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Akanyibah FA, Zhu Y, Wan A, Ocansey DKW, Xia Y, Fang AN, Mao F. Effects of DNA methylation and its application in inflammatory bowel disease (Review). Int J Mol Med 2024; 53:55. [PMID: 38695222 DOI: 10.3892/ijmm.2024.5379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) is marked by persistent inflammation, and its development and progression are linked to environmental, genetic, immune system and gut microbial factors. DNA methylation (DNAm), as one of the protein modifications, is a crucial epigenetic process used by cells to control gene transcription. DNAm is one of the most common areas that has drawn increasing attention recently, with studies revealing that the interleukin (IL)‑23/IL‑12, wingless‑related integration site, IL‑6‑associated signal transducer and activator of transcription 3, suppressor of cytokine signaling 3 and apoptosis signaling pathways are involved in DNAm and in the pathogenesis of IBD. It has emerged that DNAm‑associated genes are involved in perpetuating the persistent inflammation that characterizes a number of diseases, including IBD, providing a novel therapeutic strategy for exploring their treatment. The present review discusses DNAm‑associated genes in the pathogenesis of IBD and summarizes their application as possible diagnostic, prognostic and therapeutic biomarkers in IBD. This may provide a reference for the particular form of IBD and its related methylation genes, aiding in clinical decision‑making and encouraging therapeutic alternatives.
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Affiliation(s)
- Francis Atim Akanyibah
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| | - Yi Zhu
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu 212300, P.R. China
| | - Aijun Wan
- Zhenjiang College, Zhenjiang, Jiangsu 212028, P.R. China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yuxuan Xia
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - An-Ning Fang
- Basic Medical School, Anhui Medical College, Hefei, Anhui 230061, P.R. China
| | - Fei Mao
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
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2
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Zhao N, Lai C, Wang Y, Dai S, Gu H. Understanding the role of DNA methylation in colorectal cancer: Mechanisms, detection, and clinical significance. Biochim Biophys Acta Rev Cancer 2024; 1879:189096. [PMID: 38499079 DOI: 10.1016/j.bbcan.2024.189096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/18/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
Colorectal cancer (CRC) is one of the deadliest malignancies worldwide, ranking third in incidence and second in mortality. Remarkably, early stage localized CRC has a 5-year survival rate of over 90%; in stark contrast, the corresponding 5-year survival rate for metastatic CRC (mCRC) is only 14%. Compounding this problem is the staggering lack of effective therapeutic strategies. Beyond genetic mutations, which have been identified as critical instigators of CRC initiation and progression, the importance of epigenetic modifications, particularly DNA methylation (DNAm), cannot be underestimated, given that DNAm can be used for diagnosis, treatment monitoring and prognostic evaluation. This review addresses the intricate mechanisms governing aberrant DNAm in CRC and its profound impact on critical oncogenic pathways. In addition, a comprehensive review of the various techniques used to detect DNAm alterations in CRC is provided, along with an exploration of the clinical utility of cancer-specific DNAm alterations.
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Affiliation(s)
- Ningning Zhao
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China
| | - Chuanxi Lai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech. Ltd, Hangzhou 310000, China
| | - Sheng Dai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China.
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3
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Oh CK, Cho YS. Pathogenesis and biomarkers of colorectal cancer by epigenetic alteration. Intest Res 2024; 22:131-151. [PMID: 38295766 PMCID: PMC11079515 DOI: 10.5217/ir.2023.00115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/16/2023] [Accepted: 12/29/2023] [Indexed: 05/12/2024] Open
Abstract
Colorectal cancer (CRC) ranks third in cancer incidence and stands as the second leading cause of cancer-related deaths globally. CRC tumorigenesis results from a cumulative set of genetic and epigenetic alterations, disrupting cancer-regulatory processes like cell proliferation, metabolism, angiogenesis, cell death, invasion, and metastasis. Key epigenetic modifications observed in cancers encompass abnormal DNA methylation, atypical histone modifications, and irregularities in noncoding RNAs, such as microRNAs and long noncoding RNAs. The advancement in genomic technologies has positioned these genetic and epigenetic shifts as potential clinical biomarkers for CRC patients. This review concisely covers the fundamental principles of CRC-associated epigenetic changes, and examines in detail their emerging role as biomarkers for early detection, prognosis, and treatment response prediction.
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Affiliation(s)
- Chang Kyo Oh
- Division of Gastroenterology, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Young-Seok Cho
- Division of Gastroenterology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Mustafa SK, Khan MF, Sagheer M, Kumar D, Pandey S. Advancements in biosensors for cancer detection: revolutionizing diagnostics. Med Oncol 2024; 41:73. [PMID: 38372827 DOI: 10.1007/s12032-023-02297-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/28/2023] [Indexed: 02/20/2024]
Abstract
Cancer stands as the reigning champion of life-threatening diseases, casting a shadow with the highest global mortality rate. Unleashing the power of early cancer treatment is a vital weapon in the battle for efficient and positive outcomes. Yet, conventional screening procedures wield limitations of exorbitant costs, time-consuming endeavors, and impracticality for repeated testing. Enter bio-marker-based cancer diagnostics, which emerge as a formidable force in the realm of early detection, disease progression assessment, and ultimate cancer therapy. These remarkable devices boast a reputation for their exceptional sensitivity, streamlined setup requirements, and lightning fast response times. In this study, we embark on a captivating exploration of the most recent advancements and enhancements in the field of electrochemical marvels, targeting the detection of numerous cancer biomarkers. With each breakthrough, we inch closer to a future where cancer's grip on humanity weakens, guided by the promise of personalized treatment and improved patient outcomes. Together, we unravel the mysteries that cancer conceals and illuminate a path toward triumph against this daunting adversary. This study celebrates the relentless pursuit of progress, where electrochemical innovations take center stage in the quest for a world free from the clutches of carcinoma.
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Affiliation(s)
- Syed Khalid Mustafa
- Department of Chemistry, Faculty of Science, University of Tabuk, P.O. Box 741, Zip 71491, Tabuk, Saudi Arabia.
| | - Mohd Farhan Khan
- Faculty of Science, Gagan College of Management & Technology, Aligarh, 202002, India
| | - Mehak Sagheer
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sadanand Pandey
- Faculty of Applied Sciences and Biotechnology, School of Bioengineering and Food Technology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
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Mokhtari K, Peymani M, Rashidi M, Hushmandi K, Ghaedi K, Taheriazam A, Hashemi M. Colon cancer transcriptome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:49-82. [PMID: 37059270 DOI: 10.1016/j.pbiomolbio.2023.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.
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Affiliation(s)
- Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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6
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Müller D, Győrffy B. DNA methylation-based diagnostic, prognostic, and predictive biomarkers in colorectal cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188722. [PMID: 35307512 DOI: 10.1016/j.bbcan.2022.188722] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/21/2022] [Accepted: 03/13/2022] [Indexed: 12/12/2022]
Abstract
DNA methylation is an epigenetic mechanism regulating gene expression. Changes in DNA methylation were suggested to be useful biomarkers for diagnosis, and for the determination of prognosis and treatment response. Here, we provide an overview of methylation-based biomarkers in colorectal cancer. First, we start with the two methylation-based diagnostic biomarkers already approved for colorectal cancer, SEPT9 and the combination of NDRG4 and BMP3. Then, we provide a list-based overview of new biomarker candidates depending on the sample source including plasma, stool, urine, and surgically removed tumor tissues. The most often identified markers like SDC2, VIM, APC, MGMT, SFRP1, SFRP2, and NDRG4 have distinct functions previously linked to tumor progression. Although numerous studies have identified tumor-specific methylation changes, most of these alterations were observed in a single study only. The lack of validation in independent samples means low reproducibility and is a major limitation. The genome-wide determination of methylation status (methylome) can provide data to solve these issues. In the third section of the review, methylome studies focusing on different aspects related to CRC, including precancerous lesions, CRC-specific changes, molecular subtypes, aging, and chemotherapy response are summarized. Notably, techniques simultaneously analyzing a large set of regions can also uncover epigenetic regulation of genes which have not yet been associated with tumorigenesis previously. A remaining constraint of studies published to date is the low patient number utilized in these preventing the identification of clinically valuable biomarker candidates. Either future large-scale studies or the integration of already available methylome-level data will be necessary to uncover biomarkers sufficiently robust for clinical application.
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Affiliation(s)
- Dalma Müller
- Dept. of Bioinformatics, Semmelweis University, Budapest, Hungary; Cancer Biomarker Research Group, RCNS, Budapest, Hungary
| | - Balázs Győrffy
- Dept. of Bioinformatics, Semmelweis University, Budapest, Hungary; Cancer Biomarker Research Group, RCNS, Budapest, Hungary.
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Jafarpour S, Saberi F, Yazdi M, Nedaeinia R, Amini G, Ferns GA, Salehi R. Association between colorectal cancer and the degree of ITGA4 promoter methylation in peripheral blood mononuclear cells. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Novel Diagnostic Biomarkers in Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23020852. [PMID: 35055034 PMCID: PMC8776048 DOI: 10.3390/ijms23020852] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/27/2021] [Accepted: 01/03/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is still a leading cause of cancer death worldwide. Less than half of cases are diagnosed when the cancer is locally advanced. CRC is a heterogenous disease associated with a number of genetic or somatic mutations. Diagnostic markers are used for risk stratification and early detection, which might prolong overall survival. Nowadays, the widespread use of semi-invasive endoscopic methods and feacal blood tests characterised by suboptimal accuracy of diagnostic results has led to the detection of cases at later stages. New molecular noninvasive tests based on the detection of CRC alterations seem to be more sensitive and specific then the current methods. Therefore, research aiming at identifying molecular markers, such as DNA, RNA and proteins, would improve survival rates and contribute to the development of personalized medicine. The identification of “ideal” diagnostic biomarkers, having high sensitivity and specificity, being safe, cheap and easy to measure, remains a challenge. The purpose of this review is to discuss recent advances in novel diagnostic biomarkers for tumor tissue, blood and stool samples in CRC patients.
