1
|
Ye C, Zhao Z, Lai P, Chen C, Jian F, Liang H, Guo Q. Strategies for the detection of site-specific DNA methylation and its application, opportunities and challenges in the field of electrochemical biosensors. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5496-5508. [PMID: 39051422 DOI: 10.1039/d4ay00779d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in various biological processes. Aberrant DNA methylation is closely associated with the onset of diseases, and the specific localization of methylation sites in the genome offers further insight into the connection between methylation and diseases. Currently, there are numerous methods available for site-specific methylation detection. Electrochemical biosensors have garnered significant attention due to their distinct advantages, such as rapidity, simplicity, high sensitivity, low cost, and the potential for miniaturization. In this paper, we present a systematic review of the primary sensing strategies utilized in the past decade for analyzing site-specific methylation and their applications in electrochemical sensors, from a novel perspective focusing on the localization analysis of site-specific methylation. These strategies include bisulfite treatment, restriction endonuclease treatment, other sensing strategies, and deamination without direct bisulfite treatment. We hope that this paper can offer ideas and references for establishing site-specific methylation electrochemical analysis in clinical practice.
Collapse
Affiliation(s)
- Chenliu Ye
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Zhibin Zhao
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Penghui Lai
- The Second Hospital of Longyan, Longyan 364000, China
| | - Chunmei Chen
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Fumei Jian
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Haiying Liang
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Qiongying Guo
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| |
Collapse
|
2
|
Dar MS, Mensah IK, He M, McGovern S, Sohal IS, Whitlock HC, Bippus NE, Ceminsky M, Emerson ML, Tan HJ, Hall MC, Gowher H. Dnmt3bas coordinates transcriptional induction and alternative exon inclusion to promote catalytically active Dnmt3b expression. Cell Rep 2023; 42:112587. [PMID: 37294637 PMCID: PMC10592478 DOI: 10.1016/j.celrep.2023.112587] [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: 06/03/2022] [Revised: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 06/11/2023] Open
Abstract
Embryonic expression of DNMT3B is critical for establishing de novo DNA methylation. This study uncovers the mechanism through which the promoter-associated long non-coding RNA (lncRNA) Dnmt3bas controls the induction and alternative splicing of Dnmt3b during embryonic stem cell (ESC) differentiation. Dnmt3bas recruits the PRC2 (polycomb repressive complex 2) at cis-regulatory elements of the Dnmt3b gene expressed at a basal level. Correspondingly, Dnmt3bas knockdown enhances Dnmt3b transcriptional induction, whereas overexpression of Dnmt3bas dampens it. Dnmt3b induction coincides with exon inclusion, switching the predominant isoform from the inactive Dnmt3b6 to the active Dnmt3b1. Intriguingly, overexpressing Dnmt3bas further enhances the Dnmt3b1:Dnmt3b6 ratio, attributed to its interaction with hnRNPL (heterogeneous nuclear ribonucleoprotein L), a splicing factor that promotes exon inclusion. Our data suggest that Dnmt3bas coordinates alternative splicing and transcriptional induction of Dnmt3b by facilitating the hnRNPL and RNA polymerase II (RNA Pol II) interaction at the Dnmt3b promoter. This dual mechanism precisely regulates the expression of catalytically active DNMT3B, ensuring fidelity and specificity of de novo DNA methylation.
Collapse
Affiliation(s)
- Mohd Saleem Dar
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ikjot Singh Sohal
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Nina Elise Bippus
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Madison Ceminsky
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Martin L Emerson
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Hern J Tan
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
3
|
Das DN, Ravi N. Influences of polycyclic aromatic hydrocarbon on the epigenome toxicity and its applicability in human health risk assessment. ENVIRONMENTAL RESEARCH 2022; 213:113677. [PMID: 35714684 DOI: 10.1016/j.envres.2022.113677] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The existence of polycyclic aromatic hydrocarbons (PAHs) in ambient air is an escalating concern worldwide because of their ability to cause cancer and induce permanent changes in the genetic material. Growing evidence implies that during early life-sensitive stages, the risk of progression of acute and chronic diseases depends on epigenetic changes initiated by the influence of environmental cues. Several reports deciphered the relationship between exposure to environmental chemicals and epigenetics, and have known toxicants that alter the epigenetic states. Amongst PAHs, benzo[a]pyrene (B[a]P) is accepted as a group 1 cancer-causing agent by the International Agency for the Research on Cancer (IARC). B[a]P is a well-studied pro-carcinogen that is metabolically activated by the aryl hydrocarbon receptor (AhR)/cytochrome P450 pathway. Cytochrome P450 plays a pivotal role in the stimulation step, which is essential for DNA adduct formation. Accruing evidence suggests that epigenetic alterations assume a fundamental part in PAH-promoted carcinogenesis. This interaction between PAHs and epigenetic factors results in an altered profile of these marks, globally and locus-specific. Some of the epigenetic changes due to exposure to PAHs lead to increased disease susceptibility and progression. It is well understood that exposure to environmental carcinogens, such as PAH triggers disease pathways through changes in the genome. Several evidence reported due to the epigenome-wide association studies, that early life adverse environmental events may trigger widespread and persistent variations in transcriptional profiling. Moreover, these variations respond to DNA damage and/or a consequence of epigenetic modifications that need further investigation. Growing evidence has associated PAHs with epigenetic variations involving alterations in DNA methylation, histone modification, and micro RNA (miRNA) regulation. Epigenetic alterations to PAH exposure were related to chronic diseases, such as pulmonary disease, cardiovascular disease, endocrine disruptor, nervous system disorder, and cancer. This hormetic response gives a novel perception concerning the toxicity of PAHs and the biological reaction that may be a distinct reliance on exposure. This review sheds light on understanding the latest evidence about how PAHs can alter epigenetic patterns and human health. In conclusion, as several epigenetic change mechanisms remain unclear yet, further analyses derived from PAHs exposure must be performed to find new targets and disease biomarkers. In spite of the current limitations, numerous evidence supports the perception that epigenetics grips substantial potential for advancing our knowledge about the molecular mechanisms of environmental toxicants, also for predicting health-associated risks due to environmental circumstances exposure and individual susceptibility.
Collapse
Affiliation(s)
- Durgesh Nandini Das
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Nathan Ravi
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, 63110, USA; Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA; Institute for Public Health, Washington University in St. Louis, St. Louis, MO, 63110, USA; Veterans Affairs St. Louis Hospital, St. Louis, MO, 63106, USA.
| |
Collapse
|
4
|
Kim WR, Park EG, Lee YJ, Bae WH, Lee DH, Kim HS. Integration of TE Induces Cancer Specific Alternative Splicing Events. Int J Mol Sci 2022; 23:10918. [PMID: 36142830 PMCID: PMC9502224 DOI: 10.3390/ijms231810918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing of messenger RNA (mRNA) precursors contributes to genetic diversity by generating structurally and functionally distinct transcripts. In a disease state, alternative splicing promotes incidence and development of several cancer types through regulation of cancer-related biological processes. Transposable elements (TEs), having the genetic ability to jump to other regions of the genome, can bring about alternative splicing events in cancer. TEs can integrate into the genome, mostly in the intronic regions, and induce cancer-specific alternative splicing by adjusting various mechanisms, such as exonization, providing splicing donor/acceptor sites, alternative regulatory sequences or stop codons, and driving exon disruption or epigenetic regulation. Moreover, TEs can produce microRNAs (miRNAs) that control the proportion of transcripts by repressing translation or stimulating the degradation of transcripts at the post-transcriptional level. Notably, TE insertion creates a cancer-friendly environment by controlling the overall process of gene expression before and after transcription in cancer cells. This review emphasizes the correlative interaction between alternative splicing by TE integration and cancer-associated biological processes, suggesting a macroscopic mechanism controlling alternative splicing by TE insertion in cancer.
Collapse
Affiliation(s)
- Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| |
Collapse
|
5
|
Kasyanenko N, Qiushi Z, Bakulev V, Sokolov P, Yakovlev K. DNA Conformational Changes Induced by Its Interaction with Binuclear Platinum Complexes in Solution Indicate the Molecular Mechanism of Platinum Binding. Polymers (Basel) 2022; 14:polym14102044. [PMID: 35631926 PMCID: PMC9143540 DOI: 10.3390/polym14102044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 02/06/2023] Open
Abstract
Platinum anticancer drugs inhibit the division of cancer cells through a DNA binding mechanism. The bimetallic platinum compounds have a possibility for blocking DNA replication via the cross-linking of DNA functional groups at different distances. Many compounds with metals of the platinum group have been tested for possible antitumor activity. The main target of their biological action is a DNA molecule. A combined approach to the study of the interaction of DNA with biologically active compounds of this type is proposed. The capabilities of various methods (hydrodynamic, spectral, microscopy) in obtaining information on the type of binding of coordination compounds to DNA are compared. The analysis of DNA binding with platinum binuclear compounds containing pyrazine, tetrazole, 5- methyltetrazole, 3-propanediamine as bridging ligands in a solution was carried out with the methods of circular dichroism (CD), luminescent spectroscopy (LS), low gradient viscometry (LGV), flow birefringence (FB) and atomic force microscopy (AFM). The competitive binding of different platinum compounds to DNA and the analysis of platinum attachment to DNA after protonation of its nitrogen bases simply indicates the involvement of N7 guanine in binding. Fluorescent dye DAPI was also used to recognize the location of platinum compounds in DNA grooves. DNA conformational changes recorded by variations in persistent length, polyelectrolyte swelling, DNA secondary structure, and its stability clarify the molecular mechanism of the biological activity of platinum compounds.
Collapse
Affiliation(s)
- Nina Kasyanenko
- Department of Molecular Biophysics and Polymer Physics, Saint Petersburg State University, 7/9 Universitetskaya emb., 199034 St. Petersburg, Russia; (Z.Q.); (V.B.); (P.S.)
- Correspondence:
| | - Zhang Qiushi
- Department of Molecular Biophysics and Polymer Physics, Saint Petersburg State University, 7/9 Universitetskaya emb., 199034 St. Petersburg, Russia; (Z.Q.); (V.B.); (P.S.)
| | - Vladimir Bakulev
- Department of Molecular Biophysics and Polymer Physics, Saint Petersburg State University, 7/9 Universitetskaya emb., 199034 St. Petersburg, Russia; (Z.Q.); (V.B.); (P.S.)
| | - Petr Sokolov
- Department of Molecular Biophysics and Polymer Physics, Saint Petersburg State University, 7/9 Universitetskaya emb., 199034 St. Petersburg, Russia; (Z.Q.); (V.B.); (P.S.)
| | - Konstantin Yakovlev
- Department of Analytical Chemistry, Saint Petersburg State Chemical-Pharmaceutical Academy, 14, Prof. Popov str., 197376 St. Petersburg, Russia;
| |
Collapse
|
6
|
Paredes-Céspedes DM, Bernal-Hernández YY, Herrera-Moreno JF, Rojas-García AE, Medina-Díaz IM, González-Arias CA, Barrón-Vivanco BS. Methylation patterns of the CDKN2B and CDKN2A genes in an indigenous population exposed to pesticides. Hum Exp Toxicol 2022; 41:9603271211063161. [DOI: 10.1177/09603271211063161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The INK4 -ARF locus includes the CDKN2B and CDKN2A genes and is functionally relevant in the regulation of both cell proliferation and senescence. Studies have reported modifications of DNA methylation in this locus by exposure to environmental contaminants including pesticides; however, until now, specific methylation profiles have not been reported in genetically conserved populations exposed to occupational pesticides. The aim of this study was to determine the methylation profiles of the CDKN2B and CDKN2A genes in a genetically conserved population exposed to pesticides. A cross-sectional and analytical study was carried out in 190 Huichol indigenous persons. Information related to pesticide exposure, diet and other variables were obtained through the use of a structured questionnaire. Blood and urine samples were collected for methylation test and dialkylphosphates (DAP) determination, respectively. DNA methylation was measured by the pyrosequencing of bisulfite-treated DNA and DAP concentrations by gas chromatography-tandem mass spectrometry (GC/MS). The most frequent metabolite in the population was dimethylthiophosphate. The farmer group presented a higher methylation percentage of CDKN2B than the non-farmer group, but no differences in CDKN2A were observed between groups. A positive correlation between methylation of CpG site 3 of CDKN2B and time working in the field was observed in the farmer group. An association between methylation percentage of CDKN2B and age was also observed in the non-farmer group. These results suggest that pesticide exposure and exposure time in Huichol indigenous individuals could modify the methylation pattern of the CDKN2B gene.
