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Jung SY, Yu H, Tan X, Pellegrini M. Novel DNA methylation-based epigenetic signatures in colorectal cancer from peripheral blood leukocytes. Am J Cancer Res 2024; 14:2253-2271. [PMID: 38859857 PMCID: PMC11162685 DOI: 10.62347/mxwj1398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/21/2024] [Indexed: 06/12/2024] Open
Abstract
Colorectal cancer (CRC) is a multifactorial disease characterized by accumulation of multiple genetic and epigenetic alterations, transforming colonic epithelial cells into adenocarcinomas. Alteration of DNA methylation (DNAm) is a promising biomarker for predicting cancer risk and prognosis, but its role in CRC tumorigenesis is inconclusive. Notably, few DNAm studies have used pre-diagnostic peripheral blood (PB) DNA, causing difficulty in postulating the underlying biologic mechanism of CRC initiation. We conducted epigenome-wide association (EWA) scans in postmenopausal women from Women's Health Initiative (WHI) with their pre-diagnostic DNAm in PB leukocytes (PBLs) to prospectively evaluate CRC development. Our site-specific DNAm analyses across the genome adjusted for DNAm-age, leukocyte heterogeneities, as well as body mass index, diabetes, and insulin resistance. We validated 20 top EWA-CpGs in 2 independent CRC tissue datasets. Also, we detected differentially methylated regions (DMRs) associated with CRC, further mapped to transcriptomic profile, and finally conducted a Gene Set Enrichment Analysis. We detected multiple novel CpGs validated across WHI and tissue datasets. In particular, 2 CpGs (B4GALNT4cg10321339, SV2Bcg18144285) had the strongest effect on CRC risk. Results from our DMR scans contained MIR663cg06007966, which was also validated in EWA analyses. Also, we detected 1 methylome region in PEG10 of Chr7 shared across datasets. Our findings reflect both novel and well-established epigenomic and transcriptomic sites in CRC, warranting further functional validations. Our study contributes to better understanding of the complex interrelated mechanisms on the methylome underlying CRC tumorigenesis and suggests novel preventive DNAm-targets in PBLs for detecting at-risk individuals for CRC development.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, School of Nursing, University of CaliforniaLos Angeles, CA 90095, USA
- Department of Epidemiology, Fielding School of Public Health, University of CaliforniaLos Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of CaliforniaLos Angeles, CA 90095, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer CenterHonolulu, HI 96813, USA
| | - Xianglong Tan
- Department of Biological Chemistry, University of CaliforniaLos Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Life Sciences Division, University of CaliforniaLos Angeles, CA 90095, USA
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2
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Li NN, Lun DX, Gong N, Meng G, Du XY, Wang H, Bao X, Li XY, Song JW, Hu K, Li L, Li SY, Liu W, Zhu W, Zhang Y, Li J, Yao T, Mou L, Han X, Hao F, Hu Y, Liu L, Zhu H, Wu Y, Liu B. Targeting the chromatin structural changes of antitumor immunity. J Pharm Anal 2024; 14:100905. [PMID: 38665224 PMCID: PMC11043877 DOI: 10.1016/j.jpha.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 04/28/2024] Open
Abstract
Epigenomic imbalance drives abnormal transcriptional processes, promoting the onset and progression of cancer. Although defective gene regulation generally affects carcinogenesis and tumor suppression networks, tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes, which may have significant implications for the development and application of epigenetic therapy, cancer immunotherapy, and their combinations. Herein, we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes, DNA methylation, histone post-translational modification, and chromatin structure in tumor immunogenicity, and introduce these epigenetic research methods. We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immunotherapy through the complex interaction between cancer epigenetics and cancer immunology.
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Affiliation(s)
- Nian-nian Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Deng-xing Lun
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Ningning Gong
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Gang Meng
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, Shaanxi, 725000, China
| | - Xin-ying Du
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - He Wang
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiangxiang Bao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xin-yang Li
- Guizhou Education University, Guiyang, 550018, China
| | - Ji-wu Song
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Kewei Hu
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Lala Li
- Guizhou Normal University, Guiyang, 550025, China
| | - Si-ying Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wenbo Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wanping Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yunlong Zhang
- School of Medical Imaging, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jikai Li
- Department of Bone and Soft Tissue Oncology, Tianjin Hospital, Tianjin, 300299, China
| | - Ting Yao
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
| | - Leming Mou
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiaoqing Han
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Furong Hao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yongcheng Hu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Lin Liu
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hongguang Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yuyun Wu
- Xinqiao Hospital of Army Military Medical University, Chongqing, 400038, China
| | - Bin Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
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3
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Lu YW, Ding ZL, Mao R, Zhao GG, He YQ, Li XL, Liu J. Early results of the integrative epigenomic-transcriptomic landscape of colorectal adenoma and cancer. World J Gastrointest Oncol 2024; 16:414-435. [PMID: 38425399 PMCID: PMC10900154 DOI: 10.4251/wjgo.v16.i2.414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/24/2023] [Accepted: 12/22/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Aberrant methylation is common during the initiation and progression of colorectal cancer (CRC), and detecting these changes that occur during early adenoma (ADE) formation and CRC progression has clinical value. AIM To identify potential DNA methylation markers specific to ADE and CRC. METHODS Here, we performed SeqCap targeted bisulfite sequencing and RNA-seq analysis of colorectal ADE and CRC samples to profile the epigenomic-transcriptomic landscape. RESULTS Comparing 22 CRC and 25 ADE samples, global methylation was higher in the former, but both showed similar methylation patterns regarding differentially methylated gene positions, chromatin signatures, and repeated elements. High-grade CRC tended to exhibit elevated methylation levels in gene promoter regions compared to those in low-grade CRC. Combined with RNA-seq gene expression data, we identified 14 methylation-regulated differentially expressed genes, of which only AGTR1 and NECAB1 methylation had prognostic significance. CONCLUSION Our results suggest that genome-wide alterations in DNA methylation occur during the early stages of CRC and demonstrate the methylation signatures associated with colorectal ADEs and CRC, suggesting prognostic biomarkers for CRC.
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Affiliation(s)
- You-Wang Lu
- Department of Dermatology and Venereology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
| | - Zhao-Li Ding
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Public Technical Service Center, Kunming Institute of Zoology, Kunming 650223, Yunnan Province, China
| | - Rui Mao
- School of Stomatology, Kunming Medical University, Kunming 650500, Yunnan Province, China
| | - Gui-Gang Zhao
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, Yunnan Province, China
| | - Yu-Qi He
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, Yunnan Province, China
| | - Xiao-Lu Li
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, Yunnan Province, China
| | - Jiang Liu
- Department of Reproduction and Genetics, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
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Lu H, Liu Y, Wang J, Fu S, Wang L, Huang C, Li J, Xie L, Wang D, Li D, Zhou H, Rao Q. Detection of ovarian cancer using plasma cell-free DNA methylomes. Clin Epigenetics 2022; 14:74. [PMID: 35681212 PMCID: PMC9185905 DOI: 10.1186/s13148-022-01285-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/09/2022] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Ovarian cancer (OC) is a highly lethal gynecologic cancer, and it is hard to diagnose at an early stage. Clinically, there are no ovarian cancer-specific markers for early detection. Here, we demonstrate the use of cell-free DNA (cfDNA) methylomes to detect ovarian cancer, especially the early-stage OC. EXPERIMENTAL DESIGN Plasma from 74 epithelial ovarian cancer patients, 86 healthy volunteers, and 20 patients with benign pelvic masses was collected. The cfDNA methylomes of these samples were generated by cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq). The differentially methylated regions (DMRs) were identified by the contrasts between tumor and non-tumor groups, and the discrimination performance was evaluated with the iterative training and testing method. RESULTS The DMRs identified for cfDNA methylomes can well discriminate tumor groups and non-tumor groups (ROC values from 0.86 to 0.98). The late-stage top 300 DMRs are more late-stage-specific and failed to detect early-stage OC. However, the early-stage markers have the potential to discriminate all-stage OCs from non-tumor samples. CONCLUSIONS This study demonstrates that cfDNA methylomes generated with cfMeDIP-seq could be used to identify OC-specific biomarkers for OC, especially early OC detection. To detect early-stage OC, the biomarkers should be directly identified from early OC plasma samples rather than mix-stage ones. Further exploration of DMRs from a k larger early-stage OC cohort is warranted.
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Affiliation(s)
- Huaiwu Lu
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yunyun Liu
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jingyu Wang
- Shanghai Danbei Medical Technology Co., Ltd, Shanghai, China
| | - Shaliu Fu
- Shanghai Danbei Medical Technology Co., Ltd, Shanghai, China
| | - Lingping Wang
- Shanghai Danbei Medical Technology Co., Ltd, Shanghai, China
| | - Chunxian Huang
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jing Li
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lingling Xie
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dongyan Wang
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dan Li
- Shanghai Danbei Medical Technology Co., Ltd, Shanghai, China
| | - Hui Zhou
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Qunxian Rao
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China.
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5
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Gebrekiristos M, Melson J, Jiang A, Buckingham L. DNA methylation and miRNA expression in colon adenomas compared with matched normal colon mucosa and carcinomas. Int J Exp Pathol 2022; 103:74-82. [PMID: 35229372 DOI: 10.1111/iep.12432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/10/2021] [Accepted: 02/08/2022] [Indexed: 01/28/2023] Open
Abstract
Dysregulation of DNA methylation patterns and non-coding RNA, including miRNAs, has been implicated in colon cancer, and these changes may occur early in the development of carcinoma. In this study, the role of epigenetics as early changes in colon tumorigenesis was examined through paired sample analysis of patient-matched normal, adenoma and carcinoma samples. Global methylation was assessed by genomic 5-methyl cytosine (5-mC) and long interspersed nuclear element-1 (LINE-1) promoter methylation by pyrosequencing. KRAS mutations were also assessed by pyrosequencing. Expression of miRNA, specifically, two microRNA genes-miR-200a and let-7c-was analysed using RT-qPCR. Differences in global methylation in adenomas were not observed, compared with normal tissue. However, LINE-1 methylation was decreased in adenomas (p = .056) and carcinomas (p = .011) compared with normal tissue. Expressions of miRNA, miR-200a and let-7c were significantly higher in adenomas than normal tissues (p = .008 and p = .045 respectively). Thus the significant changes in LINE-1 methylation and microRNA expression in precancerous lesions support an early role for epigenetic changes in the carcinogenic process. Epigenetic characteristics in adenomas may provide potential diagnostic and prognostic therapeutic targets early in cancer development at the adenoma stage.