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Cao LJ, Peng XL, Xue WQ, Zhang R, Zhang JB, Zhou T, Wu ZY, Li GR, Wang TM, He YQ, Yang DW, Liao Y, Tong XT, Wang F, Chen KX, Zhang SH, Zhu LQ, Ding PR, Jia WH. A fecal-based test for the detection of advanced adenoma and colorectal cancer: a case-control and screening cohort study. BMC Med 2021; 19:250. [PMID: 34689777 PMCID: PMC8543798 DOI: 10.1186/s12916-021-02123-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/13/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the leading cause of cancer death worldwide. Screening is a confirmed way to reduce the incidence and mortality rates of CRC. This study aimed to identify a fecal-based, noninvasive, and accurate method for detection of colorectal cancer (CRC) and advanced adenoma (AA). METHODS Through detection in tissue (n = 96) and fecal samples (n = 88) and tested in an independent group of fecal samples (n = 294), the methylated DNA marker ITGA4 and bacterial markers Fusobacterium nucleatum (Fn) and Pepetostreptococcusanaerobius (Pa) were identified from the candidate biomarkers for CRC and AA detection. A prediction score (pd-score) was constructed using the selected markers and fecal immunochemical test (FIT) for distinguishing AA and CRC from healthy subjects by logistic regression method. The diagnostic performance of the pd-score was compared with FIT and validated in the external validation cohort (n = 117) and in a large CRC screening cohort. RESULTS The pd-score accurately identified AA and CRC from healthy subjects with an area under the curve (AUC) of 0.958, at a specificity of 91.37%; the pd-score showed sensitivities of 95.38% for CRC and 70.83% for AA, respectively. In the external validation cohort, the sensitivities of the pd-score for CRC and AA detection were 94.03% and 80.00%, respectively. When applied in screening, the pd-score identified 100% (11/11) of CRC and 70.83% (17/24) of AA in participants with both colonoscopy results and qualified fecal samples, showing an improvement by 41.19% compared to FIT. CONCLUSIONS The current study developed a noninvasive and well-validated approach for AA and CRC detection, which could be applied widely as a diagnostic and screening test.
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Affiliation(s)
- Lian-Jing Cao
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Department of Radiation Oncology, Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Xiao-Lin Peng
- Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, People's Republic of China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Rong Zhang
- Department of Endoscopy and Laser, Sun Yat-Sen University Cancer Center, Guangzhou, People's Republic of China
| | - Jiang-Bo Zhang
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
- Biobank of Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Zi-Yi Wu
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Gai-Rui Li
- Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, People's Republic of China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Da-Wei Yang
- School of Public Health, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Ying Liao
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Xia-Ting Tong
- School of Public Health, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Fang Wang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Ke-Xin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, Tianjin Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Shi-Hong Zhang
- Department of Laboratory Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Li-Qing Zhu
- Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, People's Republic of China
| | - Pei-Rong Ding
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China Guangzhou, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China.
- Biobank of Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China.
- School of Public Health, Sun Yat-Sen University, Guangzhou, People's Republic of China.
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Cao Y, Zhao G, Yuan M, Liu X, Ma Y, Cao Y, Miao B, Zhao S, Li D, Xiong S, Zheng M, Fei S. KCNQ5 and C9orf50 Methylation in Stool DNA for Early Detection of Colorectal Cancer. Front Oncol 2021; 10:621295. [PMID: 33585248 PMCID: PMC7878552 DOI: 10.3389/fonc.2020.621295] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/14/2020] [Indexed: 12/24/2022] Open
Abstract
Background Aberrant DNA methylation has emerged as a class of promising biomarkers for early colorectal cancer (CRC) detection, but the performance of methylated C9orf50 and methylated KCNQ5 in stool DNA has never been evaluated. Methods Methylation specific quantitative PCR (qPCR) assays for methylated C9orf50 and methylated KCNQ5 were developed. The methylation levels of C9orf50 and KCNQ5 in 198 CRC patients, 20 advanced adenoma (AA) patients, 101 small polyp (SP) patients, and 141 no evidence of disease (NED) subjects were analyzed. Results The methylation levels of both KCNQ5 and C9orf50 genes were significantly higher in CRC and AA groups than those in SP and NED groups, but showed no significant difference among different stages of CRC. The sensitivities of methylated KCNQ5 and methylated C9orf50 for CRC detection were 77.3% (95% CI: 70.7–82.8%) and 85.9% (95% CI: 80.0–90.2%) with specificities of 91.5% (95% CI: 85.3–95.3%) and 95.0% (95% CI: 89.7–97.8%), respectively. When C9orf50 and methylated KCNQ5 were combined, the clinical performance for CRC detection was similar to that of methylated C9orf50 alone. Conclusions Stool DNA based methylated C9orf50 test has the potential to become an alternative approach for CRC screening and prevention.
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Affiliation(s)
- Yaping Cao
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Guodong Zhao
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China.,State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.,Department of R&D, Suzhou VersaBio Technologies Co. Ltd., Kunshan, China
| | - Mufa Yuan
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Xiaoyu Liu
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
| | - Yong Ma
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China.,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Yang Cao
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Bei Miao
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Shuyan Zhao
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Danning Li
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Shangmin Xiong
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China.,Department of R&D, Suzhou VersaBio Technologies Co. Ltd., Kunshan, China
| | - Minxue Zheng
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China.,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Sujuan Fei
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
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11
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Laugsand EA, Brenne SS, Skorpen F. DNA methylation markers detected in blood, stool, urine, and tissue in colorectal cancer: a systematic review of paired samples. Int J Colorectal Dis 2021; 36:239-251. [PMID: 33030559 PMCID: PMC7801356 DOI: 10.1007/s00384-020-03757-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/17/2020] [Indexed: 02/04/2023]
Abstract
PURPOSE Methylated cell-free DNA in liquid biopsies are promising non-invasive biomarkers for colorectal cancer (CRC). Optimal markers would have high sensitivity and specificity for early detection of CRC and could be detected in more than one type of material from the patient. We systematically reviewed the literature on DNA methylation markers of colorectal cancer, detected in more than one type of material, regarding their potential as contributors to a panel for screening and follow-up of CRC. METHODS The databases MEDLINE, Web of Science, and Embase were systematically searched. Data extraction and review was performed by two authors independently. Agreement between methylation status in tissue and other materials (blood/stool/urine) was analyzed using the McNemar test and Cohen's kappa. RESULTS From the 51 included studies, we identified seven single markers with sensitivity ≥ 75% and specificity ≥ 90% for CRC. We also identified one promising plasma panel and two stool panels. The correspondence of methylation status was evaluated as very good for four markers, but only marginal for most of the other markers investigated (12 of 21). CONCLUSION The included studies reported only some of the variables and markers of interest and included few patients. Hence, a meta-analysis was not possible at this point. Larger, prospective studies must be designed to study the discordant detection of markers in tissue and liquid biopsies. When reporting their findings, such studies should use a standardized format.
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Affiliation(s)
- Eivor Alette Laugsand
- Department of Surgery, Levanger Hospital, Nord-Trøndelag Hospital trust, N-7600, Levanger, Norway.
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway.
| | - Siv Sellæg Brenne
- Department of Surgery, Levanger Hospital, Nord-Trøndelag Hospital trust, N-7600, Levanger, Norway
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
| | - Frank Skorpen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
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12
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Bresalier RS, Grady WM, Markowitz SD, Nielsen HJ, Batra SK, Lampe PD. Biomarkers for Early Detection of Colorectal Cancer: The Early Detection Research Network, a Framework for Clinical Translation. Cancer Epidemiol Biomarkers Prev 2020; 29:2431-2440. [PMID: 32299850 PMCID: PMC7572434 DOI: 10.1158/1055-9965.epi-20-0234] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/26/2020] [Accepted: 04/09/2020] [Indexed: 12/26/2022] Open
Abstract
Early detection by screening significantly reduces mortality from colorectal cancer, but 40% of guideline-eligible patients are not screened as recommended in the United States. Novel strategies to improve screening uptake overall and efforts to deploy best practices to underserved populations are a high priority for health care. This review focuses on existing biomarkers in practice and those in development with clinical relevance to early detection of colorectal neoplasia, with an emphasis on those developed by investigators of the NCI's Early Detection Research Network. Aberrantly methylated DNA markers (blood and stool), stool-based markers (including fecal immunochemical test-DNA), and a variety of blood-based marker assays in development (protein markers, glycoproteins including mucins, and cell-free DNA tests) are reviewed. Individual markers and biomarker panels, sample resources, and barriers to translating biomarkers to clinical practice are discussed.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Robert S Bresalier
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center and the Department of Medicine, Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington
| | - Sanford D Markowitz
- Case Comprehensive Cancer Center and the Division of Hematology-Oncology, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Hans Jørgen Nielsen
- Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark
- The Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, Omaha, Nebraska
| | - Paul D Lampe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
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13
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Zhang X, Wan S, Yu Y, Ruan W, Wang H, Xu L, Wang C, Chen S, Cao T, Peng Q, Li S, Hu T, Jiang Z, Chen Z, Fan JB. Identifying potential DNA methylation markers in early-stage colorectal Cancer. Genomics 2020; 112:3365-3373. [PMID: 32531444 DOI: 10.1016/j.ygeno.2020.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/29/2020] [Accepted: 06/03/2020] [Indexed: 01/20/2023]
Abstract
Colorectal cancer (CRC) is the second leading malignancy worldwide. Accurate screening is pivotal to early CRC detection, yet current screening modality involves invasive colonoscopy while non-invasive FIT tests have limited sensitivity. We applied a DNA methylation assay to identify biomarkers for early-stage CRC detection, risk stratification and precancerous lesion screening at tissue level. A model of biomarkers SFMBT2, ITGA4, THBD and ZNF304 showed 96.1% sensitivity and 87.0% specificity in CRC detection, with 100.0% sensitivity for advanced precancerous lesion and stage I CRC. Performances were further validated with TCGA data set, which showed a consistent AUC of 0.99 and exhibited specificity against other cancer types. KCNJ12, VAV3-AS1 and EVC were further identified for stage stratification (stage 0-I versus stage II-IV), with AUC of 0.87, 83.0% sensitivity and 71.2% specificity. Additionally, dual markers of NEUROD1 and FAM72C showed 83.2% sensitivity and 77.4% specificity in differing non-advanced precancerous lesions from inflammatory bowel diseases.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Shenmei Wan
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Yanqi Yu
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Weimei Ruan
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Hong Wang
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Linhao Xu
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Chanjuan Wang
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Shang Chen
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Tianfeng Cao
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Quanzhou Peng
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Sihui Li
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Tianliang Hu
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Zeyu Jiang
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Zhiwei Chen
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China; AnchorDx, Inc., 46305 Landing Pkwy, Fremont, CA 94538, United States.
| | - Jian-Bing Fan
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China; AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China.