Collapse
Affiliation(s)
- Diana M Paredes-Céspedes
- Posgrado en Ciencias Biológico Agropecuarias, Unidad Académica de Agricultura, Universidad Autónoma de Nayarit, Xalisco, Nayarit, México
| | - Yael Yvette Bernal-Hernández
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Tepic, Nayarit, México
| | - José Francisco Herrera-Moreno
- Posgrado en Ciencias Biológico Agropecuarias, Unidad Académica de Agricultura, Universidad Autónoma de Nayarit, Xalisco, Nayarit, México
| | - Aurora Elizabeth Rojas-García
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Tepic, Nayarit, México
| | - Irma Martha Medina-Díaz
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Tepic, Nayarit, México
| | - Cyndia A González-Arias
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Tepic, Nayarit, México
| | - Briscia Socorro Barrón-Vivanco
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Tepic, Nayarit, México
| |
Collapse
|
7
|
Li M, Sun X, Yao H, Chen W, Zhang F, Gao S, Zou X, Chen J, Qiu S, Wei H, Hu Z, Chen W. Genomic methylation variations predict the susceptibility of six chemotherapy related adverse effects and cancer development for Chinese colorectal cancer patients. Toxicol Appl Pharmacol 2021; 427:115657. [PMID: 34332992 DOI: 10.1016/j.taap.2021.115657] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/08/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) remains a major concern with high morbidity and mortality worldwide. Despite the positive influence of chemotherapy on the decline in CRC mortality, the negative influence of chemotherapy-related adverse effects (CRAEs) caused by capecitabine (Cap) remains a challenging problem. DNA methylation alteration plays a pivotal role in gene expression regulation. Here, we aimed to screen reliable and novel biomarkers for CRC diagnosis and CRAE prediction using the advanced Illumina Infinium MethylationEPIC (850 K) BeadChip. Paired tumor and normal tissues from 21 Chinese CRC patients who received Cap-based adjuvant chemotherapy were analyzed. CRC-related methylation was characterized by hypermethylated promoter islands and hypomethylated intragenic openseas; CRAE-related methylation was characterized by hyper- (or hypo-) methylated intragenic (or intergenic) regions. Based on three types of methylation profiles (differentially methylated probes, differentially methylated regions, and gene-function-differentially methylated regions), pathway enrichment analyses revealed that CRC-related genes were significantly enriched in the neuronal system, metabolism of RNA, and extracellular matrix organization; CRAE-related genes were abundantly enriched in pathways controlling regeneration functions and immune response. Finally, based on genes within the mostly related pathways and LASSO logistic regression selection, the integrated-methylation-marker systems developed here demonstrated high discriminative accuracy in both CRC diagnosis (AUROC = 1) and CRAE prediction (AUROC = 0.817-1). In conclusion, we conducted a comprehensive DNA methylation analysis of CRC patients with chemotherapy, which provided new insights into the formation of CRC and CRAEs. Most importantly, our findings identified potentially CRAE-related metabolic pathways and markers, providing a valuable reference for personalized medicine promising better safety. Trail registration:ClinicalTrials.gov,NCT03030508, Registered 25 January 2017,https://www.clinicaltrials.gov/ct2/show/NCT03030508?term=NCT03030508&draw=2&rank=1.
Collapse
Affiliation(s)
- Mingming Li
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xiaomeng Sun
- Research Institute, GloriousMed Clinical Laboratory Co., Ltd., Shanghai 201318, China
| | - Houshan Yao
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Wei Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Feng Zhang
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Shouhong Gao
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xun Zou
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Jiani Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Shi Qiu
- Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hua Wei
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Department of Pharmacy, 905th Hospital of PLA Navy, Naval Medical University, Shanghai 200052, China.
| | - Zhiqian Hu
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Department of Gastrointestinal Surgery, Tongji Hospital, Medical College of Tongji University, Shanghai 200065, China.
| | - Wansheng Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| |
Collapse
|
8
|
The association between RAPSN methylation in peripheral blood and breast cancer in the Chinese population. J Hum Genet 2021; 66:1069-1078. [PMID: 33958711 DOI: 10.1038/s10038-021-00933-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 02/05/2023]
Abstract
DNA methylation in peripheral blood is associated with breast cancer (BC) but has mainly been studied in Caucasian populations. We investigated the association between blood-based methylation of receptor-associated protein of the synapse (RAPSN) and BC in Chinese population. The methylation levels of 12 RAPSN CpG sites were quantitatively evaluated by mass spectrometry in two case-control studies with 283 sporadic BC cases and 331 controls totally. The association was analyzed by logistic regression adjusted for covariants. The RAPSN methylation levels in patients with variant clinical characteristics were investigated by non-parametric tests. We found a significant association between BC and altered RAPSN methylation in blood in women at premenopausal and perimenopausal (age < 50 years old), but not in the elder women. This was approved by two independent case-control studies as well as by combining the subjects of the two studies (taken all subjects together, age < 50 years old, per 5% of methylation, odds ratio (OR) range from 1.17 to 1.30 for two CpG sites; OR = 0.75 for one CpG site; all p values < 0.02). This age-related RAPSN methylation was further modified by human epidermal growth factor receptor 2 (HER2) status (age < 50 years old, HER2 negative, per 5% of methylation, OR range from 1.27 to 1.48 for two CpG sites; OR = 0.76 for one CpG site; all p values < 0.02). We elucidated an association between BC and blood-based RAPSN methylation influenced by age and the status of HER2 in Chinese population.
Collapse
|
9
|
Bhunia S, Barbhuiya MA, Gupta S, Shrivastava BR, Tiwari PK. Epigenetic downregulation of desmin in gall bladder cancer reveals its potential role in disease progression. Indian J Med Res 2021; 151:311-318. [PMID: 32461394 PMCID: PMC7371065 DOI: 10.4103/ijmr.ijmr_501_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background & objectives: Gall bladder cancer (GBC) is a fatal neoplasm, with a globally variable incidence rates. To improve the survival rate of patients, a newer set of biomarkers needs to be discovered for its early detection and better prognosis. Our earlier studies on GBC proteomics and whole-genome methylome data revealed expression of desmin to be significantly downregulated with correlated promoter hypermethylation during gall bladder carcinogenesis. Thus, to evaluate desmin as a potential biomarker for GBC, we carried out a detailed follow up study. Methods: Methylation-specific polymerase chain reaction (MS-PCR) (n=17, GBC and n=23, non-tumour control), real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) [n=14, GBC and n=14, adjacent non-tumour (ANT)], immunohistochemistry (n=27, GBC and n=14, non-tumour) and immunoblotting (n=13, GBC and n=13, ANT) were performed in surgically removed gall bladder tissue samples. Results: MS-PCR analysis showed methylation of desmin in 88.23 per cent (15/17) gall bladder tumour samples as compared to non-tumour tissues (39.13%, 9/23). Real-time qRT-PCR analysis revealed a significant downregulation of desmin expression in GBC as compared to ANT tissue. This was further confirmed by western blot, showing reduced expression of desmin protein in GBC, as compared to non-tumour tissue. Immunohistochemical analysis also showed a decreased level of desmin i.e., more than 95 per cent (26/27) in tumour cells compared to non-tumours (35.71%, 5/14). Interpretation & conclusions: The increased frequency of desmin promoter methylation which could be responsible for its significant downregulation, indicates its potential as a candidate biomarker for GBC. This requires further validation in a large group of patients to evaluate its clinical utility.
Collapse
Affiliation(s)
- Shushruta Bhunia
- Department of Molecular & Human Genetics, Centre for Genomics, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Mustafa Ahmed Barbhuiya
- Department of Pathology & Laboratory Medicine, Pennsylvania State University College of Medicine, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Sanjiv Gupta
- Department of Pathology, Cancer Hospital & Research Institute, Gwalior, Madhya Pradesh, India
| | - Braj Raj Shrivastava
- Department of Pathology, Cancer Hospital & Research Institute, Gwalior, Madhya Pradesh, India
| | - Pramod Kumar Tiwari
- Department of Molecular & Human Genetics, Centre for Genomics, Jiwaji University, Gwalior, Madhya Pradesh, India
| |
Collapse
|
10
|
Paredes-Céspedes DM, Rojas-García AE, Medina-Díaz IM, Ramos KS, Herrera-Moreno JF, Barrón-Vivanco BS, González-Arias CA, Bernal-Hernández YY. Environmental and socio-cultural impacts on global DNA methylation in the indigenous Huichol population of Nayarit, Mexico. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:4472-4487. [PMID: 32940839 DOI: 10.1007/s11356-020-10804-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
Alterations of global DNA methylation have been evaluated in several studies worldwide; however, Long Interspersed Nuclear Elements-1 (LINE-1) methylation in genetically conserved populations such as indigenous communities have not, to our knowledge, been reported. The aim of this study was to evaluate the relationship between LINE-1 methylation patterns and factors such as pesticide exposure and socio-cultural characteristics in the Indigenous Huichol Population of Nayarit, Mexico. A cross-sectional study was conducted in 140 Huichol indigenous individuals. A structured questionnaire was used to determine general and anthropometric characteristics, diet, harmful habits, and pesticide exposure. DNA methylation was determined by pyrosequencing of bisulfite-treated DNA. A lower level of LINE-1 methylation was found in the indigenous population when compared to a Mestizo population previously studied by our group. This difference might be due to the influence of the genetic admixture and differing dietary and lifestyle habits. The males in the indigenous population exhibited increased LINE-1 methylation in comparison to the females. Sex and alcohol consumption showed positive associations with LINE-1 methylation, while weight, current work in the field, current pesticide usage, and folate intake exhibited negative associations with LINE-1 methylation. The results suggest that ethnicity, as well as other internal and environmental factors, might influence LINE-1 methylation.
Collapse
Affiliation(s)
- Diana Marcela Paredes-Céspedes
- Posgrado en Ciencias Biológico Agropecuarias, Unidad Académica de Agricultura, Km. 9 Carretera Tepic-Compostela, Xalisco, Nayarit, México
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Aurora Elizabeth Rojas-García
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Irma Martha Medina-Díaz
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Kenneth S Ramos
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, 121 W. Holcombe Blvd, Houston, TX, 77030 m EE,UU, USA
| | - José Francisco Herrera-Moreno
- Posgrado en Ciencias Biológico Agropecuarias, Unidad Académica de Agricultura, Km. 9 Carretera Tepic-Compostela, Xalisco, Nayarit, México
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Briscia Socorro Barrón-Vivanco
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Cyndia Azucena González-Arias
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México
| | - Yael Yvette Bernal-Hernández
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n. C.P, 6300, Tepic, Nayarit, México.
| |
Collapse
|
11
|
Arthur-Farraj P, Moyon S. DNA methylation in Schwann cells and in oligodendrocytes. Glia 2020; 68:1568-1583. [PMID: 31958184 DOI: 10.1002/glia.23784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/17/2019] [Accepted: 01/10/2020] [Indexed: 12/12/2022]
Abstract
DNA methylation is one of many epigenetic marks, which directly modifies base residues, usually cytosines, in a multiple-step cycle. It has been linked to the regulation of gene expression and alternative splicing in several cell types, including during cell lineage specification and differentiation processes. DNA methylation changes have also been observed during aging, and aberrant methylation patterns have been reported in several neurological diseases. We here review the role of DNA methylation in Schwann cells and oligodendrocytes, the myelin-forming glia of the peripheral and central nervous systems, respectively. We first address how methylation and demethylation are regulating myelinating cells' differentiation during development and repair. We then mention how DNA methylation dysregulation in diseases and cancers could explain their pathogenesis by directly influencing myelinating cells' proliferation and differentiation capacities.