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Affiliation(s)
- Mezgebe Gebrekiristos
- Department of Medical Laboratory Science, Rush University College of Health Sciences, Chicago, Illinois, USA
| | - Joshua Melson
- Department of Gastroenterology, Rush University Medical Center, Chicago, Illinois, USA
| | - Alice Jiang
- Department of Gastroenterology, Rush University Medical Center, Chicago, Illinois, USA
| | - Lela Buckingham
- Department of Medical Laboratory Science, Rush University College of Health Sciences, Chicago, Illinois, USA
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6
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Heery R, Schaefer MH. DNA methylation variation along the cancer epigenome and the identification of novel epigenetic driver events. Nucleic Acids Res 2021; 49:12692-12705. [PMID: 34871444 PMCID: PMC8682778 DOI: 10.1093/nar/gkab1167] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
While large-scale studies applying various statistical approaches have identified hundreds of mutated driver genes across various cancer types, the contribution of epigenetic changes to cancer remains more enigmatic. This is partly due to the fact that certain regions of the cancer genome, due to their genomic and epigenomic properties, are more prone to dysregulated DNA methylation than others. Thus, it has been difficult to distinguish which promoter methylation changes are really driving carcinogenesis from those that are mostly just a reflection of their genomic location. By developing a novel method that corrects for epigenetic covariates, we reveal a small, concise set of potential epigenetic driver events. Interestingly, those changes suggest different modes of epigenetic carcinogenesis: first, we observe recurrent inactivation of known cancer genes across tumour types suggesting a higher convergence on common tumour suppressor pathways than previously anticipated. Second, in prostate cancer, a cancer type with few recurrently mutated genes, we demonstrate how the epigenome primes tumours towards higher tolerance of other aberrations.
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Affiliation(s)
- Richard Heery
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Martin H Schaefer
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
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7
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Nikolaienko O, Lønning PE, Knappskog S. ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions. Bioinformatics 2021; 38:133-140. [PMID: 34383893 PMCID: PMC8696093 DOI: 10.1093/bioinformatics/btab586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/26/2021] [Accepted: 08/11/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION With recent advances in the field of epigenetics, the focus is widening from large and frequent disease- or phenotype-related methylation signatures to rare alterations transmitted mitotically or transgenerationally (constitutional epimutations). Merging evidence indicate that such constitutional alterations, albeit occurring at a low mosaic level, may confer risk of disease later in life. Given their inherently low incidence rate and mosaic nature, there is a need for bioinformatic tools specifically designed to analyze such events. RESULTS We have developed a method (ramr) to identify aberrantly methylated DNA regions (AMRs). ramr can be applied to methylation data obtained by array or next-generation sequencing techniques to discover AMRs being associated with elevated risk of cancer as well as other diseases. We assessed accuracy and performance metrics of ramr and confirmed its applicability for analysis of large public datasets. Using ramr we identified aberrantly methylated regions that are known or may potentially be associated with development of colorectal cancer and provided functional annotation of AMRs that arise at early developmental stages. AVAILABILITY AND IMPLEMENTATION The R package is freely available at https://github.com/BBCG/ramr and https://bioconductor.org/packages/ramr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Per Eystein Lønning
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Oncology, Haukeland University Hospital, Bergen, Norway
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Peng Y, Zhao J, Yin F, Sharen G, Wu Q, Chen Q, Sun X, Yang J, Wang H, Zhang D. A methylation-driven gene panel predicts survival in patients with colon cancer. FEBS Open Bio 2021; 11:2490-2506. [PMID: 34184409 PMCID: PMC8409306 DOI: 10.1002/2211-5463.13242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/14/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
The accumulation of various genetic and epigenetic changes in colonic epithelial cells has been identified as one of the fundamental processes that drive the initiation and progression of colorectal cancer (CRC). This study aimed to explore functional genes regulated by DNA methylation and their potential utilization as biomarkers for the prediction of CRC prognoses. Methylation‐driven genes (MDGs) were explored by applying the integrative analysis tool (methylmix) to The Cancer Genome Atlas CRC project. The prognostic MDG panel was identified by combining the Cox regression model with the least absolute shrinkage and selection operator regularization. Gene set enrichment analysis was used to determine the pathways associated with the six‐MDG panel. Cluster of differentiation 40 (CD40) expression and methylation in CRC samples were validated by using additional datasets from the Gene Expression Omnibus. Methylation‐specific PCR and bisulfite sequencing were used to confirm DNA methylation in CRC cell lines. A prognostic MDG panel consisting of six gene members was identified: TMEM88, HOXB2, FGD1, TOGARAM1, ARHGDIB and CD40. The high‐risk phenotype classified by the six‐MDG panel was associated with cancer‐related biological processes, including invasion and metastasis, angiogenesis and the tumor immune microenvironment. The prognostic value of the six‐MDG panel was found to be independent of tumor node metastasis stage and, in combination with tumor node metastasis stage and age, could help improve survival prediction. In addition, the expression of CD40 was confirmed to be regulated by promoter region methylation in CRC samples and cell lines. The proposed six‐MDG panel represents a promising signature for estimating the prognosis of patients with CRC.
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Affiliation(s)
- Yaojun Peng
- Emergency Department, The First Medical Center, Chinese PLA General Hospital, Beijing, China.,College of Graduate, Chinese PLA General Hospital, Beijing, China
| | - Jing Zhao
- Department of Scientific Research Administration, Chinese PLA General Hospital, Beijing, China
| | - Fan Yin
- Department of Oncology, The Second Medical Center & National Clinical Research Center of Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Gaowa Sharen
- Department of Pathology, The First Affiliated Hospital of Inner Mongolia Medical University, Hohhot City, China
| | - Qiyan Wu
- Department of Oncology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qi Chen
- Department of Traditional Chinese Medicine, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaoxuan Sun
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, China.,Department of Oncology Surgery, Tianjin Cancer Hospital Airport Free Trade Zone Hospital, China
| | - Juan Yang
- Department of Cardiothoracic Surgery, Tianjin Fourth Center Hospital, China
| | - Huan Wang
- Department of Scientific Research Administration, Chinese PLA General Hospital, Beijing, China
| | - Dong Zhang
- Department of Oncology, The Second Medical Center & National Clinical Research Center of Geriatric Disease, Chinese PLA General Hospital, Beijing, China
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9
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Wang YH, Chang SC, Ansar M, Hung CS, Lin RK. Eps15 Homology Domain-Containing Protein 3 Hypermethylation as a Prognostic and Predictive Marker for Colorectal Cancer. Biomedicines 2021; 9:biomedicines9050453. [PMID: 33922189 PMCID: PMC8145505 DOI: 10.3390/biomedicines9050453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) arises from chromosomal instability, resulting from aberrant hypermethylation in tumor suppressor genes. This study identified hypermethylated genes in CRC and investigated how they affect clinical outcomes. Methylation levels of specific genes were analyzed from The Cancer Genome Atlas dataset and 20 breast cancer, 16 esophageal cancer, 33 lung cancer, 15 uterine cancer, 504 CRC, and 9 colon polyp tissues and 102 CRC plasma samples from a Taiwanese cohort. In the Asian cohort, Eps15 homology domain-containing protein 3 (EHD3) had twofold higher methylation in 44.4% of patients with colonic polyps, 37.3% of plasma from CRC patients, and 72.6% of CRC tissues, which was connected to vascular invasion and high microsatellite instability. Furthermore, EHD3 hypermethylation was detected in other gastrointestinal cancers. In the Asian CRC cohort, low EHD3 mRNA expression was found in 45.1% of patients and was connected to lymph node metastasis. Multivariate Cox proportional-hazards survival analysis revealed that hypermethylation in women and low mRNA expression were associated with overall survival. In the Western CRC cohort, EHD3 hypermethylation was also connected to overall survival and lower chemotherapy and antimetabolite response rates. In conclusion, EHD3 hypermethylation contributes to the development of CRC in both Asian and Western populations.
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Affiliation(s)
- Yu-Han Wang
- School of Medicine, Tzu Chi University, Hualien City 97071, Taiwan;
| | - Shih-Ching Chang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Muhamad Ansar
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei 11031, Taiwan;
| | - Chin-Sheng Hung
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Ruo-Kai Lin
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei 11031, Taiwan
- Clinical Trial Center, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Correspondence:
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10
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Zhang H, Xu C, Shi C, Zhang J, Qian T, Wang Z, Ma R, Wu J, Jiang F, Feng J. Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis. J Transl Med 2021; 19:98. [PMID: 33663522 PMCID: PMC7934273 DOI: 10.1186/s12967-021-02770-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The epigenetic abnormality of tumor-associated genes contributes to the pathogenesis of colorectal carcinoma (CRC). However, methylation in colorectal cancer is still poorly characterized. METHOD By integration of DNA methylation data from the GEO database and gene expression data from The Cancer Genome Atlas database, the aberrantly methylated genes involved in CRC tumorigenesis were identified. Subsequent in vitro experiments further validated their role in CRC. RESULTS We performed integrative genomic analysis and identified HPSE2, a novel tumor suppressor gene that is frequently inactivated through promoter methylation in CRC. K-M survival analysis showed that hypermethylation-low expression of heparanase 2 (HPSE2) was related to poor patient prognosis. Overexpression of HPSE2 reduced cell proliferation in vivo and in vitro. HPSE2 could regulate the p53 signaling pathway to block the cell cycle in G1 phase. CONCLUSION HPSE2, a novel tumor suppressor gene that is frequently inactivated through promoter methylation in CRC. HPSE2 performs a tumor suppressive function by activating the p53/ p21 signaling cascade. The promoter hypermethylation of HPSE2 is a potential therapeutic target in patients with CRC, especially those with late-stage CRC.
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Affiliation(s)
- Hui Zhang
- Department of General Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Chenxin Xu
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Chen Shi
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Junying Zhang
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Ting Qian
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Zhuo Wang
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Rong Ma
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Jianzhong Wu
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Feng Jiang
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China.
| | - Jifeng Feng
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China.
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11
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Bandera-Merchan B, Boughanem H, Crujeiras AB, Macias-Gonzalez M, Tinahones FJ. Ketotherapy as an epigenetic modifier in cancer. Rev Endocr Metab Disord 2020; 21:509-519. [PMID: 32514818 DOI: 10.1007/s11154-020-09567-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetic alterations in cancer play a variety of roles. Aberrant DNA methylation, as one of the epigenetic mechanisms, has been widely studied in both tumor and liquid biopsies and provide a useful bench mark for treatment response in cancer. Recently, several studies have reported an association between the type of diet and epigenetic modifications. Whereby there is a growing interest in finding the "anti-cancer diet formula", if such a thing exists. In this sense, ketogenic diets (KD) have reported potentially beneficial effects, which were able to prevent malignancies and decrease tumor growth. Some studies have even shown increased survival in cancer patients, reduced side effects of cytotoxic treatments, and intensified efficacy of cancer therapies. Although the biological mechanisms of KD are not well understood, it has been reported that KD may affect DNA methylation by modulating the expression of crucial genes involved in tumor survival and proliferation. However, there are many considerations to take into account to use ketotherapy in cancer, such as epigenetic mark, type of cancer, immunological and metabolic state or microbiota profile. In this review, we argue about ketotherapy as a potential strategy to consider as coadjuvant of cancer therapy. We will focus on mainly epigenetic mechanisms and dietary approach that could be included in the current clinical practice guidelines.
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Affiliation(s)
- Borja Bandera-Merchan
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain
| | - Hatim Boughanem
- Biomedical Research Institute of Malaga (IBIMA). Faculty of Science, University of Malaga, 29010, Málaga, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Manuel Macias-Gonzalez
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain.
