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Noehammer C, Pulverer W, Hassler MR, Hofner M, Wielscher M, Vierlinger K, Liloglou T, McCarthy D, Jensen TJ, Nygren A, Gohlke H, Trooskens G, Braspenning M, Van Criekinge W, Egger G, Weinhaeusel A. Strategies for validation and testing of DNA methylation biomarkers. Epigenomics 2015; 6:603-22. [PMID: 25531255 DOI: 10.2217/epi.14.43] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and therapeutic response prediction. Although the advent of genome-wide DNA methylation profiling in primary disease tissue has provided a manifold resource for biomarker development, only a tiny fraction of DNA methylation-based assays have reached clinical testing. Here, we provide a critical overview of different analytical methods that are suitable for biomarker validation, including general study design considerations, which might help to streamline epigenetic marker development. Furthermore, we highlight some of the recent marker validation studies and established markers that are currently commercially available for assisting in clinical management of different cancers.
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Affiliation(s)
- Christa Noehammer
- Health & Environment Department, Molecular Diagnostics, AIT Austrian Institute of Technology, Vienna, Austria
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202
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Li Y, Song L, Gong Y, He B. Detection of colorectal cancer by DNA methylation biomarker SEPT9: past, present and future. Biomark Med 2015; 8:755-69. [PMID: 25123042 DOI: 10.2217/bmm.14.8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer has become the third most common cancer in the world. Early diagnosis and treatment can significantly reduce colorectal cancer mortality. The current routinely used fecal-based screening methods do not provide satisfactory sensitivity. Although colonoscopy provides macroscopic diagnosis, the compliance is low due to its inconvenience and complications. Hence, the development of new screening methods is needed urgently. Peripheral blood SEPT9 gene methylation assay has become a potential option with promising future for early detection and screening of colorectal cancer. It is shown to be convenient, reliable with good compliance by several clinical trials. This article will review the theoretical foundation and development of the assay, focusing on its clinical trials, comparing it with other screening methods and discussing its future applications.
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Affiliation(s)
- Yuemin Li
- The Chinese PLA 309 Hospital (General Hospital of the PLA General Staff Headquarters), No. 17, HeiShanHu Road, HaiDian District, Beijing 100091, PR China
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203
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Roperch JP, Benzekri K, Mansour H, Incitti R. Improved amplification efficiency on stool samples by addition of spermidine and its use for non-invasive detection of colorectal cancer. BMC Biotechnol 2015; 15:41. [PMID: 26022272 PMCID: PMC4446959 DOI: 10.1186/s12896-015-0148-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 04/22/2015] [Indexed: 02/06/2023] Open
Abstract
Background Using quantitative methylation-specific PCR (QM-MSP) is a promising method for colorectal cancer (CRC) diagnosis from stool samples. Difficulty in eliminating PCR inhibitors of this body fluid has been extensively reported. Here, spermidine is presented as PCR facilitator for the detection of stool DNA methylation biomarkers using QM-MSP. We examined its effectiveness with NPY, PENK and WIF1, three biomarkers which we have previously shown to be of relevance to CRC. Results We determined an optimal window for the amplification of the albumin (Alb) gene (100 ng of bisulfite-treated stool DNA added of 1 mM spermidine) at which we report that spermidine acts as a PCR facilitator (AE = 1680%) for SG RT-PCR. We show that the amplification of methylated PENK, NPY and WIF1 is considerably facilitated by QM-MSP as measured by an increase of CMI (Cumulative Methylation Index, i.e. the sum of the three methylation values) by a factor of 1.5 to 23 fold in individual samples, and of 10 fold in a pool of five samples. Conclusions We contend that spermidine greatly reduces the problems of PCR inhibition in stool samples. This observed feature, after validation on a larger sampling, could be used in the development of stool-based CRC diagnosis tests. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0148-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jean-Pierre Roperch
- Profilome, Paris Biotech 24 rue du Faubourg St Jacques, Paris, 75014, France. .,OncoDiag, Agoranov 96 Bis, Boulevard Raspail, Paris, 75006, France.
| | - Karim Benzekri
- Centre d'Investigation Clinique (CIC), Henri Mondor Hospital, Créteil, France.
| | - Hicham Mansour
- King Abdullah University of Science and Technology (KAUST), Bioscience Core Laboratory Research Department, Thuwal, 23955-6900, Saudi Arabia.
| | - Roberto Incitti
- King Abdullah University of Science and Technology (KAUST), Computational Biology Research Center, Thuwal, 23955-6900, Saudi Arabia.