Collapse
Affiliation(s)
- Peter Arthur-Farraj
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Sarah Moyon
- Neuroscience Initiative Advanced Science Research Center, CUNY, New York, New York
| |
Collapse
|
12
|
Ferrari L, Carugno M, Mensi C, Pesatori AC. Circulating Epigenetic Biomarkers in Malignant Pleural Mesothelioma: State of the Art and critical Evaluation. Front Oncol 2020; 10:445. [PMID: 32318342 PMCID: PMC7146237 DOI: 10.3389/fonc.2020.00445] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare and aggressive cancer, which originates from the mesothelial cells of the pleura and is associated with asbestos exposure. In light of its aggressive nature, late diagnosis and dismal prognosis, there is an urgent need for identification of biomarkers in easily accessible samples (such as blood) for early diagnosis of MPM. In the last 10 years, epigenetic markers, such as DNA methylation and microRNAs (miRNAs), have gained popularity as possible early diagnostic and prognostic biomarkers in cancer research. The aim of this review is to provide a critical analysis of the current evidences on circulating epigenetic biomarkers for MPM and on their translational potential to the clinical practice for early diagnosis and for prognosis.
Collapse
Affiliation(s)
- Luca Ferrari
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Michele Carugno
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy.,Epidemiology Unit, Department of Preventive Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Carolina Mensi
- Epidemiology Unit, Department of Preventive Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela Cecilia Pesatori
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy.,Epidemiology Unit, Department of Preventive Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| |
Collapse
|
13
|
Xu R, Xu Q, Huang G, Yin X, Zhu J, Peng Y, Song J. Combined Analysis of the Aberrant Epigenetic Alteration of Pancreatic Ductal Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9379864. [PMID: 31956659 PMCID: PMC6949667 DOI: 10.1155/2019/9379864] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/02/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) remains one of the most fatal malignancies due to its high morbidity and mortality. DNA methylation exerts a vital part in the development of PDAC. However, a mechanistic role of mutual interactions between DNA methylation and mRNA as epigenetic regulators on transcriptomic alterations and its correlation with clinical outcomes such as survival have remained largely uncovered in cancer. Therefore, elucidation of aberrant epigenetic alteration in the development of PDAC is an urgent problem to be solved. In this work, we conduct an integrative epigenetic analysis of PDAC to identify aberrant DNA methylation-driven cancer genes during the occurrence of cancer. METHODS DNA methylation matrix and mRNA profile were obtained from the TCGA database. The integration of methylation and gene expression datasets was analyzed using an R package MethylMix. The genes with hypomethylation/hypermethylation were further validated in the Kaplan-Meier analysis. The correlation analysis of gene expression and aberrant DNA methylation was also conducted. We performed a pathway analysis on aberrant DNG methylation genes identified by MethylMix criteria using ConsensusPathDB. RESULTS 188 patients with both methylation data and mRNA data were considered eligible. A mixture model was constructed, and differential methylation genes in normal and tumor groups using the Wilcoxon rank test was performed. With the inclusion criteria, 95 differential methylation genes were detected. Among these genes, 74 hypermethylation and 21 hypomethylation genes were found. The pathway analysis revealed an increase in hypermethylation of genes involved in ATP-sensitive potassium channels, Robo4, and VEGF signaling pathways crosstalk, and generic transcription pathway. CONCLUSION Integrated analysis of the aberrant epigenetic alteration in pancreatic ductal adenocarcinoma indicated that differentially methylated genes could play a vital role in the occurrence of PDAC by bioinformatics analysis. The present work can help clinicians to elaborate on the function of differentially methylated expressed genes and pathways in PDAC. CDO1, GJD2, ID4, NOL4, PAX6, TRIM58, and ZNF382 might act as aberrantly DNA-methylated biomarkers for early screening and therapy of PDAC in the future.
Collapse
Affiliation(s)
- Rui Xu
- Department of Radiology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Qiuyan Xu
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Guanglei Huang
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Xinhai Yin
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Jianguo Zhu
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Yikun Peng
- Department of Otorhinolaryngology-Head and Neck Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Jukun Song
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| |
Collapse
|
14
|
Wang L, Guo X, Guo X, Zhang X, Ren J. Decitabine promotes apoptosis in mesenchymal stromal cells isolated from patients with myelodysplastic syndromes by inducing reactive oxygen species generation. Eur J Pharmacol 2019; 863:172676. [PMID: 31542488 DOI: 10.1016/j.ejphar.2019.172676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 09/11/2019] [Accepted: 09/18/2019] [Indexed: 10/26/2022]
Abstract
Myelodysplastic syndromes (MDSs) are a group of clonal disorders of hematopoietic stem cells, resulting in ineffective hematopoiesis. Previous studies have reported that decitabine (DAC) plays an essential role in cell cycle arrest and cell death induction in multiple cell types. Nevertheless, the effect of decitabine on mesenchymal stromal cells derived from bone marrow of patients with MDSs is not completely clarified. Here, we explored the apoptotic and anti-proliferative effect of DAC on MSCs isolated from patients with MDSs. Treatment with DAC inhibited cell growth in a concentration- and time-dependent manner by inducing apoptosis. We found a positive relationship between cell death triggered by DAC in MSCs and the death receptor family members Fas and FasL mRNA and protein levels (***P < 0.00085), cleaved caspase (-3, -8, and -9) activity, and mitochondrial membrane potential reduction. Additionally, DAC-induced apoptosis was inhibited by Kp7-6, a FasL/Fas antagonist, indicating a crucial role of FasL/Fas, a cell death receptor, in mediating the apoptotic effect of DAC. DAC also induced reactive oxygen species (ROS) generation in MSCs derived from MDSs patients (*P = 0.038). Furthermore, N-acetyl-L-cysteine (NAC), a widely accepted ROS scavenger, efficiently reversed DAC-induced apoptosis by inhibiting ROS generation (***P < 0.00051) in mitochondria and restoring mitochondrial membrane potential. Furthermore, ROS production was found to be a consequence of caspase activation via caspases inhibition. Our data imply that DAC triggers ROS production in human MSCs, which serves as a crucial factor for mitochondrial membrane potential reduction, and DAC induces cell death prior to FasL/Fas stimulation.
Collapse
Affiliation(s)
- Lihua Wang
- Department of Hematology, Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Xiaonan Guo
- Department of Hematology, Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Xiaoling Guo
- Department of Hematology, Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Xiaolei Zhang
- Department of Hematology, Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Jinhai Ren
- Department of Hematology, Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
| |
Collapse
|
15
|
Arora I, Sharma M, Tollefsbol TO. Combinatorial Epigenetics Impact of Polyphenols and Phytochemicals in Cancer Prevention and Therapy. Int J Mol Sci 2019; 20:ijms20184567. [PMID: 31540128 PMCID: PMC6769666 DOI: 10.3390/ijms20184567] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/08/2019] [Accepted: 09/11/2019] [Indexed: 12/24/2022] Open
Abstract
Polyphenols are potent micronutrients that can be found in large quantities in various food sources and spices. These compounds, also known as phenolics due to their phenolic structure, play a vital nutrient-based role in the prevention of various diseases such as diabetes, cardiovascular diseases, neurodegenerative diseases, liver disease, and cancers. However, the function of polyphenols in disease prevention and therapy depends on their dietary consumption and biological properties. According to American Cancer Society statistics, there will be an expected rise of 23.6 million new cancer cases by 2030. Due to the severity of the increased risk, it is important to evaluate various preventive measures associated with cancer. Relatively recently, numerous studies have indicated that various dietary polyphenols and phytochemicals possess properties of modifying epigenetic mechanisms that modulate gene expression resulting in regulation of cancer. These polyphenols and phytochemicals, when administrated in a dose-dependent and combinatorial-based manner, can have an enhanced effect on epigenetic changes, which play a crucial role in cancer prevention and therapy. Hence, this review will focus on the mechanisms of combined polyphenols and phytochemicals that can impact various epigenetic modifications such as DNA methylation and histone modifications as well as regulation of non-coding miRNAs expression for treatment and prevention of various types of cancer.
Collapse
Affiliation(s)
- Itika Arora
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Manvi Sharma
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
- Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA.
- Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA.
- Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA.
- Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
| |
Collapse
|
16
|
Humphrey KM, Pandey S, Martin J, Hagoel T, Grand'Maison A, Ohm JE. Establishing a role for environmental toxicant exposure induced epigenetic remodeling in malignant transformation. Semin Cancer Biol 2019; 57:86-94. [PMID: 30453042 PMCID: PMC6522338 DOI: 10.1016/j.semcancer.2018.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/05/2018] [Accepted: 11/14/2018] [Indexed: 01/01/2023]
Abstract
Humans are exposed to a wide variety of environmental exposures throughout their lifespan. These include both naturally occurring toxins and chemical toxicants like pesticides, herbicides, and industrial chemicals, many of which have been implicated as possible contributors to human disease susceptibility [1-3]. We, and others, have hypothesized that environmental exposures may cause adaptive epigenetic changes in regenerative cell populations and developing organisms, leading to abnormal gene expression and increased disease susceptibility later in life [3]. Common epigenetic changes include changes in miRNA expression, covalent histone modifications, and methylation of DNA. Importantly, due to their heritable nature, abnormal epigenetic modifications which occur within stem cells may be particularly deleterious. Abnormal epigenetic changes in regenerative cell linages can be passed onto a large population of daughter cells and can persist for long periods of time. It is well established that an accumulation of epigenetic changes can lead to many human diseases including cancer [4-6]. Subsequently, it is imperative that we increase our understanding of how common environmental toxins and toxicants can induce epigenetic changes, particularly in stem cell populations. In this review, we will discuss how common environmental exposures in the United States and around the world may lead to epigenetic changes and discuss potential links to human disease, including cancer.
Collapse
Affiliation(s)
- Kristen M Humphrey
- Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY, United States
| | - Sumali Pandey
- Minnesota State University Moorhead, Moorhead, MN, United States
| | - Jeffery Martin
- Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY, United States
| | - Tamara Hagoel
- Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY, United States
| | - Anne Grand'Maison
- Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY, United States
| | - Joyce E Ohm
- Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY, United States.
| |
Collapse
|
17
|
Ferrari L, Pavanello S, Bollati V. Molecular and epigenetic markers as promising tools to quantify the effect of occupational exposures and the risk of developing non-communicable diseases. LA MEDICINA DEL LAVORO 2019; 110:168-190. [PMID: 31268425 PMCID: PMC7812541 DOI: 10.23749/mdl.v110i3.8538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 06/06/2019] [Indexed: 12/18/2022]
Abstract
Non-communicable diseases (NCDs) are chronic diseases that are by far the leading cause of death in the world. Many occupational hazards, together with social, economic and demographic factors, have been associated to NCDs development. Genetic susceptibility or environmental exposures alone are not usually sufficient to explain the pathogenesis of NCDs, but can be integrated in a more complex scenario that can result in pathological phenotypes. Epigenetics is a crucial component of this scenario, as its changes are related to specific exposures, therefore potentially able to display the effects of environment on the genome, filling the gap between genetic asset and environment in explaining disease development. To date, the most promising biomarkers have been assessed in occupational cohorts as well as in case/control studies and include DNA methylation, histone modifications, microRNA expression, extracellular vesicles, telomere length, and mitochondrial alterations.
