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Ng JMK, Yu J. Promoter hypermethylation of tumour suppressor genes as potential biomarkers in colorectal cancer. Int J Mol Sci 2015; 16:2472-96. [PMID: 25622259 PMCID: PMC4346847 DOI: 10.3390/ijms16022472] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/02/2014] [Accepted: 01/14/2015] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a common malignancy and the fourth leading cause of cancer deaths worldwide. It results from the accumulation of multiple genetic and epigenetic changes leading to the transformation of colon epithelial cells into invasive adenocarcinomas. In CRC, epigenetic changes, in particular promoter CpG island methylation, occur more frequently than genetic mutations. Hypermethylation contributes to carcinogenesis by inducing transcriptional silencing or downregulation of tumour suppressor genes and currently, over 600 candidate hypermethylated genes have been identified. Over the past decade, a deeper understanding of epigenetics coupled with technological advances have hinted at the potential of translating benchtop research into biomarkers for clinical use. DNA methylation represents one of the largest bodies of literature in epigenetics, and hence has the highest potential for minimally invasive biomarker development. Most progress has been made in the development of diagnostic markers and there are currently two, one stool-based and one blood-based, biomarkers that are commercially available for diagnostics. Prognostic and predictive methylation markers are still at their infantile stages.
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Affiliation(s)
- Jennifer Mun-Kar Ng
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China.
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152
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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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153
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Detection of methylated CDO1 in plasma of colorectal cancer; a PCR study. PLoS One 2014; 9:e113546. [PMID: 25469504 PMCID: PMC4254285 DOI: 10.1371/journal.pone.0113546] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 10/25/2014] [Indexed: 02/06/2023] Open
Abstract
Background Cysteine biology is important for the chemosensitivity of cancer cells. Our research has focused on the epigenetic silencing of cysteine dioxygenase type 1 (CDO1) in colorectal cancer (CRC). In this study, we describe detection of CDO1 methylation in the plasma of CRC patients using methylation specific PCR (Q-MSP) and extensive analysis of the PCR reaction. Methods DNA was extracted from plasma, and analysed for methylation of the CDO1 gene using Q-MSP. The detection rate of CDO1 gene methylation was calculated and compared with that of diluted DNA extracted from “positive control” DLD1 cells. CDO1 gene methylation in the plasma of 40 CRC patients that were clinicopathologically analysed was then determined. Results (1) The cloned sequence analysis detected 93.3% methylation of the promoter CpG islands of the CDO1 gene of positive control DLD1 cells and 4.7% methylation of the negative control HepG2 CDO1 gene. (2) DLD1 CDO1 DNA could not be detected in this assay if the extracted DNA was diluted ∼1000 fold. The more DNA that was used for the PCR reaction, the more effectively it was amplified in Q-MSP. (3) By increasing the amount of DNA used, methylated CDO1 could be clearly detected in the plasma of 8 (20%) of the CRC patients. However, the percentage of CRC patients detected by methylated CDO1 in plasma was lower than that detected by CEA (35.9%) or CA19-9 (23.1%) in preoperative serum. Combination of CEA/CA19-9 plus plasma methylated CDO1 could increase the rate of detection of curable CRC patients (39.3%) as compared to CEA/CA19-9 (25%). Conclusion We have described detection of CDO1 methylation in the plasma of CRC patients. Although CDO1 methylation was not detected as frequently as conventional tumor markers, analysis of plasma CDO1 methylation in combination with CEA/CA19-9 levels increases the detection rate of curable CRC patients.
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Hochberg FH, Atai NA, Gonda D, Hughes MS, Mawejje B, Balaj L, Carter RS. Glioma diagnostics and biomarkers: an ongoing challenge in the field of medicine and science. Expert Rev Mol Diagn 2014; 14:439-52. [PMID: 24746164 DOI: 10.1586/14737159.2014.905202] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glioma is the most common brain tumor. For the more aggressive form, glioblastoma, standard treatment includes surgical resection, irradiation with adjuvant temozolomide and, on recurrence, experimental chemotherapy. However, the survival of patients remains poor. There is a critical need for minimally invasive biomarkers for diagnosis and as measures of response to therapeutic interventions. Glioma shed extracellular vesicles (EVs), which invade the surrounding tissue and circulate within both the cerebrospinal fluid and the systemic circulation. These tumor-derived EVs and their content serve as an attractive source of biomarkers. In this review, we discuss the current state of the art of biomarkers for glioma with emphasis on their EV derivation.
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Affiliation(s)
- Fred H Hochberg
- Department of Neurology and Program in Neuroscience, Massachusetts General Hospital and Harvard Medical School, Suite 340, 175 Cambridge Street, Boston, MA 02114, USA
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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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156
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Deregulation of MYC and TP53 through genetic and epigenetic alterations in gallbladder carcinomas. Clin Exp Med 2014; 15:421-6. [PMID: 25200035 DOI: 10.1007/s10238-014-0311-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/26/2014] [Indexed: 12/11/2022]
Abstract
Gallbladder cancer is a rare malignancy and presents a poor prognosis. MYC and p53 have been implicated in gallbladder carcinogenesis. However, little is known about the molecular mechanisms involved in their regulation in this neoplasia. Here, we evaluated the MYC and TP53 copy numbers in gallbladder tumors and their possible association with protein expression. We also investigated whether MYC may be controlled by mutations and DNA promoter methylation. In the present study, 15 samples of invasive gallbladder carcinomas and six control samples were analyzed. On the other hand, the expression of MYC and p53 was more frequent in gallbladder carcinomas than in control samples (p = 0.002, p = 0.046, respectively). Gain of copies of the MYC and TP53 genes was detected in 86.7 and 50 % of gallbladder carcinomas, respectively. MYC and TP53 amplifications were associated with immunoreactivity of their protein (p = 0.029, p = 0.001, respectively). MYC hypomethylation was only detected in tumoral samples and was associated with its protein expression (p = 0.029). MYC mutations were detected in 80 % of tumor samples. The G allele at rs117856857 was associated with the presence of gallbladder tumors (p = 0.019) and with MYC expression (p = 0.044). Moreover, two tumors presented a pathogenic mutation in MYC exon 2 (rs28933407). Our study highlights that the gain of MYC and TP53 copies seems to be a frequent finding in gallbladder cancer. In addition, gain of copies, hypomethylation and point mutations at MYC may contribute to overexpression of its protein in this type of cancer.
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Katsiampoura A, Kopetz S. Clinical Applications of Liquid Biopsies in Gastrointestinal Oncology. GASTROINTESTINAL CANCER RESEARCH : GCR 2014; 7:S8-S12. [PMID: 27053977 PMCID: PMC4812842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Accumulating knowledge in colorectal cancer (CRC) biology has led to an understanding of the role of genetic and epigenetic alterations in tumorigenesis and progression of the disease. Numerous studies have focused on the identification of novel biomarkers in circulating free (cf)DNA that have the potential of guiding clinical practice. These markers are specifically attractive for the characterization of molecular profiles in patients with limited tissue access, the monitoring of therapeutic responses and the development of recurrent disease, the monitoring of the tumor evolution with therapy, and the response to therapy. Moreover, cfDNA can be useful for early detection and detection of minimal residual disease and to improve characterization of the pharmacodynamic effects of a drug. This review will focus on recent advances of cfDNA analysis and novel discoveries that have the potential to guide treatment of CRC.