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204
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Colorectal Cancer Biomarkers: Where Are We Now? BIOMED RESEARCH INTERNATIONAL 2015; 2015:149014. [PMID: 26106599 PMCID: PMC4461726 DOI: 10.1155/2015/149014] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/19/2015] [Indexed: 12/18/2022]
Abstract
Colorectal cancer is one of the major causes of cancer-related death in the Western world. Patient survival is highly dependent on the tumor stage at the time of diagnosis. Reduced sensitivity to chemotherapy is still a major obstacle in effective treatment of advanced disease. Due to the fact that colorectal cancer is mostly asymptomatic until it progresses to advanced stages, the implementation of screening programs aimed at early detection is essential to reduce incidence and mortality rates. Current screening and diagnostic methods range from semi-invasive procedures such as colonoscopy to noninvasive stool-based tests. The combination of the absence of symptoms, the semi-invasive nature of currently used methods, and the suboptimal accuracy of fecal blood tests results in colorectal cancer diagnosis at advanced stages in a significant number of individuals. Alterations in gene expression leading to colorectal carcinogenesis are reflected in dysregulated levels of nucleic acids and proteins, which can be used for the development of novel, minimally invasive molecular biomarkers. The purpose of this review is to discuss the commercially available colorectal cancer molecular diagnostic methods as well as to highlight some of the new candidate predictive and prognostic molecular markers for tumor, stool, and blood samples.
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205
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Kok-Sin T, Mokhtar NM, Ali Hassan NZ, Sagap I, Mohamed Rose I, Harun R, Jamal R. Identification of diagnostic markers in colorectal cancer via integrative epigenomics and genomics data. Oncol Rep 2015; 34:22-32. [PMID: 25997610 PMCID: PMC4484611 DOI: 10.3892/or.2015.3993] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/30/2015] [Indexed: 12/12/2022] Open
Abstract
Apart from genetic mutations, epigenetic alteration is a common phenomenon that contributes to neoplastic transformation in colorectal cancer. Transcriptional silencing of tumor-suppressor genes without changes in the DNA sequence is explained by the existence of promoter hypermethylation. To test this hypothesis, we integrated the epigenome and transcriptome data from a similar set of colorectal tissue samples. Methylation profiling was performed using the Illumina InfiniumHumanMethylation27 BeadChip on 55 paired cancer and adjacent normal epithelial cells. Fifteen of the 55 paired tissues were used for gene expression profiling using the Affymetrix GeneChip Human Gene 1.0 ST array. Validation was carried out on 150 colorectal tissues using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) technique. PCA and supervised hierarchical clustering in the two microarray datasets showed good separation between cancer and normal samples. Significant genes from the two analyses were obtained based on a ≥2-fold change and a false discovery rate (FDR) p-value of <0.05. We identified 1,081 differentially hypermethylated CpG sites and 36 hypomethylated CpG sites. We also found 709 upregulated and 699 downregulated genes from the gene expression profiling. A comparison of the two datasets revealed 32 overlapping genes with 27 being hypermethylated with downregulated expression and 4 hypermethylated with upregulated expression. One gene was found to be hypomethylated and downregulated. The most enriched molecular pathway identified was cell adhesion molecules that involved 4 overlapped genes, JAM2, NCAM1, ITGA8 and CNTN1. In the present study, we successfully identified a group of genes that showed methylation and gene expression changes in well-defined colorectal cancer tissues with high purity. The integrated analysis gives additional insight regarding the regulation of colorectal cancer-associated genes and their underlying mechanisms that contribute to colorectal carcinogenesis.
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Affiliation(s)
- Teow Kok-Sin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Norfilza Mohd Mokhtar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nur Zarina Ali Hassan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Ismail Sagap
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Isa Mohamed Rose
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Roslan Harun
- Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Guzzetta AA, Pisanic Ii TR, Sharma P, Yi JM, Stark A, Wang TH, Ahuja N. The promise of methylation on beads for cancer detection and treatment. Expert Rev Mol Diagn 2015; 14:845-52. [PMID: 25136840 DOI: 10.1586/14737159.2014.943665] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Despite numerous technical hurdles, the realization of true personalized medicine is becoming a progressive reality for the future of patient care. With the development of new techniques and tools to measure the genetic signature of tumors, biomarkers are increasingly being used to detect occult tumors, determine the choice of treatment and predict outcomes. Methylation of CpG islands at the promoter region of genes is a particularly exciting biomarker as it is cancer-specific. Older methods to detect methylation were cumbersome, operator-dependent and required large amounts of DNA. However, a newer technique called methylation on beads has resulted in a more uniform, streamlined and efficient assay. Furthermore, methylation on beads permits the extraction and processing of miniscule amounts of methylated tumor DNA in the peripheral blood. Such a technique may aid in the clinical detection and treatment of cancers in the future.
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207
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Jin P, Kang Q, Wang X, Yang L, Yu Y, Li N, He YQ, Han X, Hang J, Zhang J, Song L, Han Y, Sheng JQ. Performance of a second-generation methylated SEPT9 test in detecting colorectal neoplasm. J Gastroenterol Hepatol 2015; 30:830-3. [PMID: 25471329 DOI: 10.1111/jgh.12855] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/17/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIM Screening and early detection reduces mortality due to colorectal cancer (CRC). Methylated Septin 9 (SEPT9) is a new blood-based biomarker for CRC. We evaluated the performance of the second-generation SEPT9 assay for the detection of colorectal neoplasm, and compared it with fecal immunochemical test (FIT). METHODS A total of 135 patients with CRC, 169 with adenomatous polyps, 81 with hyperplastic polyps, and 91 healthy controls were included. The clinical status of all subjects was verified by colonoscopy. In all patients, peripheral blood samples were taken for SEPT9 testing using Epi proColon 2.0 test. For 177 patients, both SEPT9 and FIT were performed. RESULTS The sensitivity and specificity of SEPT9 for CRC were 74.8% (95% confidence interval [CI]: 67.0-81.6%) and 87.4% (vs non-CRC, 95% CI: 83.5-90.6%), respectively. SEPT9 was positive in 66.7% of stage I, 82.6% of stage II, 84.1% of stage III, and 100% of stage IV CRCs. The sensitivity of SEPT9 for advanced adenomas was 27.4% (95% CI: 18.7-37.6%). The sensitivity and specificity of FIT for CRC was 58.0% (95% CI: 46.1-69.2%) and 82.4% (95% CI: 74.4-88.7%), respectively. SEPT9 showed better performance in CRC detection than FIT, but similar among advanced adenomas. CONCLUSIONS With improved performance characteristics in detecting CRC, the second-generation SEPT9 assay could play an important role in CRC screening and early detection.