Collapse
Affiliation(s)
- Luca Ferrari
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, via San Barnaba 8, 20122 Milan, Italy..
| | | | | |
Collapse
|
18
|
Jiang Y, Zong W, Ju S, Jing R, Cui M. Promising member of the short interspersed nuclear elements ( Alu elements): mechanisms and clinical applications in human cancers. J Med Genet 2019; 56:639-645. [PMID: 30852527 DOI: 10.1136/jmedgenet-2018-105761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/13/2019] [Accepted: 01/31/2019] [Indexed: 12/11/2022]
Abstract
Alu elements are one of most ubiquitous repetitive sequences in human genome, which were considered as the junk DNA in the past. Alu elements have been found to be associated with human diseases including cancers via events such as amplification, insertion, recombination or RNA editing, which provide a new perspective of oncogenesis at both DNA and RNA levels. Due to the prevalent distribution, Alu elements are widely used as target molecule of liquid biopsy. Alu-based cell-free DNA shows feasible application value in tumour diagnosis, postoperative monitoring and adjuvant therapy. In this review, the special tumourigenesis mechanism of Alu elements in human cancers is discussed, and the application of Alu elements in various tumour liquid biopsy is summarised.
Collapse
Affiliation(s)
- Yun Jiang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Wei Zong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Ming Cui
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| |
Collapse
|
19
|
Azimzadeh-Isfanjani A, Safaralizadeh R, Hosseinpour-Feizi M, Shokouhi B, Nemati M, Moaddab SY. Expression of miR-520c in intestinal type gastric adenocarcinoma. J Gastrointest Oncol 2018; 9:1184-1189. [PMID: 30603140 DOI: 10.21037/jgo.2018.08.09] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background MicroRNAs are small non-coding RNAs that participate in post-transcriptional gene regulation in cells thereby playing active role in pathological conditions and have been nominated as new class of biomarkers in disease including cancer. miR-520c has been reported as potential oncogenic micro-RNA in several previous studies. Gastric cancer is the most common cancer of digestive tract and the fourth prevalent cancer worldwide with the intestinal-type gastric adenocarcinoma (IGA) the dominant type of gastric malignancies. This study aimed to explore miR-520c putative role, in IGA and patient's clinicopathological features. Methods Total RNA was first extracted from 42 pairs of IGA tissues and relevant non-tumorous adjacent tissues. cDNA was synthesized from extracted RNAs using specific primers for miR-520c. The level of miR-520c was quantified using SYBER Green Real-Time PCR master mix. The relationship between miR-520c expression and clinicopathological features were examined. Results Our study resulted in no differential expression of miR-520c in IGA. There was no significant correlation between miR-520c expression and clinicopathological features including tumor grade, genus and age groups. Conclusions To our knowledge, this is the first report about exploring miR-520c expression in IGA tissue samples. Our results do not verify miR-520c previously established oncogenic role in IGA.
Collapse
Affiliation(s)
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | - Behrouz Shokouhi
- Pathology Department, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masuomeh Nemati
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Seyyed-Yaghoub Moaddab
- Liver and Gastroenterology Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
20
|
Uli N, Michelen-Gomez E, Ramos EI, Druley TE. Age-specific changes in genome-wide methylation enrich for Foxa2 and estrogen receptor alpha binding sites. PLoS One 2018; 13:e0203147. [PMID: 30256791 PMCID: PMC6157835 DOI: 10.1371/journal.pone.0203147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/15/2018] [Indexed: 12/26/2022] Open
Abstract
The role of DNA methylation patterns in complex phenotypes remains unclear. To explore this question, we adapted our methods for rare variant analysis to characterize genome-wide murine DNA hybridization array to investigate methylation at CpG islands, shores, and regulatory elements. We have applied this platform to compare age and tissue- specific methylation differences in the brain and spleen of young and aged mice. As expected from prior studies, there are clear global differences in organ-specific, but not age-specific, methylation due mostly to changes at repetitive elements. Surprisingly, out of 200,000 loci there were only 946 differentially methylated cytosines (DMCs) between young and old samples (529 hypermethylated, 417 hypomethylated in aged mice) compared to thousands of tissue-specific DMCs. Hypermethylated loci were clustered around the promoter region of Sfi1, exon 2 of Slc11a2, Drg1, Esr1 and Foxa2 transcription factor binding sites. In particular, there were 75 hypermethylated Foxa2 binding sites across a 2.7 Mb region of chromosome 11. Hypomethylated loci were clustered around Mid1, Isoc2b and genome-wide loci with binding sites for Foxa2 and Esr1, which are known to play important roles in development and aging. These data suggest discreet tissue-independent methylation changes associated with aging processes such as cell division (Sfi1, Mid1), energy production (Drg1, Isoc2b) and cell death (Foxa2, Esr1).
Collapse
Affiliation(s)
- Nishanth Uli
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Eduardo Michelen-Gomez
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Enrique I. Ramos
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Todd E. Druley
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
| |
Collapse
|
21
|
Wu C, Peng S, Sun W, Luo M, Su B, Liu D, Hu G. Association of E-cadherin methylation with risk of nasopharyngeal cancer: A meta-analysis. Head Neck 2018; 40:2538-2545. [PMID: 29947108 DOI: 10.1002/hed.25319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 03/13/2018] [Accepted: 04/03/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Various studies have assessed the association between E-cadherin methylation and risk of nasopharyngeal cancer (NPC) but the conclusion remains unclear. This meta-analysis was conducted to evaluate the effects of E-cadherin methylation on the incidence and clinicopathological characteristics of NPC. METHODS Ten studies published up to June 30, 2016, were collected. Odds ratios (ORs) with corresponding confidence intervals (CIs) were calculated and summarized, respectively. RESULTS The E-cadherin methylation in NPC was significantly higher than those in normal groups (OR 16.23; 95% CI 8.34-31.60; P < .001). Ethnicity-stratified analysis indicated that E-cadherin methylation was strongly correlated with NPC among both Asians (OR 16.98; 95% CI 8.45-34.14; P < .001) and North Africans (OR 10.67; 95% CI 1.21-93.72; P = .033). However, further analysis showed that E-cadherin methylation was not strongly associated with clinicopathological feathers in patients with NPC. CONCLUSION The E-cadherin methylation is strongly associated with the incidence of NPC, which can serve as an effective biomarker for early detection of NPC.
Collapse
Affiliation(s)
- Cheng Wu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Shan Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Wei Sun
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Min Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Beibei Su
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Dongbo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Guoqing Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| |
Collapse
|
22
|
Estekizadeh A, Landázur N, Bartek J, Beltoft Brøchner C, Davoudi B, Broholm H, Karimi M, Ekström TJ, Rahbar A. Increased cytomegalovirus replication by 5-Azacytidine and viral-induced cytoplasmic expression of DNMT‑1 in medulloblastoma and endothelial cells. Int J Oncol 2018; 52:1317-1327. [PMID: 29484388 DOI: 10.3892/ijo.2018.4286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/24/2018] [Indexed: 11/06/2022] Open
Abstract
Among all brain tumors diagnosed in children, medulloblastomas (MBs) are associated with a poor prognosis. The etiology of MB is not fully understood, yet the impact of epigenetic alterations of oncogenes has previously been established. During the past decade, the human cytomegalovirus (HCMV) has been detected in several types of cancer, including MB. Since DNA methylation occurs in the cell nucleus and this is considered a host defence response, we studied the impact of HCMV infection on DNA methyltransferase (DNMT‑1) in MB (D324) cells, human umbilical vein endothelial cells (HUVECs) as well as in MB tissue sections. We hypothesized that infection and DNMT‑1 intracellular localization are linked. Uninfected and HCMV‑infected D324 cells and HUVECs were analyzed for HCMV immediate early (HCMV‑IE) protein, HCMV‑glycoprotein B (HCMV‑gB) and DNMT‑1 using immunofluorescence staining and quantitative ELISA. DNMT‑1 localized to the nucleus of uninfected and HCMV‑IE- expressing D324 cells and HUVECs, but accumulated in the extra nuclear space in all HCMV‑gB-positive cells. Inhibition of HCMV late protein expression by Cymevene® (ganciclovir) prevented the cytoplasmic localization of DNMT‑1. Treatment of HCMV‑ infected D324 cells and HUVECs with the methylation inhibitor 5-Azacytidine (5AZA), significantly increased HCMV‑IE and HCMV‑gB gene transcription and protein expression. Immunohistochemical staining of DNMT‑1 and HCMV proteins in MB cancer tissue sections revealed both nuclear and cytoplasmic DNMT‑1 localization. In conclusion, DNMT‑1 resides in the cytoplasm of HCMV‑gB-expressing HUVECs and D324 cells. Increased viral protein synthesis in 5AZA-treated cells suggests that HCMV replication may benefit from a DNA methyltransferase-free cellular environment. Our findings emphasize the importance of assessing potential viral activation in the treatment of MB patients with epigenetic drugs.
Collapse
Affiliation(s)
- Atosa Estekizadeh
- Department of Clinical Neuroscience and Center for Molecular Medicine, Karolinska Institutet, SE_17176 Stockholm, Sweden
| | - Natalia Landázur
- Department of Clinical Neuroscience and Center for Molecular Medicine, Karolinska Institutet, SE_17176 Stockholm, Sweden
| | - Jiri Bartek
- Department of Medicine, Solna and Center for Molecular Medicine, Karolinska Institutet, SE_17176 Stockholm, Sweden
| | | | - Belghis Davoudi
- Department of Medicine, Solna and Center for Molecular Medicine, Karolinska Institutet, SE_17176 Stockholm, Sweden
| | - Helle Broholm
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Mohsen Karimi
- Department of Medicine, Solna and Center for Molecular Medicine, Karolinska Institutet, SE_17176 Stockholm, Sweden
| | - Tomas J Ekström
- Department of Clinical Neuroscience and Center for Molecular Medicine, Karolinska Institutet, SE_17176 Stockholm, Sweden
| | - Afsar Rahbar
- Department of Medicine, Solna and Center for Molecular Medicine, Karolinska Institutet, SE_17176 Stockholm, Sweden
| |
Collapse
|
23
|
Liu J, Li M, Wang Y, Luo J. Curcumin sensitizes prostate cancer cells to radiation partly via epigenetic activation of miR-143 and miR-143 mediated autophagy inhibition. J Drug Target 2017; 25:645-652. [PMID: 28391715 DOI: 10.1080/1061186x.2017.1315686] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Curcumin has been reported as a radiosensitizer in prostate cancer. But the underlying mechanism is not well understood. In this study, we firstly assessed how curcumin affects the expression of miR-143/miR-145 cluster. Then, we investigated whether miR-143 is involved in regulation of radiosensitivity and its association with autophagy in prostate cancer cells. Our data showed that PC3, DU145 and LNCaP cells treated with curcumin had significantly restored miR-143 and miR-145 expression. Curcumin showed similar effect as 5-AZA-dC on reducing methylation of CpG dinucleotides in miR-143 promoter. In addition, curcumin treatment reduced the expression of DNMT1 and DNMT3B, which contribute to promoter hypermethylation of the miR-143/miR-145 cluster. Therefore, we infer that curcumin can restore miR-143 and miR-145 expression via hypomethylation. MiR-143 overexpression and curcumin pretreatment enhanced radiation induced cancer cell growth inhibition and apoptosis. MiR-143 and curcumin remarkably reduced radiation-induced autophagy in PC3 and DU145 cells. MiR-143 overexpression alone also reduced the basal level of autophagy in DU145 cells. Mechanistically, miR-143 can suppress autophagy in prostate cancer cells at least via downregulating ATG2B. Based on these findings, we infer that curcumin sensitizes prostate cancer cells to radiation partly via epigenetic activation of miR-143 and miR-143 mediated autophagy inhibition.