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Affiliation(s)
- Anastasia Katsiampoura
- Department of Gastrointestinal Medical Oncology University of Texas MD Anderson Cancer Center Houston, TX
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology University of Texas MD Anderson Cancer Center Houston, TX
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158
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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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159
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Barrow TM, Michels KB. Epigenetic epidemiology of cancer. Biochem Biophys Res Commun 2014; 455:70-83. [PMID: 25124661 DOI: 10.1016/j.bbrc.2014.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/15/2014] [Accepted: 08/01/2014] [Indexed: 02/06/2023]
Abstract
Epigenetic epidemiology includes the study of variation in epigenetic traits and the risk of disease in populations. Its application to the field of cancer has provided insight into how lifestyle and environmental factors influence the epigenome and how epigenetic events may be involved in carcinogenesis. Furthermore, it has the potential to bring benefit to patients through the identification of diagnostic markers that enable the early detection of disease and prognostic markers that can inform upon appropriate treatment strategies. However, there are a number of challenges associated with the conduct of such studies, and with the identification of biomarkers that can be applied to the clinical setting. In this review, we delineate the challenges faced in the design of epigenetic epidemiology studies in cancer, including the suitability of blood as a surrogate tissue and the capture of genome-wide DNA methylation. We describe how epigenetic epidemiology has brought insight into risk factors associated with lung, breast, colorectal and bladder cancer and review relevant research. We discuss recent findings on the identification of epigenetic diagnostic and prognostic biomarkers for these cancers.
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Affiliation(s)
- Timothy M Barrow
- Institute for Prevention and Tumor Epidemiology, Freiburg Medical Center, University of Freiburg, 79106, Germany; German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Karin B Michels
- Institute for Prevention and Tumor Epidemiology, Freiburg Medical Center, University of Freiburg, 79106, Germany; Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.
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160
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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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161
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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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162
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Imperiale TF, Ransohoff DF, Itzkowitz SH, Levin TR, Lavin P, Lidgard GP, Ahlquist DA, Berger BM. Multitarget stool DNA testing for colorectal-cancer screening. N Engl J Med 2014; 370:1287-97. [PMID: 24645800 DOI: 10.1056/nejmoa1311194] [Citation(s) in RCA: 1098] [Impact Index Per Article: 109.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND An accurate, noninvasive test could improve the effectiveness of colorectal-cancer screening. METHODS We compared a noninvasive, multitarget stool DNA test with a fecal immunochemical test (FIT) in persons at average risk for colorectal cancer. The DNA test includes quantitative molecular assays for KRAS mutations, aberrant NDRG4 and BMP3 methylation, and β-actin, plus a hemoglobin immunoassay. Results were generated with the use of a logistic-regression algorithm, with values of 183 or more considered to be positive. FIT values of more than 100 ng of hemoglobin per milliliter of buffer were considered to be positive. Tests were processed independently of colonoscopic findings. RESULTS Of the 9989 participants who could be evaluated, 65 (0.7%) had colorectal cancer and 757 (7.6%) had advanced precancerous lesions (advanced adenomas or sessile serrated polyps measuring ≥1 cm in the greatest dimension) on colonoscopy. The sensitivity for detecting colorectal cancer was 92.3% with DNA testing and 73.8% with FIT (P=0.002). The sensitivity for detecting advanced precancerous lesions was 42.4% with DNA testing and 23.8% with FIT (P<0.001). The rate of detection of polyps with high-grade dysplasia was 69.2% with DNA testing and 46.2% with FIT (P=0.004); the rates of detection of serrated sessile polyps measuring 1 cm or more were 42.4% and 5.1%, respectively (P<0.001). Specificities with DNA testing and FIT were 86.6% and 94.9%, respectively, among participants with nonadvanced or negative findings (P<0.001) and 89.8% and 96.4%, respectively, among those with negative results on colonoscopy (P<0.001). The numbers of persons who would need to be screened to detect one cancer were 154 with colonoscopy, 166 with DNA testing, and 208 with FIT. CONCLUSIONS In asymptomatic persons at average risk for colorectal cancer, multitarget stool DNA testing detected significantly more cancers than did FIT but had more false positive results. (Funded by Exact Sciences; ClinicalTrials.gov number, NCT01397747.).
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Affiliation(s)
- Thomas F Imperiale
- From the Department of Medicine, Indiana University School of Medicine, the Regenstrief Institute, the Simon Cancer Center, and the Center for Innovation at Roudebush Veterans Affairs Medical Center - all in Indianapolis (T.F.I.); the Departments of Medicine and Epidemiology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill (D.F.R.); the Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York (S.H.I.); Kaiser Permanente Medical Center, Walnut Creek, CA (T.R.L.); Boston Biostatistics Research Foundation, Framingham MA (P.L.); Exact Sciences, Madison, WI (G.P.L., B.M.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (D.A.A.)
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163
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Xiao Z, Li B, Wang G, Zhu W, Wang Z, Lin J, Xu A, Wang X. Validation of methylation-sensitive high-resolution melting (MS-HRM) for the detection of stool DNA methylation in colorectal neoplasms. Clin Chim Acta 2014; 431:154-63. [PMID: 24518356 DOI: 10.1016/j.cca.2014.01.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/18/2014] [Accepted: 01/26/2014] [Indexed: 12/18/2022]
Abstract
BACKGROUND Methylation-sensitive high-resolution melting (MS-HRM) is a new technique for assaying DNA methylation, but its feasibility for assaying stool in patients with colorectal cancer (CRC) is unknown. METHODS First, the MS-HRM and methylation-specific PCR (MSP) detection limits were tested. Second, the methylation statuses of SFRP2 and VIM were analyzed in stool samples by MS-HRM, and in matching tumor and normal colon tissues via bisulfite sequencing PCR (BSP). Third, a case-control study evaluated the diagnostic sensitivity and specificity of MS-HRM relative to results obtained with MSP and the fecal immunochemical test (FIT). Finally, the linearity and reproducibility of MS-HRM were assessed. RESULTS The detection limits of MS-HRM and MSP were 1% and 5%, respectively. The diagnostic sensitivities of MS-HRM (87.3%, 55/63) in stool and BSP in matching tumor tissue (92.1%, 58/63) were highly consistent (κ=0.744). The MS-HRM assay detected 92.5% (37/40) methylation in CRCs, 94.4% (34/36) in advanced adenomas, and 8.8% (5/57) in normal controls. The results of MS-HRM analysis were stable and reliable and showed fairly good linearity for both SFRP2 (P<0.001, R(2)=0.957) and VIM (P<0.001, R(2)=0.954). CONCLUSIONS MS-HRM shows potential for CRC screening.
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Affiliation(s)
- Zhujun Xiao
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China
| | - Bingsheng Li
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Gastroenterology, Huizhou First Hospital, Huizhou 516003, China
| | - Guozhen Wang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China
| | - Weisi Zhu
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China
| | - Zhongqiu Wang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China
| | - Jinfeng Lin
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China
| | - Angao Xu
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Huizhou Medicine Institute, Huizhou 516003, China.
| | - Xinying Wang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China.
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Walter K, Holcomb T, Januario T, Yauch RL, Du P, Bourgon R, Seshagiri S, Amler LC, Hampton GM, S Shames D. Discovery and development of DNA methylation-based biomarkers for lung cancer. Epigenomics 2014; 6:59-72. [DOI: 10.2217/epi.13.81] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Lung cancer remains the primary cause of cancer-related deaths worldwide. Improved tools for early detection and therapeutic stratification would be expected to increase the survival rate for this disease. Alterations in the molecular pathways that drive lung cancer, which include epigenetic modifications, may provide biomarkers to help address this major unmet clinical need. Epigenetic changes, which are defined as heritable changes in gene expression that do not alter the primary DNA sequence, are one of the hallmarks of cancer, and prevalent in all types of cancer. These modifications represent a rich source of biomarkers that have the potential to be implemented in clinical practice. This perspective describes recent advances in the discovery of epigenetic biomarkers in lung cancer, specifically those that result in the methylation of DNA at CpG sites. We discuss one approach for methylation-based biomarker assay development that describes the discovery at a genome-scale level, which addresses some of the practical considerations for design of assays that can be implemented in the clinic. We emphasize that an integrated technological approach will enable the development of clinically useful DNA methylation-based biomarker assays. While this article focuses on current literature and primary research findings in lung cancer, the principles we describe here apply to the discovery and development of epigenetic biomarkers for other types of cancer.