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Affiliation(s)
- Peng Jin
- Third Military Medical University, Chongqing, China; Department of Gastroenterology, Beijing Military General Hospital, Beijing, China
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208
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Andresen K, Boberg KM, Vedeld HM, Honne H, Jebsen P, Hektoen M, Wadsworth CA, Clausen OP, Lundin KE, Paulsen V, Foss A, Mathisen Ø, Aabakken L, Schrumpf E, Lothe RA, Lind GE. Four DNA methylation biomarkers in biliary brush samples accurately identify the presence of cholangiocarcinoma. Hepatology 2015; 61:1651-9. [PMID: 25644509 PMCID: PMC4832263 DOI: 10.1002/hep.27707] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 01/12/2015] [Indexed: 12/19/2022]
Abstract
UNLABELLED Early detection of the highly aggressive malignancy cholangiocarcinoma (CCA) remains a challenge but has the potential to render the tumor curable by surgical removal. This study evaluates a biomarker panel for the diagnosis of CCA by DNA methylation analyses of biliary brush samples. The methylation status of 13 candidate genes (CDO1, CNRIP1, DCLK1, FBN1, INA, MAL, SEPT9, SFRP1, SNCA, SPG20, TMEFF2, VIM, and ZSCAN18) was investigated in 93 tissue samples (39 CCAs and 54 nonmalignant controls) using quantitative methylation-specific polymerase chain reaction. The 13 genes were further analyzed in a test series of biliary brush samples (15 CCAs and 20 nonmalignant primary sclerosing cholangitis controls), and the methylation status of the four best performing markers was validated (34 CCAs and 34 primary sclerosing cholangitis controls). Receiver operating characteristic curve analyses were used to evaluate the performance of individual biomarkers and the combination of biomarkers. The 13 candidate genes displayed a methylation frequency of 26%-82% in tissue samples. The four best-performing genes (CDO1, CNRIP1, SEPT9, and VIM) displayed individual methylation frequencies of 45%-77% in biliary brushes from CCA patients. Across the test and validation biliary brush series, this four-gene biomarker panel achieved a sensitivity of 85% and a specificity of 98%, with an area under the receiver operating characteristic curve of 0.944. CONCLUSION We report a straightforward biomarker assay with high sensitivity and specificity for CCA, outperforming standard brush cytology, and suggest that the biomarker panel, potentially in combination with cytological evaluation, may improve CCA detection, particularly among primary sclerosing cholangitis patients.
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Affiliation(s)
- Kim Andresen
- Department of Molecular OncologyInstitute for Cancer ResearchOslo University Hospital–The Norwegian Radium HospitalOsloNorway,Centre for Cancer Biomedicine, Faculty of MedicineUniversity of OsloOsloNorway,Norwegian PSC Research Center, Division of Cancer, Surgery and TransplantationOslo University HospitalOsloNorway
| | - Kirsten Muri Boberg
- Norwegian PSC Research Center, Division of Cancer, Surgery and TransplantationOslo University HospitalOsloNorway,Institute for Clinical MedicineUniversity of OsloOsloNorway
| | - Hege Marie Vedeld
- Department of Molecular OncologyInstitute for Cancer ResearchOslo University Hospital–The Norwegian Radium HospitalOsloNorway,Centre for Cancer Biomedicine, Faculty of MedicineUniversity of OsloOsloNorway
| | - Hilde Honne
- Department of Molecular OncologyInstitute for Cancer ResearchOslo University Hospital–The Norwegian Radium HospitalOsloNorway,Centre for Cancer Biomedicine, Faculty of MedicineUniversity of OsloOsloNorway
| | - Peter Jebsen
- Department of Pathology, Division of Diagnostics and InterventionOslo University HospitalOsloNorway
| | - Merete Hektoen
- Department of Molecular OncologyInstitute for Cancer ResearchOslo University Hospital–The Norwegian Radium HospitalOsloNorway,Centre for Cancer Biomedicine, Faculty of MedicineUniversity of OsloOsloNorway
| | - Christopher A. Wadsworth
- Hepatology and Gastroenterology Section, Division of Diabetes, Endocrinology and Metabolism, Department of MedicineImperial College LondonLondonUK
| | - Ole Petter Clausen
- Department of Pathology, Division of Diagnostics and InterventionOslo University HospitalOsloNorway
| | - Knut E.A. Lundin
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery, and TransplantationOslo University HospitalOsloNorway
| | - Vemund Paulsen
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery, and TransplantationOslo University HospitalOsloNorway
| | - Aksel Foss