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Francisco J Tinahones
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain
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12
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Sobhani I, Rotkopf H, Khazaie K. Bacteria-related changes in host DNA methylation and the risk for CRC. Gut Microbes 2020; 12:1800898. [PMID: 32931352 PMCID: PMC7575230 DOI: 10.1080/19490976.2020.1800898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/17/2020] [Indexed: 02/03/2023] Open
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer deaths in men and women combined. Colon-tumor growth is multistage and the result of the accumulation of spontaneous mutations and epigenetic events that silence tumor-suppressor genes and activate oncogenes. Environmental factors are primary contributors to these somatic gene alterations, which account for the increase in incidence of CRC in western countries. In recent decades, gut microbiota and their metabolites have been recognized as essential contributing factors to CRC, and now serve as biomarkers for the diagnosis and prognosis of CRC. In the present review, we highlight holistic approaches to understanding how gut microbiota contributes to CRC. We particularly focus herein on bacteria-related changes in host DNA methylation and the risk for CRC.
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Affiliation(s)
- Iradj Sobhani
- Head of the Department of Gastroenterology, Consultant in GI Oncology, Hopital Henri Mondor, APHP. Créteil-France; Head of the Research Team EC2M3, Université Paris-Est Créteil (UPEC), Créteil, France
| | - Hugo Rotkopf
- Department of Gastroenterology Hospital Henri Mondor, APHP. Créteil-France; Member of Research Team EC2M3, Université Paris-Est Créteil (UPEC). Créteil, France
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13
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Abstract
Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide. Although targeted therapy in combination with chemotherapy in CRC prolongs the overall survival of patients with metastatic disease, acquired resistance and relapse hinder their clinical benefits. Moreover, patients with some specific genetic profile are unlikely to benefit from targeted therapy, suggesting the need for safe and effective treatment strategies. Retinoids, comprising of natural and synthetic analogs, are a class of chemical compounds that regulate cellular proliferation, differentiation, and cell death. Retinoids have been used in the clinic for several leukemias and solid tumors, either as single agents or in combination therapy. Furthermore, retinoids have shown potent chemotherapeutic and chemopreventive properties in different cancer models, including CRC. In this review, we summarize the major preclinical findings in CRC in which natural and synthetic retinoids showed promising antitumor activities and stress on the proposed mechanisms of action. Understanding of the retinoids' antitumor mechanisms would provide insights to support and warrant their development in the management of CRC.
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14
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Tsumura K, Arai E, Tian Y, Shibuya A, Nishihara H, Yotani T, Yamada Y, Takahashi Y, Maeshima AM, Fujimoto H, Nakagawa T, Kume H, Homma Y, Yoshida T, Kanai Y. Establishment of permutation for cancer risk estimation in the urothelium based on genome-wide DNA methylation analysis. Carcinogenesis 2020; 40:1308-1319. [PMID: 31241739 DOI: 10.1093/carcin/bgz112] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 05/25/2019] [Accepted: 06/22/2019] [Indexed: 02/02/2023] Open
Abstract
The aim of this study was to establish permutation for cancer risk estimation in the urothelium. Twenty-six samples of normal control urothelium obtained from patients without urothelial carcinomas (C), 47 samples of non-cancerous urothelium without noticeable morphological changes obtained from patients with urothelial carcinomas (N), and 46 samples of the corresponding cancerous tissue (T) in the learning cohort and 64 N samples in the validation cohort, i.e. 183 tissue samples in total, were analyzed. Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylation 450K BeadChip, and DNA methylation levels were verified using pyrosequencing and MassARRAY. Amplicon sequencing was performed using the GeneRead DNAseq Targeted Panels V2. Although N samples rarely showed genetic mutations or copy number alterations, they showed DNA methylation alterations at 2502 CpG sites compared to C samples, and such alterations were inherited by or strengthened in T samples, indicating that DNA methylation alterations may participate in field cancerization in the urothelium. Receiver operating characteristic curve analysis confirmed the feasibility of cancer risk estimation to identify urothelium at the precancerous stage by DNA methylation quantification. Cancer risk estimation permutation was established using a combination of two marker CpG loci on the HOXC4, TENM3 and TLR1 genes (sensitivity and specificity 96-100%). Among them, the diagnostic impact of 10 patterns of permutation was successfully validated in the validation cohort (sensitivity and specificity 94-98%). These data suggest that cancer risk estimation using procedures such as urine tests during health checkups might become applicable for clinical use.
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Affiliation(s)
- Koji Tsumura
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Ayako Shibuya
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Takuya Yotani
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd, Ryugasaki, Japan
| | - Yuriko Yamada
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd, Ryugasaki, Japan
| | - Yoriko Takahashi
- Biomedical Department, Cloud Service Division, IT Infrastructure Services Unit, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Akiko Miyagi Maeshima
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital, Tokyo, Japan
| | - Tohru Nakagawa
- Department of Urology, Teikyo University School of Medicine, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukio Homma
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Shinanomachi, Shinjuku-ku, Tokyo, Japan
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15
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Costea T, Vlad OC, Miclea LC, Ganea C, Szöllősi J, Mocanu MM. Alleviation of Multidrug Resistance by Flavonoid and Non-Flavonoid Compounds in Breast, Lung, Colorectal and Prostate Cancer. Int J Mol Sci 2020; 21:E401. [PMID: 31936346 PMCID: PMC7013436 DOI: 10.3390/ijms21020401] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 12/12/2022] Open
Abstract
The aim of the manuscript is to discuss the influence of plant polyphenols in overcoming multidrug resistance in four types of solid cancers (breast, colorectal, lung and prostate cancer). Effective treatment requires the use of multiple toxic chemotherapeutic drugs with different properties and targets. However, a major cause of cancer treatment failure and metastasis is the development of multidrug resistance. Potential mechanisms of multidrug resistance include increase of drug efflux, drug inactivation, detoxification mechanisms, modification of drug target, inhibition of cell death, involvement of cancer stem cells, dysregulation of miRNAs activity, epigenetic variations, imbalance of DNA damage/repair processes, tumor heterogeneity, tumor microenvironment, epithelial to mesenchymal transition and modulation of reactive oxygen species. Taking into consideration that synthetic multidrug resistance agents have failed to demonstrate significant survival benefits in patients with different types of cancer, recent research have focused on beneficial effects of natural compounds. Several phenolic compounds (flavones, phenolcarboxylic acids, ellagitannins, stilbens, lignans, curcumin, etc.) act as chemopreventive agents due to their antioxidant capacity, inhibition of proliferation, survival, angiogenesis, and metastasis, modulation of immune and inflammatory responses or inactivation of pro-carcinogens. Moreover, preclinical and clinical studies revealed that these compounds prevent multidrug resistance in cancer by modulating different pathways. Additional research is needed regarding the role of phenolic compounds in the prevention of multidrug resistance in different types of cancer.
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Affiliation(s)
- Teodora Costea
- Department of Pharmacognosy, Phytochemistry and Phytotherapy, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Oana Cezara Vlad
- Department of Biophysics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.C.V.); (C.G.)
| | - Luminita-Claudia Miclea
- Department of Biophysics and Cellular Biotechnology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
- Research Excellence Center in Biophysics and Cellular Biotechnology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Constanta Ganea
- Department of Biophysics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.C.V.); (C.G.)
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Maria-Magdalena Mocanu
- Department of Biophysics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (O.C.V.); (C.G.)
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16
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Yang C, Zhang Y, Xu X, Li W. Molecular subtypes based on DNA methylation predict prognosis in colon adenocarcinoma patients. Aging (Albany NY) 2019; 11:11880-11892. [PMID: 31852837 PMCID: PMC6949097 DOI: 10.18632/aging.102492] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/17/2019] [Indexed: 12/25/2022]
Abstract
Tumor heterogeneity makes early diagnosis and effective treatment of colon adenocarcinoma difficult. As an important regulator of gene expression, DNA methylation can influence tumor heterogeneity. In this study, we explored the prognostic value of subtypes based on DNA methylation status in 424 colon adenocarcinoma samples from the Cancer Genome Atlas database. Differences in DNA methylation levels were associated with differences in T, N, and M category, age, stage, and prognosis. Seven subgroups were identified based on consensus clustering using 356 CpG sites that significantly influenced survival. Finally, a prognostic model was constructed and used to classify samples in a testing dataset into seven DNA methylation subgroups based on the classification results of a training dataset. These specific classifications based on DNA methylation may help account for heterogeneity within previously established molecular subgroups of colon adenocarcinoma and could potentially aid in the development of more effective personalized treatments.
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Affiliation(s)
- Changshun Yang
- Department of Surgical Oncology, Fujian Provincial Hospital, Fuzhou 350001, China
| | - Yu Zhang
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350001, China
| | - Xiaoqin Xu
- School of Public Health, Fujian Medical University, Fuzhou 350001, China
| | - Weihua Li
- Department of Surgical Oncology, Fujian Provincial Hospital, Fuzhou 350001, China
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17
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Ying X, Pan R, Zhong J, Wu B, Jiang Y, Ying J, Zhou C, Dai J, Zhao S, Shen Y, Zhang W, Duan S. Significant association of EED promoter hypomethylation with colorectal cancer. Oncol Lett 2019; 18:1564-1570. [PMID: 31423224 DOI: 10.3892/ol.2019.10432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/12/2019] [Indexed: 01/02/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common and serious types of malignancy worldwide. The embryonic ectoderm development (EED) gene is important to maintain transcriptional repressive states of genes over successive cell generations. The present study aimed to investigate the association between EED methylation and CRC. A total of 111 CRC tissue samples, 111 paired para-tumor tissues and 20 colorectal normal tissues were obtained for EED methylation assay, which was performed using a quantitative methylation-specific polymerase chain reaction. The percentage of methylated reference was calculated to represent the DNA methylation level. A dual-luciferase reporter gene assay was used to detect the gene promoter activity of a EED fragment. The current results revealed a significant difference in the EED methylation levels among tumor, para-tumor and normal colorectal tissues (tumor vs. para-tumor vs. normal, 5.03±4.61 vs. 8.65±11.50 vs. 40.12±45.31; F=45.014; P<0.0001). The dual-luciferase reporter gene assay demonstrated that the transcriptional activity of recombinant pGL3-EED plasmid was significantly higher compared with that of the pGL3-Basic control vector (fold-change, 3.15; P=0.014), which suggests the EED fragment can promote gene expression. In conclusion, the present study demonstrated that EED hypomethylation may be an important factor associated with CRC.