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Affiliation(s)
- Kimberly Walter
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Thomas Holcomb
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Tom Januario
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Robert L Yauch
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Pan Du
- Department of Bioinformatics & Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Richard Bourgon
- Department of Bioinformatics & Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Lukas C Amler
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Garret M Hampton
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - David S Shames
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
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165
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Kraus S, Nabiochtchikov I, Shapira S, Arber N. Recent advances in personalized colorectal cancer research. Cancer Lett 2014; 347:15-21. [PMID: 24491406 DOI: 10.1016/j.canlet.2014.01.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 01/20/2014] [Accepted: 01/24/2014] [Indexed: 12/13/2022]
Abstract
Colorectal cancer is one of the most prevalent cancers and a leading cause ofcancer-related death. It is also curable if detected early. The prognosis for metastatic colorectal cancer remains poor and resistance to chemotherapy is still a major obstacle in effective treatment. While many patients do not clinically benefit from chemotherapy, others experience adverse reactions resulting in dose modifications or treatment withdrawal, thereby reducing treatment efficacy. Researchefforts attempt to identify reliable biomarkers which will guide clinicians in decision making, while matching suitable therapeutic regimens. We here review currently known molecular biomarkers used for the personalized treatment of colorectal cancer.
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Affiliation(s)
- Sarah Kraus
- The Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ilana Nabiochtchikov
- The Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shiran Shapira
- The Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nadir Arber
- The Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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166
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Liu Y, Tham CK, Ong SYK, Ho KS, Lim JF, Chew MH, Lim CK, Zhao Y, Tang CL, Eu KW. Serum methylation levels of TAC1. SEPT9 and EYA4 as diagnostic markers for early colorectal cancers: a pilot study. Biomarkers 2014; 18:399-405. [PMID: 23862763 DOI: 10.3109/1354750x.2013.798745] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To identify methylated genes in serum with diagnostic potentials for early colorectal cancer (CRC). METHODS Serum methylation levels of up to 12 genes were measured in two sets of serum samples with the second set from 26 stage I CRC patients and 26 age/gender-matched controls. RESULTS Serum methylation levels of TAC1, SEPT9, and EYA4 were significant discriminants between stage I CRC and healthy controls. Combination of TAC1 and SEPT9 rendered 73.1% sensitivity with 92.3% specificity. CONCLUSION Serum methylation levels of TAC1. SEPT9 and EYA4 may be useful biomarkers for early detection of CRC though a validation study is necessary.
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Affiliation(s)
- Yanqun Liu
- Department of Colorectal Surgery, Singapore General Hospital, Singapore.
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167
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Abstract
Genotyping tumor tissue in search of somatic genetic alterations for actionable information has become routine practice in clinical oncology. Although these sequence alterations are highly informative, sampling tumor tissue has significant inherent limitations; tumor tissue is a single snapshot in time, is subject to selection bias resulting from tumor heterogeneity, and can be difficult to obtain. Cell-free fragments of DNA are shed into the bloodstream by cells undergoing apoptosis or necrosis, and the load of circulating cell-free DNA (cfDNA) correlates with tumor staging and prognosis. Moreover, recent advances in the sensitivity and accuracy of DNA analysis have allowed for genotyping of cfDNA for somatic genomic alterations found in tumors. The ability to detect and quantify tumor mutations has proven effective in tracking tumor dynamics in real time as well as serving as a liquid biopsy that can be used for a variety of clinical and investigational applications not previously possible.
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Affiliation(s)
- Luis A Diaz
- Luis A. Diaz Jr, Swim Across America Laboratory and Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD; and Alberto Bardelli, Institute for Cancer Research and Treatment at Candiolo, University of Torino, Candiolo, and the Fondazione Italiana per la Ricerca sul Cancro Institute of Molecular Oncology, Milan, Italy
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168
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VanInsberghe M, Heyries KA, Hansen CL. Should genetic testing go digital? Expert Rev Mol Diagn 2014; 12:111-4. [DOI: 10.1586/erm.12.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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169
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Marzese DM, Hirose H, Hoon DSB. Diagnostic and prognostic value of circulating tumor-related DNA in cancer patients. Expert Rev Mol Diagn 2014; 13:827-44. [DOI: 10.1586/14737159.2013.845088] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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170
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Abstract
The promise of precision medicine is now a clinical reality. Advances in our understanding of the molecular genetics of colorectal cancer (CRC) are leading to the development of a variety of biomarkers that are being used as early detection markers, prognostic markers, and markers for predicting treatment responses. This is no more evident than in the recent advances in testing CRCs for specific molecular alterations in order to guide treatment with the monoclonal antibody therapies cetuximab and panitumumab, which target the epidermal growth factor receptor. In this review, we update a prior review published in 2010 and describe our current understanding of the molecular pathogenesis of CRC and how these alterations relate to emerging biomarkers for early detection and risk stratification (diagnostic markers), prognosis (prognostic markers), and the prediction of treatment responses (predictive markers).
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Affiliation(s)
- William M Grady
- 1Clinical Research Division, Fred Hutchison Cancer Research Center, Seattle, Washington, USA
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171
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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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172
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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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173
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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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174
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Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1161-74. [PMID: 23938249 DOI: 10.1016/j.bbagrm.2013.08.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 02/06/2023]
Abstract
Ever since the discovery of DNA methylation at cytosine residues, the role of this so called fifth base has been extensively studied and debated. Until recently, the majority of DNA methylation studies focused on the analysis of CpG islands associated to promoter regions. However, with the upcoming possibilities to study DNA methylation in a genome-wide context, this epigenetic mark can now be studied in an unbiased manner. As a result, recent studies have shown that not only promoters but also intragenic and intergenic regions are widely modulated during physiological processes and disease. In particular, it is becoming increasingly clear that DNA methylation in the gene body is not just a passive witness of gene transcription but it seems to be actively involved in multiple gene regulation processes. In this review we discuss the potential role of intragenic DNA methylation in alternative promoter usage, regulation of short and long non-coding RNAs, alternative RNA processing, as well as enhancer activity. Furthermore, we summarize how the intragenic DNA methylome is modified both during normal cell differentiation and neoplastic transformation.
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175
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Dorff KC, Chambwe N, Zeno Z, Simi M, Shaknovich R, Campagne F. GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. PLoS One 2013; 8:e69666. [PMID: 23936070 PMCID: PMC3720652 DOI: 10.1371/journal.pone.0069666] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/11/2013] [Indexed: 01/04/2023] Open
Abstract
We present GobyWeb, a web-based system that facilitates the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension mechanism. Analyses currently supported include quantification of gene expression for messenger and small RNA sequencing, estimation of DNA methylation (i.e., reduced bisulfite sequencing and whole genome methyl-seq), or the detection of pathogens in sequenced data. In contrast to previous analysis pipelines developed for analysis of HTS data, GobyWeb requires significantly less storage space, runs analyses efficiently on a parallel grid, scales gracefully to process tens or hundreds of multi-gigabyte samples, yet can be used effectively by researchers who are comfortable using a web browser. We conducted performance evaluations of the software and found it to either outperform or have similar performance to analysis programs developed for specialized analyses of HTS data. We found that most biologists who took a one-hour GobyWeb training session were readily able to analyze RNA-Seq data with state of the art analysis tools. GobyWeb can be obtained at http://gobyweb.campagnelab.org and is freely available for non-commercial use. GobyWeb plugins are distributed in source code and licensed under the open source LGPL3 license to facilitate code inspection, reuse and independent extensions http://github.com/CampagneLaboratory/gobyweb2-plugins.