- Institute for Clinical MedicineUniversity of OsloOsloNorway,Section for Transplantation Surgery, Department of Transplantation Medicine, Division of Cancer Medicine, Surgery, and TransplantationOslo University HospitalOsloNorway
| | - Øystein Mathisen
- Section for Hepatopancreatic and Biliary Surgery, Department of Gastrointestinal Surgery, Division of Cancer, Surgery, and TransplantationOslo University HospitalOsloNorway
| | - Lars Aabakken
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery, and TransplantationOslo University HospitalOsloNorway,Institute for Clinical MedicineUniversity of OsloOsloNorway
| | - Erik Schrumpf
- Norwegian PSC Research Center, Division of Cancer, Surgery and TransplantationOslo University HospitalOsloNorway,Institute for Clinical MedicineUniversity of OsloOsloNorway
| | - Ragnhild A. Lothe
- Department of Molecular OncologyInstitute for Cancer ResearchOslo University Hospital–The Norwegian Radium HospitalOsloNorway,Centre for Cancer Biomedicine, Faculty of MedicineUniversity of OsloOsloNorway
| | - Guro E. Lind
- Department of Molecular OncologyInstitute for Cancer ResearchOslo University Hospital–The Norwegian Radium HospitalOsloNorway,Centre for Cancer Biomedicine, Faculty of MedicineUniversity of OsloOsloNorway
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A two-gene blood test for methylated DNA sensitive for colorectal cancer. PLoS One 2015; 10:e0125041. [PMID: 25928810 PMCID: PMC4416022 DOI: 10.1371/journal.pone.0125041] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/08/2015] [Indexed: 02/06/2023] Open
Abstract
Background Specific genes are methylated with high frequency in colorectal neoplasia, and may leak into blood. Detection of multiple methylated DNA biomarkers in blood may improve assay sensitivity for colorectal cancer (CRC) relative to a single marker. We undertook a case-control study evaluating the presence of two methylation DNA markers, BCAT1 and IKZF1, in circulation to determine if they were complementary for detection of CRC. Methods Methylation-specific PCR assays were developed to measure the level of methylated BCAT1 and IKZF1 in DNA extracted from plasma obtained from colonoscopy-confirmed 144 healthy controls and 74 CRC cases. Results DNA yields ranged from 2 to 730 ng/mL plasma (mean 18.6ng/mL; 95% CI 11-26 ng/mL) and did not correlate with gender, age or CRC status. Methylated BCAT1 and IKZF1 DNA were detected in respectively 48 (65%) and 50 (68%) of the 74 cancers. In contrast, only 5 (4%) and 7 (5%) controls were positive for BCAT1 and IKZF1 DNA methylation, respectively. A two-gene classifier model (“either or” rule) improved segregation of CRC from controls, with 57 of 74 cancers (77%) compared to only 11 of 144 (7.6%) controls being positive for BCAT1 and/or IKZF1 DNA methylation. Increasing levels of methylated DNA were observed as CRC stage progressed. Conclusions Detection of methylated BCAT1 and/or IKZF1 DNA in plasma may have clinical application as a novel blood test for CRC. Combining the results from the two methylation-specific PCR assays improved CRC detection with minimal change in specificity. Further validation of this two-gene blood test with a view to application in screening is now indicated.
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210
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Yi JM, Kim TO. Epigenetic alterations in inflammatory bowel disease and cancer. Intest Res 2015; 13:112-21. [PMID: 25931995 PMCID: PMC4414752 DOI: 10.5217/ir.2015.13.2.112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 12/15/2022] Open
Abstract
Overwhelming evidences supports the idea that inflammatory bowel disease (IBD) is caused by a complex interplay between genetic alterations of multiple genes and an aberrant interaction with environmental factors. There is growing evidence that epigenetic factors can play a significant part in the pathogenesis of IBD. Significant effort has been invested in uncovering genetic and epigenetic factors, which may increase the risk of IBD, but progress has been slow, and few IBD-specific factors have been detected so far. It has been known for decades that DNA methylation is the most well studied epigenetic modification, and analysis of DNA methylation is leading to a new generation of cancer biomarkers. Therefore, in this review, we summarize the role of DNA methylation alteration in IBD pathogenesis, and discuss specific genes or genetic loci using recent molecular technology advances. Here, we suggest that DNA methylation should be studied in depth to understand the molecular pathways of IBD pathogenesis, and discuss epigenetic studies of IBD that may have a significant impact on the field of IBD research.