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Affiliation(s)
- Xiuru Ying
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Ranran Pan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Boyi Wu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yuting Jiang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jieer Ying
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Cong Zhou
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Dai
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Shuangying Zhao
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yinan Shen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Wei Zhang
- Department of Preventive Medicine and The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
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18
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Cabrera-Mulero A, Crujeiras AB, Izquierdo AG, Torres E, Ayers D, Casanueva FF, Tinahones FJ, Morcillo S, Macias-Gonzalez M. Novel SFRP2 DNA Methylation Profile Following Neoadjuvant Therapy in Colorectal Cancer Patients with Different Grades of BMI. J Clin Med 2019; 8:jcm8071041. [PMID: 31319558 PMCID: PMC6678889 DOI: 10.3390/jcm8071041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/13/2022] Open
Abstract
The relationship between body weight and different cancers is now well-recognized and among such cancers, colorectal cancer (CRC) is reported most frequently. Our group recently published findings, through an epigenome-wide association study, suggesting that body mass index (BMI) could act as a relevant risk factor in the CRC. In addition, aberrant SFRP2 methylation is one of the major mechanisms for Wnt signaling activation in CRC. Conversely, neoadjuvant chemo-radiotherapy appears to alter the rectal cancer epigenome. This study was aimed to evaluate the effect of obesity, measured by BMI, on the methylation of SFRP2 in tumor samples of patients with CRC. Non-treated CRC patients and CRC patients treated with pre-operative neoadjuvant therapy from 2011 to 2013 were included and classified by BMI < 25.0 kg/m2 and BMI > 25.0 kg/m2. SFRP2 DNA methylation in tumor samples was measured by pyrosequencing. Our findings suggest a possible interaction between SFRP2 methylation levels and BMI in CRC tumor samples. The correlation of SFRP2 hypomethylation with an elevated BMI was stronger within the non-treated CRC patient group than within the treated CRC patient group. We have successfully demonstrated that the beneficial association of tumor SFRP2 hypomethylation is dependent on patient BMI in non-treated CRC, suggesting a possible tumor suppressor role for SFRP2 in overweight and obese patients. Additional studies of clinical pathologies would be necessary to strengthen these preliminary results.
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Affiliation(s)
- Amanda Cabrera-Mulero
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010 Málaga, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition CB06/03/0018), "Instituto de Salud Carlos III", 28029 Madrid, Spain
| | - Ana B Crujeiras
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition CB06/03/0018), "Instituto de Salud Carlos III", 28029 Madrid, Spain
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain
| | - Andrea G Izquierdo
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition CB06/03/0018), "Instituto de Salud Carlos III", 28029 Madrid, Spain
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain
| | - Esperanza Torres
- Unidad de Gestión Clínica de Oncología Intercentros Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Duncan Ayers
- Centre for Molecular Medicine and Biobanking, University of Malta, 2080 Msida MSD, Malta
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M1 7DN, UK
| | - Felipe F Casanueva
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition CB06/03/0018), "Instituto de Salud Carlos III", 28029 Madrid, Spain
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain
| | - Francisco J Tinahones
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010 Málaga, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition CB06/03/0018), "Instituto de Salud Carlos III", 28029 Madrid, Spain
| | - Sonsoles Morcillo
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010 Málaga, Spain.
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition CB06/03/0018), "Instituto de Salud Carlos III", 28029 Madrid, Spain.
- Laboratorio Investigación Biomédica 1ª Planta, Hospital Universitario Virgen de la Victoria, Campus de Teatinos s/n 29010, 29010 Málaga, Spain.
| | - Manuel Macias-Gonzalez
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010 Málaga, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition CB06/03/0018), "Instituto de Salud Carlos III", 28029 Madrid, Spain
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19
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Leung PHM, Subramanya R, Mou Q, Lee KTW, Islam F, Gopalan V, Lu CT, Lam AKY. Characterization of Mucosa-Associated Microbiota in Matched Cancer and Non-neoplastic Mucosa From Patients With Colorectal Cancer. Front Microbiol 2019; 10:1317. [PMID: 31244818 PMCID: PMC6581718 DOI: 10.3389/fmicb.2019.01317] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 05/27/2019] [Indexed: 12/21/2022] Open
Abstract
Colonic microbiota play important roles in the development of colorectal cancer. We aim to characterise the mucosa-associated microbiota in the tumour as well as the matched non-neoplastic mucosa from patients with colorectal cancer. Microbiota profiling in these samples was done using high-throughput 16S rRNA amplicon sequencing. Our results showed that the microbiota richness and diversity were similar between the tumour and non-neoplastic mucosae. Linear discriminant analysis effect size (LEfSe) analysis identified Fusobacterium and Campylobacter as the key genera of the tumour while Brevundimonas as the key genus of the non-neoplastic mucosa. In patients with shorter survival period, the relative abundance of Fusobacterium and Campylobacter was significantly higher in the tumour. Besides, regardless of the sites, tumour showed higher abundance of Fusobacterium. On the other hand, the relative abundance of Brevundimonas was significantly lower in the tumour. When validated with quantitative ddPCR, we found the absolute numbers of both Fusobacterium and F. nucleatum were significantly higher in the carcinoma from patients with shorter survival period, conventional type of adenocarcinoma in the distal portion of the large intestine (descending colon, sigmoidal colon, and rectum). In conclusion, our study showed a compositional alteration in the mucosa-associated microbiota in the tumour, which may contribute to the progression of colorectal cancer.
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Affiliation(s)
- Polly H M Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Rao Subramanya
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Qianqian Mou
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Katherine Ting-Wei Lee
- Pathology, School of Medicine, Gold Coast Campus, Griffith University, Gold Coast, QLD, Australia
| | - Farhadul Islam
- Pathology, School of Medicine, Gold Coast Campus, Griffith University, Gold Coast, QLD, Australia.,Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Vinod Gopalan
- Pathology, School of Medicine, Gold Coast Campus, Griffith University, Gold Coast, QLD, Australia
| | - Cu-Tai Lu
- Department of Surgery, Gold Coast University Hospital, Gold Coast, QLD, Australia
| | - Alfred King-Yin Lam
- Pathology, School of Medicine, Gold Coast Campus, Griffith University, Gold Coast, QLD, Australia
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20
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Rezapour S, Hosseinzadeh E, Marofi F, Hassanzadeh A. Epigenetic-based therapy for colorectal cancer: Prospect and involved mechanisms. J Cell Physiol 2019; 234:19366-19383. [PMID: 31020647 DOI: 10.1002/jcp.28658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022]
Abstract
Epigenetic modifications are heritable variations in gene expression not encoded by the DNA sequence. According to reports, a large number of studies have been performed to characterize epigenetic modification during normal development and also in cancer. Epigenetics can be regarded more widely to contain all of the changes in expression of genes that make by adjusted interactions between the regulatory portions of DNA or messenger RNAs that lead to indirect variation in the DNA sequence. In the last decade, epigenetic modification importance in colorectal cancer (CRC) pathogenesis was demonstrated powerfully. Although developments in CRC therapy have been made in the last years, much work is required as it remains the second leading cause of cancer death. Nowadays, epigenetic programs and genetic change have pivotal roles in the CRC incidence as well as progression. While our knowledge about epigenetic mechanism in CRC is not comprehensive, selective histone modifications and resultant chromatin conformation together with DNA methylation most likely regulate CRC pathogenesis that involved genes expression. Undoubtedly, the advanced understanding of epigenetic-based gene expression regulation in the CRC is essential to make epigenetic drugs for CRC therapy. The major aim of this review is to deliver a summary of valuable results that represent evidence of principle for epigenetic-based therapeutic approaches employment in CRC with a focus on the advantages of epigenetic-based therapy in the inhibition of the CRC metastasis and proliferation.
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Affiliation(s)
- Saleheh Rezapour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Hosseinzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faroogh Marofi
- Division of Hematology, Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Hassanzadeh
- Division of Hematology, Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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21
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Lee JA, Park HE, Yoo SY, Jeong S, Cho NY, Kang GH, Kim JH. CpG Island Methylation in Sessile Serrated Adenoma/Polyp of the Colorectum: Implications for Differential Diagnosis of Molecularly High-Risk Lesions among Non-dysplastic Sessile Serrated Adenomas/Polyps. J Pathol Transl Med 2019; 53:225-235. [PMID: 30887794 PMCID: PMC6639709 DOI: 10.4132/jptm.2019.03.12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 03/12/2019] [Indexed: 01/01/2023] Open
Abstract
Background Although colorectal sessile serrated adenomas/polyps (SSA/Ps) with morphologic dysplasia are regarded as definite high-risk premalignant lesions, no reliable grading or risk-stratifying system exists for non-dysplastic SSA/Ps. The accumulation of CpG island methylation is a molecular hallmark of progression of SSA/Ps. Thus, we decided to classify non-dysplastic SSA/Ps into risk subgroups based on the extent of CpG island methylation. Methods The CpG island methylator phenotype (CIMP) status of 132 non-dysplastic SSA/Ps was determined using eight CIMP-specific promoter markers. SSA/Ps with CIMP-high and/or MLH1 promoter methylation were regarded as a high-risk subgroup. Results Based on the CIMP analysis results, methylation frequency of each CIMP marker suggested a sequential pattern of CpG island methylation during progression of SSA/P, indicating MLH1 as a late-methylated marker. Among the 132 non-dysplastic SSA/Ps, 34 (26%) were determined to be high-risk lesions (33 CIMP-high and 8 MLH1-methylated cases; seven cases overlapped). All 34 high-risk SSA/Ps were located exclusively in the proximal colon (100%, p = .001) and were significantly associated with older age (≥ 50 years, 100%; p = .003) and a larger histologically measured lesion size (> 5 mm, 100%; p = .004). In addition, the high-risk SSA/Ps were characterized by a relatively higher number of typical base-dilated serrated crypts. Conclusions Both CIMP-high and MLH1 methylation are late-step molecular events during progression of SSA/Ps and rarely occur in SSA/Ps of young patients. Comprehensive consideration of age (≥ 50), location (proximal colon), and histologic size (> 5 mm) may be important for the prediction of high-risk lesions among non-dysplastic SSA/Ps.
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Affiliation(s)
- Ji Ae Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hye Eun Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Seung-Yeon Yoo
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Seorin Jeong
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Nam-Yun Cho
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Jung Ho Kim
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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22
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Wu W, Tan W, Ye S, Zhou Y, Quan J. Analysis of the promoter region of the human miR-32 gene in colorectal cancer. Oncol Lett 2019; 17:3743-3750. [PMID: 30881496 PMCID: PMC6403515 DOI: 10.3892/ol.2019.10042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022] Open
Abstract
The pathogenesis of colorectal cancer (CRC) is poorly understood. MicroRNA (miR)-32 upregulation in CRC tissues was previously reported, where it increased the proliferation, migration and invasion, and reduced apoptosis of CRC cells by inhibiting the expression of phosphatase and tensin homolog (PTEN). However, the mechanism underlying miR-32 upregulation remains unknown. miR-32 is an intronic miRNA located within intron 14 of the transmembrane protein 245 gene (TMEM245). The present study aimed to elucidate the biological pathways underlying miR-32 regulation in CRC. A truncated promoter containing the 5′-flanking region of TMEM245/miR-32 gene was constructed. The promoter region was analyzed by dual luciferase reporter assay in CRC cells. DNA pull-down assay and mass spectrometry (MS) were used to identify proteins binding to the core promoter. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and transcription factor (TF) analyses were used to identify the binding proteins. The −320 to −1 bp fragment of the 5′-flanking region exhibited the highest luciferase activity. The regions spanning −606 to −320 bp exhibited a significant decrease in luciferase activity, compared with the −320 to −1 bp fragment. DNA pull-down assay and MS revealed 403 potential miR-32 promoter binding proteins. GO and KEGG pathway analysis indicated that these proteins were involved in numerous physiological and biochemical processes, including ‘structural molecule activity’, ‘RNA binding’, ‘small molecule metabolic process’ and ‘biogenesis’. Furthermore, TF analysis revealed 10 potential interacting TFs, including SMAD family member 1 (SMAD1), signal transducer and activator of transcription 1 (STAT1) and forkhead box K1 (Foxk1). These results suggested that the core promoter region may be located within-320 to −1 bp of the 5′-flanking region of TMEM245/miR-32 gene, while the region from −606 to −320 bp may harbor repressive regulatory elements. The TFs SMAD1, STAT1 and Foxk1 may be involved in the transcriptional regulation of miR-32.