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Affiliation(s)
- Kevin C. Dorff
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, The Weill Cornell Medical College, New York, New York, United States of America
| | - Nyasha Chambwe
- Department of Physiology and Biophysics, The Weill Cornell Medical College, New York, New York, United States of America
- Tri-Institutional Training Program in Computational Biology and Medicine, The Weill Cornell Medical College, New York, New York, United States of America
| | - Zachary Zeno
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, The Weill Cornell Medical College, New York, New York, United States of America
| | - Manuele Simi
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, The Weill Cornell Medical College, New York, New York, United States of America
| | - Rita Shaknovich
- Department of Pathology and Department of Medicine; The Weill Cornell Medical College, New York, New York, United States of America
| | - Fabien Campagne
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, The Weill Cornell Medical College, New York, New York, United States of America
- Department of Physiology and Biophysics, The Weill Cornell Medical College, New York, New York, United States of America
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176
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BEAMing and Droplet Digital PCR Analysis of Mutant IDH1 mRNA in Glioma Patient Serum and Cerebrospinal Fluid Extracellular Vesicles. MOLECULAR THERAPY-NUCLEIC ACIDS 2013; 2:e109. [PMID: 23881452 PMCID: PMC3732870 DOI: 10.1038/mtna.2013.28] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/06/2013] [Indexed: 02/06/2023]
Abstract
Development of biofluid-based molecular diagnostic tests for cancer is an important step towards tumor characterization and real-time monitoring in a minimally invasive fashion. Extracellular vesicles (EVs) are released from tumor cells into body fluids and can provide a powerful platform for tumor biomarkers because they carry tumor proteins and nucleic acids. Detecting rare point mutations in the background of wild-type sequences in biofluids such as blood and cerebrospinal fluid (CSF) remains a major challenge. Techniques such as BEAMing (beads, emulsion, amplification, magnetics) PCR and droplet digital PCR (ddPCR) are substantially more sensitive than many other assays for mutant sequence detection. Here, we describe a novel approach that combines biofluid EV RNA and BEAMing RT-PCR (EV-BEAMing), as well droplet digital PCR to interrogate mutations from glioma tumors. EVs from CSF of patients with glioma were shown to contain mutant IDH1 transcripts, and we were able to reliably detect and quantify mutant and wild-type IDH1 RNA transcripts in CSF of patients with gliomas. EV-BEAMing and EV-ddPCR represent a valuable new strategy for cancer diagnostics, which can be applied to a variety of biofluids and neoplasms.
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177
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Timp W, Feinberg AP. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer 2013; 13:497-510. [PMID: 23760024 PMCID: PMC4636434 DOI: 10.1038/nrc3486] [Citation(s) in RCA: 410] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although at the genetic level cancer is caused by diverse mutations, epigenetic modifications are characteristic of all cancers, from apparently normal precursor tissue to advanced metastatic disease, and these epigenetic modifications drive tumour cell heterogeneity. We propose a unifying model of cancer in which epigenetic dysregulation allows rapid selection for tumour cell survival at the expense of the host. Mechanisms involve both genetic mutations and epigenetic modifications that disrupt the function of genes that regulate the epigenome itself. Several exciting recent discoveries also point to a genome-scale disruption of the epigenome that involves large blocks of DNA hypomethylation, mutations of epigenetic modifier genes and alterations of heterochromatin in cancer (including large organized chromatin lysine modifications (LOCKs) and lamin-associated domains (LADs)), all of which increase epigenetic and gene expression plasticity. Our model suggests a new approach to cancer diagnosis and therapy that focuses on epigenetic dysregulation and has great potential for risk detection and chemoprevention.
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Affiliation(s)
- Winston Timp
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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178
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Pang JMB, Dobrovic A, Fox SB. DNA methylation in ductal carcinoma in situ of the breast. Breast Cancer Res 2013; 15:206. [PMID: 23826974 PMCID: PMC3707020 DOI: 10.1186/bcr3420] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ductal carcinoma in situ (DCIS) is a non-obligate precursor lesion of invasive carcinoma of the breast. Current prognostic markers based on histopathological examination are unable to accurately predict which DCIS cases will progress to invasive carcinoma or recur after surgical excision. Epigenetic changes have been shown to be a significant driver of tumorigenesis, and DNA methylation of specific gene promoters provides predictive and prognostic markers in many types of cancer, including invasive breast cancer. In general, the spectrum of genes that are methylated in DCIS strongly resembles that seen in invasive ductal carcinoma. The identification of specific prognostic markers in DCIS remains elusive and awaits additional work investigating a large panel of methylatable genes by using sensitive and reproducible technologies. This review critically appraises the role of methylation in DCIS and its use as a biomarker.
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179
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Tänzer M, Liebl M, Quante M. Molecular biomarkers in esophageal, gastric, and colorectal adenocarcinoma. Pharmacol Ther 2013; 140:133-47. [PMID: 23791941 DOI: 10.1016/j.pharmthera.2013.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 06/06/2013] [Indexed: 02/06/2023]
Abstract
Cancers of the esophagus, stomach and colon contribute to a major health burden worldwide and over 20% of all cancer deaths. Biomarkers that should indicate pathogenic process and are measureable in an objective manner for these tumors are rare and not established in the clinical setting. In general biomarkers can be very useful for cancer management as they can improve clinical decision-making regarding diagnosis, surveillance, and therapy. Biomarkers can be different types of molecular entities (such as DNA, RNA or proteins), which can be detected, in different tissues or body fluids. However, more important is the type of biomarker itself, which allows diagnostic, prognostic or predictive analyses for different clinical problems. This review aims to systematically summarize the recent findings of genetic and epigenetic markers for gastrointestinal tumors within the last decade. While many biomarkers seem to be very promising, especially if used as panels, further development is urgently needed to address practical considerations of biomarkers in cancer treatment.
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Affiliation(s)
- Marc Tänzer
- II. Medizinische Klinik, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675 München, Germany
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180
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Skally M, Hanly P, Sharp L. Cost effectiveness of fecal DNA screening for colorectal cancer: a systematic review and quality appraisal of the literature. APPLIED HEALTH ECONOMICS AND HEALTH POLICY 2013; 11:181-192. [PMID: 23549792 DOI: 10.1007/s40258-013-0010-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
BACKGROUND Fecal DNA (fDNA) testing is a noninvasive potential alternative to current colorectal cancer screening tests. OBJECTIVE We conducted a systematic review and quality assessment of studies of cost-effectiveness of fDNA as a colorectal cancer screening tool (compared with no screening and other screening modalities), and identified key variables that impinged on cost-effectiveness. DATA SOURCES We searched MEDLINE, Embase, and the Centre for Reviews and Dissemination for cost-effectiveness studies of fDNA-based screening, published in English by September 2011. STUDY SELECTION Studies that undertook an economic evaluation of fDNA, using either a cost-effectiveness or cost-utility analysis, compared with other relevant screening modalities and/or no screening were included. Additional inclusion criteria related to the presentation of data pertaining to model variables including time horizon, costs, fDNA performance characteristics, screening uptake, and comparators. A total of 369 articles were initially identified for review. After removing duplicates and applying inclusion and exclusion criteria, seven articles were included in the final review. STUDY APPRAISAL Data was abstracted on key descriptor variables including screening scenarios, time horizon, costs, test performance characteristics, screening uptake, comparators, and incremental cost-effectiveness ratios. Quality assessment was undertaken using a standard checklist for economic evaluations. Studies cited by cost-effectiveness articles as the source of data on fDNA test performance characteristics were also reviewed. RESULTS Seven cost-effectiveness studies were included, from the USA (4), Canada (1), Israel (1), and Taiwan (1). Markov models (5), a partially observable Markov decision process model (1) and MISCAN and SimCRC (1) microsimulation models were used. All studies took a third-party payer perspective and one included, in addition, a societal perspective. Comparator screening tests, screening intervals, and specific fDNA tests varied between studies. fDNA sensitivity and specificity parameters were derived from 12 research studies and one meta-analysis. Outcomes assessed were life-years gained and quality-adjusted life-years gained. fDNA was cost-effective when compared with no screening in six studies. Compared with other screening modalities, fDNA was not considered cost-effective in any of the base-case analyses: in five studies it was dominated by all alternatives considered. Sensitivity analyses identified cost, compliance, and test parameters as key influential parameters. In general, poor presentation of "study design" and "data collection" details lowered the quality of included articles. LIMITATIONS Although the literature searches were designed for high sensitivity, the possibility cannot be excluded that some eligible studies may have been missed. Reports (such as Health Technology Assessments produced by government agencies) and other forms of grey literature were excluded because they are difficult to identify systematically and/or may not report methods and results in sufficient detail for assessment. CONCLUSION On the basis of the available (albeit limited) evidence, while fDNA is cost-effective when compared with no screening, it is currently dominated by most of the other available screening options. Cost and test performance appear to be the main influences on cost-effectiveness.