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Affiliation(s)
- Joo Mi Yi
- Research Institute, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan, Korea
| | - Tae Oh Kim
- Department of Internal Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea
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211
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Warton K, Samimi G. Methylation of cell-free circulating DNA in the diagnosis of cancer. Front Mol Biosci 2015; 2:13. [PMID: 25988180 PMCID: PMC4428375 DOI: 10.3389/fmolb.2015.00013] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/07/2015] [Indexed: 01/04/2023] Open
Abstract
A range of molecular alterations found in tumor cells, such as DNA mutations and DNA methylation, is reflected in cell-free circulating DNA (circDNA) released from the tumor into the blood, thereby making circDNA an ideal candidate for the basis of a blood-based cancer diagnosis test. In many cancer types, mutations driving tumor development and progression are present in a wide range of oncogenes and tumor suppressor genes. However, even when a gene is consistently mutated in a particular cancer, the mutations can be spread over very large regions of its sequence, making evaluation difficult. This diversity of sequence changes in tumor DNA presents a challenge for the development of blood tests based on DNA mutations for cancer diagnosis. Unlike mutations, DNA methylation that can be consistently measured, as it tends to occur in specific regions of the DNA called CpG islands. Since DNA methylation is reflected within circDNA, detection of tumor-specific DNA methylation in patient plasma is a feasible approach for the development of a blood-based test. Aberrant circDNA methylation has been described in most cancer types and is actively being investigated for clinical applications. A commercial blood test for colorectal cancer based on the methylation of the SEPT9 promoter region in circDNA is under review for approval by the Federal Drug Administration (FDA) for clinical use. In this paper, we review the state of research in circDNA methylation as an application for blood-based diagnostic tests in colorectal, breast, lung, pancreatic and ovarian cancers, and we consider some of the future directions and challenges in this field. There are a number of potential circDNA biomarkers currently under investigation, and experience with SEPT9 shows that the time to clinical translation can be relatively rapid, supporting the promise of circDNA as a biomarker.
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Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Goli Samimi
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
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212
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Marzese DM, Hoon DS. Emerging technologies for studying DNA methylation for the molecular diagnosis of cancer. Expert Rev Mol Diagn 2015; 15:647-64. [PMID: 25797072 DOI: 10.1586/14737159.2015.1027194] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is an epigenetic mechanism that plays a key role in regulating gene expression and other functions. Although this modification is seen in different sequence contexts, the most frequently detected DNA methylation in mammals involves cytosine-guanine dinucleotides. Pathological alterations in DNA methylation patterns are described in a variety of human diseases, including cancer. Unlike genetic changes, DNA methylation is heavily influenced by subtle modifications in the cellular microenvironment. In all cancers, aberrant DNA methylation is involved in the alteration of a large number of oncological pathways with relevant theranostic utility. Several technologies for DNA methylation mapping have been developed recently and successfully applied in cancer studies. The scope of these technologies varies from assessing a single cytosine-guanine locus to genome-wide distribution of DNA methylation. Here, we review the strengths and weaknesses of these approaches in the context of clinical utility for the molecular diagnosis of human cancers.
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Affiliation(s)
- Diego M Marzese
- Department of Molecular Oncology, Saint John's Health Center, John Wayne Cancer Institute, 2200 Santa Monica Blvd, Santa Monica, CA 90404, USA
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213
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Zhang X, Song YF, Lu HN, Wang DP, Zhang XS, Huang SL, Sun BL, Huang ZG. Combined detection of plasma GATA5 and SFRP2 methylation is a valid noninvasive biomarker for colorectal cancer and adenomas. World J Gastroenterol 2015; 21:2629-2637. [PMID: 25759530 PMCID: PMC4351212 DOI: 10.3748/wjg.v21.i9.2629] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/31/2014] [Accepted: 12/01/2014] [Indexed: 02/07/2023] Open
Abstract
AIM: To investigate GATA5, SFRP2, and ITGA4 methylation in plasma DNA as noninvasive biomarkers for colorectal cancer (CRC) or adenomas.
METHODS: There were 57 CRC patients, 30 adenomas patients, and 47 control patients enrolled in this study. Methylation-specific polymerase chain reaction was used to determine the promoter methylation status of GATA5, SFRP2, and ITGA4 genes in plasma DNA, and their association with clinical outcome in CRC. The predictive ability of GATA5, SFRP2, and ITGA4 methylation, individually or in combination, to detect CRC or adenomas was further analyzed.
RESULTS: Hypermethylated GATA5 was detected in plasma in 61.4% (35/57) of CRC cases, 43.33% (13/30) of adenoma cases, and 21.28% (10/47) of control cases. The hypermethylation of SFRP2 was detected in 54.39% (31/57), 40.00% (12/30), and 27.66% (13/47) in plasma samples from CRC, adenomas, and controls, respectively. ITGA4 methylation was detected in 36.84% (21/57) of plasma samples of CRC patients and in 30.00% (9/30) of plasma samples from patients with colorectal adenomas, and the specificity of this individual biomarker was 80.85% (9/47). Moreover, GATA5 methylation in the plasma was significantly correlated with larger tumor size (P = 0.019), differentiation status (P = 0.038), TNM stage (P = 0.008), and lymph node metastasis (P = 0.008). SFRP2 and ITGA4 methylation in plasma significantly correlated with differentiation status (SFRP2, P = 0.012; ITGA4, P = 0.007), TNM stage (SFRP2, P = 0.034; ITGA4, P = 0.021), and lymph node metastasis (SFRP2, P = 0.034; ITGA4, P = 0.021). From the perspective of predictive power and cost-performance, using GATA5 and SFRP2 together as methylation markers seemed the most favorable predictor for CRC (OR = 8.06; 95%CI: 2.54-25.5; P < 0.01) and adenomas (OR = 3.35; 95%CI: 1.29-8.71; P = 0.012).