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14
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Liu X, Wen J, Li C, Wang H, Wang J, Zou H. High-Yield Methylation Markers for Stool-Based Detection of Colorectal Cancer. Dig Dis Sci 2020; 65:1710-1719. [PMID: 31720923 DOI: 10.1007/s10620-019-05908-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Many methylation markers associated with colorectal cancer have been reported, but few of them are actually used in clinical practice. AIMS This study was designed to identify promising methylation markers for stool-based detection of colorectal cancer. METHODS We first tested 324 reported methylated genes in colorectal cancer cell lines. A total of 111 heavily methylated genes were selected for further evaluation with a pilot set of colorectal cancer and adjacent normal tissues. Ten high-yield methylated markers were further studied in 319 tissue samples. Eventually, the four best markers, namely methylated COL4A1, COL4A2, TLX2, and ITGA4, were validated in 240 stool samples. Methylation-specific PCR (MSP) and real-time MSP (qMSP) were employed for methylation detection. RESULTS After hierarchical selection, ten differentially methylated genes demonstrated high sensitivity and specificity for the detection of colorectal cancer in tissue. When validated in stool samples, the four with the best performance-COL4A1, COL4A2, TLX2, and ITGA4-were able to detect 82.5-92.5% of colorectal cancers and 41.6-58.4% of adenomas (≥ 1 cm) with specificity of 88.0-96.4%. The best combination, COL4A2 and TLX2, detected 91.3% of CRCs and 51.9% of advanced adenomas in stool with 97.6% specificity. CONCLUSIONS Methylated COL4A1, COL4A2, TLX2, and ITGA4 demonstrated high accuracy for the detection of colorectal neoplasms in stool. They are potentially valuable markers for the detection of colorectal cancer.
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Affiliation(s)
- Xianglin Liu
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Yuancun Erheng Road, Guangzhou, 510655, Guangdong, China
| | - Jialing Wen
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Yuancun Erheng Road, Guangzhou, 510655, Guangdong, China
| | - Chujun Li
- Digestive Endoscopy Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Wang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jianping Wang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Yuancun Erheng Road, Guangzhou, 510655, Guangdong, China.,Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongzhi Zou
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Yuancun Erheng Road, Guangzhou, 510655, Guangdong, China. .,Creative Biosciences (Guangzhou) CO., Ltd., Guangzhou, Guangdong, China.
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15
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Liu R, Su X, Long Y, Zhou D, Zhang X, Ye Z, Ma J, Tang T, Wang F, He C. A systematic review and quantitative assessment of methylation biomarkers in fecal DNA and colorectal cancer and its precursor, colorectal adenoma. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 779:45-57. [PMID: 31097151 DOI: 10.1016/j.mrrev.2019.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/15/2018] [Accepted: 01/16/2019] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) arises from accumulated genetic and epigenetic alterations, which provide the possibility to identify tumor-specific biomarkers by analyzing fecal DNA. Methylation status in human genes from tumor tissue is highlighted as promising biomarker in the early detection of CRC. A number of studies have documented altered methylation levels in DNA extracted from stool samples, but generated heterogeneous results. We performed a systematic review and quantitative assessment of existing studies to compare levels of DNA methylation in most frequently studied genes and their diagnostic value in CRC and its precursor, colorectal adenoma, with their counterparts in healthy subjects. Robust searches of the literature were performed in our study with explicit strategies and definite inclusion/exclusion criteria. Pooled data revealed that methylation levels of SFRP2, SFRP1, TFPI2, BMP3, NDRG4, SPG20, and BMP3 plus NDRG4 genes exceeded a sensitivity of 70% and a specificity of 80% for CRC detection. The DOR of the seven candidate biomarkers ranged from 19.80 to 334.33, indicating a good diagnostic power in discriminating cancer from normal tissues. The AUC range was from 0.88 to 0.95, indicating a good or very good discriminatory performance. When test results for BMP3 and NDRG4 were combined, the DOR of CRC detection was 98.36, which was higher than that for BMP3 and NDRG4 separately. As for adenoma detection, the DOR of methylated NDRG4 is higher than that for CRC (CRC vs. adenoma: 54.86 vs. 57.22). Both the sensitivity and specificity of NDRG4 for adenoma detection exceeded 70%. These findings demonstrate the eligibility and feasibility of DNA methylation as a minimally invasive biomarker in feces in the diagnosis of CRC and adenoma. The use of DNA from human stools has the potential to be readily applicable to detect aberrant DNA methylation levels among many subjects for CRC early screening.
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Affiliation(s)
- Rongbin Liu
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China; Department of Ultrasound, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuan Su
- Department of Head and Neck, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, China
| | - Yakang Long
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Dalei Zhou
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xiao Zhang
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zulu Ye
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jiangjun Ma
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Tao Tang
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Fang Wang
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Caiyun He
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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16
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Barault L, Amatu A, Siravegna G, Ponzetti A, Moran S, Cassingena A, Mussolin B, Falcomatà C, Binder A, Cristiano C, Oddo D, Cancelliere C, Bustreo S, Bencardino K, Maden S, Vanzati A, Zavattari P, Truini M, Grady WM, Racca P, Michels KB, Siena S, Esteller M, Bardelli A, Sartore-Bianchi A, Di Nicolantonio F, Sartore-Bianchi A, Di Nicolantonio F. Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer. Gut 2018; 67:1995-2005. [PMID: 28982739 PMCID: PMC5897187 DOI: 10.1136/gutjnl-2016-313372] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Mutations in cell-free circulating DNA (cfDNA) have been studied for tracking disease relapse in colorectal cancer (CRC). This approach requires personalised assay design due to the lack of universally mutated genes. In contrast, early methylation alterations are restricted to defined genomic loci allowing comprehensive assay design for population studies. Our objective was to identify cancer-specific methylated biomarkers which could be measured longitudinally in cfDNA (liquid biopsy) to monitor therapeutic outcome in patients with metastatic CRC (mCRC). DESIGN Genome-wide methylation microarrays of CRC cell lines (n=149) identified five cancer-specific methylated loci (EYA4, GRIA4, ITGA4, MAP3K14-AS1, MSC). Digital PCR assays were employed to measure methylation of these genes in tumour tissue DNA (n=82) and cfDNA from patients with mCRC (n=182). Plasma longitudinal assessment was performed in a patient subset treated with chemotherapy or targeted therapy. RESULTS Methylation in at least one marker was detected in all tumour tissue samples and in 156 mCRC patient cfDNA samples (85.7%). Plasma marker prevalence was 71.4% for EYA4, 68.5% for GRIA4, 69.7% for ITGA4, 69.1% for MAP3K14-AS1% and 65.1% for MSC. Dynamics of methylation markers was not affected by treatment type and correlated with objective tumour response and progression-free survival. CONCLUSION This five-gene methylation panel can be used to circumvent the absence of patient-specific mutations for monitoring tumour burden dynamics in liquid biopsy under different therapeutic regimens. This method might be proposed for assessing pharmacodynamics in clinical trials or when conventional imaging has limitations.
