed to investigate the dynamic expression of MBD family and assess the potential association of MBD family in the progression of CHB. METHODS Quantitative real-time polymerase chain reaction (RT-PCR) was used to determine the mRNA levels of MBD family in peripheral blood mononuclear cells (PBMCs) from 223 patients with CHB as training cohort, 146 patients with CHB as validation cohort [immune-tolerant (IT), immune clearance (IC), non/low-replicative (LR) and HBeAg negative hepatitis (ENH)], and 14 healthy controls (HCs). RESULTS The mRNA levels of MeCP2, MBD1, MBD2 and MBD4 were upregulated in patients with CHB compared with HCs. MBD1 mRNA was highest expressed in IT phase than other phases. The optimal cut-off value for MBD1 mRNA in discriminating IT phase from CHB was 0.0305 in both training and validation cohorts. Both MBD2 and MBD4 mRNA were highest expressed in IC phase than other phases. Moreover, the optimal cut-off values for MBD2 and MBD4 mRNA in discriminating IC phase from CHB were 0.0069 and 0.00099. Furthermore, MBD2 plus MBD4 performed better than MBD2 alone for discriminating IC phase from CHB in training (area under the curve of receiver operating characteristics [AUC] 0.736 vs. 0.671, P=0.0225) and validation cohorts (AUC 0.754 vs. 0.665, P=0.004). MeCP2 mRNA was highest expressed in patients with S3+S4. MeCP2 mRNA has higher AUC than APRI score for predicting S3+S4 and S4 in fibrosis. CONCLUSIONS MBD family is involved in the pathogenesis of CHB and is correlated with disease progression, suggesting the value in evaluating disease severity.
Collapse
Affiliation(s)
- Jing Zhao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Institute of Hepatology, Shandong University, Jinan 250012, China
| | - Long-Yan Chen
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Institute of Hepatology, Shandong University, Jinan 250012, China
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Institute of Hepatology, Shandong University, Jinan 250012, China
| | - Feng Li
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Institute of Hepatology, Shandong University, Jinan 250012, China.
| |
Collapse
|
44
|
Sato T, Issa JPJ, Kropf P. DNA Hypomethylating Drugs in Cancer Therapy. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026948. [PMID: 28159832 DOI: 10.1101/cshperspect.a026948] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aberrant DNA methylation is a critically important modification in cancer cells, which, through promoter and enhancer DNA methylation changes, use this mechanism to activate oncogenes and silence of tumor-suppressor genes. Targeting DNA methylation in cancer using DNA hypomethylating drugs reprograms tumor cells to a more normal-like state by affecting multiple pathways, and also sensitizes these cells to chemotherapy and immunotherapy. The first generation hypomethylating drugs azacitidine and decitabine are routinely used for the treatment of myeloid leukemias and a next-generation drug (guadecitabine) is currently in clinical trials. This review will summarize preclinical and clinical data on DNA hypomethylating drugs as a cancer therapy.
Collapse
Affiliation(s)
- Takahiro Sato
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140.,Fox Chase Cancer Center, Temple Health, Philadelphia, Pennsylvania 19111
| | - Patricia Kropf
- Fox Chase Cancer Center, Temple Health, Philadelphia, Pennsylvania 19111
| |
Collapse
|
45
|
Ratovitski EA. Anticancer Natural Compounds as Epigenetic Modulators of Gene Expression. Curr Genomics 2017; 18:175-205. [PMID: 28367075 PMCID: PMC5345332 DOI: 10.2174/1389202917666160803165229] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/24/2015] [Accepted: 11/29/2015] [Indexed: 11/30/2022] Open
Abstract
Accumulating evidence shows that hallmarks of cancer include: "genetic and epigenetic alterations leading to inactivation of cancer suppressors, overexpression of oncogenes, deregulation of intracellular signaling cascades, alterations of cancer cell metabolism, failure to undergo cancer cell death, induction of epithelial to mesenchymal transition, invasiveness, metastasis, deregulation of immune response and changes in cancer microenvironment, which underpin cancer development". Natural compounds as bioactive ingredients isolated from natural sources (plants, fungi, marine life forms) have revolutionized the field of anticancer therapeutics and rapid developments in preclinical studies are encouraging. Natural compounds could affect the epigenetic molecular mechanisms that modulate gene expression, as well as DNA damage and repair mechanisms. The current review will describe the latest achievements in using naturally produced compounds targeting epigenetic regulators and modulators of gene transcription in vitro and in vivo to generate novel anticancer therapeutics.