CONCLUSION: A combination of GATA5 and SFRP2 methylation could be promising as a marker for the detection and diagnosis of CRC and adenomas.
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214
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Bresalier RS, Kopetz S, Brenner DE. Blood-based tests for colorectal cancer screening: do they threaten the survival of the FIT test? Dig Dis Sci 2015; 60:664-71. [PMID: 25680874 DOI: 10.1007/s10620-015-3575-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 01/31/2015] [Indexed: 02/06/2023]
Abstract
Colorectal cancer is the second leading cause of cancer death in industrialized nations, accounting for 10% of the total cancer burden with an individual lifetime risk of ~6% in the USA (Siegel et al. in CA Cancer J Clin 62:9-29, 2014, American Cancer Society in Colorectal cancer facts and figures 2011-2013. American Cancer Society, Atlanta, 2011, Siegel et al. in CA Cancer J Clin 61:212-236, 2011). Although numerous screening methods have been incorporated into guidelines for colorectal cancer screening, no guideline includes a noninvasive blood-based test as a recommended option.
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Affiliation(s)
- Robert S Bresalier
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1466, Houston, TX, 77030, USA,
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Sun GP, Tang YX, Meng J, Liang GF, Zhang YW, Lu XB, Li XX. WITHDRAWN: SEPT9 DNA methylation as an early diagnostic marker in colorectal cancer. Cancer Genet 2015:S2210-7762(15)00026-5. [PMID: 25908231 DOI: 10.1016/j.cancergen.2015.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/22/2015] [Accepted: 02/17/2015] [Indexed: 11/18/2022]
Abstract
The publisher regrets that this article has been temporarily removed. A replacement will appear as soon as possible in which the reason for the removal of the article will be specified, or the article will be reinstated. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Gong-Ping Sun
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, P.R. China
| | - Yuan-Xin Tang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, P.R. China
| | - Jin Meng
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, P.R. China
| | - Gao-Feng Liang
- Department of Breast Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, P.R. China
| | - Yun-Wei Zhang
- Department of Breast Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, P.R. China
| | - Xiao-Bo Lu
- School of Public Health China Medical University, Shenyang, P.R. China
| | - Xiao-Xia Li
- Department of Breast Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, P.R. China
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216
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Vatandoost N, Ghanbari J, Mojaver M, Avan A, Ghayour-Mobarhan M, Nedaeinia R, Salehi R. Early detection of colorectal cancer: from conventional methods to novel biomarkers. J Cancer Res Clin Oncol 2015; 142:341-51. [PMID: 25687380 DOI: 10.1007/s00432-015-1928-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 01/23/2015] [Indexed: 02/06/2023]
Abstract
PURPOSE Colorectal cancer (CRC) is one of the major health problems worldwide and is often diagnosed at late stage. There is growing body of evidence in early detection of this disease with novel screening modalities to reduce compliance and increase specificity of available methods. The aim of current review is to give an overview on currently available screening methods (e.g., fecal occult blood testing (FOBT), flexible sigmoidoscopy, and colonoscopy), with their own merits and disadvantages, and new genetic/epigenetic/protein markers, as novel screening modalities. RESULT There are several serum and fecal biomarkers that can predict CRC and polyps. Overall sensitivities for detection by fecal DNA markers ranged from 53 to 87%, while a panel of serum protein markers provides a sensitivity/specificity up to 85% for CRC. In particular, DNA methylation markers (e.g., SEPT9, SFRP2, and ALX4), circulating microRNAs (e.g., microRNA21), SNPs in microRNAs binding site (e.g., rs4596 located within a target region of the predicted miR-518a-5p and miR-527), protein markers (e.g., carcinoembryonic antigen, N-methyltransferase), or microsatellites instability in tumors with deficient mismatch repair of some genes are among the most interesting and promising biomarkers. CONCLUSION Increasing evidence supports the use of combined fecal and serum biomarkers with sigmoidoscopy and colonoscopy screening in order to maximize the benefits and reduce the number of false-positive tests and patients undergoing invasive methods, which in turn could overcome the limitations of the current screening methods for early detection of CRC and adenomas.
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Affiliation(s)
- Nasimeh Vatandoost
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jahanafrooz Ghanbari
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahboobeh Mojaver
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Amir Avan
- Molecular Medicine Group, Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Ghayour-Mobarhan
- Biochemistry of Nutrition Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Nedaeinia
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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217
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Benton SC, Seaman HE, Halloran SP. Faecal occult blood testing for colorectal cancer screening: the past or the future. Curr Gastroenterol Rep 2015; 17:428. [PMID: 25673567 DOI: 10.1007/s11894-015-0428-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Screening for colorectal cancer (CRC) reduces CRC mortality; many countries have implemented population-based CRC screening programmes and many more are poised to do so. Whilst several different CRC screening modalities are available, choice will be influenced by cost, available resources (e.g. high-quality colonoscopy) and acceptability of the test by the invited population. For CRC screening, no screening test has so far surpassed the practicality, affordability and effectiveness of tests for the presence of blood in faeces (faecal occult blood tests, FOBt). The results of several large FOBt-based randomised controlled trials provide the best clinical evidence to support their use in population-based CRC screening. This review considers the current options for CRC screening and the future for FOBt.