Collapse
Affiliation(s)
- Jianbo Liu
- a Department of Radiation Oncology , Henan Provincial People's Hospital , Zhengzhou , PR China
| | - Min Li
- b Department of ICU , Henan Provincial People's Hospital , Zhengzhou , PR China
| | - Yuewei Wang
- a Department of Radiation Oncology , Henan Provincial People's Hospital , Zhengzhou , PR China
| | - Jianchao Luo
- a Department of Radiation Oncology , Henan Provincial People's Hospital , Zhengzhou , PR China
| |
Collapse
|
24
|
Efficient Remyelination Requires DNA Methylation. eNeuro 2017; 4:eN-NWR-0336-16. [PMID: 28451635 PMCID: PMC5394940 DOI: 10.1523/eneuro.0336-16.2017] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/28/2017] [Accepted: 01/31/2017] [Indexed: 12/05/2022] Open
Abstract
Oligodendrocyte progenitor cells (OPCs) are the principal source of new myelin in the central nervous system. A better understanding of how they mature into myelin-forming cells is of high relevance for remyelination. It has recently been demonstrated that during developmental myelination, the DNA methyltransferase 1 (DNMT1), but not DNMT3A, is critical for regulating proliferation and differentiation of OPCs into myelinating oligodendrocytes (OLs). However, it remains to be determined whether DNA methylation is also critical for the differentiation of adult OPCs during remyelination. After lysolecithin-induced demyelination in the ventrolateral spinal cord white matter of adult mice of either sex, we detected increased levels of DNA methylation and higher expression levels of the DNA methyltransferase DNMT3A and lower levels of DNMT1 in differentiating adult OLs. To functionally assess the role of DNMT1 and DNMT3 in adult OPCs, we used mice with inducible and lineage-specific ablation of Dnmt3a and/or Dnmt1 (i.e., Plp-creER(t);Dnmt3a-flox, Plp-creER(t);Dnmt1-flox, Plp-creER(t);Dnmt1-flox;Dnmt3a-flox). Upon lysolecithin injection in the spinal cord of these transgenic mice, we detected defective OPC differentiation and inefficient remyelination in the Dnmt3a null and Dnmt1/Dnmt3a null mice, but not in the Dnmt1 null mice. Taken together with previous results in the developing spinal cord, these data suggest an age-dependent role of distinct DNA methyltransferases in the oligodendrocyte lineage, with a dominant role for DNMT1 in neonatal OPCs and for DNMT3A in adult OPCs.
Collapse
|
25
|
Moyon S, Casaccia P. DNA methylation in oligodendroglial cells during developmental myelination and in disease. NEUROGENESIS 2017; 4:e1270381. [PMID: 28203606 DOI: 10.1080/23262133.2016.1270381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/23/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
Abstract
Oligodendrocyte progenitor cells (OPC) are the myelinating cells of the central nervous system (CNS). During development, they differentiate into mature oligodendrocytes (OL) and ensheath axons, providing trophic and functional support to the neurons. This process is regulated by the dynamic expression of specific transcription factors, which, in turn, is controlled by epigenetic marks such as DNA methylation. Here we discuss recent findings showing that DNA methylation levels are differentially regulated in the oligodendrocyte lineage during developmental myelination, affecting both genes expression and alternative splicing events. Based on the phenotypic characterization of mice with genetic ablation of DNA methyltransferase 1 (Dnmt1) we conclude that DNA methylation is critical for efficient OPC expansion and for developmental myelination. Previous work suggests that in the context of diseases such as multiple sclerosis (MS) or gliomas, DNA methylation is differentially regulated in the CNS of affected individuals compared with healthy controls. In this commentary, based on the results of previous work, we propose the potential role of DNA methylation in adult oligodendroglial lineage cells in physiologic and pathological conditions, and delineate potential research approaches to be undertaken to test this hypothesis. A better understanding of this epigenetic modification in adult oligodendrocyte progenitor cells is essential, as it can potentially result in the design of new therapeutic strategies to enhance remyelination in MS patients or reduce proliferation in glioma patients.
Collapse
Affiliation(s)
- Sarah Moyon
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai , New York, NY, USA
| | - Patrizia Casaccia
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Neuroscience Initiative Advanced Science Research Center, CUNY, New York, NY, USA
| |
Collapse
|
26
|
Rodríguez-Rodero S, Delgado-Álvarez E, Díaz-Naya L, Martín Nieto A, Menéndez Torre E. Epigenetic modulators of thyroid cancer. ACTA ACUST UNITED AC 2017; 64:44-56. [PMID: 28440770 DOI: 10.1016/j.endinu.2016.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 09/14/2016] [Accepted: 09/20/2016] [Indexed: 12/14/2022]
Abstract
There are some well known factors involved in the etiology of thyroid cancer, including iodine deficiency, radiation exposure at early ages, or some genetic changes. However, epigenetic modulators that may contribute to development of these tumors and be helpful to for both their diagnosis and treatment have recently been discovered. The currently known changes in DNA methylation, histone modifications, and non-coding RNAs in each type of thyroid carcinoma are reviewed here.
Collapse
Affiliation(s)
- Sandra Rodríguez-Rodero
- Department of Endocrinology and Nutrition, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain; Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Elías Delgado-Álvarez
- Department of Endocrinology and Nutrition, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain
| | - Lucía Díaz-Naya
- Department of Endocrinology and Nutrition, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain
| | - Alicia Martín Nieto
- Department of Endocrinology and Nutrition, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain
| | - Edelmiro Menéndez Torre
- Department of Endocrinology and Nutrition, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain.
| |
Collapse
|
27
|
Jezkova E, Kajo K, Zubor P, Grendar M, Malicherova B, Mendelova A, Dokus K, Lasabova Z, Plank L, Danko J. Methylation in promoter regions of PITX2 and RASSF1A genes in association with clinicopathological features in breast cancer patients. Tumour Biol 2016; 37:10.1007/s13277-016-5324-3. [PMID: 27744628 DOI: 10.1007/s13277-016-5324-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/06/2016] [Indexed: 01/31/2023] Open
Abstract
Breast cancer is a heterogeneous disease with very different responses to therapy and different length of survival. In many cases, however, the determination of the stage and histopathological characteristics of breast cancer is insufficient to predict prognosis and response to treatment for the vast heterogeneity of the disease. To understand the molecular signature of subtypes of breast cancer, we attempted to identify the methylation status of key tumour suppressor gene Ras association (RalGDS/AF-6) domain family member 1 isoform a (RASSF1A) and a member of the paired-like homeodomain transcription factor family which functions in left-right asymmetry development (PITX2) and to correlate results with known clinicopathological features of breast cancer. Formalin-fixed, paraffin-embedded (FFPE) tissues of breast carcinomas (n = 149) were used for DNA extraction. DNA was modified by bisulphite conversion. Detection of the methylation level of the genes mentioned above was performed by methylation-sensitive high-resolution melting assay (MS-HRM). Based on MS-HRM results for RASSF1A and PITX2, we subdivided the samples into four groups according to methylation level (≤50 % methylated, >50 % methylated, 100 % methylated and completely unmethylated alleles). All degrees of methylation status for both genes underwent analysis of dependence with known clinicopathological features, and we found significant associations. In 134 of 149 (89.9 %) primary breast carcinomas, the RASSF1A promoter was methylated. Total hypermethylation of PITX2 was observed in 60 of 135 (44.4 %) breast cancer cases. RASSF1A hypermethylation had significant association with increased age (p < 0.05), tumour grade (p < 0.0001) and stage (p < 0.0001) in the 100 % methylated group. There was significant association of PITX2 hypermethylation with tumour grade (p < 0.0001) and stage (p < 0.0001). Association between the methylation level of both investigated genes and tumour type was significant for ductal invasive carcinoma cases only (p < 0.0001). This study shows different levels of heterogeneous methylation acquired by MS-HRM assay of the promoter region of RASSF1A and PITX2 and its relationship with clinicopathological features of 149 breast cancer patients. We noticed that immunohistopathological subtypes of breast cancer contain distinct promoter methylation patterns. All these data suggest that hypermethylation of the CpG island promoters of RASSF1A and PITX2 might play an essential role in the very early stages of breast cancer pathogenesis.
Collapse
Affiliation(s)
- Eva Jezkova
- Department of Oncology JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia.
- Clinic of Gynaecology and Obstetrics, Jessenius Faculty of Medicine, Martin University Hospital, Kollarova 2, 036 01, Martin, Slovakia.
| | - Karol Kajo
- St. Elizabeth Cancer Institute Hospital, Heydukova 10, 812 50, Bratislava, Slovakia
| | - Pavol Zubor
- Department of Oncology JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia
- Clinic of Gynaecology and Obstetrics, Jessenius Faculty of Medicine, Martin University Hospital, Kollarova 2, 036 01, Martin, Slovakia
| | - Marian Grendar
- Department of Oncology JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia
| | - Bibiana Malicherova
- Department of Oncology JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia
| | - Andrea Mendelova
- Department of Molecular Medicine JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia
| | - Karol Dokus
- Clinic of Gynaecology and Obstetrics, Jessenius Faculty of Medicine, Martin University Hospital, Kollarova 2, 036 01, Martin, Slovakia
| | - Zora Lasabova
- Department of Oncology JFM CU, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4C, 036 01, Martin, Slovakia
| | - Lukas Plank
- Department of Pathological Anatomy, Jessenius Faculty of Medicine, Martin University Hospital, Kollarova 2, 036 01, Martin, Slovakia
| | - Jan Danko
- Clinic of Gynaecology and Obstetrics, Jessenius Faculty of Medicine, Martin University Hospital, Kollarova 2, 036 01, Martin, Slovakia
| |
Collapse
|
28
|
Chang HF, Wu CC, Sun CA, Chu CM, Lin FG, Hsieh JF, Hsu CH, Huang CH, Yang T, Tsai YM, Kuan JC, Chou YC. Clinical stage and risk of recurrence and mortality: interaction of DNA methylation factors in patients with colorectal cancer. J Investig Med 2016; 64:1200-7. [PMID: 27296458 DOI: 10.1136/jim-2016-000086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2016] [Indexed: 12/12/2022]
Abstract
Aberrant DNA methylation plays a crucial role in cancer development; however, prospective evidence of an interaction between molecular biomarkers and cancer staging for predicting the prognosis of colorectal cancer (CRC) is still limited. We examined DNA methylation in tumors and adjacent normal tissues from patients who underwent CRC surgical resection, and evaluated the interaction between cancer staging (advanced vs local) and DNA methylation to predict the prognosis of CRC. We recruited 132 patients with CRC from Tri-Service General Hospital in Taiwan and used the candidate gene approach to select 3 tumor suppressor genes involved in carcinogenesis pathways. ORs and 95% CIs were computed using logistic regression analyses while adjusting for potential covariates. Advanced cancer stage was correlated with cancer recurrence (OR 7.22, 95% CI 2.82 to 18.45; p<0.001). In addition, after stratification by promoter methylation in 3 combined genes in the matched normal tissues, we observed a joint effect after adjusting for sex, age at surgery, and adjuvant chemotherapy, yielding a significant OR of 20.35 (95% CI 4.16 to 99.57; p<0.001). DNA methylation status would significantly increase the recurrence risk of CRC with a significant impact on joint effect between DNA methylation and clinical stage, particularly in matched normal tissues. This was attributed to molecular changes that could not be examined on the basis of clinical pathology. Our interaction results may serve as a reference marker for evaluating the risk of recurrence in future studies.
Collapse
Affiliation(s)
- Hsien-Feng Chang
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Chang-Chieh Wu
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chien-An Sun
- Department of Public Health, College of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Chi-Ming Chu
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Fu-Gong Lin
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Jih-Fu Hsieh
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Hsiung Hsu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Chi-Hua Huang
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Tsan Yang
- Department of Health Business Administration, Meiho University, Pingtung, Taiwan
| | - Yang-Ming Tsai
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Jen-Chun Kuan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| |
Collapse
|
29
|
Moyon S, Liang J, Casaccia P. Epigenetics in NG2 glia cells. Brain Res 2016; 1638:183-198. [PMID: 26092401 PMCID: PMC4683112 DOI: 10.1016/j.brainres.2015.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/11/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022]
Abstract
The interplay of transcription and epigenetic marks is essential for oligodendrocyte progenitor cell (OPC) proliferation and differentiation during development. Here, we review the recent advances in this field and highlight mechanisms of transcriptional repression and activation involved in OPC proliferation, differentiation and plasticity. We also describe how dysregulation of these epigenetic events may affect demyelinating disorders, and consider potential ways to manipulate NG2 cell behavior through modulation of the epigenome. This article is part of a Special Issue entitled SI:NG2-glia(Invited only).