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Affiliation(s)
- Mairead Skally
- National Cancer Registry Ireland, Building 6800, Cork Airport Business Park, Kinsale Road, Cork, Ireland.
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181
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Affiliation(s)
- Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - David Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 90033
| | - Robert Haile
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 90033
| | - David Duggan
- The Translational Genomics Research Institute (TGen), Phoenix, Arizona 85004
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182
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de Souza CRT, Leal MF, Calcagno DQ, Costa Sozinho EK, Borges BDN, Montenegro RC, Dos Santos AKCR, Dos Santos SEB, Ribeiro HF, Assumpção PP, de Arruda Cardoso Smith M, Burbano RR. MYC deregulation in gastric cancer and its clinicopathological implications. PLoS One 2013; 8:e64420. [PMID: 23717612 PMCID: PMC3661519 DOI: 10.1371/journal.pone.0064420] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/12/2013] [Indexed: 12/13/2022] Open
Abstract
Our study investigated the relationship between MYC alterations and clinicopathological features in gastric cancers. We evaluated the effect of MYC mRNA expression and its protein immunoreactivity, as well as copy number variation, promoter DNA methylation, and point mutations, in 125 gastric adenocarcinoma and 67 paried non-neoplastic tissues. We observed that 77% of the tumors presented MYC immunoreactivity which was significantly associated with increased mRNA expression (p<0.05). These observations were associated with deeper tumor extension and the presence of metastasis (p<0.05). MYC protein expression was also more frequently observed in intestinal-type than in diffuse-type tumors (p<0.001). Additionally, MYC mRNA and protein expression were significantly associated with its copy number (p<0.05). The gain of MYC copies was associated with late-onset, intestinal-type, advanced tumor stage, and the presence of distant metastasis (p<0.05). A hypomethylated MYC promoter was detected in 86.4% of tumor samples. MYC hypomethylation was associated with diffuse-type, advanced tumor stage, deeper tumor extension, and the presence of lymph node metastasis (p<0.05). Moreover, eighteen tumor samples presented at least one known mutation. The presence of MYC mutations was associated with diffuse-type tumor (p<0.001). Our results showed that MYC deregulation was mainly associated with poor prognostic features and also reinforced the presence of different pathways involved in intestinal-type and diffuse-type gastric carcinogenesis. Thus, our findings suggest that MYC may be a useful marker for clinical stratification and prognosis.
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183
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Qu Y, Dang S, Hou P. Gene methylation in gastric cancer. Clin Chim Acta 2013; 424:53-65. [PMID: 23669186 DOI: 10.1016/j.cca.2013.05.002] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 05/03/2013] [Accepted: 05/03/2013] [Indexed: 02/07/2023]
Abstract
Gastric cancer is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide. Over 70% of new cases and deaths occur in developing countries. In the early years of the molecular biology revolution, cancer research mainly focuses on genetic alterations, including gastric cancer. Epigenetic mechanisms are essential for normal development and maintenance of tissue-specific gene expression patterns in mammals. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Recent advancements in the rapidly evolving field of cancer epigenetics have shown extensive reprogramming of every component of the epigenetic machinery in cancer, including DNA methylation, histone modifications, nucleosome positioning, noncoding RNAs, and microRNAs. Aberrant DNA methylation in the promoter regions of gene, which leads to inactivation of tumor suppressor and other cancer-related genes in cancer cells, is the most well-defined epigenetic hallmark in gastric cancer. The advantages of gene methylation as a target for detection and diagnosis of cancer in biopsy specimens and non-invasive body fluids such as serum and gastric washes have led to many studies of application in gastric cancer. This review focuses on the most common and important phenomenon of epigenetics, DNA methylation, in gastric cancer and illustrates the impact epigenetics has had on this field.
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Key Words
- 5-hmC
- 5-hydroxymethylcytosine
- 5-mC
- 5-methylcytosine
- ADAM metallopeptidase domain 23
- ADAM metallopeptidase with thrombospondin type 1 motif, 9
- ADAM23
- ADAMTS9
- AML
- APC
- ARID1A
- AT motif-binding factor 1
- AT rich interactive domain 1A (SWI-like)
- ATBF1
- Acute myelocytic leukemia
- Adenomatosis polyposis coli
- B-cell translocation gene 4
- BCL2/adenovirus E1B 19kDa interacting protein 3
- BMP-2
- BNIP3
- BS
- BTG4
- Biomarkers
- Bisulfite sequencing
- Bone morphogenetic protein 2
- C-MET
- CACNA1G
- CACNA2D3
- CD44
- CD44 molecule (Indian blood group)
- CDH1
- CDK4
- CDK6
- CDKN1C
- CDKN2A
- CDX2
- CGI
- CHD5
- CHFR
- CKLF-like MARVEL transmembrane domain containing 3
- CMTM3
- CNS
- CRBP1
- Cadherin 1 or E-cadherin
- Calcium channel, voltage-dependent, T type, alpha 1G subunit
- Calcium channel, voltage-dependent, alpha 2/delta subunit 3
- Caudal type homeobox 2
- Central nervous system
- Checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase
- Chromodomain helicase DNA binding protein 5
- Chromosome 2 open reading frame 40
- Clinical outcomes
- CpG islands
- Cyclin-dependent kinase 4
- Cyclin-dependent kinase 6
- Cyclin-dependent kinase inhibitor 1A
- Cyclin-dependent kinase inhibitor 1B
- Cyclin-dependent kinase inhibitor 1C
- Cyclin-dependent kinase inhibitor 2A
- Cyclin-dependent kinase inhibitor 2B
- DAB2 interacting protein
- DACT1
- DAPK
- DNA
- DNA methylatransferases
- DNA mismatch repair
- DNMT
- Dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)
- Death-associated protein kinase
- Deoxyribose Nucleic Acid
- Dickkopf 3 homolog (Xenopus laevis)
- Dkk-3
- EBV
- ECRG4
- EDNRB
- EGCG
- ERBB4
- Endothelin receptor type B
- Epigallocatechin gallate
- Epigenetics
- Epstein–Barr Virus
- FDA
- FLNc
- Filamin C
- Food and Drug Administration
- GC
- GDNF
- GI endoscopy
- GPX3
- GRIK2
- GSTP1
- Gastric cancer
- Gene methylation
- Glutamate receptor, ionotropic, kainate 2
- Glutathione S-transferase pi 1
- Glutathione peroxidase 3 (plasma)
- H. pylori
- HACE1
- HAI-2/SPINT2
- HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1
- HGFA
- HLTF
- HOXA1
- HOXA10
- HRAS-like suppressor
- HRASLS
- Helicase-like transcription factor
- Helicobacter pylori
- Homeobox A1
- Homeobox A10
- Homeobox D10
- HoxD10
- IGF-1
- IGF-1R
- IGFBP3
- IL-1β
- ITGA4
- Insulin-like growth factor 1 (somatomedin C)
- Insulin-like growth factor I receptor
- Insulin-like growth factor binding protein 3
- Integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)
- Interleukin 1, beta
- KL
- KRAS
- Klotho
- LL3
- LMP2A
- LOX
- LRP1B
- Low density lipoprotein receptor-related protein 1B
- Lysyl oxidase
- MAPK
- MBPs
- MDS
- MGMT
- MINT25
- MLF1
- MLL
- MMR
- MSI
- MSP
- Matrix metallopeptidase 24 (membrane-inserted)
- Met proto-oncogene (hepatocyte growth factor receptor)
- Methyl-CpG binding proteins
- Methylation-specific PCR
- Microsatellite instability
- Myeloid leukemia factor 1
- Myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)
- Myeloid/lymphoid or mixed-lineage leukemia 3
- NDRG family member 2
- NDRG2
- NPR1
- NR3C1
- Natriuretic peptide receptor A/guanylate cyclase A
- Notch 1
- Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)
- O-6-methylguanine-DNA methyltransferase
- PCDH10
- PCDH17
- PI3K/Akt
- PIK3CA
- PR domain containing 5
- PRDM5
- PTCH1
- Patched 1
- Phosphatidylethanolamine binding protein 1
- Protein tyrosine phosphatase, non-receptor type 6
- Protocadherin 10
- Protocadherin 17
- Q-MSP