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Affiliation(s)
- Ludovic Barault
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Corresponding authors: Ludovic Barault, PhD or Dr Federica Di Nicolantonio, PhD, Department of Oncology, University of Torino, Candiolo Cancer Institute – FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, Torino, Italy, Phone: +39-011-9933523, Fax: +39-011-9933225, (; )
| | - Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Giulia Siravegna
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy,FIRC Institute of Molecular Oncology (IFOM), Milano, Italy
| | - Agostino Ponzetti
- Colorectal Cancer Unit, Medical Oncology Division 1, AOU Città della Salute e della Scienza, San Giovanni Battista Hospital, Turin, Italy
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L’Hospitalet, Barcelona, Catalonia, Spain
| | - Andrea Cassingena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Benedetta Mussolin
- Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy
| | - Chiara Falcomatà
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy
| | - Alexandra Binder
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
| | - Carmen Cristiano
- Colorectal Cancer Unit, Medical Oncology Division 1, AOU Città della Salute e della Scienza, San Giovanni Battista Hospital, Turin, Italy
| | - Daniele Oddo
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy
| | - Carlotta Cancelliere
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy
| | - Sara Bustreo
- Colorectal Cancer Unit, Medical Oncology Division 1, AOU Città della Salute e della Scienza, San Giovanni Battista Hospital, Turin, Italy
| | - Katia Bencardino
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Sean Maden
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Alice Vanzati
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Patrizia Zavattari
- Unit of Biology and Genetics, Dept. Biomedical Sciences, University of Cagliari, Italy
| | - Mauro Truini
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA,Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Patrizia Racca
- Colorectal Cancer Unit, Medical Oncology Division 1, AOU Città della Salute e della Scienza, San Giovanni Battista Hospital, Turin, Italy
| | - Karin B. Michels
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy,Università degli Studi di Milano, Milan, Italy
| | - Manel Esteller
- Colorectal Cancer Unit, Medical Oncology Division 1, AOU Città della Salute e della Scienza, San Giovanni Battista Hospital, Turin, Italy,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain,Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Alberto Bardelli
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy
| | | | - Federica Di Nicolantonio
- Department of Oncology, University of Torino, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Candiolo Cancer Institute-FPO, IRCCS, SP 142 km 3.95, 10060 Candiolo (TO), Italy,Corresponding authors: Ludovic Barault, PhD or Dr Federica Di Nicolantonio, PhD, Department of Oncology, University of Torino, Candiolo Cancer Institute – FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, Torino, Italy, Phone: +39-011-9933523, Fax: +39-011-9933225, (; )
| | | | - Federica Di Nicolantonio
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
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17
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Oh TJ, Oh HI, Seo YY, Jeong D, Kim C, Kang HW, Han YD, Chung HC, Kim NK, An S. Feasibility of quantifying SDC2 methylation in stool DNA for early detection of colorectal cancer. Clin Epigenetics 2017; 9:126. [PMID: 29225717 PMCID: PMC5715626 DOI: 10.1186/s13148-017-0426-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/23/2017] [Indexed: 01/04/2023] Open
Abstract
Background Colorectal cancer (CRC) screening is the most efficient strategy to reduce disease-related mortality. Frequent aberrant DNA methylation is known to occur in selected genes and early during CRC development, which has emerged as a new epigenetic biomarker for early detection of CRC. Previously, we reported that we identified that CpG sites of SDC2 were aberrantly methylated in tumor tissues of most CRC patients through comprehensive methylation analysis and demonstrated a high potential of quantification of SDC2 methylation in blood for early detection of colorectal cancer. In this study, we aim to investigate the feasibility of quantifying SDC2 methylation in stool DNA for the early detection of CRC. The objective of this study was to confirm a high frequency of SDC2 methylation in tumor tissues at various stages of CRC and investigate the feasibility of a quantitative test for SDC2 methylation in fecal DNA by highly sensitive and accurate real-time PCR for early detection of CRC. Methods Bisulfite-pyrosequencing assay was performed to measure the SDC2 methylation status in tissue samples. For methylation analysis in stool DNA, a highly sensitive and accurate method was applied which implements consecutive two rounds of PCR consisting of unidirectional linear target enrichment (LTE) of SDC2 and quantitative methylation-specific real time PCR (qMSP) for SDC2, named as meSDC2 LTE-qMSP assay. Its limit of detection was 0.1% methylation (corresponding to ~ 6 copies in total ~ 6200 genome copies). Results Positive SDC2 methylation was observed in 100% of primary tumors, 90.6% of adenomatous polyps, 94.1% of hyperplastic polyps, and 0% of normal tissues. SDC2 methylation level also significantly (P < 0.01) increased according to the severity of lesions. In stool DNA test for SDC2 methylation by LTE-qMSP comparing CRC patients with various stages (I to IV) (n = 50) and precancerous lesions (n = 21) with healthy subjects (n = 22), the overall sensitivity was 90.0% for detecting CRC and 33.3% for detecting small polyps, with a specificity of 90.9%. Conclusions Taken together, our result indicates that stool DNA-based SDC2 methylation test by LTE-qMSP is a potential noninvasive diagnostic tool for early detection of CRC.
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Affiliation(s)
- Tae Jeong Oh
- Genomictree, Inc, 44-6 Techno 10-ro Yuseong-gu, Daejeon, 34027 South Korea
| | - Hyun Il Oh
- Genomictree, Inc, 44-6 Techno 10-ro Yuseong-gu, Daejeon, 34027 South Korea
| | - Yang Yei Seo
- Genomictree, Inc, 44-6 Techno 10-ro Yuseong-gu, Daejeon, 34027 South Korea
| | - Dongjun Jeong
- Department of Pathology, College of Medicine, Soonchunhyang University, 23-20 Byeongmyeong-dong Dongnam-gu, Cheonan, Chungcheongnam-do 31151 South Korea
| | - Changjin Kim
- Department of Pathology, College of Medicine, Soonchunhyang University, 23-20 Byeongmyeong-dong Dongnam-gu, Cheonan, Chungcheongnam-do 31151 South Korea
| | - Hyoun Woo Kang
- Department of Internal Medicine, Dongguk University Ilsan Hospital, College of Medicine, Dongguk University, 27 Dongguk-ro Ilsandong-gu, Goyang-si, Gyeonggi-do 10326 South Korea
| | - Yoon Dae Han
- Department of Surgery, Yonsei University College of Medicine, 50-1 Yonsei-ro Seodaemun-gu, Seoul, 03722 South Korea
| | - Hyun Cheol Chung
- Yonsei Cancer Center Yonsei University College of Medicine, 50-1 Yonsei-ro Seodaemun-gu, Seoul, 03722 South Korea
| | - Nam Kyu Kim
- Department of Surgery, Yonsei University College of Medicine, 50-1 Yonsei-ro Seodaemun-gu, Seoul, 03722 South Korea
| | - Sungwhan An
- Genomictree, Inc, 44-6 Techno 10-ro Yuseong-gu, Daejeon, 34027 South Korea
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18
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Hashimoto Y, Zumwalt TJ, Goel A. DNA methylation patterns as noninvasive biomarkers and targets of epigenetic therapies in colorectal cancer. Epigenomics 2016; 8:685-703. [PMID: 27102979 DOI: 10.2217/epi-2015-0013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aberrant DNA methylation is frequently detected in gastrointestinal tumors, and can therefore potentially be used to screen, diagnose, prognosticate, and predict colorectal cancers (CRCs). Although colonoscopic screening remains the gold standard for CRC screening, this procedure is invasive, expensive, and suffers from poor patient compliance. Methylated DNA is an attractive choice for a biomarker substrate because CRCs harbor hundreds of aberrantly methylated genes. Furthermore, abundance in extracellular environments and resistance to degradation and enrichment in serum, stool, and other noninvasive bodily fluids, allows quantitative measurements of methylated DNA biomarkers. This article describes the most important studies that investigated the efficacy of serum- or stool-derived methylated DNA as population-based screening biomarkers in CRC, details several mechanisms and factors that control DNA methylation, describes a better use of prevailing technologies that discover novel DNA methylation biomarkers, and illustrates the diversity of demethylating agents and their applicability toward clinical impact.
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Affiliation(s)
- Yutaka Hashimoto
- Center for Translational Genomics & Oncology, Baylor Scott & White Research Institute & Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Timothy J Zumwalt
- Center for Translational Genomics & Oncology, Baylor Scott & White Research Institute & Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Ajay Goel
- Center for Translational Genomics & Oncology, Baylor Scott & White Research Institute & Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
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19
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Xue M, Wang LJ. Value of DNA methylation markers in colorectal cancer screening. Shijie Huaren Xiaohua Zazhi 2015; 23:4626-4635. [DOI: 10.11569/wcjd.v23.i29.4626] [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] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors in the world. Recognizing CRC at an early stage by population-based screening is crucial in the prevention and treatment of CRC. Numerous candidate genes, which play important roles in the development and progression of CRC, have been found to be hyper-methylated in the promoter regions in recent studies. The promoter fragments of those hyper-methylated genes in tumor tissues have also been detected in the blood and fecal specimens, with higher sensitivity and specificity than traditional markers in the screening of CRC, including carcino-embryonic antigen (CEA) and fecal occult blood test. Here, we will discuss what we have already known about the DNA methylation markers for CRC screening and the potential research direction in the future.
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Okugawa Y, Grady WM, Goel A. Epigenetic Alterations in Colorectal Cancer: Emerging Biomarkers. Gastroenterology 2015; 149:1204-1225.e12. [PMID: 26216839 PMCID: PMC4589488 DOI: 10.1053/j.gastro.2015.07.011] [Citation(s) in RCA: 515] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/13/2015] [Accepted: 07/20/2015] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. One of the fundamental processes driving the initiation and progression of CRC is the accumulation of a variety of genetic and epigenetic changes in colonic epithelial cells. Over the past decade, major advances have been made in our understanding of cancer epigenetics, particularly regarding aberrant DNA methylation, microRNA (miRNA) and noncoding RNA deregulation, and alterations in histone modification states. Assessment of the colon cancer "epigenome" has revealed that virtually all CRCs have aberrantly methylated genes and altered miRNA expression. The average CRC methylome has hundreds to thousands of abnormally methylated genes and dozens of altered miRNAs. As with gene mutations in the cancer genome, a subset of these epigenetic alterations, called driver events, are presumed to have a functional role in CRC. In addition, the advances in our understanding of epigenetic alterations in CRC have led to these alterations being developed as clinical biomarkers for diagnostic, prognostic, and therapeutic applications. Progress in this field suggests that these epigenetic alterations will be commonly used in the near future to direct the prevention and treatment of CRC.
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Affiliation(s)
- Yoshinaga Okugawa
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington.
| | - Ajay Goel
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, Texas.
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Hypermethylation of ITGA4, TFPI2 and VIMENTIN promoters is increased in inflamed colon tissue: putative risk markers for colitis-associated cancer. J Cancer Res Clin Oncol 2015; 141:2097-107. [PMID: 25902909 DOI: 10.1007/s00432-015-1972-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 04/13/2015] [Indexed: 12/18/2022]
Abstract
PURPOSE Epigenetic silencing of tumor suppressor genes is involved in early transforming events and has a high impact on colorectal carcinogenesis. Likewise, colon cancers that derive from chronically inflamed bowel diseases frequently exhibit epigenetic changes. But there is little data about epigenetic aberrations causing colorectal cancer in chronically inflamed tissue. The aim of the present study was to evaluate the aberrant gain of methylation in the gene promoters of VIM, TFPI2 and ITGA4 as putative early markers in the development from inflamed tissue via precancerous lesions toward colorectal cancer. METHODS Initial screening of different cancer cell lines by using methylation-specific PCR revealed a putative colon cancer-specific methylation pattern. Additionally, a demethylation assay was performed to investigate the methylation-dependent gene silencing of ITGA4. The candidate markers were analyzed in colonic tissue specimens from patients with colorectal cancer (n = 15), adenomas (n = 76), serrated lesions (n = 13), chronic inflammation (n = 10) and normal mucosal samples (n = 9). RESULTS A high methylation frequency of VIM (55.6 %) was observed in normal colon tissue, whereas ITGA4 and TFPI2 were completely unmethylated in controls. A significant gain of methylation frequency with progression of disease as well as an age-dependent effect was detectable for TFPI2. ITGA4 methylation frequency was high in precancerous and cancerous tissues as well as in inflammatory bowel diseases (IBD). CONCLUSION The already established methylation marker VIM does not permit a specific and sensitive discrimination of healthy and neoplastic tissue. The methylation markers ITGA4 and TFPI2 seem to be suitable risk markers for inflammation-associated colon cancer.