Collapse
Affiliation(s)
- Sarah Moyon
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jialiang Liang
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrizia Casaccia
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| |
Collapse
|
30
|
Chappell G, Pogribny IP, Guyton KZ, Rusyn I. Epigenetic alterations induced by genotoxic occupational and environmental human chemical carcinogens: A systematic literature review. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2016; 768:27-45. [PMID: 27234561 PMCID: PMC4884606 DOI: 10.1016/j.mrrev.2016.03.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/24/2016] [Accepted: 03/25/2016] [Indexed: 01/30/2023]
Abstract
Accumulating evidence suggests that epigenetic alterations play an important role in chemically-induced carcinogenesis. Although the epigenome and genome may be equally important in carcinogenicity, the genotoxicity of chemical agents and exposure-related transcriptomic responses have been more thoroughly studied and characterized. To better understand the evidence for epigenetic alterations of human carcinogens, and the potential association with genotoxic endpoints, we conducted a systematic review of published studies of genotoxic carcinogens that reported epigenetic endpoints. Specifically, we searched for publications reporting epigenetic effects for the 28 agents and occupations included in Monograph Volume 100F of the International Agency for the Research on Cancer (IARC) that were classified as "carcinogenic to humans" (Group 1) with strong evidence of genotoxic mechanisms of carcinogenesis. We identified a total of 158 studies that evaluated epigenetic alterations for 12 of these 28 carcinogenic agents and occupations (1,3-butadiene, 4-aminobiphenyl, aflatoxins, benzene, benzidine, benzo[a]pyrene, coke production, formaldehyde, occupational exposure as a painter, sulfur mustard, and vinyl chloride). Aberrant DNA methylation was most commonly studied, followed by altered expression of non-coding RNAs and histone changes (totaling 85, 59 and 25 studies, respectively). For 3 carcinogens (aflatoxins, benzene and benzo[a]pyrene), 10 or more studies reported epigenetic effects. However, epigenetic studies were sparse for the remaining 9 carcinogens; for 4 agents, only 1 or 2 published reports were identified. While further research is needed to better identify carcinogenesis-associated epigenetic perturbations for many potential carcinogens, published reports on specific epigenetic endpoints can be systematically identified and increasingly incorporated in cancer hazard assessments.
Collapse
Affiliation(s)
- Grace Chappell
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Igor P Pogribny
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | | | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
31
|
Mauro M, Caradonna F, Klein CB. Dysregulation of DNA methylation induced by past arsenic treatment causes persistent genomic instability in mammalian cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:137-50. [PMID: 26581878 PMCID: PMC5008255 DOI: 10.1002/em.21987] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 10/29/2015] [Accepted: 10/31/2015] [Indexed: 05/21/2023]
Abstract
The mechanisms by which arsenic-induced genomic instability is initiated and maintained are poorly understood. To investigate potential epigenetic mechanisms, in this study we evaluated global DNA methylation levels in V79 cells and human HaCaT keratinocytes at several time points during expanded growth of cell cultures following removal of arsenite exposures. We have found altered genomic methylation patterns that persisted up to 40 cell generations in HaCaT cells after the treatments were withdrawn. Moreover, mRNA expression levels were evaluated by RT-PCR for DNMT1, DNMT3A, DNMT3B, HMLH1, and HMSH2 genes, demonstrating that the down regulation of DNMT3A and DNMT3B genes, but not DNMT1, occurred in an arsenic dose-dependent manner, and persisted for many cell generations following removal of the arsenite, offering a plausible mechanism of persistently genotoxic arsenic action. Analyses of promoter methylation status of the DNA mismatch repair genes HMLH1 and HMSH2 show that HMSH2, but not HMLH1, was epigenetically regulated by promoter hypermethylation changes following arsenic treatment. The results reported here demonstrate that arsenic exposure promptly induces genome-wide global DNA hypomethylation, and some specific gene promoter methylation changes, that persist for many cell generations following withdrawal of arsenite, supporting the hypothesis that the cells undergo epigenetic reprogramming at both the gene and genome level that is durable over many cell generations in the absence of further arsenic treatment. These DNA methylation changes, in concert with other known epigenome alterations, are likely contributing to long-lasting arsenic-induced genomic instability that manifests in several ways, including aberrant chromosomal effects.
Collapse
Affiliation(s)
- Maurizio Mauro
- Dipartimento Di Scienze E Tecnologie Biologiche Chimiche E Farmaceutiche (STEBICEF, Sezione Di Biologia Cellulare) Universita Di Palermo, Italia
| | - Fabio Caradonna
- Dipartimento Di Scienze E Tecnologie Biologiche Chimiche E Farmaceutiche (STEBICEF, Sezione Di Biologia Cellulare) Universita Di Palermo, Italia
| | - Catherine B. Klein
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York 10987
| |
Collapse
|
32
|
Identification of a DNA methylation signature to predict disease-free survival in locally advanced rectal cancer. Oncotarget 2015; 5:8123-35. [PMID: 25261372 PMCID: PMC4226671 DOI: 10.18632/oncotarget.2347] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In locally advanced rectal cancer a preoperative predictive biomarker is necessary to adjust treatment specifically for those patients expected to suffer relapse. We applied whole genome methylation CpG island array analyses to an initial set of patients (n=11) to identify differentially methylated regions (DMRs) that separate a good from a bad prognosis group. Using a quantitative high-resolution approach, candidate DMRs were first validated in a set of 61 patients (test set) and then confirmed DMRs were further validated in additional independent patient cohorts (n=71, n=42). We identified twenty highly discriminative DMRs and validated them in the test set using the MassARRAY technique. Ten DMRs could be confirmed which allowed separation into prognosis groups (p=0.0207, HR=4.09). The classifier was validated in two additional cohorts (n=71, p=0.0345, HR=3.57 and n=42, p=0.0113, HR=3.78). Interestingly, six of the ten DMRs represented regions close to the transcriptional start sites of genes which are also marked by the Polycomb Repressor Complex component EZH2. In conclusion we present a classifier comprising 10 DMRs which predicts patient prognosis with a high degree of accuracy. These data may now help to discriminate between patients that may respond better to standard treatments from those that may require alternative modalities.
Collapse
|
33
|
Ngollo M, Dagdemir A, Karsli-Ceppioglu S, Judes G, Pajon A, Penault-Llorca F, Boiteux JP, Bignon YJ, Guy L, Bernard-Gallon DJ. Epigenetic modifications in prostate cancer. Epigenomics 2015; 6:415-26. [PMID: 25333850 DOI: 10.2217/epi.14.34] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer is the most common cancer in men and the second leading cause of cancer deaths in men in France. Apart from the genetic alterations in prostate cancer, epigenetics modifications are involved in the development and progression of this disease. Epigenetic events are the main cause in gene regulation and the three most epigenetic mechanisms studied include DNA methylation, histone modifications and microRNA expression. In this review, we summarized epigenetic mechanisms in prostate cancer. Epigenetic drugs that inhibit DNA methylation, histone methylation and histone acetylation might be able to reactivate silenced gene expression in prostate cancer. However, further understanding of interactions of these enzymes and their effects on transcription regulation in prostate cancer is needed and has become a priority in biomedical research. In this study, we summed up epigenetic changes with emphasis on pharmacologic epigenetic target agents.
Collapse
Affiliation(s)
- Marjolaine Ngollo
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Abstract
Stem cell decline is an important cellular driver of aging-associated pathophysiology in multiple tissues. Epigenetic regulation is central to establishing and maintaining stem cell function, and emerging evidence indicates that epigenetic dysregulation contributes to the altered potential of stem cells during aging. Unlike terminally differentiated cells, the impact of epigenetic dysregulation in stem cells is propagated beyond self; alterations can be heritably transmitted to differentiated progeny, in addition to being perpetuated and amplified within the stem cell pool through self-renewal divisions. This Review focuses on recent studies examining epigenetic regulation of tissue-specific stem cells in homeostasis, aging, and aging-related disease.
Collapse
Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA.
| |
Collapse
|
35
|
Kuan JC, Wu CC, Sun CA, Chu CM, Lin FG, Hsu CH, Kan PC, Lin SC, Yang T, Chou YC. DNA methylation combinations in adjacent normal colon tissue predict cancer recurrence: evidence from a clinical cohort study. PLoS One 2015; 10:e0123396. [PMID: 25815725 PMCID: PMC4376718 DOI: 10.1371/journal.pone.0123396] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/18/2015] [Indexed: 12/13/2022] Open
Abstract
Accumulating evidence has suggested the requirement for further stratification of patients in the same tumor stage according to molecular factors. We evaluate the combination of cancer stage and DNA methylation status as an indicator of the risk of recurrence and mortality among patients with colorectal cancer (CRC). A cohort study of 215 patients with CRC (mean age 64.32 years; 50.5% of men) from Tri-Service General Hospital in Taiwan examined the association between cancer stage and risk of CRC recurrence and mortality. A Cox proportional hazard model was used to analyze patient methylation status and clinical information at study entry, and their associations with CRC recurrence and mortality during follow-up. The advanced stage patients with p16, hMLH1, and MGMT methylation were associated with higher risk of CRC recurrence compared with the local stage patients with unmethylation status in tumor tissues, with adjusted hazard ratios (HRs) (95% confidence interval [CI]) of 9.64 (2.92-31.81), 8.29 (3.40-20.22), and 11.83 (3.49-40.12), respectively. When analyzing normal tissues, we observed similar risk of CRC recurrence with adjusted HRs (95% CI) of 10.85 (4.06-28.96), 9.04 (3.79-21.54), and 12.61 (4.90-32.44), respectively. For combined analyses, the risk of recurrence in the patients in advanced stage with DNA methylation in both normal and tumor tissues, compared with local stage with unmethylation, was increased with adjusted HR (95% CI) of 9.37 (3.36-26.09). In the advanced stage patients, methylation status and tissue subtype were associated with increased risk of 5-year cumulative CRC recurrence (p < 0.001). This study demonstrates that clustering DNA methylation status according to cancer stage and tissue subtype is critical for the assessment of risk of recurrence in CRC patients and also indicated an underlying mechanism.
Collapse
Affiliation(s)
- Jen Chun Kuan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (R.O.C.)
| | - Chang Chieh Wu
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan (R.O.C.)
| | - Chien An Sun
- Department of Public Health, College of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan (R.O.C.)
| | - Chi Ming Chu
- School of Public Health, National Defense Medical Center, Taipei, Taiwan (R.O.C.)
| | - Fu Gong Lin
- School of Public Health, National Defense Medical Center, Taipei, Taiwan (R.O.C.)
| | - Chih Hsiung Hsu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan (R.O.C.)
| | - Po-Chieh Kan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (R.O.C.)
| | - Shih-Chieh Lin
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (R.O.C.)
| | - Tsan Yang
- Department of Health Business Administration, Meiho University, Pingtung, Taiwan
| | - Yu-Ching Chou
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (R.O.C.); School of Public Health, National Defense Medical Center, Taipei, Taiwan (R.O.C.)
| |
Collapse
|
36
|
Lu TP, Hsiao CK, Lai LC, Tsai MH, Hsu CP, Lee JM, Chuang EY. Identification of regulatory SNPs associated with genetic modifications in lung adenocarcinoma. BMC Res Notes 2015; 8:92. [PMID: 25889623 PMCID: PMC4384239 DOI: 10.1186/s13104-015-1053-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/11/2015] [Indexed: 11/28/2022] Open
Abstract
Background Although much research effort has been devoted to elucidating lung cancer, the molecular mechanism of tumorigenesis still remains unclear. A major challenge to improve the understanding of lung cancer is the difficulty of identifying reproducible differentially expressed genes across independent studies, due to their low consistency. To enhance the reproducibility of the findings, an integrated analysis was performed to identify regulatory SNPs. Thirty-two pairs of tumor and adjacent normal lung tissue specimens were analyzed using Affymetrix U133plus2.0, Affymetrix SNP 6.0, and Illumina Infinium Methylation microarrays. Copy number variations (CNVs) and methylation alterations were analyzed and paired t-tests were used to identify differentially expressed genes. Results A total of 505 differentially expressed genes were identified, and their dysregulated patterns moderately correlated with CNVs and methylation alterations based on the hierarchical clustering analysis. Subsequently, three statistical approaches were performed to explore regulatory SNPs, which revealed that the genotypes of 551 and 66 SNPs were associated with CNV and changes in methylation, respectively. Among them, downstream transcriptional dysregulation was observed in 9 SNPs for CNVs and 4 SNPs for methylation alterations. Conclusions In summary, these identified SNPs concurrently showed the same direction of gene expression changes with genetic modifications, suggesting their pivotal roles in the genome for non-smoking women with lung adenocarcinoma. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1053-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tzu-Pin Lu
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan.
| | - Chuhsing K Hsiao
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan. .,Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan.
| | - Liang-Chuan Lai
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan. .,Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan.