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Affiliation(s)
- Sally C Benton
- NHS Bowel Cancer Screening Southern Programme Hub, 20 Priestley Road, Surrey Research Park, Guildford, Surrey, GU2 7YS, UK,
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218
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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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219
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Abstract
Colorectal cancer (CRC) is one of most common malignancies and a leading cause of cancer related deaths worldwide. Epigenetic change is an important mechanism of colorectal carcinogenesis. Accumulation of epigenetic changes was found in colorectal cancer and other tumors. Aberrant changes in DNA methylation, histone modification, imprinting, and noncoding RNAs were frequently found in human colorectal cancer. Epigenetic changes may serve as a diagnostic, prognostic, and chemo-sensitive marker. It also becomes a cancer preventive or therapeutic target in some circumstances.
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Affiliation(s)
- Wenji Yan
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853, China
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220
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Miozzo M, Vaira V, Sirchia SM. Epigenetic alterations in cancer and personalized cancer treatment. Future Oncol 2015; 11:333-48. [DOI: 10.2217/fon.14.237] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT Based on the pivotal importance of epigenetics for transcription regulation, it is not surprising that cancer is characterized by several epigenetic abnormalities. Conversely to genetic alterations, epigenetic changes are not permanent, thus represent opportunities for therapeutic strategies designed to reverse transcriptional abnormalities, and cancer is the first disease in which epigenetic therapies with chromatin remodeling agents were introduced. The role of miRNAs in gene regulation supports their potential as innovative therapeutic strategy. Recent evidences have proven that the environment can profoundly influence the epigenome: diet, smoking and alcohol consumption can negatively impact the expression profile. Given the plasticity of epigenetic marks, it is challenging the idea that the epigenetic alterations are ‘druggable’ sites using specific food components.
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Affiliation(s)
- Monica Miozzo
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy
| | - Valentina Vaira
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
- Istituto Nazionale di Genetica Molecolare ‘Romeo ed Enrica Invernizzi’, Integrative Biology Unit, Milano, Italy
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Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive tumor and the fourth common cause of cancer death in the Western world. The lack of effective therapeutic strategies is due to the late diagnosis of this disease. Methylation markers could improve early detection and help in the surveillance of PDAC after treatment. Analysis of hypermethylation in the tumor tissue might help to identify new therapeutic strategies and aid in the understanding of the pathophysiological changes occurring in pancreatic cancer. There are several methods for the detection of methylated events, but methylation-specific PCR (MSP-PCR) is the method of choice if a small number of genes will be tested in a larger set of patients samples. After isolation of the DNA by standard procedure, the DNA is then modified using sodium bisulfide.
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Affiliation(s)
- Christian Pilarsky
- Department of Surgery, Medizinische Fakultät Carl Gustav Carus, TU Dresden, Fetscherstr. 74, 01307, Dresden, Germany,
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222
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Melotte V, Yi JM, Lentjes MHFM, Smits KM, Van Neste L, Niessen HEC, Wouters KAD, Louwagie J, Schuebel KE, Herman JG, Baylin SB, van Criekinge W, Meijer GA, Ahuja N, van Engeland M. Spectrin repeat containing nuclear envelope 1 and forkhead box protein E1 are promising markers for the detection of colorectal cancer in blood. Cancer Prev Res (Phila) 2014; 8:157-64. [PMID: 25538088 DOI: 10.1158/1940-6207.capr-14-0198] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Identifying biomarkers in body fluids may improve the noninvasive detection of colorectal cancer. Previously, we identified N-Myc downstream-regulated gene 4 (NDRG4) and GATA binding protein 5 (GATA5) methylation as promising biomarkers for colorectal cancer in stool DNA. Here, we examined the utility of NDRG4, GATA5, and two additional markers [Forkhead box protein E1 (FOXE1) and spectrin repeat containing nuclear envelope 1 (SYNE1)] promoter methylation as biomarkers in plasma DNA. Quantitative methylation-specific PCR was performed on plasma DNA from 220 patients with colorectal cancer and 684 noncancer controls, divided in a training set and a test set. Receiver operating characteristic analysis was performed to measure the area under the curve of GATA5, NDRG4, SYNE1, and FOXE1 methylation. Functional assays were performed in SYNE1 and FOXE1 stably transfected cell lines. The sensitivity of NDRG4, GATA5, FOXE1, and SYNE1 methylation in all stages of colorectal cancer (154 cases, 444 controls) was 27% [95% confidence interval (CI), 20%-34%), 18% (95% CI, 12%-24%), 46% (95% CI, 38%-54%), and 47% (95% CI, 39%-55%), with a specificity of 95% (95% CI, 93%-97%), 99% (95% CI, 98%-100%), 93% (95% CI, 91%-95%), and 96% (95% CI, 94%-98%), respectively. Combining SYNE1 and FOXE1, increased the sensitivity to 56% (95% CI, 48%-64%), while the specificity decreased to 90% (95% CI, 87%-93%) in the training set and to 58% sensitivity (95% CI, 46%-70%) and 91% specificity (95% CI, 80%-100%) in a test set (66 cases, 240 controls). SYNE1 overexpression showed no major differences in cell proliferation, migration, and invasion compared with controls. Overexpression of FOXE1 significantly decreased the number of colonies in SW480 and HCT116 cell lines. Overall, our data suggest that SYNE1 and FOXE1 are promising markers for colorectal cancer detection.