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Affiliation(s)
- Weiyun Wu
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Wenkai Tan
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Shicai Ye
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Yu Zhou
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Juanhua Quan
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
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Significant association between KDM1A promoter hypomethylation and colorectal cancer in Han Chinese. Pathol Res Pract 2018; 215:532-538. [PMID: 30638951 DOI: 10.1016/j.prp.2018.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/15/2018] [Accepted: 12/05/2018] [Indexed: 02/06/2023]
Abstract
Lysine-specific histone demethylase 1A gene (KDM1A) promotes tumorigenesis. The aim of this study was to investigate the association between KDM1A methylation and colorectal cancer (CRC). Currently, we collected 37 paired CRC tissues and adjacent non-tumor tissues from Jiangsu province and 75 paired CRC tissues and adjacent non-tumor tissues from Zhejiang province to conduct a two-stage experiment to study the association between KDM1A methylation and CRC. We used qMSP to measure the KDM1A promoter methylation, and the percentage of methylation reference (PMR) to quantify the KDM1A promoter methylation level. To investigate the effect of the selected KDM1A fragment on gene expression regulation, we also performed a dual luciferase reporter gene assay. In the stage I study, the KDM1A promoter methylation level in CRC tumor tissues was significantly lower than that in adjacent non-tumor tissues (median PMR: 6.93% vs 10.25%, P = 0.033). The results of the stage II study were similar to those of the stage I study (mean PMR: 12.94% versus 17.42%, P = 0.016). In addition, a clinical pathology subgroup analysis found that KDM1A hypomethylation was associated with CRC only in patients with well-differentiated CRC (stage I: P = 0.047; stage II: P = 0.040). The dual luciferase reporter assay showed that the transcriptional activity of the recombinant pGL3-KDM1A plasmid was significantly higher (fold change = 2, P = 0.0009). In conclusion, our results suggest that KDM1A hypomethylation is significantly associated with CRC.
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24
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Costea T, Hudiță A, Ciolac OA, Gălățeanu B, Ginghină O, Costache M, Ganea C, Mocanu MM. Chemoprevention of Colorectal Cancer by Dietary Compounds. Int J Mol Sci 2018; 19:E3787. [PMID: 30487390 PMCID: PMC6321468 DOI: 10.3390/ijms19123787] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/18/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is one of the leading causes of death, and the third most diagnosed type of cancer, worldwide. It is most common amongst men and women over 50 years old. Risk factors include smoking, alcohol, diet, physical inactivity, genetics, alterations in gut microbiota, and associated pathologies (diabetes, obesity, chronic inflammatory bowel diseases). This review will discuss, in detail, the chemopreventive properties of some dietary compounds (phenolic compounds, carotenoids, iridoids, nitrogen compounds, organosulfur compounds, phytosterols, essential oil compounds, polyunsaturated fatty acids and dietary fiber) against colorectal cancer. We present recent data, focusing on in vitro, laboratory animals and clinical trials with the previously mentioned compounds. The chemopreventive properties of the dietary compounds involve multiple molecular and biochemical mechanisms of action, such as inhibition of cell growth, inhibition of tumor initiation, inhibition of adhesion, migration and angiogenesis, apoptosis, interaction with gut microbiota, regulation of cellular signal transduction pathways and xenobiotic metabolizing enzymes, etc. Moreover, this review will also focus on the natural dietary compounds' bioavailability, their synergistic protective effect, as well as the association with conventional therapy. Dietary natural compounds play a major role in colorectal chemoprevention and continuous research in this field is needed.
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Affiliation(s)
- Teodora Costea
- Department of Pharmacognosy, Phytochemistry and Phytotherapy, "Carol Davila" University of Medicine and Pharmacy, 020956 Bucharest, Romania.
| | - Ariana Hudiță
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania.
| | - Oana-Alina Ciolac
- Department of Biophysics, "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania.
| | - Bianca Gălățeanu
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania.
| | - Octav Ginghină
- Department of Surgery, "Sf. Ioan" Emergency Clinical Hospital, 042122 Bucharest, Romania.
- Department II, Faculty of Dental Medicine, "Carol Davila" University of Medicine and Pharmacy, 030167 Bucharest, Romania.
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania.
| | - Constanța Ganea
- Department of Biophysics, "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania.
| | - Maria-Magdalena Mocanu
- Department of Biophysics, "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania.
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25
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Effects of dietary interventions on DNA methylation in adult humans: systematic review and meta-analysis. Br J Nutr 2018; 120:961-976. [DOI: 10.1017/s000711451800243x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractDNA methylation is a key component of the epigenetic machinery that is responsible for regulating gene expression and, therefore, cell function. Patterns of DNA methylation change during development and ageing, differ between cell types, are altered in multiple diseases and can be modulated by dietary factors. However, evidence about the effects of dietary factors on DNA methylation patterns in humans is fragmentary. This study was initiated to collate evidence for causal links between dietary factors and changes in DNA methylation patterns. We carried out a systematic review of dietary intervention studies in adult humans using Medline, EMBASE and Scopus. Out of 22 149 screened titles, sixty intervention studies were included, of which 65% were randomised (n 39). Most studies (53%) reported data from blood analyses, whereas 27% studied DNA methylation in colorectal mucosal biopsies. Folic acid was the most common intervention agent (33%). There was great heterogeneity in the methods used for assessing DNA methylation and in the genomic loci investigated. Meta-analysis of the effect of folic acid on global DNA methylation revealed strong evidence that supplementation caused hypermethylation in colorectal mucosa (P=0·009). Meta-regression analysis showed that the dose of supplementary folic acid was the only identified factor (P<0·001) showing a positive relationship. In summary, there is limited evidence from intervention studies of effects of dietary factors, other than folic acid, on DNA methylation patterns in humans. In addition, the application of multiple different assays and investigations of different genomic loci makes it difficult to compare, or to combine, data across studies.
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26
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Gao HL, Wang X, Sun HR, Zhou JD, Lin SQ, Xing YH, Zhu L, Zhou HB, Zhao YS, Chi Q, Liu YP. Methylation Status of Transcriptional Modulatory Genes Associated with Colorectal Cancer in Northeast China. Gut Liver 2018; 12:173-182. [PMID: 29291617 PMCID: PMC5832342 DOI: 10.5009/gnl17163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/08/2017] [Accepted: 05/22/2017] [Indexed: 12/13/2022] Open
Abstract
Background/Aims Methylation status plays a causal role in carcinogenesis in targeted tissues. However, the relationship between the DNA methylation status of multiple genes in blood leukocytes and colorectal cancer (CRC) susceptibility as well as interactions between dietary factors and CRC risks are unclear. Methods We performed a case-control study with 466 CRC patients and 507 cancer-free controls to investigate the association among the methylation status of individual genes, multiple CpG site methylation (MCSM), multiple CpG site heterogeneous methylation and CRC susceptibility. Peripheral blood DNA methylation levels were detected by performing methylation-sensitive high-resolution melting. Results Total heterogeneous methylation of CA10 and WT1 conferred a significantly higher risk of CRC (adjusted odds ratio [ORadjusted], 5.445; 95% confidence interval [CI], 3.075 to 9.643; ORadjusted, 1.831; 95% CI, 1.100 to 3.047; respectively). Subjects with high-level MCSM (MCSM-H) status demonstrated a higher risk of CRC (ORadjusted, 4.318; 95% CI, 1.529 to 12.197). Additionally, interactions between the high-level intake of fruit and CRH, WT1, and MCSM on CRC were statistically significant. Conclusions The gene methylation status of blood leukocytes may be associated with CRC risk. MCSM-H of blood leukocytes was associated with CRC, especially in younger people. Some dietary factors may affect hypermethylation status and influence susceptibility to CRC.
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Affiliation(s)
- Han-Lu Gao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Xuan Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Hong-Ru Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Jun-De Zhou
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shang-Qun Lin
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Yu-Hang Xing
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Lin Zhu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Hai-Bo Zhou
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Ya-Shuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Qiang Chi
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu-Peng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
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27
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Coppedè F, Stoccoro A, Lazzarotti A, Spisni R, Migliore L. Investigation of GHSR and GHRL methylation in colorectal cancer. Epigenomics 2018; 10:1525-1539. [PMID: 29963901 DOI: 10.2217/epi-2018-0030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM To investigate GHSR and GHRL methylation in 73 pairs of colorectal cancer (CRC) tissues and healthy adjacent mucosa. METHODS Methylation was assessed with methylation-sensitive high-resolution melting. RESULTS GHSR was significantly hypermethylated in CRC tissues than in healthy mucosa (p < 1 × 10-5), but no significant changes of GHRL methylation were observed. GHSR hypermethylation was already detectable at the adenoma stage and maintained in later stages independently of age, gender, anatomical location, histological grading, MLH1 deficiency, as well as of major polymorphisms in folate-pathway genes, yielding an area under the curve of 0.824 for discriminating cancers from respective non-neoplastic mucosa specimens. CONCLUSION GHSR hypermethylation occurs early in CRC, but is not paralleled by significant changes of GHRL methylation.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy
| | - Andrea Stoccoro
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy
| | - Alessandro Lazzarotti
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy
| | - Roberto Spisni
- Department of Surgery, Medical, Molecular, & Critical Area Pathology, University of Pisa, Pisa, Italy
| | - Lucia Migliore
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy
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28
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Buoncervello M, Romagnoli G, Buccarelli M, Fragale A, Toschi E, Parlato S, Lucchetti D, Macchia D, Spada M, Canini I, Sanchez M, Falchi M, Musella M, Biffoni M, Belardelli F, Capone I, Sgambato A, Vitiani LR, Gabriele L. IFN-α potentiates the direct and immune-mediated antitumor effects of epigenetic drugs on both metastatic and stem cells of colorectal cancer. Oncotarget 2018; 7:26361-73. [PMID: 27028869 PMCID: PMC5041985 DOI: 10.18632/oncotarget.8379] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 03/02/2016] [Indexed: 01/29/2023] Open
Abstract
Epigenetic alterations, including dysregulated DNA methylation and histone modifications, govern the progression of colorectal cancer (CRC). Cancer cells exploit epigenetic regulation to control cellular pathways, including apoptotic and metastatic signals. Since aberrations in epigenome can be pharmacologically reversed by DNA methyltransferase and histone deacetylase inhibitors, epigenetics in combination with standard agents are currently envisaged as a new therapeutic frontier in cancer, expected to overcome drug resistance associated with current treatments. In this study, we challenged this idea and demonstrated that the combination of azacitidine and romidepsin with IFN-α owns a high therapeutic potential, targeting the most aggressive cellular components of CRC, such as metastatic cells and cancer stem cells (CSCs), via tight control of key survival and death pathways. Moreover, the antitumor efficacy of this novel pharmacological approach is associated with induction of signals of immunogenic cell death. Of note, a previously undisclosed key role of IFN-α in inducing both antiproliferative and pro-apoptotic effects on CSCs of CRC was also found. Overall, these findings open a new frontier on the suitability of IFN-α in association with epigenetics as a novel and promising therapeutic approach for CRC management.