- Quantitative methylation-specific PCR
- RAR-related orphan receptor A
- RARRES1
- RARß
- RAS/RAF/MEK/ERK
- RASSF1A
- RASSF2
- RBP1
- RKIP
- RORA
- ROS
- RUNX3
- Ras association (RalGDS/AF-6) domain family member 1
- Ras association (RalGDS/AF-6) domain family member 2
- Rb
- Retinoic acid receptor responder (tazarotene induced) 1
- Retinoic acid receptor, beta
- Retinol binding protein 1, cellular
- Runt-related transcription factor 3
- S-adenosylmethionine
- SAM
- SFRP2
- SFRP5
- SHP1
- SOCS-1
- STAT3
- SYK
- Secreted frizzled-related protein 2
- Secreted frizzled-related protein 5
- Serine peptidase inhibitor, Kunitz type, 2
- Spleen tyrosine kinase
- Suppressor of cytokine signaling 1
- TCF4
- TET
- TFPI2
- TGF-β
- TIMP metallopeptidase inhibitor 3
- TIMP3
- TNM
- TP73
- TSP1
- Thrombospondin 1
- Tissue factor pathway inhibitor 2
- Transcription factor 4
- Tumor Node Metastasis
- Tumor protein p73
- V-erb-a erythroblastic leukemia viral oncogene homolog 4
- ZFP82 zinc finger protein
- ZIC1
- ZNF545
- Zinc finger protein of the cerebellum 1
- gastrointestinal endoscopy
- glial cell derived neurotrophic factor
- hDAB2IP
- hMLH1
- hepatocyte growth factor activator
- latent membrane protein
- mutL homolog 1
- myelodysplastic syndromes
- p15
- p16
- p21
- p27
- p53
- p73
- phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha
- phosphoinositide 3-kinase (PI3K)/Akt
- reactive oxygen species
- retinoblastoma
- signal transducer and activator of transcription-3
- ten-eleven translocation
- transforming growth factor-β
- tumor protein p53
- tumor protein p73
- v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
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Affiliation(s)
- Yiping Qu
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, People's Republic of China
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184
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Non-invasive prenatal diagnosis of fetal trisomy 21 using cell-free fetal DNA in maternal blood. Obstet Gynecol Sci 2013; 56:58-66. [PMID: 24327983 PMCID: PMC3784100 DOI: 10.5468/ogs.2013.56.2.58] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/08/2013] [Accepted: 02/08/2013] [Indexed: 01/04/2023] Open
Abstract
Since the existence of cell-free fetal DNA (cff-DNA) in maternal circulation was discovered, it has been identified as a promising source of fetal genetic material in the development of reliable methods for non-invasive prenatal diagnosis (NIPD) of fetal trisomy 21 (T21). Currently, a prenatal diagnosis of fetal T21 is achieved through invasive techniques, such as chorionic villus sampling or amniocentesis. However, such invasive diagnostic tests are expensive, require expert technicians, and have a miscarriage risk approximately 1%. Therefore, NIPD using cff-DNA in the detection of fetal T21 is significant in prenatal care. Recently, the application of new techniques using single-molecular counting methods and the development of fetal-specific epigenetic markers has opened up new possibilities in the NIPD of fetal T21 using cff-DNA. These new technologies will facilitate safer, more sensitive and accurate prenatal tests in the near future. In this review, we investigate the recent methods for the NIPD of fetal T21 and discuss their implications in future clinical practice.
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185
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Kahi CJ, Anderson JC, Rex DK. Screening and surveillance for colorectal cancer: state of the art. Gastrointest Endosc 2013; 77:335-50. [PMID: 23410695 DOI: 10.1016/j.gie.2013.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 01/01/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Charles J Kahi
- Department of Medicine, Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, IN, USA
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186
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Agarose droplet microfluidics for highly parallel and efficient single molecule emulsion PCR. Methods Mol Biol 2013; 949:413-22. [PMID: 23329457 DOI: 10.1007/978-1-62703-134-9_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Agarose emulsion droplet microfluidic technology for single copy emulsion PCR (ePCR) is a suitable technique for the detection of single copy DNA molecules. It improves the traditional ePCR by employing agarose with low melting and low gelling temperatures, which is coupled with PCR forward primers using Schiff-base reaction. Highly uniform monodisperse nanoliter agarose droplets each containing PCR reagents and single copy template are produced with a microfabricated emulsion generator. Following PCR, the cooled droplets transform to microbeads carrying amplicons to maintain the monocolonity of each droplet, which can be further analyzed. This method allows high-throughput generation of uniform droplets and enables high PCR efficiency, making it a promising platform for many single copy genetic studies.
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187
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Sipos F, Mũzes G, Patai AV, Fũri I, Péterfia B, Hollósi P, Molnár B, Tulassay Z. Genome-wide screening for understanding the role of DNA methylation in colorectal cancer. Epigenomics 2013; 5:569-81. [PMID: 24059802 DOI: 10.2217/epi.13.52] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA methylation analysis methods have undergone an impressive revolution over the past 15 years. Regarding colorectal cancer (CRC), the localization and distribution of several differently methylated genes have been determined by genome-wide DNA methylation assays. These genes do not just influence the pathogenesis of CRC, but can be used further as diagnostic or prognostic markers. Moreover, the identified four DNA methylation-based subgroups of CRC have important clinical and therapeutic merit. Since genome-wide DNA methylation analyzes result in a large amount of data, there is a need for complex bioinformatic and pathway analysis. Future challenges in epigenetic alterations of CRC include the demand for comprehensive identification and experimental validation of gene abnormalities. By introduction of genome-wide DNA methylation profiling into clinical practice not only the patients' risk stratification but development of targeted therapies will also be possible.
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Affiliation(s)
- Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
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188
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Abstract
The functional impact of aberrant DNA methylation and the widespread alterations in DNA methylation in cancer development have led to the development of a variety of methods to characterize the DNA methylation patterns. This chapter critiques and describes the major approaches to analyzing DNA methylation.
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189
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Mikeska T, Bock C, Do H, Dobrovic A. DNA methylation biomarkers in cancer: progress towards clinical implementation. Expert Rev Mol Diagn 2012; 12:473-87. [PMID: 22702364 DOI: 10.1586/erm.12.45] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Altered DNA methylation is ubiquitous in human cancers and specific methylation changes are often correlated with clinical features. DNA methylation biomarkers, which use those specific methylation changes, provide a range of opportunities for early detection, diagnosis, prognosis, therapeutic stratification and post-therapeutic monitoring. Here we review current approaches to developing and applying DNA methylation biomarkers in cancer therapy. We discuss the obstacles that have so far limited the routine use of DNA methylation biomarkers in clinical settings and describe ways in which these obstacles can be overcome. Finally, we summarize the current state of clinical implementation for some of the most widely studied and well-validated DNA methylation biomarkers, including SEPT9, VIM, SHOX2, PITX2 and MGMT.