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan. .,Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.
| | - Chung-Ping Hsu
- Division of Thoracic Surgery, Taichung Veterans General Hospital, Taichung, Taiwan.
| | - Jang-Ming Lee
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan.
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan. .,Graduate Institute of Biomedical Electronics and Bioinformatics and Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
37
|
Liu WJ, Ren JG, Li T, Yu GZ, Zhang J, Li CS, Liu ZS, Liu QY. 5-Aza-2<-deoxycytidine induces hepatoma cell apoptosis via enhancing methionine adenosyltransferase 1A expression and inducing S-adenosylmethionine production. Asian Pac J Cancer Prev 2015; 14:6433-8. [PMID: 24377546 DOI: 10.7314/apjcp.2013.14.11.6433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In hepatocellular cancer (HCC), lack of response to chemotherapy and radiation treatment can be caused by a loss of epigenetic modifications of cancer cells. Methionine adenosyltransferase 1A is inactivated in HCC and may be stimulated by an epigenetic change involving promoter hypermethylation. Therefore, drugs releasing epigenetic repression have been proposed to reverse this process. We studied the effect of the demethylating reagent 5-aza-2<-deoxycitidine (5-Aza-CdR) on MAT1A gene expression, DNA methylation and S-adenosylmethionine (SAMe) production in the HCC cell line Huh7. We found that MAT1A mRNA and protein expression were activated in Huh7 cells with the treatment of 5-Aza-CdR; the status of promoter hypermethylation was reversed. At the same time, MAT2A mRNA and protein expression was significantly reduced in Huh7 cells treated with 5-Aza-CdR, while SAMe production was significantly induced. However, 5-Aza-CdR showed no effects on MAT2A methylation. Furthermore, 5-Aza-CdR inhibited the growth of Huh7 cells and induced apoptosis and through down-regulation of Bcl-2, up-regulation of Bax and caspase-3. Our observations suggest that 5-Aza- CdR exerts its anti-tumor effects in Huh7 cells through an epigenetic change involving increased expression of the methionine adenosyltransferase 1A gene and induction of S-adenosylmethionine production.
Collapse
Affiliation(s)
- Wei-Jun Liu
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital, Wuhan University, Wuhan, China E-mail : lqy@whu. edu.cn,
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Henning SM, Wang P, Carpenter CL, Heber D. Epigenetic effects of green tea polyphenols in cancer. Epigenomics 2014; 5:729-41. [PMID: 24283885 DOI: 10.2217/epi.13.57] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Epigenetics describes heritable alterations of gene expression and chromatin organization without changes in DNA sequence. Both hypermethylation and hypomethylation of DNA can affect gene expression and the multistep process of carcinogenesis. Epigenetic changes are reversible and may be targeted by dietary interventions. Bioactive compounds from green tea (GT) such as (-)-epigallocatechin gallate have been shown to alter DNA methyltransferase activity in studies of esophageal, oral, skin, Tregs, lung, breast and prostate cancer cells, which may contribute to the chemopreventive effect of GT. Three out of four mouse model studies have confirmed the inhibitory effect of (-)-epigallocatechin gallate on DNA methylation. A human study demonstrated that decreased methylation of CDX2 and BMP-2 in gastric carcinoma was associated with higher GT consumption. It is the goal of this review to summarize our current knowledge of the potential of GT to alter epigenetic processes, which may be useful in chemoprevention.
Collapse
Affiliation(s)
- Susanne M Henning
- Center for Human Nutrition, David Geffen School of Medicine, University of California Los Angeles, 900 Veteran Avenue, Warren Hall 14-166, Los Angeles, CA 90095, USA
| | | | | | | |
Collapse
|
39
|
Krasilnikova MM. Complexes between two GAA Repeats within DNA introduced into Cos-1 cells. Mob Genet Elements 2014; 2:267-271. [PMID: 23481169 PMCID: PMC3575420 DOI: 10.4161/mge.23194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We have recently shown that GAA repeats severely impede replication elongation during the first replication cycle of transfected DNA wherein the chromatin is still at the formation stage.1 Here we extend this study by showing that two GAA repeats located within the same plasmid in the direct orientation can form complexes upon transient transfection of mammalian Cos-1 cells. However, these complexes do not form in DNA that went through several replication rounds in mammalian cells. We suggest that formation of such complexes in mammalian genomes can contribute to genomic instability.
Collapse
|
40
|
Abstract
INTRODUCTION There is certain degree of frustration and discontent in the area of microarray gene expression data analysis of cancer datasets. It arises from the mathematical problem called 'curse of dimensionality,' which is due to the small number of samples available in training sets, used for calculating transcriptional signatures from the large number of differentially expressed (DE) genes, measured by microarrays. The new generation of causal reasoning algorithms can provide solutions to the curse of dimensionality by transforming microarray data into activity of a small number of cancer hallmark pathways. This new approach can make feature space dimensionality optimal for mathematical signature calculations. AREAS COVERED The author reviews the reasons behind the current frustration with transcriptional signatures derived from DE genes in cancer. He also provides an overview of the novel methods for signature calculations based on differentially variable genes and expression regulators. Furthermore, the authors provide perspectives on causal reasoning algorithms that use prior knowledge about regulatory events described in scientific literature to identify expression regulators responsible for the differential expression observed in cancer samples. EXPERT OPINION The author advocates causal reasoning methods to calculate cancer pathway activity signatures. The current challenge for these algorithms is in ensuring quality of the knowledgebase. Indeed, the development of cancer hallmark pathway collections, together with statistical algorithms to transform activity of expression regulators into pathway activity, are necessary for causal reasoning to be used in cancer research.
Collapse
Affiliation(s)
- Anton Yuryev
- Elsevier, Inc. , 5635 Fishers Lane, Rockville, MD 20852 USA
| |
Collapse
|
41
|
Watanabe Y, Shibata K, Maekawa M. Cell line differences in replication timing of human glutamate receptor genes and other large genes associated with neural disease. Epigenetics 2014; 9:1350-9. [PMID: 25437050 PMCID: PMC4622467 DOI: 10.4161/15592294.2014.967585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/04/2014] [Accepted: 09/11/2014] [Indexed: 01/30/2023] Open
Abstract
There is considerable current interest in the function of epigenetic mechanisms in neuroplasticity with regard to learning and memory formation and to a range of neural diseases. Previously, we described replication timing on human chromosome 21q in the THP-1 human cell line (2n = 46, XY) and showed that several genes associated with neural diseases, such as the neuronal glutamate receptor subunit GluR-5 (GRIK1) and amyloid precursor protein (APP), were located in regions where replication timing transitioned from early to late S phase. Here, we compared replication timing of all known human glutamate receptor genes (26 genes in total) and APP in 6 different human cell lines including human neuron-related cell lines. Replication timings were obtained by integrating our previously reported data with new data generated here and information from the online database ReplicationDomain. We found that many of the glutamate receptor genes were clearly located in replication timing transition zones in neural precursor cells, but this relationship was less clear in embryonic stem cells before neural differentiation; in the latter, the genes were often located in later replication timing zones that displayed DNA hypermethylation. Analysis of selected large glutamate receptor genes (> 200 kb), and of APP, showed that their precise replication timing patterns differed among the cell lines. We propose that the transition zones of DNA replication timing are altered by epigenetic mechanisms, and that these changes may affect the neuroplasticity that is important to memory and learning, and may also have a role in the development of neural diseases.
Collapse
Affiliation(s)
- Yoshihisa Watanabe
- Department of Laboratory Medicine; Hamamatsu University School of Medicine; Hamamatsu, Japan
| | - Kiyoshi Shibata
- Research Equipment Center; Hamamatsu University School of Medicine; Hamamatsu, Japan
| | - Masato Maekawa
- Department of Laboratory Medicine; Hamamatsu University School of Medicine; Hamamatsu, Japan
| |
Collapse
|
42
|
Batra V, Verma P. Dietary l-methionine supplementation mitigates gamma-radiation induced global DNA hypomethylation: Enhanced metabolic flux towards S-adenosyl-l-methionine (SAM) biosynthesis increases genomic methylation potential. Food Chem Toxicol 2014; 69:46-54. [DOI: 10.1016/j.fct.2014.03.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/11/2014] [Accepted: 03/28/2014] [Indexed: 01/23/2023]
|
43
|
Gorlov IP, Yang JY, Byun J, Logothetis C, Gorlova OY, Do KA, Amos C. How to get the most from microarray data: advice from reverse genomics. BMC Genomics 2014; 15:223. [PMID: 24656147 PMCID: PMC3997969 DOI: 10.1186/1471-2164-15-223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 03/10/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Whole-genome profiling of gene expression is a powerful tool for identifying cancer-associated genes. Genes differentially expressed between normal and tumorous tissues are usually considered to be cancer associated. We recently demonstrated that the analysis of interindividual variation in gene expression can be useful for identifying cancer associated genes. The goal of this study was to identify the best microarray data-derived predictor of known cancer associated genes. RESULTS We found that the traditional approach of identifying cancer genes--identifying differentially expressed genes--is not very efficient. The analysis of interindividual variation of gene expression in tumor samples identifies cancer-associated genes more effectively. The results were consistent across 4 major types of cancer: breast, colorectal, lung, and prostate. We used recently reported cancer-associated genes (2011-2012) for validation and found that novel cancer-associated genes can be best identified by elevated variance of the gene expression in tumor samples. CONCLUSIONS The observation that the high interindividual variation of gene expression in tumor tissues is the best predictor of cancer-associated genes is likely a result of tumor heterogeneity on gene level. Computer simulation demonstrates that in the case of heterogeneity, an assessment of variance in tumors provides a better identification of cancer genes than does the comparison of the expression in normal and tumor tissues. Our results thus challenge the current paradigm that comparing the mean expression between normal and tumorous tissues is the best approach to identifying cancer-associated genes; we found that the high interindividual variation in expression is a better approach, and that using variation would improve our chances of identifying cancer-associated genes.
Collapse
Affiliation(s)
- Ivan P Gorlov
- Department of Genitourinary Medical Oncology, Unit 1374, The University of Texas MD Anderson Cancer Center, 1155 Pressler Street, Houston, TX 77030-3721, USA.
| | | | | | | | | | | | | |
Collapse
|
44
|
E2F1 coregulates cell cycle genes and chromatin components during the transition of oligodendrocyte progenitors from proliferation to differentiation. J Neurosci 2014; 34:1481-93. [PMID: 24453336 DOI: 10.1523/jneurosci.2840-13.2014] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cell cycle exit is an obligatory step for the differentiation of oligodendrocyte progenitor cells (OPCs) into myelinating cells. A key regulator of the transition from proliferation to quiescence is the E2F/Rb pathway, whose activity is highly regulated in physiological conditions and deregulated in tumors. In this paper we report a lineage-specific decline of nuclear E2F1 during differentiation of rodent OPC into oligodendrocytes (OLs) in developing white matter tracts and in cultured cells. Using chromatin immunoprecipitation (ChIP) and deep-sequencing in mouse and rat OPCs, we identified cell cycle genes (i.e., Cdc2) and chromatin components (i.e., Hmgn1, Hmgn2), including those modulating DNA methylation (i.e., Uhrf1), as E2F1 targets. Binding of E2F1 to chromatin on the gene targets was validated and their expression assessed in developing white matter tracts and cultured OPCs. Increased expression of E2F1 gene targets was also detected in mouse gliomas (that were induced by retroviral transformation of OPCs) compared with normal brain. Together, these data identify E2F1 as a key transcription factor modulating the expression of chromatin components in OPC during the transition from proliferation to differentiation.