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Affiliation(s)
- Maria Buoncervello
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Giulia Romagnoli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Mariachiara Buccarelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Fragale
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Elena Toschi
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Stefania Parlato
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Donatella Lucchetti
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Daniele Macchia
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Massimo Spada
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Irene Canini
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Massimo Sanchez
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome, Italy
| | - Mario Falchi
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Martina Musella
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Mauro Biffoni
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Filippo Belardelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Imerio Capone
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandro Sgambato
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Lucia Ricci Vitiani
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lucia Gabriele
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
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El Bairi K, Tariq K, Himri I, Jaafari A, Smaili W, Kandhro AH, Gouri A, Ghazi B. Decoding colorectal cancer epigenomics. Cancer Genet 2018; 220:49-76. [PMID: 29310839 DOI: 10.1016/j.cancergen.2017.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/01/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is very heterogeneous and presents different types of epigenetic alterations including DNA methylation, histone modifications and microRNAs. These changes are considered as characteristics of various observed clinical phenotypes. Undoubtedly, the discovery of epigenetic pathways with novel epigenetic-related mechanisms constitutes a promising advance in cancer biomarker discovery. In this review, we provide an evidence-based discussing of the current understanding of CRC epigenomics and its role in initiation, epithelial-to-mesenchymal transition and metastasis. We also discuss the recent findings regarding the potential clinical perspectives of these alterations as potent biomarkers for CRC diagnosis, prognosis, and therapy in the era of liquid biopsy.
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Affiliation(s)
- Khalid El Bairi
- Independent Research Team in Cancer Biology and Bioactive Compounds, Mohamed 1(st) University, Oujda, Morocco.
| | - Kanwal Tariq
- B-10 Jumani Center, Garden East, Karachi 74400, Pakistan
| | - Imane Himri
- Laboratory of Biochemistry, Faculty of Sciences, Mohamed I(st) Universiy, Oujda, Morocco; Delegation of the Ministry of Health, Oujda, Morocco
| | - Abdeslam Jaafari
- Laboratoire de Génie Biologique, Equipe d'Immunopharmacologie, Faculté des Sciences et Techniques, Université Sultan Moulay Slimane, Beni Mellal, Maroc
| | - Wiam Smaili
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohamed V, Rabat, Maroc; Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc
| | - Abdul Hafeez Kandhro
- Department of Biochemistry, Healthcare Molecular and Diagnostic Laboratory, Hyderabad, Pakistan
| | - Adel Gouri
- Laboratory of Medical Biochemistry, Ibn Rochd University Hospital, Annaba, Algeria
| | - Bouchra Ghazi
- National Laboratory of Reference, Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
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Lin RK, Hung WY, Huang YF, Chang YJ, Lin CH, Chen WY, Chiu SF, Chang SC, Tsai SF. Hypermethylation of BEND5 contributes to cell proliferation and is a prognostic marker of colorectal cancer. Oncotarget 2017; 8:113431-113443. [PMID: 29371920 PMCID: PMC5768337 DOI: 10.18632/oncotarget.22266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 05/10/2017] [Indexed: 01/05/2023] Open
Abstract
Aberrant hypermethylation of CpG islands in tumor suppressor genes (TSGs) contributes to colorectal tumorigenesis. To identify new colorectal cancer (CRC) screening marker, we investigated DNA methylation alterations in novel TSGs. Using HumanMethylation450 BeadChip arrays, CpG regions in BEND5 were the most highly methylated among all genomic regions in 26 colorectal tumors compared to paired non-neoplastic tissues from a Taiwan cohort. Therefore, BEND5 was selected for further analysis. Quantitative methylation-specific real-time PCR revealed that 86.7% (117/135) of CRC patients exhibited hypermethylated BEND5. Real-time reverse transcription PCR identified that BEND5 mRNA expression was downregulated in 68% (32/47) of the analyzed samples. BEND5 hypermethylation was associated with poor overall survival (OS) in Taiwan patients with early-stage CRC (P = 0.037). In a CRC tissue set from South Korea, OS was higher in patients with high BEND5 protein expression than in those with low BEND5 protein expression (P = 0.037) by using immunohistochemistry assays. Consistently, BEND5 hypermethylation was associated with poor OS in patients with early-stage CRC in The Cancer Genome Atlas (TCGA) data set (P = 0.003). Multivariate Cox proportional hazards regression analysis further supported that hypermethylation of BEND5 genes was significantly associated with OS in Taiwan and TCGA CRC patients (P = 0.023 and 0.033, respectively). Finally, the cell model assay with transient transfection of BEND5 or si-BEND5 knockdown indicated that BEND5 inhibited cancer cell proliferation. In conclusion, epigenetic alteration in the candidate TSG BEND5 contributes to colorectal cancer development and is a prognostic marker of CRC.
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Affiliation(s)
- Ruo-Kai Lin
- Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, Taiwan, R.O.C.,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei Medical University, Taipei, Taiwan, R.O.C.,PH.D Program for Clinical Drug Development of Chinese Herbal Medicine, Ph.D Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Wan-Yu Hung
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Yu-Fang Huang
- Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Yu-Jia Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Chien-Hsing Lin
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Wei-Yu Chen
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, R.O.C.,Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Shih-Feng Chiu
- Professional Master Program in Pharmaceutics and Biotechnology, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Shih-Ching Chang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
| | - Shih-Feng Tsai
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
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31
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Yang Y, Chu FH, Xu WR, Sun JQ, Sun X, Ma XM, Yu MW, Yang GW, Wang XM. Identification of regulatory role of DNA methylation in colon cancer gene expression via systematic bioinformatics analysis. Medicine (Baltimore) 2017; 96:e8487. [PMID: 29381923 PMCID: PMC5708922 DOI: 10.1097/md.0000000000008487] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Colon cancer arises from the accumulations of genetic and epigenetic changes. Currently, profiles of DNA methylation and gene expression of colon cancer have not been elucidated clearly. This articles aims to characterize the profile of DNA methylation and gene expression of colon cancer systemically, and acquire candidate genes potentially regulated by altered methylation for this disease.Data were downloaded from The Cancer Genome Atlas database. Differentially methylated CpG sites (DMCs) and differentially methylated regions (DMRs) were calculated via COHCAP. Differentially expressed genes (DEGs) were identified by DESeq2. Weighted gene co-expression network analysis (WGCNA) package in R was applied for WGCNA.Data of 275 solid tumor tissues and 19 adjacent tumor tissues of colon cancer were obtained. A total of 1828 DMCs, including 1390 hypermethylated and 438 hypomethylated CpG sites, were identified between tumor and normal groups. A total of 789 DEGs, containing 435 upregulated genes and 354 downregulated genes were observed. It revealed that 8 DMRs-DEGs and 95 DMCs-DEGs pairs were significantly correlated. Furthermore, genes of yellow and brown modules from WGCNA were significantly correlated with tumor/normal status, and significantly enriched in peroxisome proliferator activated receptor signaling pathway, glutamatergic synapse, and neuroactive ligand-receptor interaction. Genes in the above 2 modules were also significantly enriched in DMCs or DMRs-associated genes. Specifically, ADHFE1, HAND2, and GNAO1 were hypermethylated and downregulated in colon cancer, suggesting that the low expression levels of these genes may be regulated by DNA hypermethylation. In addition, the 3 genes were involved in brown module of WGCNA, indicating their important roles in colon cancer.The investigation of the relationship between DNA methylation and gene expression may help to understand the effect of DNA methylation alteration on genes expression, especially gene co-expression network in the development of colon cancer. Genes such as ADHFE1, HAND2, and GNAO1 may be served as potential candidates for diagnosis and therapy targets in colon cancer.
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Affiliation(s)
- Yong Yang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Fu-Hao Chu
- Department of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Wei-Ru Xu
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Jia-Qi Sun
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Xu Sun
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Xue-Man Ma
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Ming-Wei Yu
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Guo-Wang Yang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
| | - Xiao-Min Wang
- Department of Oncology, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University
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Puccini A, Berger MD, Naseem M, Tokunaga R, Battaglin F, Cao S, Hanna DL, McSkane M, Soni S, Zhang W, Lenz HJ. Colorectal cancer: epigenetic alterations and their clinical implications. Biochim Biophys Acta Rev Cancer 2017; 1868:439-448. [PMID: 28939182 DOI: 10.1016/j.bbcan.2017.09.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/16/2017] [Accepted: 09/17/2017] [Indexed: 12/20/2022]
Abstract
Colorectal cancer (CRC) is a heterogeneous disease with distinct molecular and clinical features, which reflects the wide range of prognostic outcomes and treatment responses observed among CRC patients worldwide. Our understanding of the CRC epigenome has been largely developed over the last decade and it is now believed that among thousands of epigenetic alterations present in each tumor, a small subgroup of these may be considered as a CRC driver event. DNA methylation profiles have been the most widely studied in CRC, which includes a subset of patients with distinct molecular and clinical features now categorized as CpG island methylator phenotype (CIMP). Major advances have been made in our capacity to detect epigenetic alterations, providing us with new potential biomarkers for diagnostic, prognostic and therapeutic purposes. This review aims to summarize our current knowledge about epigenetic alterations occurring in CRC, underlying their potential future clinical implications in terms of diagnosis, prognosis and therapeutic strategies for CRC patients.
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Affiliation(s)
- Alberto Puccini
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Martin D Berger
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Madiha Naseem
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ryuma Tokunaga
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shu Cao
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Diana L Hanna
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michelle McSkane
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA.
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Hanley MP, Hahn MA, Li AX, Wu X, Lin J, Wang J, Choi AH, Ouyang Z, Fong Y, Pfeifer GP, Devers TJ, Rosenberg DW. Genome-wide DNA methylation profiling reveals cancer-associated changes within early colonic neoplasia. Oncogene 2017; 36:5035-5044. [PMID: 28459462 PMCID: PMC5578878 DOI: 10.1038/onc.2017.130] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 03/04/2017] [Accepted: 03/14/2017] [Indexed: 12/15/2022]
Abstract
Colorectal cancer (CRC) is characterized by genome-wide alterations to DNA methylation that influence gene expression and genomic stability. Less is known about the extent to which methylation is disrupted in the earliest stages of CRC development. In this study we have combined laser-capture microdissection (LCM) with reduced representation bisulfite sequencing (RRBS) to identify cancer-associated DNA methylation changes in human aberrant crypt foci (ACF), the earliest putative precursor to CRC. Using this approach, methylation profiles have been generated for 10 KRAS-mutant ACF and 10 CRCs harboring a KRAS mutation, as well as matched samples of normal mucosa. Of 811 differentially methylated regions (DMRs) identified in ACF, 537 (66%) were hypermethylated and 274 (34%) were hypomethylated. DMRs located within intergenic regions were heavily enriched for AP-1 transcription factor binding sites and were frequently hypomethylated. Furthermore, gene ontology (GO) analysis demonstrated that DMRs associated with promoters were enriched for genes involved in intestinal development, including homeobox genes and targets of the Polycomb repressive complex 2 (PRC2). Consistent with their role in the earliest stages of colonic neoplasia, 75% of the loci harboring methylation changes in ACF were also altered in CRC samples, though the magnitude of change at these sites was lesser in ACF. While aberrant promoter methylation was associated with altered gene expression in CRC, this was not the case in ACF, suggesting the insufficiency of methylation changes to modulate gene expression in early colonic neoplasia. Together, these data demonstrate that DNA methylation changes, including significant hypermethylation, occur more frequently in early colonic neoplasia than previously believed, and identify epigenomic features of ACF that may provide new targets for cancer chemoprevention or lead to the development of new biomarkers for CRC risk.