Collapse
Affiliation(s)
- Edward A. Ratovitski
- Head and Neck Cancer Research Division, Department of Otolaryngology/Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
| |
Collapse
|
46
|
Özbayer C, Üstüner D, Ak GA, Saydam F, Metintaş M, Değirmenci İ. Akciğer Kanserli Hastalarda Plazma DNA Metiltransferaz ve Metil-CpG’ye Bağlanan Protein Seviyelerinin Değerlendirilmesi. DICLE MEDICAL JOURNAL 2017. [DOI: 10.5798/dicletip.298604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
47
|
Menga A, Palmieri EM, Cianciulli A, Infantino V, Mazzone M, Scilimati A, Palmieri F, Castegna A, Iacobazzi V. SLC25A26 overexpression impairs cell function via mtDNA hypermethylation and rewiring of methyl metabolism. FEBS J 2017; 284:967-984. [PMID: 28118529 DOI: 10.1111/febs.14028] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 12/01/2016] [Accepted: 01/20/2017] [Indexed: 12/22/2022]
Abstract
Cancer cells down-regulate different genes to give them a selective advantage in invasiveness and/or metastasis. The SLC25A26 gene encodes the mitochondrial carrier that catalyzes the import of S-adenosylmethionine (SAM) into the mitochondrial matrix, required for mitochondrial methylation processes, and is down-regulated in cervical cancer cells. In this study we show that SLC25A26 is down-regulated due to gene promoter hypermethylation, as a mechanism to promote cell survival and proliferation. Furthermore, overexpression of SLC25A26 in CaSki cells increases mitochondrial SAM availability and promotes hypermethylation of mitochondrial DNA, leading to decreased expression of key respiratory complex subunits, reduction of mitochondrial ATP and release of cytochrome c. In addition, increased SAM transport into mitochondria leads to impairment of the methionine cycle with accumulation of homocysteine at the expense of glutathione, which is strongly reduced. All these events concur to arrest the cell cycle in the S phase, induce apoptosis and enhance chemosensitivity of SAM carrier-overexpressing CaSki cells to cisplatin.
Collapse
Affiliation(s)
- Alessio Menga
- National Cancer Research Center, Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Erika M Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari 'Aldo Moro', Italy
| | - Antonia Cianciulli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari 'Aldo Moro', Italy
| | | | - Massimiliano Mazzone
- Laboratory of Molecular Oncology and Angiogenesis, Department of Oncology, Vesalius Research Center, KU Leuven, Belgium
| | | | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari 'Aldo Moro', Italy
| | - Alessandra Castegna
- National Cancer Research Center, Istituto Tumori 'Giovanni Paolo II', Bari, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari 'Aldo Moro', Italy
| | - Vito Iacobazzi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari 'Aldo Moro', Italy
| |
Collapse
|
48
|
Sweet TJ, Ting AH. WOMEN IN CANCER THEMATIC REVIEW: Diverse functions of DNA methylation: implications for prostate cancer and beyond. Endocr Relat Cancer 2016; 23:T169-T178. [PMID: 27605446 DOI: 10.1530/erc-16-0306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 12/31/2022]
Abstract
Prostate cancer is one of the most common malignancies in men worldwide. Current clinical screening ensures that most prostate cancers are diagnosed while still organ confined, but disease outcome is highly variable. Thus, a better understanding of the molecular features contributing to prostate cancer aggressiveness is being sought. For many cancers, aberrant genome-wide patterns of cytosine DNA methylation in CpG dinucleotides distinguish tumor from normal tissue and contribute to disease progression by altering the transcriptome. In prostate cancer, recent genomic studies identified cancer and high grade-specific differential DNA methylation in gene promoters, gene bodies, gene 3' ends and at distal regulatory elements. Using examples from developmental and disease systems, we will discuss how DNA methylation in each of these genomic contexts can contribute to transcriptome diversity by modulating transcription initiation, alternative transcription start site selection, alternative pre-mRNA splicing and alternative polyadenylation. Alternative transcripts from the same gene often exhibit altered protein-coding potential, translatability, stability and/or localization. All of these can have functional consequences in cells. In future work, it will be important to determine if DNA methylation abnormalities in prostate cancer modify the transcriptome through some or all of these mechanisms and if these DNA methylation-mediated transcriptome alterations impact prostate tumorigenesis and aggressiveness.