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Affiliation(s)
- Thomas Mikeska
- Molecular Pathology Research & Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett Street, Melbourne, Victoria 8006, Australia
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190
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Castellanos-Rizaldos E, Milbury CA, Makrigiorgos GM. Enrichment of mutations in multiple DNA sequences using COLD-PCR in emulsion. PLoS One 2012; 7:e51362. [PMID: 23236486 PMCID: PMC3516544 DOI: 10.1371/journal.pone.0051362] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/01/2012] [Indexed: 01/04/2023] Open
Abstract
Background Multiplex detection of low-level mutant alleles in the presence of wild-type DNA would be useful for several fields of medicine including cancer, pre-natal diagnosis and infectious diseases. COLD-PCR is a recently developed method that enriches low-level mutations during PCR cycling, thus enhancing downstream detection without the need for special reagents or equipment. The approach relies on the differential denaturation of DNA strands which contain Tm-lowering mutations or mismatches, versus ‘homo-duplex’ wild-type DNA. Enabling multiplex-COLD-PCR that can enrich mutations in several amplicons simultaneously is desirable but technically difficult to accomplish. Here we describe the proof of principle of an emulsion-PCR based approach that demonstrates the feasibility of multiplexed-COLD-PCR within a single tube, using commercially available mutated cell lines. This method works best with short amplicons; therefore, it could potentially be used on highly fragmented samples obtained from biological material or FFPE specimens. Methods Following a multiplex pre-amplification of TP53 exons from genomic DNA, emulsions which incorporate the multiplex product, PCR reagents and primers specific for a given TP53 exon are prepared. Emulsions with different TP53 targets are then combined in a single tube and a fast-COLD-PCR program that gradually ramps up the denaturation temperature over several PCR cycles is applied (temperature-tolerant, TT-fast-eCOLD-PCR). The range of denaturation temperatures applied encompasses the critical denaturation temperature (Tc) corresponding to all the amplicons included in the reaction, resulting to a gradual enrichment of mutations within all amplicons encompassed by emulsion. Results Validation for TT-fast-eCOLD-PCR is provided for TP53 exons 6–9. Using dilutions of mutated cell-line into wild-type DNA, we demonstrate simultaneous mutation enrichment between 7 to 15-fold in all amplicons examined. Conclusions TT-fast-eCOLD-PCR expands the versatility of COLD-PCR and enables high-throughput enrichment of low-level mutant alleles over multiple sequences in a single tube.
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Affiliation(s)
- Elena Castellanos-Rizaldos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Coren Audrey Milbury
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - G. Mike Makrigiorgos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Medical Physics and Biophysics, Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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191
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Goel A, Boland CR. Epigenetics of colorectal cancer. Gastroenterology 2012; 143:1442-1460.e1. [PMID: 23000599 PMCID: PMC3611241 DOI: 10.1053/j.gastro.2012.09.032] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 09/04/2012] [Accepted: 09/13/2012] [Indexed: 12/18/2022]
Abstract
In the early years of the molecular biology revolution, cancer research was mainly focused on genetic changes (ie, those that altered DNA sequences). Although this has been extremely useful as our understanding of the pathogenesis and biology of cancer has grown and matured, there is another realm in tumor development that does not involve changing the sequence of cellular DNA. This field is called "epigenetics" and broadly encompasses changes in the methylation of cytosines in DNA, changes in histone and chromatin structure, and alterations in the expression of microRNAs, which control the stability of many messenger RNAs and serve as "master regulators" of gene expression. This review focuses on the epigenetics of colorectal cancer and illustrates the impact epigenetics has had on this field.
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Affiliation(s)
- Ajay Goel
- Gastrointestinal Cancer Research Laboratory, Division of Gastroenterology, Department of Internal Medicine, Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, Texas, USA.
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192
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Genome-scale discovery of DNA-methylation biomarkers for blood-based detection of colorectal cancer. PLoS One 2012; 7:e50266. [PMID: 23209692 PMCID: PMC3508917 DOI: 10.1371/journal.pone.0050266] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/17/2012] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND There is an increasing demand for accurate biomarkers for early non-invasive colorectal cancer detection. We employed a genome-scale marker discovery method to identify and verify candidate DNA methylation biomarkers for blood-based detection of colorectal cancer. METHODOLOGY/PRINCIPAL FINDINGS We used DNA methylation data from 711 colorectal tumors, 53 matched adjacent-normal colonic tissue samples, 286 healthy blood samples and 4,201 tumor samples of 15 different cancer types. DNA methylation data were generated by the Illumina Infinium HumanMethylation27 and the HumanMethylation450 platforms, which determine the methylation status of 27,578 and 482,421 CpG sites respectively. We first performed a multistep marker selection to identify candidate markers with high methylation across all colorectal tumors while harboring low methylation in healthy samples and other cancer types. We then used pre-therapeutic plasma and serum samples from 107 colorectal cancer patients and 98 controls without colorectal cancer, confirmed by colonoscopy, to verify candidate markers. We selected two markers for further evaluation: methylated THBD (THBD-M) and methylated C9orf50 (C9orf50-M). When tested on clinical plasma and serum samples these markers outperformed carcinoembryonic antigen (CEA) serum measurement and resulted in a high sensitive and specific test performance for early colorectal cancer detection. CONCLUSIONS/SIGNIFICANCE Our systematic marker discovery and verification study for blood-based DNA methylation markers resulted in two novel colorectal cancer biomarkers, THBD-M and C9orf50-M. THBD-M in particular showed promising performance in clinical samples, justifying its further optimization and clinical testing.
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193
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Abstract
BACKGROUND Identifying an accurate, reliable, affordable, and acceptable noninvasive screening test for colorectal cancer (CRC) would greatly facilitate population screening. METHODS Published literature from 2000 through February 2012 on noninvasive CRC screening tests was identified, reviewed, and summarized. RESULTS The highest quality evidence for noninvasive screening exists for guaiac-based fecal occult blood tests (gFOBTs), for which the CRC-specific incidence and mortality reductions are modest. Fecal immunochemical tests (FITs) offer better sensitivity and comparable specificity. Cross-sectional studies comparing gFOBTs and FITs suggest that FITs provide higher detection of advanced neoplasia. Modeling studies favor FITs over gFOBTs with respect to effectiveness and cost-effectiveness. A myriad of studies report the performance of fecal-based and blood-based genetic and protein-based biomarkers; the studies differ in patient population assembled, marker selection, and assay methods. Several markers and panels of markers are promising, although nearly all studies focus on new markers and/or assay methods on small sets of referred patients rather than validating markers using optimal assays in a screening setting. CONCLUSION In the absence of long-term randomized trials, adoption of the noninvasive tests will require cross-sectional data on test characteristics obtained from the screening setting, where CRC prevalence is low and the full spectrum of colorectal findings exists, along with estimates of cumulative risks, benefits, and cost-effectiveness. Test adoption will ultimately depend on test characteristics, availability, affordability, and user appeal. There is no noninvasive substitute for the currently recommended screening tests. FITs should replace gFOBTs wherever gFOBTs are used for screening.
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Affiliation(s)
- Thomas F Imperiale
- Indiana University School of Medicine, Regenstrief Institute, Inc. and Richard L. Roudebush VA Medical Center, Indianapolis, Indiana 46202, USA.