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Affiliation(s)
- M P Hanley
- Center for Molecular Medicine, School of Medicine, UConn Health, Farmington, CT, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - M A Hahn
- Department of Surgery, City of Hope, Duarte, CA, USA
| | - A X Li
- Department of Information Sciences, City of Hope, Duarte, CA, USA
| | - X Wu
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - J Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - J Wang
- Integrative Genomics Core, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - A H Choi
- Department of Surgery, City of Hope, Duarte, CA, USA
| | - Z Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Y Fong
- Department of Surgery, City of Hope, Duarte, CA, USA
| | - G P Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - T J Devers
- Division of Gastroenterology, School of Medicine, UConn Health, Farmington, CT, USA
| | - D W Rosenberg
- Center for Molecular Medicine, School of Medicine, UConn Health, Farmington, CT, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.,Colon Cancer Prevention Program, Neag Comprehensive Cancer Center, UConn Health, Farmington, CT, USA
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Hyper-Methylated Loci Persisting from Sessile Serrated Polyps to Serrated Cancers. Int J Mol Sci 2017; 18:ijms18030535. [PMID: 28257124 PMCID: PMC5372551 DOI: 10.3390/ijms18030535] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/22/2017] [Indexed: 12/13/2022] Open
Abstract
Although serrated polyps were historically considered to pose little risk, it is now understood that progression down the serrated pathway could account for as many as 15%-35% of colorectal cancers. The sessile serrated adenoma/polyp (SSA/P) is the most prevalent pre-invasive serrated lesion. Our objective was to identify the CpG loci that are persistently hyper-methylated during serrated carcinogenesis, from the early SSA/P lesion through the later cancer phases of neoplasia development. We queried the loci hyper-methylated in serrated cancers within our rightsided SSA/Ps from the New Hampshire Colonoscopy Registry, using the Illumina Infinium Human Methylation 450 k panel to comprehensively assess the DNA methylation status. We identified CpG loci and regions consistently hyper-methylated throughout the serrated carcinogenesis spectrum, in both our SSA/P specimens and in serrated cancers. Hyper-methylated CpG loci included the known the tumor suppressor gene RET (p = 5.72 x 10-10), as well as loci in differentially methylated regions for GSG1L, MIR4493, NTNG1, MCIDAS, ZNF568, and RERG. The hyper-methylated loci that we identified help characterize the biology of SSA/P development, and could be useful as therapeutic targets, or for future identification of patients who may benefit from shorter surveillance intervals.
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Alexander M, Burch JB, Steck SE, Chen CF, Hurley TG, Cavicchia P, Shivappa N, Guess J, Zhang H, Youngstedt SD, Creek KE, Lloyd S, Jones K, Hébert JR. Case-control study of candidate gene methylation and adenomatous polyp formation. Int J Colorectal Dis 2017; 32:183-192. [PMID: 27771773 PMCID: PMC5288296 DOI: 10.1007/s00384-016-2688-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/12/2016] [Indexed: 02/04/2023]
Abstract
PURPOSE Colorectal cancer (CRC) is one of the most common and preventable forms of cancer but remains the second leading cause of cancer-related death. Colorectal adenomas are precursor lesions that develop in 70-90 % of CRC cases. Identification of peripheral biomarkers for adenomas would help to enhance screening efforts. This exploratory study examined the methylation status of 20 candidate markers in peripheral blood leukocytes and their association with adenoma formation. METHODS Patients recruited from a local endoscopy clinic provided informed consent and completed an interview to ascertain demographic, lifestyle, and adenoma risk factors. Cases were individuals with a histopathologically confirmed adenoma, and controls included patients with a normal colonoscopy or those with histopathological findings not requiring heightened surveillance (normal biopsy, hyperplastic polyp). Methylation-specific polymerase chain reaction was used to characterize candidate gene promoter methylation. Odds ratios (ORs) and 95 % confidence intervals (95% CIs) were calculated using unconditional multivariable logistic regression to test the hypothesis that candidate gene methylation differed between cases and controls, after adjustment for confounders. RESULTS Complete data were available for 107 participants; 36 % had adenomas (men 40 %, women 31 %). Hypomethylation of the MINT1 locus (OR 5.3, 95% CI 1.0-28.2) and the PER1 (OR 2.9, 95% CI 1.1-7.7) and PER3 (OR 11.6, 95% CI 1.6-78.5) clock gene promoters was more common among adenoma cases. While specificity was moderate to high for the three markers (71-97 %), sensitivity was relatively low (18-45 %). CONCLUSION Follow-up of these epigenetic markers is suggested to further evaluate their utility for adenoma screening or surveillance.
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Affiliation(s)
- M Alexander
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
| | - J B Burch
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA.
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA.
- William Jennings Bryant Dorn Department of Veterans Affairs Medical Center, Columbia, SC, USA.
| | - S E Steck
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
| | - C-F Chen
- Center for Molecular Studies, Greenwood Genetic Center, Greenwood, SC, USA
| | - T G Hurley
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
| | - P Cavicchia
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
- Division of Community Health Promotion, Florida Department of Health, Tallahassee, FL, USA
| | - N Shivappa
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
| | - J Guess
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
| | - H Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - S D Youngstedt
- College of Nursing and Health Innovation, College of Health Solutions, Arizona State University and Phoenix VA Health Care System, Phoenix, AZ, USA
| | - K E Creek
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - S Lloyd
- South Carolina Medical Endoscopy Center, and Department of Family Medicine, University of South Carolina School of Medicine, Columbia, SC, USA
| | - K Jones
- Center for Molecular Studies, Greenwood Genetic Center, Greenwood, SC, USA
| | - J R Hébert
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
- Department of Family and Preventive Medicine, School of Medicine, University of South Carolin, Columbia, SC, USA
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Aberrant DNA methylation of acute myeloid leukemia and colorectal cancer in a Chinese pedigree with a MLL3 germline mutation. Tumour Biol 2016; 37:12609-12618. [PMID: 27405564 DOI: 10.1007/s13277-016-5130-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/29/2016] [Indexed: 12/14/2022] Open
Abstract
Unlike genetic aberrations, epigenetic alterations do not modify the deoxyribonucleic acid (DNA) coding sequence and can be reversed pharmacologically. Identifying a particular epigenetic alteration such as abnormal DNA methylation may provide better understanding of cancers and improve current therapy. In a Chinese pedigree with colorectal carcinoma and acute myeloid leukemia, we examined the genome-wide DNA methylation level of cases and explored the role of methylation in pathogenesis and progression. DNA methylation status in the four cases, which all harbor a MLL3 germline mutation, differed from that of the normal control, and hypermethylation was more prevalent. Also, more CpG sites were hypermethylated in the acute-phase AML patient than in the AML patient in remission. Fifty-nine hyper- or hypomethylated genes were identified as common to all four cases. Genome-wide DNA methylation analysis demonstrated that differentially methylated sites among acute myeloid leukemia and colorectal carcinoma cases and the control were in both promoters (CpG island) and gene body regions (shelf/shore areas). Hypermethylation was more prevalent in cancer cases. The study supports the suggestion that the level of DNA methylation changes in AML progression.
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37
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Procaine Induces Epigenetic Changes in HCT116 Colon Cancer Cells. GENETICS RESEARCH INTERNATIONAL 2016; 2016:8348450. [PMID: 27843649 PMCID: PMC5098101 DOI: 10.1155/2016/8348450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/25/2016] [Accepted: 09/29/2016] [Indexed: 12/17/2022]
Abstract
Colon cancer is the third most commonly diagnosed cancer in the world, and it is the major cause of morbidity and mortality throughout the world. The present study aimed at treating colon cancer cell line (HCT116) with different chemotherapeutic drug/drug combinations (procaine, vorinostat “SAHA,” sodium phenylbutyrate, erlotinib, and carboplatin). Two different final concentrations were applied: 3 μM and 5 μM. Trypan blue test was performed to assess the viability of the cell before and after being treated with the drugs. The data obtained showed that there was a significant decrease in the viability of cells after applying the chemotherapeutic drugs/drug combinations. Also, DNA fragmentation assay was carried out to study the effect of these drugs on the activation of apoptosis-mediated DNA degradation process. The results indicated that all the drugs/drug combinations had a severe effect on inducing DNA fragmentation. Global DNA methylation quantification was performed to identify the role of these drugs individually or in combination in hypo- or hypermethylating the CpG dinucleotide all over the genome of the HCT116 colon cancer cell line. Data obtained indicated that different combinations had different effects in reducing or increasing the level of methylation, which might indicate the effectiveness of combining drugs in treating colon cancer cells.
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Choi B, Han TS, Min J, Hur K, Lee SM, Lee HJ, Kim YJ, Yang HK. MAL and TMEM220 are novel DNA methylation markers in human gastric cancer. Biomarkers 2016; 22:35-44. [DOI: 10.1080/1354750x.2016.1201542] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Semaan A, van Ellen A, Meller S, Bergheim D, Branchi V, Lingohr P, Goltz D, Kalff JC, Kristiansen G, Matthaei H, Pantelis D, Dietrich D. SEPT9 and SHOX2 DNA methylation status and its utility in the diagnosis of colonic adenomas and colorectal adenocarcinomas. Clin Epigenetics 2016; 8:100. [PMID: 27660666 PMCID: PMC5028994 DOI: 10.1186/s13148-016-0267-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/13/2016] [Indexed: 02/06/2023] Open
Abstract
Background Colorectal cancer (CRC) appear to arise from precursor lesions in a well-characterized adenoma-carcinoma sequence. Significant efforts have been invested to develop biomarkers that identify early adenocarcinomas and adenomas with high-grade dysplasia, since these are believed to harbor a particularly high risk for malignant transition and thus require resection. Promoter methylation of SEPT9 and SHOX2 has been suggested as a biomarker for various solid malignant tumors. Hence, the present study aimed to test their biomarker potential in CRC and precursor lesions. Results Assessment of promoter methylation of SEPT9 distinguished adenomas and CRC from controls as well as advanced from non-advanced adenomas (all p < 0.001). Correspondingly, SHOX2 methylation levels in adenomas and colorectal carcinomas were significantly higher compared to those in normal control tissues (p < 0.001). Histologic transition from adenomas to CRC was paralleled by amplification of the SEPT9 gene locus. Conclusions SEPT9/SHOX2 methylation assays may help to distinguish colorectal cancer and adenomas from normal and inflammatory colonic tissue, as well as advanced from non-advanced adenomas. Further studies need to validate these findings before introduction in clinical routine.