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Zhang X, Song YF, Lu HN, Wang DP, Zhang XS, Huang SL, Sun BL, Huang ZG. Combined detection of plasma GATA5 and SFRP2 methylation is a valid noninvasive biomarker for colorectal cancer and adenomas. World J Gastroenterol 2015; 21:2629-2637. [PMID: 25759530 PMCID: PMC4351212 DOI: 10.3748/wjg.v21.i9.2629] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/31/2014] [Accepted: 12/01/2014] [Indexed: 02/07/2023] Open
Abstract
AIM: To investigate GATA5, SFRP2, and ITGA4 methylation in plasma DNA as noninvasive biomarkers for colorectal cancer (CRC) or adenomas.
METHODS: There were 57 CRC patients, 30 adenomas patients, and 47 control patients enrolled in this study. Methylation-specific polymerase chain reaction was used to determine the promoter methylation status of GATA5, SFRP2, and ITGA4 genes in plasma DNA, and their association with clinical outcome in CRC. The predictive ability of GATA5, SFRP2, and ITGA4 methylation, individually or in combination, to detect CRC or adenomas was further analyzed.
RESULTS: Hypermethylated GATA5 was detected in plasma in 61.4% (35/57) of CRC cases, 43.33% (13/30) of adenoma cases, and 21.28% (10/47) of control cases. The hypermethylation of SFRP2 was detected in 54.39% (31/57), 40.00% (12/30), and 27.66% (13/47) in plasma samples from CRC, adenomas, and controls, respectively. ITGA4 methylation was detected in 36.84% (21/57) of plasma samples of CRC patients and in 30.00% (9/30) of plasma samples from patients with colorectal adenomas, and the specificity of this individual biomarker was 80.85% (9/47). Moreover, GATA5 methylation in the plasma was significantly correlated with larger tumor size (P = 0.019), differentiation status (P = 0.038), TNM stage (P = 0.008), and lymph node metastasis (P = 0.008). SFRP2 and ITGA4 methylation in plasma significantly correlated with differentiation status (SFRP2, P = 0.012; ITGA4, P = 0.007), TNM stage (SFRP2, P = 0.034; ITGA4, P = 0.021), and lymph node metastasis (SFRP2, P = 0.034; ITGA4, P = 0.021). From the perspective of predictive power and cost-performance, using GATA5 and SFRP2 together as methylation markers seemed the most favorable predictor for CRC (OR = 8.06; 95%CI: 2.54-25.5; P < 0.01) and adenomas (OR = 3.35; 95%CI: 1.29-8.71; P = 0.012).
CONCLUSION: A combination of GATA5 and SFRP2 methylation could be promising as a marker for the detection and diagnosis of CRC and adenomas.
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Fleischhacker M, Schmidt B. Extracellular Nucleic Acids and Cancer. ADVANCES IN PREDICTIVE, PREVENTIVE AND PERSONALISED MEDICINE 2015. [DOI: 10.1007/978-94-017-9168-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Zhang H, Qi J, Wu YQ, Zhang P, Jiang J, Wang QX, Zhu YQ. Accuracy of early detection of colorectal tumours by stool methylation markers: A meta-analysis. World J Gastroenterol 2014; 20:14040-14050. [PMID: 25320544 PMCID: PMC4194590 DOI: 10.3748/wjg.v20.i38.14040] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/24/2014] [Accepted: 06/26/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To evaluate the accuracy of methylation of genes in stool samples for diagnosing colorectal tumours.
METHODS: Electronic databases including PubMed, Web of Science, Chinese Journals Full-Text Database and Wanfang Journals Full-Text Database were searched to find relevant original articles about methylated genes to be used in diagnosing colorectal tumours. A quality assessment of diagnostic accuracy studies tool (QADAS) was used to evaluate the quality of the included articles, and the Meta-disc 1.4 and SPSS 13.0 software programs were used for data analysis.
RESULTS: Thirty-seven articles met the inclusion criteria, and 4484 patients were included. The sensitivity and specificity for the detection of colorectal cancer (CRC) were 73% (95%CI: 71%-75%) and 92% (95%CI: 90%-93%), respectively. For adenoma, the sensitivity and specificity were 51% (95%CI: 47%-54%) and 92% (95%CI: 90%-93%), respectively. Pooled diagnostic performance of SFRP2 methylation for CRC provided the following results: the sensitivity was 79% (95%CI: 75%-82%), the specificity was 93% (95%CI: 90%-96%), the diagnostic OR was 47.57 (95%CI: 20.08-112.72), the area under the curve was 0.9565. Additionally, the results of accuracy of SFRP2 methylation for detecting colorectal adenomas were as follows: sensitivity was 43% (95%CI: 38%-49%), specificity was 94% (95%CI: 91%-97%), the diagnostic OR was 11.06 (95%CI: 5.77-21.18), and the area under the curve was 0.9563.
CONCLUSION: Stool-based DNA testing may be useful for noninvasively diagnosing colorectal tumours and SFRP2 methylation is a promising marker that has great potential in early CRC diagnosis.
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Toiyama Y, Okugawa Y, Goel A. DNA methylation and microRNA biomarkers for noninvasive detection of gastric and colorectal cancer. Biochem Biophys Res Commun 2014; 455:43-57. [PMID: 25128828 DOI: 10.1016/j.bbrc.2014.08.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 07/22/2014] [Accepted: 08/01/2014] [Indexed: 02/06/2023]
Abstract
Cancer initiation and progression is controlled by both genetic and epigenetic events. Epigenetics refers to the study of mechanisms that alter gene expression without permanently altering the DNA sequence. Epigenetic alterations are reversible and heritable, and include changes in histone modifications, DNA methylation, and non-coding RNA-mediated gene silencing. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Aberrant epigenetic modifications occur at the earliest stages of neoplastic transformation and are now believed to be essential players in cancer initiation and progression. Recent advances in epigenetics have not only offered a deeper understanding of the underlying mechanism(s) of carcinogenesis, but have also allowed identification of clinically relevant putative biomarkers for the early detection, disease monitoring, prognosis and risk assessment of cancer patients. At this moment, DNA methylation and non-coding RNA including with microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) represent the largest body of available literature on epigenetic biomarkers with the highest potential for cancer diagnosis. Following identification of cell-free nucleic acids in systematic circulation, increasing evidence has demonstrated the potential of cell-free epigenetic biomarkers in the blood or other body fluids for cancer detection. In this article, we summarize the current state of knowledge on epigenetic biomarkers - primarily DNA methylation and non-coding RNAs - as potential substrates for cancer detection in gastric and colorectal cancer, the two most frequent cancers within the gastrointestinal tract. We also discuss the obstacles that have limited the routine use of epigenetic biomarkers in the clinical settings and provide our perspective on approaches that might help overcome these hurdles, so that these biomarkers can be readily developed for clinical management of cancer patients.
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Affiliation(s)
- Yuji Toiyama
- Gastrointestinal Cancer Research Laboratory, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, 3500 Gaston Avenue, Dallas, TX 75246, USA; Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie 514-8507, Japan
| | - Yoshinaga Okugawa
- Gastrointestinal Cancer Research Laboratory, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, 3500 Gaston Avenue, Dallas, TX 75246, USA; Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Graduate School of Medicine, Mie University, Mie 514-8507, Japan
| | - Ajay Goel
- Gastrointestinal Cancer Research Laboratory, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, 3500 Gaston Avenue, Dallas, TX 75246, USA.
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Lu H, Huang S, Zhang X, Wang D, Zhang X, Yuan X, Zhang Q, Huang Z. DNA methylation analysis of SFRP2, GATA4/5, NDRG4 and VIM for the detection of colorectal cancer in fecal DNA. Oncol Lett 2014; 8:1751-1756. [PMID: 25202404 PMCID: PMC4156205 DOI: 10.3892/ol.2014.2413] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 07/18/2014] [Indexed: 01/22/2023] Open
Abstract
Aberrantly methylated genes are increasingly being established as biomarkers for the detection of colorectal cancer (CRC). In the present study, the methylation levels of the secreted frizzled-related protein gene 2 (SFRP2), GATA binding protein 4/5 (GATA4/5), N-Myc downstream-regulated gene 4 (NDRG4) and vimentin (VIM) promoters were evaluated for their use as markers in the noninvasive detection of CRC. Methylation-specific polymerase chain reaction was performed to analyze promoter CpG methylation of SFRP2, GATA4/5, NDRG4 and VIM in the fecal DNA of 56 patients with CRC and 40 individuals exhibiting normal colonoscopy results. Promoter methylation levels of SFRP2, GATA4/5, NDRG4 and VIM in CRC patients were 57.1% (32/56), 42.9% (24/56), 83.9% (47/56), 28.6% (16/56) and 41.1% (23/56), respectively. Furthermore, the specificity of the genes were 90.0% (4/40), 95.0% (2/40), 82.5% (7/40), 97.5% (4/40) and 85.0% (6/40), respectively. The overall sensitivity of detection for fecal DNA with at least one methylated gene was 96.4% (54/56) in CRC patients. By contrast, only 14 of the 40 normal individuals exhibited methylated DNA in the aforementioned promoter regions. Methylation of the SFRP2, GATA4/5, NDRG4 and VIM promoters in fecal DNA is associated with the presence of colorectal tumors. Therefore, the detection of aberrantly methylated DNA in fecal samples may present a promising, noninvasive screening method for CRC.