Collapse
|
45
|
Wang Y, Kong CZ, Zhang Z, Yang CM, Li J. Role of CDH1 promoter polymorphism and DNA methylation in bladder carcinogenesis: a meta-analysis. DNA Cell Biol 2014; 33:205-16. [PMID: 24491043 DOI: 10.1089/dna.2013.2100] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Increasing scientific evidences suggest that CDH1 gene promoter polymorphism and DNA methylation may contribute to the development and progression of bladder cancer, but many existing studies have yielded inconclusive results. This meta-analysis aims to assess the role of CDH1 gene promoter polymorphism and methylation in bladder carcinogenesis. An extensive literature search for relevant studies was conducted in PubMed, Embase, Web of Science, Cochrane Library, and CBM databases from their inception through April 1, 2013. This meta-analysis was performed using the STATA 12.0 software. The crude odds ratio with 95% confidence interval was calculated. Fifteen studies were included in this meta-analysis with a total of 824 bladder cancer patients and 818 healthy controls being assessed. Our meta-analysis revealed that the A variant of CDH1 -160C/A polymorphism was associated with an increased risk of bladder cancer. Further analysis by pathological subtype indicated that patients with invasive carcinoma had a higher frequency of CDH1 -160A variant than those with superficial carcinoma. We analyzed the methylation frequency of CDH1 gene in 608 bladder cancer samples and 338 normal bladder samples. Our data strongly suggest that the CDH1 promoter methylation frequencies in bladder cancer tissues were greater than those in normal control tissues. In conclusion, our meta-analysis indicates that promoter polymorphism and methylation of CDH1 gene may be involved in the development and progression of bladder cancer. CDH1 gene promoter polymorphism and methylation might be promising biomarkers for the diagnosis and prognosis of bladder cancer.
Collapse
Affiliation(s)
- Yi Wang
- Department of Urology, The First Affiliated Hospital of China Medical University , Shenyang, People's Republic of China
| | | | | | | | | |
Collapse
|
46
|
Fang L, Wuptra K, Chen D, Li H, Huang SK, Jin C, Yokoyama KK. Environmental-stress-induced Chromatin Regulation and its Heritability. ACTA ACUST UNITED AC 2014; 5. [PMID: 25045581 PMCID: PMC4101908 DOI: 10.4172/2157-2518.1000156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatin is subject to proofreading and repair mechanisms during the process of DNA replication, as well as repair to maintain genetic and epigenetic information and genome stability. The dynamic structure of chromatin modulates various nuclear processes, including transcription and replication, by altering the accessibility of the DNA to regulatory factors. Structural changes in chromatin are affected by the chemical modification of histone proteins and DNA, remodeling of nucleosomes, incorporation of variant histones, noncoding RNAs, and nonhistone DNA-binding proteins. Phenotypic diversity and fidelity can be balanced by controlling stochastic switching of chromatin structure and dynamics in response to the environmental disruptors and endogenous stresses. The dynamic chromatin remodeling can, therefore, serve as a sensor, through which environmental and/or metabolic agents can alter gene expression, leading to global cellular changes involving multiple interactive networks. Furthermore its recent evidence also suggests that the epigenetic changes are heritable during the development. This review will discuss the environmental sensing system for chromatin regulation and genetic and epigenetic controls from developmental perspectives.
Collapse
Affiliation(s)
- Lei Fang
- Department of Environmental Medicine, NYU School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
| | - Kenly Wuptra
- Center of Environmental Medicine, Graduate Institute of Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Rd, San Ming District, Kaohsiung 807, Taiwan ; Division of Environmental Health and Occupational Medicine, National Health Research Institutes, 35 Keyan Rd, Zhunan, Miaoli County 350, Taiwan
| | - Danqi Chen
- Department of Environmental Medicine, NYU School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
| | - Hongjie Li
- Department of Environmental Medicine, NYU School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
| | - Shau-Ku Huang
- Division of Environmental Health and Occupational Medicine, National Health Research Institutes, 35 Keyan Rd, Zhunan, Miaoli County 350, Taiwan ; Johns Hopkins Asthma and Allergy Center, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Chunyuan Jin
- Department of Environmental Medicine, NYU School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
| | - Kazunari K Yokoyama
- Center of Environmental Medicine, Graduate Institute of Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Rd, San Ming District, Kaohsiung 807, Taiwan
| |
Collapse
|
47
|
Stefanoli M, La Rosa S, Sahnane N, Romualdi C, Pastorino R, Marando A, Capella C, Sessa F, Furlan D. Prognostic relevance of aberrant DNA methylation in g1 and g2 pancreatic neuroendocrine tumors. Neuroendocrinology 2014; 100:26-34. [PMID: 25011998 DOI: 10.1159/000365449] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/23/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND/AIMS The occurrence and clinical relevance of DNA hypermethylation and global hypomethylation in pancreatic neuroendocrine tumours (PanNETs) are still unknown. We evaluated the frequency of both epigenetic alterations in PanNETs to assess the relationship between methylation profiles and chromosomal instability, tumour phenotypes and prognosis. METHODS In a well-characterized series of 56 sporadic G1 and G2 PanNETs, methylation-sensitive multiple ligation-dependent probe amplification was performed to assess hypermethylayion of 33 genes and copy number alterations (CNAs) of 53 chromosomal regions. Long interspersed nucleotide element-1 (LINE-1) hypomethylation was quantified by pyrosequencing. RESULTS Unsupervised hierarchical clustering allowed to identify a subset of 22 PanNETs (39%) exhibiting high frequency of gene-specific methylation and low CNA percentages. This tumour cluster was significantly associated with stage IV (p = 0.04) and with poor prognosis in univariable analysis (p = 0.004). LINE-1 methylation levels in PanNETs were significantly lower than in normal samples (p < 0.01) and were approximately normally distributed. 12 tumours (21%) were highly hypomethylated, showing variable levels of CNA. Interestingly, only 5 PanNETs (9%) were observed to show simultaneously LINE-1 hypomethylation and high frequency of gene-specific methylation. LINE-1 hypomethylation was strongly correlated with advanced stage (p = 0.002) and with poor prognosis (p < 0.0001). In the multivariable analysis, low LINE-1 methylation status and methylation clusters were the only independent significant predictors of outcome (p = 0.034 and p = 0.029, respectively). CONCLUSION The combination of global DNA hypomethylation and gene hypermethylation analyses may be useful to define distinct subsets of PanNETs. Both alterations are common in PanNETs and could be directly correlated with tumour progression.
Collapse
Affiliation(s)
- Michele Stefanoli
- Section of Anatomic Pathology, Department of Surgical and Morphological Sciences, University of Insubria and Ospedale di Circolo, Varese, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Chen H, Kazemier HG, de Groote ML, Ruiters MHJ, Xu GL, Rots MG. Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter. Nucleic Acids Res 2013; 42:1563-74. [PMID: 24194590 PMCID: PMC3919596 DOI: 10.1093/nar/gkt1019] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxidation. Aberrant DNA methylation profiles are associated with many diseases. For example in cancer, hypermethylation results in silencing of tumor suppressor genes. Such silenced genes can be re-expressed by epigenetic drugs, but this approach has genome-wide effects. In this study, fusions of designer DNA binding domains to TET dioxygenase family members (TET1, -2 or -3) were engineered to target epigenetically silenced genes (ICAM-1, EpCAM). The effects on targeted CpGs’ methylation and on expression levels of the target genes were assessed. The results indicated demethylation of targeted CpG sites in both promoters for targeted TET2 and to a lesser extent for TET1, but not for TET3. Interestingly, we observed re-activation of transcription of ICAM-1. Thus, our work suggests that we provided a mechanism to induce targeted DNA demethylation, which facilitates re-activation of expression of the target genes. Furthermore, this Epigenetic Editing approach is a powerful tool to investigate functions of epigenetic writers and erasers and to elucidate consequences of epigenetic marks.
Collapse
Affiliation(s)
- Hui Chen
- Epigenetic Editing, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein1, 9713 GZ Groningen, The Netherlands, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and Synvolux Therapeutics Inc., LJ. Zielstraweg 1, 9713 GX Groningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
49
|
Ammal Kaidery N, Tarannum S, Thomas B. Epigenetic landscape of Parkinson's disease: emerging role in disease mechanisms and therapeutic modalities. Neurotherapeutics 2013; 10:698-708. [PMID: 24030213 PMCID: PMC3805874 DOI: 10.1007/s13311-013-0211-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Parkinson's disease (PD) is a complex multifactorial disorder marked by extensive system-wide pathology, including a substantial loss of nigrostriatal dopaminergic neurons. The etiology of PD remains elusive, but there is considerable evidence that, in addition to well-defined genetic mechanisms environmental factors play a crucial role in disease pathogenesis. How the environment might influence the genetic factors and contribute to disease development and progression remains unclear. In recent years, epigenetic mechanisms such as DNA methylation, chromatin remodeling and alterations in gene expression via non-coding RNAs have begun to be revealed as potential factors in PD pathogenesis. Epigenetic modulation exists throughout life, beginning in prenatal stages, is dependent on the lifestyle, environmental exposure and genetic makeup of an individual and may serve as a missing link between PD risk factors and development of the disease. This chapter sheds light on the emerging role of epigenetics in disease pathogenesis and on prospective interventional strategies for the therapeutic modulation of PD.
Collapse
Affiliation(s)
- Navneet Ammal Kaidery
- />Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents University, 1459 Laney Walker Blvd, CB-3618, 30912 Augusta, Georgia
| | - Shaista Tarannum
- />Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents University, 1459 Laney Walker Blvd, CB-3618, 30912 Augusta, Georgia
| | - Bobby Thomas
- />Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents University, 1459 Laney Walker Blvd, CB-3618, 30912 Augusta, Georgia
- />Department of Neurology, Medical College of Georgia, Georgia Regents University, 1459 Laney Walker Blvd, CB-3618, 30912 Augusta, Georgia
| |
Collapse
|
50
|
The conceptualization and measurement of comorbidity: a review of the interprofessional discourse. Nurs Res Pract 2013; 2013:192782. [PMID: 24187618 PMCID: PMC3800641 DOI: 10.1155/2013/192782] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 08/16/2013] [Indexed: 11/17/2022] Open
Abstract
Background. Chronic medical conditions often occur in combination. Understanding underlying mechanisms causing diseases and their interactions may make it possible to address multiple complex conditions with single or consolidated treatment approaches and improve patients' health outcomes while reducing costs. Objectives. We present a synthesis of the current interprofessional discourse on the issues surrounding comorbidities. Methods. A targeted review of the literature was conducted using published editorials, commentaries, and review articles. Results. Errors in conceptualization and measurement plague our current understanding of comorbidities. Two potential paths to generating knowledge involve the use of etiological or epidemiological approach. An etiological approach investigates the risk factors and underlying mechanisms potentially leading to consolidation of diagnosis and treatments. Because of the rudimentary stage of knowledge development in this area, this approach will require time and significant research investments. In contrast, the epidemiological approach relies on statistical identification of disease entities that cooccur beyond random chance; this approach carries an accompanying risk of diagnostic and treatment proliferation. Discussion. The concept of comorbidity, its nature, and measurement is in need of meaningful debate by the scientific and clinical communities. Recommendations in the domains of conceptualization, research, and measurement are discussed.
Collapse
|