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Affiliation(s)
- Alexander Semaan
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Anne van Ellen
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Sebastian Meller
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Dominik Bergheim
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Vittorio Branchi
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Philipp Lingohr
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Diane Goltz
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Jörg C Kalff
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Glen Kristiansen
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Hanno Matthaei
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Dimitrios Pantelis
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Dimo Dietrich
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
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Babaei H, Mohammadi M, Salehi R. DNA methylation analysis of secreted frizzled-related protein 2 gene for the early detection of colorectal cancer in fecal DNA. Niger Med J 2016; 57:242-5. [PMID: 27630389 PMCID: PMC4995817 DOI: 10.4103/0300-1652.188357] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background: The early detection of colorectal cancer (CRC) with high sensitivity screening is essential for the reduction of cancer-specific mortality. Abnormally methylated genes that are responsible for the pathogenesis of cancers can be used as biomarkers for the detection of CRC. The methylation status of the secreted frizzled-related protein 2 (SFRP2) gene was evaluated for their use as a marker in the noninvasive detection of CRC. Materials and Methods: Methylation-specific polymerase chain reaction was performed to analyze the promoter CpG methylation of SFRP2 in the fecal DNA of 25 patients with CRC and 25 individuals exhibiting normal colonoscopy results. Results: Promoter methylation levels of SFRP2 in CRC patients and in healthy controls were 60% and 8%, respectively. Methylation of the SFRP2 promoter in fecal DNA is associated with the presence of colorectal tumors. Conclusion: Hence, the detection of aberrantly methylated DNA in fecal samples may present a promising, noninvasive screening method for CRC.
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Affiliation(s)
- Hadi Babaei
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohsen Mohammadi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Sameer AS, Nissar S. Understanding Epigenetics: an Alternative Mechanism of Colorectal Carcinogenesis. CURRENT COLORECTAL CANCER REPORTS 2016. [DOI: 10.1007/s11888-016-0317-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Abstract
Rhabdomyosarcoma is the most common soft tissue sarcoma of childhood and adolescence. Despite advances in therapy, patients with histological variant of rhabdomyosarcoma known as alveolar rhabdomyosarcoma (ARMS) have a 5-year survival of less than 30%. Caveolin-1 (CAV1), encoding the structural component of cellular caveolae, is a suggested tumor suppressor gene involved in cell signaling. In the present study we report that compared to other forms of rhabdomyosarcoma (RMS) CAV1 expression is either undetectable or very low in ARMS cell lines and tumor samples. DNA methylation analysis of the promoter region and azacytidine-induced re-expression suggest the involvement of epigenetic mechanisms in the silencing of CAV1. Reintroduction of CAV1 in three of these cell lines impairs their clonogenic capacity and promotes features of muscular differentiation. In vitro, CAV1-expressing cells show high expression of Caveolin-3 (CAV3), a muscular differentiation marker. Blockade of MAPK signaling is also observed. In vivo, CAV1-expressing xenografts show growth delay, features of muscular differentiation and increased cell death. In summary, our results suggest that CAV1 could function as a potent tumor suppressor in ARMS tumors. Inhibition of CAV1 function therefore, could contribute to aberrant cell proliferation, leading to ARMS development.
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Liao Q, He W, Liu J, Cen Y, Luo L, Yu C, Li Y, Chen S, Duan S. Identification and functional annotation of lncRNA genes with hypermethylation in colorectal cancer. Gene 2015; 572:259-65. [PMID: 26172871 DOI: 10.1016/j.gene.2015.07.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/28/2015] [Accepted: 07/08/2015] [Indexed: 02/08/2023]
Abstract
Colorectal cancer (CRC) is one of the leading causes of mortality worldwide. DNA methylation is an important epigenetic modification for CRC. Although currently a number of studies about DNA methylation of protein coding genes have been carried out, only a few are about the methylation of genes encoding the long noncoding RNAs (lncRNAs). In this study, we identified 761 lncRNA genes with DNA hypermethylation in CRC using a free MethylCap-seq dataset. Integration of lncRNA expression and methylation datasets showed that the expression of lncRNAs is negatively correlated with DNA methylation (p<0.01). Co-methylation network was also constructed to annotate the functions of unknown lncRNAs. Our results showed that a total of 364 lncRNAs were annotated with at least one GO biological process term. The current data-mining work is likely to provide informative clues for biological researchers to further understand the role of lncRNAs in the development of CRC.
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Affiliation(s)
- Qi Liao
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Weiling He
- Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Jianfa Liu
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Yi Cen
- Yinzhou Branch of Ningbo Public Security Bureau, Ningbo, Zhejiang 315100, China
| | - Liang Luo
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Chengliang Yu
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Yang Li
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Sitong Chen
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.
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Abstract
The trillions of bacteria that naturally reside in the human gut collectively constitute the complex system known the gut microbiome, a vital player for the host's homeostasis and health. However, there is mounting evidence that dysbiosis, a state of pathological imbalance in the gut microbiome is present in many disease states. In this review, we present recent insights concerning the gut microbiome's contribution to the development of colorectal adenomas and the subsequent progression to colorectal cancer (CRC). In the United States alone, CRC is the second leading cause of cancer deaths. As a result, there is a high interest in identifying risk factors for adenomas, which are intermediate precursors to CRC. Recent research on CRC and the microbiome suggest that modulation of the gut bacterial composition and structure may be useful in preventing adenomas and CRC. We highlight the known risk factors for colorectal adenomas and the potential mechanisms by which microbial dysbiosis may contribute to the etiology of CRC. We also underscore novel findings from recent studies on the gut microbiota and colorectal adenomas along with current knowledge gaps. Understanding the microbiome may provide promising new directions towards novel diagnostic tools, biomarkers, and therapeutic interventions for CRC.
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Keku TO, Dulal S, Deveaux A, Jovov B, Han X. The gastrointestinal microbiota and colorectal cancer. Am J Physiol Gastrointest Liver Physiol 2015; 308:G351-63. [PMID: 25540232 PMCID: PMC4346754 DOI: 10.1152/ajpgi.00360.2012] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The human gut is home to a complex and diverse microbiota that contributes to the overall homeostasis of the host. Increasingly, the intestinal microbiota is recognized as an important player in human illness such as colorectal cancer (CRC), inflammatory bowel diseases, and obesity. CRC in itself is one of the major causes of cancer mortality in the Western world. The mechanisms by which bacteria contribute to CRC are complex and not fully understood, but increasing evidence suggests a link between the intestinal microbiota and CRC as well as diet and inflammation, which are believed to play a role in carcinogenesis. It is thought that the gut microbiota interact with dietary factors to promote chronic inflammation and CRC through direct influence on host cell physiology, cellular homeostasis, energy regulation, and/or metabolism of xenobiotics. This review provides an overview on the role of commensal gut microbiota in the development of human CRC and explores its association with diet and inflammation.
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Affiliation(s)
- Temitope O. Keku
- 1Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina; ,2Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, North Carolina; and
| | - Santosh Dulal
- 1Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina; ,2Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, North Carolina; and
| | - April Deveaux
- 1Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina; ,2Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, North Carolina; and
| | - Biljana Jovov
- 1Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina; ,2Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, North Carolina; and
| | - Xuesong Han
- 3Surveillance and Health Services Research, American Cancer Society, Atlanta, Georgia
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Coppedè F, Grossi E, Lopomo A, Spisni R, Buscema M, Migliore L. Application of artificial neural networks to link genetic and environmental factors to DNA methylation in colorectal cancer. Epigenomics 2015; 7:175-86. [PMID: 25942531 DOI: 10.2217/epi.14.77] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
AIMS We applied artificial neural networks (ANNs) to understand the connections among polymorphisms of genes involved in folate metabolism, clinico-pathological features and promoter methylation levels of MLH1, APC, CDKN2A(INK4A), MGMT and RASSF1A in 83 sporadic colorectal cancer (CRC) tissues, and to link dietary and lifestyle factors with gene promoter methylation. MATERIALS & METHODS Promoter methylation was assessed by means of methylation-sensitive high-resolution melting and genotyping by PCR-RFLP technique. Data were analyzed with the Auto Contractive Map, a special kind of ANN able to define the strength of the association of each variable with all the others and to visually show the map of the main connections. RESULTS We observed a strong connection between the low methylation levels of the five CRC genes and the MTR 2756AA genotype. Several other connections were revealed, including those between dietary and lifestyle factors and the methylation levels of CRC genes. CONCLUSION ANNs revealed the complexity of the interconnections among factors linked to DNA methylation in CRC.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & New Technologies in Medicine & Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy
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Abstract
Colorectal cancer (CRC) results from a stepwise accumulation of genetic and epigenetic alterations that transform the normal colonic epithelium into cancer. DNA methylation represents one of the most studied epigenetic marks in CRC, and three common epigenotypes have been identified characterized by high, intermediate and low methylation profiles, respectively. Combining DNA methylation data with gene mutations and cytogenetic alterations occurring in CRC is nowadays allowing the characterization of different CRC subtypes, but the crosstalk between DNA methylation and other epigenetic mechanisms, such as histone tail modifications and the deregulated expression of non-coding RNAs is not yet clearly defined. Epigenetic biomarkers are increasingly recognized as promising diagnostic and prognostic tools in CRC, and the potential of therapeutic applications aimed at targeting the epigenome is under investigation.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy
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Yamaguchi K, Matsumura N, Mandai M, Baba T, Konishi I, Murphy SK. Epigenetic and genetic dispositions of ovarian carcinomas. Oncoscience 2014; 1:574-9. [PMID: 25594067 PMCID: PMC4278339 DOI: 10.18632/oncoscience.82] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 09/15/2014] [Indexed: 12/17/2022] Open
Abstract
Ovarian clear cell carcinoma has unique clinical characteristics with slow growth and a stress-resistant phenotype that is epigenetically induced during cancer progression in an inflammatory microenvironment. We refer to this as an epigenetic disposition, which is frequently associated with unique biomolecular features including prominent alterations in methylation, microsatellite instability and ARID1A mutations. This characteristic methylation profile also affects glucose metabolism, commonly known as the Warburg effect. In contrast, high-grade ovarian serous adenocarcinoma has a genetic disposition that is accompanied by rapid growth, TP53 mutations and chromosomal instability. The concept of epigenetic and genetic dispositions is applicable to various malignancies, including gastric and colorectal cancers. These disposition classifications are based on fundamental characteristics of malignancies and may provide a new vantage point for development of individualized therapies.
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Affiliation(s)
- Ken Yamaguchi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507 Japan
| | - Noriomi Matsumura
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507 Japan
| | - Masaki Mandai
- Department of Obstetrics and Gynecology, Kinki University, Faculty of Medicine, Osakasayama, Osaka, 589-8511 Japan
| | - Tsukasa Baba
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507 Japan
| | - Ikuo Konishi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507 Japan
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham NC, 27708 USA
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