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194
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Pedersen JW, Gentry-Maharaj A, Fourkala EO, Dawnay A, Burnell M, Zaikin A, Pedersen AE, Jacobs I, Menon U, Wandall HH. Early detection of cancer in the general population: a blinded case-control study of p53 autoantibodies in colorectal cancer. Br J Cancer 2012; 108:107-14. [PMID: 23169294 PMCID: PMC3553520 DOI: 10.1038/bjc.2012.517] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Recent reports from cancer screening trials in high-risk populations suggest that autoantibodies can be detected before clinical diagnosis. However, there is minimal data on the role of autoantibody signatures in cancer screening in the general population. Methods: Informative p53 peptides were identified in sera from patients with colorectal cancer using an autoantibody microarray with 15-mer overlapping peptides covering the complete p53 sequence. The selected peptides were evaluated in a blinded case–control study using stored serum from the multimodal arm of the United Kingdom Collaborative Trial of Ovarian Cancer Screening where women gave annual blood samples. Cases were postmenopausal women who developed colorectal cancer following recruitment, with 2 or more serum samples preceding diagnosis. Controls were age-matched women with no history of cancer. Results: The 50 640 women randomised to the multimodal group were followed up for a median of 6.8 (inter-quartile range 5.9–8.4) years. Colorectal cancer notification was received in 101 women with serial samples of whom 97 (297 samples) had given consent for secondary studies. They were matched 1 : 1 with 97 controls (296 serial samples). The four most informative peptides identified 25.8% of colorectal cancer patients with a specificity of 95%. The median lead time was 1.4 (range 0.12–3.8) years before clinical diagnosis. Conclusion: Our findings suggest that in the general population, autoantibody signatures are detectable during preclinical disease and may be of value in cancer screening. In colorectal cancer screening in particular, where the current need is to improve compliance, it suggests that p53 autoantibodies may contribute towards risk stratification.
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Affiliation(s)
- J W Pedersen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N, DK-2200, Denmark
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195
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The expanding scope of DNA sequencing. Nat Biotechnol 2012; 30:1084-94. [PMID: 23138308 DOI: 10.1038/nbt.2421] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 10/15/2012] [Indexed: 01/04/2023]
Abstract
In just seven years, next-generation technologies have reduced the cost and increased the speed of DNA sequencing by four orders of magnitude, and experiments requiring many millions of sequencing reads are now routine. In research, sequencing is being applied not only to assemble genomes and to investigate the genetic basis of human disease, but also to explore myriad phenomena in organismic and cellular biology. In the clinic, the utility of sequence data is being intensively evaluated in diverse contexts, including reproductive medicine, oncology and infectious disease. A recurrent theme in the development of new sequencing applications is the creative 'recombination' of existing experimental building blocks. However, there remain many potentially high-impact applications of next-generation DNA sequencing that are not yet fully realized.
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196
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Moinova H, Leidner RS, Ravi L, Lutterbaugh J, Barnholtz-Sloan JS, Chen Y, Chak A, Markowitz SD, Willis JE. Vimentin in Upper Gastrointestinal Pathologies—Response. Cancer Epidemiol Biomarkers Prev 2012. [DOI: 10.1158/1055-9965.epi-12-0952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Helen Moinova
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
| | - Rom S. Leidner
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
| | - Lakshmeswari Ravi
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
| | - James Lutterbaugh
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
| | - Jill S. Barnholtz-Sloan
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
| | - Yanwen Chen
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
| | - Amitabh Chak
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
| | - Sanford D. Markowitz
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
| | - Joseph E. Willis
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
- Authors' Affiliations: Departments of 1Medicine, 2Pathology, and 3Case Comprehensive Cancer Center, Case Western Reserve University, and 4Case Medical Center, Cleveland, Ohio
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197
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Olkhov-Mitsel E, Bapat B. Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers. Cancer Med 2012; 1:237-60. [PMID: 23342273 PMCID: PMC3544446 DOI: 10.1002/cam4.22] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 06/29/2012] [Accepted: 07/02/2012] [Indexed: 12/13/2022] Open
Abstract
DNA methylation, consisting of the addition of a methyl group at the fifth-position of cytosine in a CpG dinucleotide, is one of the most well-studied epigenetic mechanisms in mammals with important functions in normal and disease biology. Disease-specific aberrant DNA methylation is a well-recognized hallmark of many complex diseases. Accordingly, various studies have focused on characterizing unique DNA methylation marks associated with distinct stages of disease development as they may serve as useful biomarkers for diagnosis, prognosis, prediction of response to therapy, or disease monitoring. Recently, novel CpG dinucleotide modifications with potential regulatory roles such as 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine have been described. These potential epigenetic marks cannot be distinguished from 5-methylcytosine by many current strategies and may potentially compromise assessment and interpretation of methylation data. A large number of strategies have been described for the discovery and validation of DNA methylation-based biomarkers, each with its own advantages and limitations. These strategies can be classified into three main categories: restriction enzyme digestion, affinity-based analysis, and bisulfite modification. In general, candidate biomarkers are discovered using large-scale, genome-wide, methylation sequencing, and/or microarray-based profiling strategies. Following discovery, biomarker performance is validated in large independent cohorts using highly targeted locus-specific assays. There are still many challenges to the effective implementation of DNA methylation-based biomarkers. Emerging innovative methylation and hydroxymethylation detection strategies are focused on addressing these gaps in the field of epigenetics. The development of DNA methylation- and hydroxymethylation-based biomarkers is an exciting and rapidly evolving area of research that holds promise for potential applications in diverse clinical settings.
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Affiliation(s)
- Ekaterina Olkhov-Mitsel
- Samuel Lunenfeld Research Institute, Mount Sinai HospitalToronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, Ontario, Canada
| | - Bharati Bapat
- Samuel Lunenfeld Research Institute, Mount Sinai HospitalToronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, Ontario, Canada
- Department of Pathology, University Health Network, University of TorontoToronto, Ontario, Canada
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Liu S. Epigenetics advancing personalized nanomedicine in cancer therapy. Adv Drug Deliv Rev 2012; 64:1532-43. [PMID: 22921595 DOI: 10.1016/j.addr.2012.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/27/2012] [Accepted: 08/09/2012] [Indexed: 02/06/2023]
Abstract
Personalized medicine aims to deliver the right drug to a right patient at the right time. It offers unique opportunities to integrate new technologies and concepts to disease prognosis, diagnosis and therapeutics. While selective personalized therapies are conceptually impressive, the majority of cancer therapies have dismal outcome. Such therapeutic failure could result from no response, drug resistance, disease relapse or severe side effect from improper drug delivery. Nanomedicine, the application of nanotechnology in medicine, has a potential to advance the identification of diagnostic and prognostic biomarkers and the delivery of right drug to disease sites. Epigenetic aberrations dynamically contribute to cancer pathogenesis. Given the individualized traits of epigenetic biomarkers, epigenetic considerations would significantly refine personalized nanomedicine. This review aims to dissect the interface of personalized medicine with nanomedicine and epigenetics. I will outline the progress and highlight challenges and areas that can be further explored perfecting the personalized health care.
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Promoter CpG island methylation in colorectal cancer:. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Draht MXG, Riedl RR, Niessen H, Carvalho B, Meijer GA, Herman JG, van Engeland M, Melotte V, Smits KM. Promoter CpG island methylation markers in colorectal cancer: the road ahead. Epigenomics 2012; 4:179-94. [PMID: 22449189 DOI: 10.2217/epi.12.9] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite increasing knowledge on the biology, detection and treatment of colorectal cancer (CRC), the disease is still a major health problem. Hypermethylation of promoter regions of genes has been studied extensively as a contributor in CRC carcinogenesis. In addition, it is the topic of many studies focusing on biomarkers for the early detection, prediction of prognosis and treatment outcome. Methylation markers may be preferred over current screening and test methods as they are stable and easy to detect. However, almost no methylation marker is currently being used in clinical practice, often due to a lack of sensitivity, specificity, or validation of the results. This review summarizes the current knowledge of hypermethylation biomarkers for CRC detection, progression and treatment outcome.
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Affiliation(s)
- Muriel X G Draht
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
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