Collapse
Affiliation(s)
- Thomas J Sweet
- Genomic Medicine InstituteLerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Angela H Ting
- Genomic Medicine InstituteLerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| |
Collapse
|
49
|
Brotons A, Sanjuán I, Foster CW, Banks CE, Vidal-Iglesias FJ, Solla-Gullón J, Iniesta J. A Facile and Cost-effective Electroanalytical Strategy for the Quantification of Deoxyguanosine and Deoxyadenosine in Oligonucleotides Using Screen-printed Graphite Electrodes. ELECTROANAL 2016. [DOI: 10.1002/elan.201600272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ariadna Brotons
- Institute of Electrochemistry; University of Alicante; 03690 San Vicente del Raspeig Alicante Spain
| | - Ignacio Sanjuán
- Institute of Electrochemistry; University of Alicante; 03690 San Vicente del Raspeig Alicante Spain
| | - Christopher W. Foster
- Faculty of Science and Engineering; School of Science and the Environment; Division of Chemistry and Environmental Science; Manchester Metropolitan University; Chester Street Manchester M1 5GD UK
| | - Craig E. Banks
- Faculty of Science and Engineering; School of Science and the Environment; Division of Chemistry and Environmental Science; Manchester Metropolitan University; Chester Street Manchester M1 5GD UK
| | | | - José Solla-Gullón
- Institute of Electrochemistry; University of Alicante; 03690 San Vicente del Raspeig Alicante Spain
| | - Jesús Iniesta
- Institute of Electrochemistry; University of Alicante; 03690 San Vicente del Raspeig Alicante Spain
- Physical Chemistry Department; University of Alicante; 03690 San Vicente del Raspeig Alicante Spain
| |
Collapse
|
50
|
Wood KH, Zhou Z. Emerging Molecular and Biological Functions of MBD2, a Reader of DNA Methylation. Front Genet 2016; 7:93. [PMID: 27303433 PMCID: PMC4880565 DOI: 10.3389/fgene.2016.00093] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/10/2016] [Indexed: 01/25/2023] Open
Abstract
DNA methylation is an epigenetic mark that is essential for many biological processes and is linked to diseases such as cancer. Methylation is usually associated with transcriptional silencing, but new research has challenged this model. Both transcriptional activation and repression have recently been found to be associated with DNA methylation in a context-specific manner. How DNA methylation patterns are interpreted into different functional output remains poorly understood. One mechanism involves the protein ‘readers’ of methylation, which includes the methyl-CpG binding domain (MBD) family of proteins. This review examines the molecular and biological functions of MBD2, which binds to CpG methylation and is an integral part of the nucleosome remodeling and histone deacetylation (NuRD) complex. MBD2 has been linked to immune system function and tumorigenesis, yet little is known about its functions in vivo. Recent studies have found the MBD2 protein is ubiquitously expressed, with relatively high levels in the lung, liver, and colon. Mbd2 null mice surprisingly show relatively mild phenotypes compared to mice with loss of function of other MBD proteins. This evidence has previously been interpreted as functional redundancy between the MBD proteins. Here, we examine and contextualize research that suggests MBD2 has unique properties and functions among the MBD proteins. These functions translate to recently described roles in the development and differentiation of multiple cell lineages, including pluripotent stem cells and various cell types of the immune system, as well as in tumorigenesis. We also consider possible models for the dynamic interactions between MBD2 and NuRD in different tissues in vivo. The functions of MBD2 may have direct therapeutic implications for several areas of human disease, including autoimmune conditions and cancer, in addition to providing insights into the actions of NuRD and chromatin regulation.
Collapse
Affiliation(s)
- Kathleen H Wood
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Zhaolan Zhou
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| |
Collapse
|