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Affiliation(s)
- Hongna Lu
- Ningbo Medical Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China ; Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Shiliang Huang
- Ningbo Medical Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Xie Zhang
- Ningbo Medical Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Danping Wang
- Medical School of Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Xuesong Zhang
- Ningbo Medical Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Xiaogang Yuan
- Ningbo Medical Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Qiubo Zhang
- Ningbo Medical Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Zhigang Huang
- Ningbo Medical Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
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Binefa G, Rodríguez-Moranta F, Teule &A, Medina-Hayas M. Colorectal cancer: from prevention to personalized medicine. World J Gastroenterol 2014; 20:6786-808. [PMID: 24944469 PMCID: PMC4051918 DOI: 10.3748/wjg.v20.i22.6786] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 01/16/2014] [Accepted: 03/06/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a very heterogeneous disease that is caused by the interaction of genetic and environmental factors. CRC develops through a gradual accumulation of genetic and epigenetic changes, leading to the transformation of normal colonic mucosa into invasive cancer. CRC is one of the most prevalent and incident cancers worldwide, as well as one of the most deadly. Approximately 1235108 people are diagnosed annually with CRC, and 609051 die from CRC annually. The World Health Organization estimates an increase of 77% in the number of newly diagnosed cases of CRC and an increase of 80% in deaths from CRC by 2030. The incidence of CRC can benefit from different strategies depending on its stage: health promotion through health education campaigns (when the disease is not yet present), the implementation of screening programs (for detection of the disease in its early stages), and the development of nearly personalized treatments according to both patient characteristics (age, sex) and the cancer itself (gene expression). Although there are different strategies for screening and although the number of such strategies is increasing due to the potential of emerging technologies in molecular marker application, not all strategies meet the criteria required for screening tests in population programs; the three most accepted tests are the fecal occult blood test (FOBT), colonoscopy and sigmoidoscopy. FOBT is the most used method for CRC screening worldwide and is also the primary choice in most population-based screening programs in Europe. Due to its non-invasive nature and low cost, it is one of the most accepted techniques by population. CRC is a very heterogeneous disease, and with a few exceptions (APC, p53, KRAS), most of the genes involved in CRC are observed in a small percentage of cases. The design of genetic and epigenetic marker panels that are able to provide maximum coverage in the diagnosis of colorectal neoplasia seems a reasonable strategy. In recent years, the use of DNA, RNA and protein markers in different biological samples has been explored as strategies for CRC diagnosis. Although there is not yet sufficient evidence to recommend the analysis of biomarkers such as DNA, RNA or proteins in the blood or stool, it is likely that given the quick progression of technology tools in molecular biology, increasingly sensitive and less expensive, these tools will gradually be employed in clinical practice and will likely be developed in mass.
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Wang X, Kuang YY, Hu XT. Advances in epigenetic biomarker research in colorectal cancer. World J Gastroenterol 2014; 20:4276-4287. [PMID: 24764665 PMCID: PMC3989963 DOI: 10.3748/wjg.v20.i15.4276] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/05/2013] [Accepted: 01/15/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) causes approximately 600000 deaths annually and is the third leading cause of cancer mortality worldwide. Despite significant advancements in treatment options, CRC patient survival is still poor owing to a lack of effective tools for early diagnosis and a limited capacity for optimal therapeutic decision making. Since there exists a need to find new biomarkers to improve diagnosis of CRC, the research on epigenetic biomarkers for molecular diagnostics encourages the translation of this field from the bench to clinical practice. Epigenetic alterations are thought to hold great promise as tumor biomarkers. In this review, we will primarily focus on recent advances in the study of epigenetic biomarkers for colorectal cancer and discuss epigenetic biomarkers, including DNA methylation, microRNA expression and histone modification, in cancer tissue, stool, plasma, serum, cell lines and xenografts. These studies have improved the chances that epigenetic biomarkers will find a place in the clinical practices of screening, early diagnosis, prognosis, therapy choice and recurrence surveillance for CRC patients. However, these studies have typically been small in size, and evaluation at a larger scale of well-controlled randomized clinical trials is the next step that is necessary to increase the quality of epigenetic biomarkers and ensure their widespread clinical use.
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Koga Y, Yamazaki N, Matsumura Y. New molecular diagnosis and screening methods for colorectal cancer using fecal protein, DNA and RNA. Expert Rev Mol Diagn 2013; 14:107-20. [PMID: 24308334 DOI: 10.1586/14737159.2014.863152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Several screening methods for reducing the mortality rate of colorectal cancer (CRC) have been reported in recent decades. Fecal occult blood tests (FOBTs) are widely used for CRC screening and immunochemical FOBTs perform better than guaiac FOBTs; however, the sensitivity and specificity of immunochemical FOBTs remain unsatisfactory. To resolve this problem, novel fecal molecular methods based on fecal protein, DNA and RNA analyses have been developed. Regarding fecal proteins, several marker proteins indicating intestinal bleeding and cancer cell-specific proteins have been investigated. Regarding fecal DNA, numerous gene mutation and gene methylation analyses have been reported. Consequently, fecal DNA analysis was recommended as a CRC screening method in 2008. In addition, gene expression analyses of CRC-specific genes and miRNAs in fecal RNA have been investigated over the last decade. This review article summarizes molecular methods using fecal samples for CRC screening, focusing on reports within the last 5 years.
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Affiliation(s)
- Yoshikatsu Koga
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa 277-8577, Japan
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Zhang H, Zhu YQ, Qi J, Wang QX, Cai SS, Zhu SY, Zhu XW, Wang XT. Accuracy of early detection of colorectal tumours using stool methylation markers: A meta-analysis. World J Meta-Anal 2013; 1:147-156. [DOI: 10.13105/wjma.v1.i3.147] [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: 07/09/2013] [Revised: 10/07/2013] [Accepted: 11/05/2013] [Indexed: 02/05/2023] Open
Abstract
AIM: To evaluate the accuracy of methylation of genes in stool samples for diagnosing colorectal tumours.
METHODS: Electronic databases including PubMed, Web of Science, Chinese Journal Full Text Database and Wanfang Journals Full-text Database were searched to find relevant original articles about methylated genes used in diagnosing colorectal tumours. Quality assessment of diagnostic accuracy studies items were used to evaluate the quality of the included articles, and the Meta-disc 1.4 and SPSS 13.0 software programs were used for data analysis.
RESULTS: Thirty-four articles met the inclusion criteria, and 4151 patients were included. Pooled diagnostic performances of SFRP2 methylation for colorectal cancer (CRC) provided the following results: the sensitivity was 79% (95%CI: 75%-82%), the specificity was 93% (95%CI: 90%-96%), the diagnostic odds ratio (DOR) was 47.57 (95%CI: 20.08-112.72), and the area under the curve was 0.9565. Additionally, the results of accuracy of SFRP2 methylation for detecting colorectal adenomas were as follows: the sensitivity was 43% (95%CI: 38%-49%), the specificity was 94% (95%CI: 91%-97%), the DOR was 11.06 (95%CI: 5.77-21.18), and the area under the curve was 0.9563.
CONCLUSION: Stool-based DNA testing may be useful for non-invasively diagnosing colorectal tumours, and SFRP2 methylation is a promising marker that has great potential in early CRC diagnosis.
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Lu HN, Zhang X, Wang DP, Dong XW, Huang ZG. Detection of fecal DNA methylation for colorectal neoplasia screening: A meta-analysis. Shijie Huaren Xiaohua Zazhi 2013; 21:3585-3591. [DOI: 10.11569/wcjd.v21.i32.3585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To systemically evaluate the feasibility of using methylated genes as biomarkers for the detection of colorectal neoplasia.
METHODS: We searched PubMed, the Web of Science and On-line Visual Display Unit Interrogation of Data Bases (OVID) with the key words "colorectal cancer/colorectal adenoma/colorectal polyps", "methylation", "stool/fecal DNA" for studies that used hypermethylated genes as biomarkers for the detection of colorectal cancer (CRC) or adenomas. This meta-analysis used the sensitivity, specificity and 95% confidence intervals (95%CI) as effect measurements, and the Stata statistical software (version 11.0) was used to perform statistical analyses.
RESULTS: A total of 24 studies including 3555 patients were selected into the final analysis. The sensitivity and specificity of detecting single methylated gene in fecal DNA for the detection of colorectal neoplasia (CRC and adenomas) were 0.58 (95%CI: 0.51-0.66) and 0.93 (95%CI: 0.89-0.96), respectively. The sensitivity and specificity of detecting multiple methylated genes in fecal DNA for the detection of colorectal neoplasia were 0.79 (95%CI: 0.67-0.81) and 0.88 (95%CI: 0.86-0.91), respectively.
CONCLUSION: Analysis of stool DNA methylation has a reasonable sensitivity and specificity for the detection of CRC, and may provide a promising and noninvasive screening method for colorectal cancer. Combined detection of multiple methylated genes in fecal DNA is superior to the single gene detection method for colorectal neoplasia screening.
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Silva TD, Vidigal VM, Felipe AV, DE Lima JM, Neto RA, Saad SS, Forones NM. DNA methylation as an epigenetic biomarker in colorectal cancer. Oncol Lett 2013; 6:1687-1692. [PMID: 24260063 PMCID: PMC3834199 DOI: 10.3892/ol.2013.1606] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 09/12/2013] [Indexed: 02/06/2023] Open
Abstract
Sporadic colorectal cancer (CRC) is a consequence of the accumulation of genetic and epigenetic alterations that result in the transformation of normal colonic epithelial cells to adenocarcinomas. Studies have indicated that a common event in the tumorigenesis of CRC is the association of global hypomethylation with discrete hypermethylation at the promoter regions of specific genes that are involved in cell cycle regulation, DNA repair, apoptosis, angiogenesis, adhesion and invasion. The present study aimed to investigate the epigenetic changes (DNA methylation) in 24 candidate genes in CRC. A total of 10 candidate hypermethylated (HM) and unmethylated (UM) genes were identified that may be useful epigenetic markers for non-invasive CRC screening. The five genes that had the highest average UM percentages in the control group were MLH1 (71.7%), DKK2 (69.6%), CDKN2A (68.4%), APC (67.5%) and hsa-mir-342 (67.4%). RUNX3 (58.9%), PCDH10 (55.5%), SFRP5 (52.1%), IGF2 (50.4%) and Hnf1b (50.0%) were the five genes with the highest average HM percentages in the test group. In summary, the present preliminary study identified the methylation profiles of normal and cancerous colonic epithelial tissues, and provided the groundwork for future large-scale methylation studies.
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Affiliation(s)
- Tiago Donizetti Silva
- Oncology Group, Gastroenterology Division, Federal University of São Paulo, São Paulo 04023-900, Brazil
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Naumov VA, Generozov EV, Zaharjevskaya NB, Matushkina DS, Larin AK, Chernyshov SV, Alekseev MV, Shelygin YA, Govorun VM. Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips. Epigenetics 2013; 8:921-34. [PMID: 23867710 DOI: 10.4161/epi.25577] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Illumina's Infinium HumanMethylation450 BeadChip arrays were used to examine genome-wide DNA methylation profiles in 22 sample pairs from colorectal cancer (CRC) and adjacent tissues and 19 colon tissue samples from cancer-free donors. We show that the methylation profiles of tumors and healthy tissue samples can be clearly distinguished from one another and that the main source of methylation variability is associated with disease status. We used different statistical approaches to evaluate the methylation data. In general, at the CpG-site level, we found that common CRC-specific methylation patterns consist of at least 15,667 CpG sites that were significantly different from either adjacent healthy tissue or tissue from cancer-free subjects. Of these sites, 10,342 were hypermethylated in CRC, and 5,325 were hypomethylated. Hypermethylated sites were common in the maximum number of sample pairs and were mostly located in CpG islands, where they were significantly enriched for differentially methylated regions known to be cancer-specific. In contrast, hypomethylated sites were mostly located in CpG shores and were generally sample-specific. Despite the considerable variability in methylation data, we selected a panel of 14 highly robust candidates showing methylation marks in genes SND1, ADHFE1, OPLAH, TLX2, C1orf70, ZFP64, NR5A2, and COL4A. This set was successfully cross-validated using methylation data from 209 CRC samples and 38 healthy tissue samples from The Cancer Genome Atlas consortium (AUC = 0.981 [95% CI: 0.9677-0.9939], sensitivity = 100% and specificity = 82%). In summary, this study reports a large number of loci with novel differential methylation statuses, some of which may serve as candidate markers for diagnostic purposes.
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Affiliation(s)
- Vladimir A Naumov
- Research Institute of Physical Chemical Medicine of Federal Medical Biology Agency of Russian Federation; Moscow, Russia
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Hong L, Ahuja N. DNA methylation biomarkers of stool and blood for early detection of colon cancer. Genet Test Mol Biomarkers 2013; 17:401-6. [PMID: 23406208 DOI: 10.1089/gtmb.2012.0478] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Detection of colorectal cancer at an early stage may significantly decrease mortality from the disease. The current screening test of colonoscopy is of high efficacy, but its acceptance in the general public is rather low. Availability of a blood- or stool-based test of DNA methylation markers is expected to improve the screening compliance for colon cancer in the general population. The goal of this review is to describe the recent advances in DNA methylation markers of stool and blood for early detection of colon cancer, and envisage future developments toward their clinical availability. More investigations should be performed to promote both basic and clinical research of DNA methylation markers in patients with colon cancer.
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Affiliation(s)
- Liu Hong
- Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China.
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Ahmed D, Danielsen SA, Aagesen TH, Bretthauer M, Thiis-Evensen E, Hoff G, Rognum TO, Nesbakken A, Lothe RA, Lind GE. A tissue-based comparative effectiveness analysis of biomarkers for early detection of colorectal tumors. Clin Transl Gastroenterol 2012; 3:e27. [PMID: 23324654 PMCID: PMC3535074 DOI: 10.1038/ctg.2012.21] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES: We recently identified a six-gene methylation-based biomarker panel suitable for early detection of colorectal cancer (CRC). In this study, we compared the performance of this novel epi-panel with that of previously identified DNA methylation markers in the same clinical tissue sample sets. METHODS: Quantitative methylation-specific PCR was used to analyze the promoter region of SEPT9 and VIM in a total of 485 tissue samples, divided into test and validation sets. ITGA4, NTRK2, OSMR, and TUBG2 were also included in the analyses. Receiver operating characteristic (ROC) curves were used to compare the performances of the individual biomarkers with that of the novel epi-panel. RESULTS: SEPT9 and VIM were methylated in 82 and 67% of CRCs (n=169) and in 88 and 54% of the adenomas (n=104). Only 3% of the normal mucosa samples (n=107) were methylated for these genes, confirming that the methylation was highly cancer-specific. Areas under the ROC curve (AUC), distinguishing CRCs from normal mucosa, were 0.94 for SEPT9 and 0.81 for VIM. AUC values for separating adenomas from normal mucosa samples were 0.96 and 0.81 for the same genes. In comparison, the novel epi-panel achieved an AUC of 0.98 (CRC) and 0.97 (adenomas). ITGA4, OSMR, NTRK2, and TUBG2 were methylated in 90, 78, 7, and 1% of the CRCs, and in 76, 77, 3, and 0% of the adenomas. Between 0 and 2% of the normal mucosa samples were methylated for the same genes. ITGA4 and OSMR achieved an AUC of 0.96 and 0.92 (CRC vs. normal mucosa), and 0.93 and 0.92 (adenomas vs. normal mucosa). CONCLUSIONS: We have confirmed the high performance of some of the previously identified DNA methylation markers. Furthermore, we showed that a recently reported epi-panel performed better than the individual DNA methylation biomarkers when analyzed in the same tissue samples. This observation was also true for VIM and SEPT9, which are included in commercially available noninvasive tests for CRC. These results further underscore the value of combining a manageable number of individual markers into a panel, which in addition to having a higher sensitivity and specificity might provide a more profound robustness to a noninvasive test compared with single markers.
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Affiliation(s)
- Deeqa Ahmed
- 1] Department of Cancer Prevention, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway [2] Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
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Chen Z, Mantha RR, Chen JS, Slivano OJ, Takahashi H. Non-invasive genotyping of transgenic animals using fecal DNA. Lab Anim (NY) 2012; 41:102-7. [DOI: 10.1038/laban0412-102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/10/2012] [Indexed: 11/09/2022]
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Herbst A, Kolligs FT. Detection of DNA hypermethylation in remote media of patients with colorectal cancer: new biomarkers for colorectal carcinoma. Tumour Biol 2012; 33:297-305. [PMID: 22362383 DOI: 10.1007/s13277-012-0346-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 02/03/2012] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer is the third most common cancer and a major cause of cancer-related mortality. The lifetime risk to develop colorectal cancer is 6% in the Western world, and one third of the affected people will ultimately die from this disease. Colorectal carcinomas develop slowly over a period of several years. Therefore, identifying people with precancerous lesions holds the potential to reduce the incidence and mortality of colorectal cancer. Apart from mutations and chromosomal imbalances, inactivation of tumor suppressor genes by DNA hypermethylation has been recognized as an important mechanism driving colorectal carcinogenesis. In recent years, screening tests have been developed that rely on the detection of DNA hypermethylation in remote media to identify people suffering from asymptomatic colorectal cancers at early stages. Apart from their diagnostic value, methylation markers hold the potential to be used as prognostic markers. Here, we summarize the recent development of DNA methylation markers for colorectal cancer in remote media with regard to their diagnostic and prognostic value.
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Affiliation(s)
- Andreas Herbst
- Department of Medicine II, University of Munich, Marchioninistrasse 15, 81377, Munich, Germany.
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Luo YX, Chen DK, Song SX, Wang L, Wang JP. Aberrant methylation of genes in stool samples as diagnostic biomarkers for colorectal cancer or adenomas: a meta-analysis. Int J Clin Pract 2011; 65:1313-20. [PMID: 22093539 DOI: 10.1111/j.1742-1241.2011.02800.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND An increasing number of hypermethylated genes in stool samples have been reported as biomarkers for the detection of colorectal cancer (CRC) or adenomas. We aimed to comprehensively review and compare the evidence for feasibility of using these biomarkers for the detection of colorectal neoplasia. METHODS We searched Medline, the Web of Science and OVID for studies that used hypermethylated genes as biomarkers for the detection of CRC or adenomas. A meta-analysis was carried out using the random-effect model with diagnostic odd ratios (DOR) and 95% confidence intervals (CI) as effect measurements. RESULTS A total of 19 studies including 2,356 patients were eligible for final analysis. The sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and DOR for the detection of CRC or adenomas were 0.62 (95% CI: 0.51-0.71), 0.89 (95% CI: 0.86-0.92), 5.66 (95% CI: 4.68-6.83), 0.43 (95% CI: 0.34-0.55) and 13.15 (95% CI: 9.82-17.60) respectively. Of these, the sensitivity and specificity for the detection of adenoma were 0.54 (95% CI: 0.39-0.68) and 0.88 (95% CI: 0.83-0.92) respectively. CONCLUSIONS Hypermethylated gene panels are not currently accurate enough to be used alone for colorectal neoplasia screening. The discovery and evaluation of additional biomarkers with improved sensitivity and specificity is necessary.
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Affiliation(s)
- Y-X Luo
- Department of Colorectal Surgery, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
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Fecal molecular markers for colorectal cancer screening. Gastroenterol Res Pract 2011; 2012:184343. [PMID: 22969796 PMCID: PMC3226355 DOI: 10.1155/2012/184343] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 09/26/2011] [Indexed: 02/06/2023] Open
Abstract
Despite multiple screening techniques, including colonoscopy, flexible sigmoidoscopy, radiological imaging, and fecal occult blood testing, colorectal cancer remains a leading cause of death. As these techniques improve, their sensitivity to detect malignant lesions is increasing; however, detection of precursor lesions remains problematic and has generated a lack of general acceptance for their widespread usage. Early detection by an accurate, noninvasive, cost-effective, simple-to-use screening technique is central to decreasing the incidence and mortality of this disease. Recent advances in the development of molecular markers in faecal specimens are encouraging for its use as a screening tool. Genetic mutations and epigenetic alterations that result from the carcinogenetic process can be detected by coprocytobiology in the colonocytes exfoliated from the lesion into the fecal matter. These markers have shown promising sensitivity and specificity in the detection of both malignant and premalignant lesions and are gaining popularity as a noninvasive technique that is representative of the entire colon. In this paper, we summarize the genetic and epigenetic fecal molecular markers that have been identified as potential targets in the screening of colorectal cancer.
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Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. It results from an accumulation of genetic and epigenetic changes in colon epithelial cells, which transforms them into adenocarcinomas. Over the past decade, major advances have been made in understanding cancer epigenetics, particularly regarding aberrant DNA methylation. Assessment of the colon cancer epigenome has revealed that virtually all CRCs have aberrantly methylated genes and that the average CRC methylome has hundreds to thousands of abnormally methylated genes. As with gene mutations in the cancer genome, a subset of these methylated genes, called driver genes, is presumed to have a functional role in CRC. The assessment of methylated genes in CRCs has also revealed a unique molecular subgroup of CRCs called CpG island methylator phenotype (CIMP) cancers; these tumors have a particularly high frequency of methylated genes. These advances in our understanding of aberrant methylation in CRC have led to epigenetic alterations being developed as clinical biomarkers for diagnostic, prognostic and therapeutic applications. Progress in this field suggests that these epigenetic alterations will be commonly used in the near future to direct the prevention and treatment of CRC.
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Affiliation(s)
- Victoria Valinluck Lao
- Department of Surgery, University of Washington, Seattle, WA,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA,Department of Medicine, University of Washington Medical School, Seattle, WA
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Bosch LJW, Carvalho B, Fijneman RJA, Jimenez CR, Pinedo HM, van Engeland M, Meijer GA. Molecular tests for colorectal cancer screening. Clin Colorectal Cancer 2011; 10:8-23. [PMID: 21609931 DOI: 10.3816/ccc.2011.n.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Detecting and removing high-risk adenomas and early colorectal cancer (CRC) can reduce mortality of this disease. The noninvasive fecal occult blood test (FOBT; guaiac-based or immunochemical) is widely used in screening programs and although effective, it leaves room for improvement in terms of test accuracy. Molecular tests are expected to be more sensitive, specific and informative than current detection tests, and are promising future tools for CRC screening. This review provides an overview of the performances of DNA, RNA, and protein markers for CRC detection in stool and blood. Most emphasis currently is on DNA and protein markers. Among DNA markers there is trend to move away from mutation markers in favor of methylation markers. The recent boost in proteomics research leads to many new candidate protein markers. Usually in small series, some markers show better performance than the present FOBT. Evaluation in large well-controlled randomized trials is the next step needed to take molecular markers for CRC screening to the next level and warrant implementation in a screening setting.
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Affiliation(s)
- Linda J W Bosch
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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Lind GE, Danielsen SA, Ahlquist T, Merok MA, Andresen K, Skotheim RI, Hektoen M, Rognum TO, Meling GI, Hoff G, Bretthauer M, Thiis-Evensen E, Nesbakken A, Lothe RA. Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas. Mol Cancer 2011; 10:85. [PMID: 21777459 PMCID: PMC3166273 DOI: 10.1186/1476-4598-10-85] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 07/21/2011] [Indexed: 12/16/2022] Open
Abstract
Background The presence of cancer-specific DNA methylation patterns in epithelial colorectal cells in human feces provides the prospect of a simple, non-invasive screening test for colorectal cancer and its precursor, the adenoma. This study investigates a panel of epigenetic markers for the detection of colorectal cancer and adenomas. Methods Candidate biomarkers were subjected to quantitative methylation analysis in test sets of tissue samples from colorectal cancers, adenomas, and normal colonic mucosa. All findings were verified in independent clinical validation series. A total of 523 human samples were included in the study. Receiver operating characteristic (ROC) curve analysis was used to evaluate the performance of the biomarker panel. Results Promoter hypermethylation of the genes CNRIP1, FBN1, INA, MAL, SNCA, and SPG20 was frequent in both colorectal cancers (65-94%) and adenomas (35-91%), whereas normal mucosa samples were rarely (0-5%) methylated. The combined sensitivity of at least two positives among the six markers was 94% for colorectal cancers and 93% for adenoma samples, with a specificity of 98%. The resulting areas under the ROC curve were 0.984 for cancers and 0.968 for adenomas versus normal mucosa. Conclusions The novel epigenetic marker panel shows very high sensitivity and specificity for both colorectal cancers and adenomas. Our findings suggest this biomarker panel to be highly suitable for early tumor detection.
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Affiliation(s)
- Guro E Lind
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
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Oster B, Thorsen K, Lamy P, Wojdacz TK, Hansen LL, Birkenkamp-Demtröder K, Sørensen KD, Laurberg S, Orntoft TF, Andersen CL. Identification and validation of highly frequent CpG island hypermethylation in colorectal adenomas and carcinomas. Int J Cancer 2011; 129:2855-66. [PMID: 21400501 DOI: 10.1002/ijc.25951] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 12/27/2010] [Indexed: 01/11/2023]
Abstract
In our study, whole-genome methylation arrays were applied to identify novel genes with tumor specific DNA methylation of promoter CpG islands in pre-malignant and malignant colorectal lesions. Using a combination of Illumina HumanMethylation27 beadchips, Methylation-Sensitive High Resolution Melting (MS-HRM) analysis, and Exon arrays (Affymetrix) the DNA methylation pattern of ∼14,000 genes and their transcript levels were investigated in six normal mucosas, six adenomas and 30 MSI and MSS carcinomas. Sixty eight genes with tumor-specific hypermethylation were identified (p < 0.005). Identified hypermethylated sites were validated in an independent sample set of eight normal mucosas, 12 adenomas, 40 MSS and nine MSI cancer samples. The methylation patterns of 15 selected genes, hypermethylated in adenomas and carcinomas (FLI1, ST6GALNAC5, TWIST1, ADHFE1, JAM2, IRF4, CNRIP1, NRG1 and EYA4), in carcinomas only (ABHD9, AOX1 and RERG), or in MSI but not MSS carcinomas (RAMP2, DSC3 and MLH1) were validated using MS-HRM. Four of these genes (MLH1, AOX1, EYA4 and TWIST1) had previously been reported to be hypermethylated in CRC. Eleven genes, not previously known to be affected by CRC specific hypermethylation, were identified and validated. Inverse correlation to gene expression was observed for six of the 15 genes with Spearman correlation coefficients ranging from -0.39 to -0.60. For six of these genes the altered methylation patterns had a profound transcriptional association, indicating that methylation of these genes may play a direct regulatory role. The hypermethylation changes often occurred already in adenomas, indicating that they may be used as biomarkers for early detection of CRC.
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Affiliation(s)
- Bodil Oster
- Department of Molecular Medicine, Aarhus University Hospital, Skejby, Denmark
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Oghamian S, Sodir NM, Bashir MU, Shen H, Cullins AE, Carroll CA, Kundu P, Shibata D, Laird PW. Reduction of pancreatic acinar cell tumor multiplicity in Dnmt1 hypomorphic mice. Carcinogenesis 2011; 32:829-35. [PMID: 21362628 DOI: 10.1093/carcin/bgr039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In human pancreatic cancers, promoter CpG island hypermethylation is observed in both benign and malignant tumors. It is thought that silencing of key growth-controlling genes by promoter hypermethylation may play a role in pancreatic oncogenesis. We have shown previously that sufficient levels of DNA methyltransferase (Dnmt) 1 expression are required for the development of murine intestinal tumors. Here, we report the results of a large-scale triple cross (progeny n = 761) between Apc(Min/+), Trp53(-/-) and Dnmt1 hypomorphic mice to investigate the role of Dnmt levels in the Apc(Min/+), Trp53(-/-) mouse models of acinar cell pancreatic cancer. Mutations of both APC and TP53 are observed in human pancreatic cancer. We found that tumor burden, but not tumor size, is significantly reduced with decreasing Dnmt1 levels, suggesting that DNA methylation is involved in pancreatic tumorigenesis in this mouse model. Detailed analyses showed that the reduction in tumor burden is the result of a decrease in both early- and late-stage lesions. We observed decreased levels of DNA methylation at candidate genes in the normal pancreas of Dnmt1 hypomorphic mice. Some of these genes showed increased methylation associated with tumorigenesis, suggesting that the tumor-suppressive effects of Dnmt1 hypomorphic alleles may be mediated in part through reduced promoter hypermethylation. Our work is the first in vivo study to show the effects of reduced Dnmt levels on pancreatic tumor development.
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Affiliation(s)
- Shirley Oghamian
- Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA 90089-9176, USA
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Molecular detection of colorectal neoplasia. Gastroenterology 2010; 138:2127-39. [PMID: 20420950 DOI: 10.1053/j.gastro.2010.01.055] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 01/12/2010] [Accepted: 01/20/2010] [Indexed: 02/06/2023]
Abstract
A variety of noninvasive molecular approaches to colorectal cancer screening are emerging with potential to improve screening effectiveness and user-friendliness. These approaches are based on the sensitive assay of molecular markers in stool, blood, and urine samples. New methods, especially next generation stool-based tests, have been shown to detect both colorectal cancers and precancerous lesions with high accuracy. Validation of these technologies in average-risk populations are needed to establish their role for general colorectal cancer screening. This review addresses the biological rationale, technical advances, recent clinical performance data, and remaining issues with molecular screening for colorectal cancer.
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Abstract
Colorectal cancer (CRC) arises as a consequence of the accumulation of genetic and epigenetic alterations in colonic epithelial cells during neoplastic transformation. Epigenetic modifications, particularly DNA methylation in selected gene promoters, are recognized as common molecular alterations in human tumors. Substantial efforts have been made to determine the cause and role of aberrant DNA methylation ("epigenomic instability") in colon carcinogenesis. In the colon, aberrant DNA methylation arises in tumor-adjacent, normal-appearing mucosa. Aberrant methylation also contributes to later stages of colon carcinogenesis through simultaneous methylation in key specific genes that alter specific oncogenic pathways. Hypermethylation of several gene clusters has been termed CpG island methylator phenotype and appears to define a subgroup of colon cancer distinctly characterized by pathological, clinical, and molecular features. DNA methylation of multiple promoters may serve as a biomarker for early detection in stool and blood DNA and as a tool for monitoring patients with CRC. DNA methylation patterns may also be predictors of metastatic or aggressive CRC. Therefore, the aim of this review is to understand DNA methylation as a driving force in colorectal neoplasia and its emerging value as a molecular marker in the clinic.
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Affiliation(s)
- Myoung Sook Kim
- Department of Otolaryngology, Head and Neck Surgery, The Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB II-5M, Baltimore, MD, 21231, USA
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