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Affiliation(s)
- Veerle Melotte
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Joo Mi Yi
- Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, South Korea
| | - Marjolein H F M Lentjes
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Kim M Smits
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands. Department of Radiation Oncology (MAASTRO), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leander Van Neste
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands. MDxHealth, Herstal, Belgium
| | - Hanneke E C Niessen
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Kim A D Wouters
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | | | - Kornel E Schuebel
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James G Herman
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephen B Baylin
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Nita Ahuja
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland. Department of Surgery, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland. Department of Urology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Manon van Engeland
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands.
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223
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Lin PC, Lin JK, Lin CH, Lin HH, Yang SH, Jiang JK, Chen WS, Chou CC, Tsai SF, Chang SC. Clinical Relevance of Plasma DNA Methylation in Colorectal Cancer Patients Identified by Using a Genome-Wide High-Resolution Array. Ann Surg Oncol 2014; 22 Suppl 3:S1419-27. [PMID: 25472652 DOI: 10.1245/s10434-014-4277-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND DNA methylation is a potential tumor marker for several cancers, including colorectal cancer (CRC), because of its heritable and stable characteristics. METHODS Using a high-resolution, genome-wide approach, we epigenotyped >450,000 CpG sites in tumor and adjacent non-tumor tissues from 23 microsatellite instability (MSI)/microsatellite stability (MSS) CRC cases. Using matrix-assisted laser desorption ionization-time of flight mass spectrometry, the methylation status of five frequently hypermethylated genes were confirmed in 75 independent CRC series and 353 CRC patients with available plasma. RESULTS Compared with non-tumor tissues, 13 MSI tumors had 34,836 (7 %) aberrant methylation sites, 87 % of which were hypermethylated. In contrast, only 9,806 (2 %) differentially methylated sites were identified in ten MSS cases (62 % hypermethylated). In both MSI and MSS, 228 promoter-associated CpG islands were hypermethylated, with AGBL4, ZNF625, MDFI, TWIST1, and FLI1 being most frequently hypermethylated. In an independent set of 35 MSI and 40 MSS cases, the methylation status of these five genes significantly differed between tumor and adjacent non-tumor tissues. Of 353 CRC patients, 230 (65.2 %), 232 (65.7 %), and 247 (70.0 %) had AGBL4, FLI1, and TWIST1 promoter hypermethylation in circulating cell-free DNA, respectively. In patients without metastasis, the sensitivity of any two or three hypermethylation markers was 52.8-57.8 and 27.9-38.9 %, respectively. The sensitivity of any two or three markers was significantly high in patients with stage IV disease (73.0 and 55.6 %, respectively). The prognostic value of these epimarkers was inconclusive. CONCLUSION DNA methylation patterns differed in CRC subtypes. The identified hypermethylation markers in CRC patients may have good sensitivity in different CRC stages.
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Affiliation(s)
- Pei-Ching Lin
- Department of Clinical Pathology, Yang-Ming Branch, Taipei City Hospital, Taipei, Taiwan
| | - Jen-Kou Lin
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chien-Hsing Lin
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Hung-Hsin Lin
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Shung-Haur Yang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jeng-Kai Jiang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wei-Shone Chen
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Chi Chou
- Department of Life Sciences and Genome Research Center and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Feng Tsai
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan. .,Department of Life Sciences and Genome Research Center and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan.
| | - Shih-Ching Chang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan. .,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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224
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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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225
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Fung KYY, Dai L, Trimble WS. Cell and molecular biology of septins. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 310:289-339. [PMID: 24725429 DOI: 10.1016/b978-0-12-800180-6.00007-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Septins are a family of GTP-binding proteins that assemble into cytoskeletal filaments. Unlike other cytoskeletal components, septins form ordered arrays of defined stoichiometry that can polymerize into long filaments and bundle laterally. Septins associate directly with membranes and have been implicated in providing membrane stability and serving as diffusion barriers for membrane proteins. In addition, septins bind other proteins and have been shown to function as multimolecular scaffolds by recruiting components of signaling pathways. Remarkably, septins participate in a spectrum of cellular processes including cytokinesis, ciliogenesis, cell migration, polarity, and cell-pathogen interactions. Given their breadth of functions, it is not surprising that septin abnormalities have also been linked to human diseases. In this review, we discuss the current knowledge of septin structure, assembly and function, and discuss these in the context of human disease.
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Affiliation(s)
- Karen Y Y Fung
- Cell Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Lu Dai
- Cell Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Physiology, University of Toronto, Toronto, Canada
| | - William S Trimble
- Cell Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Biochemistry, University of Toronto, Toronto, Canada; Department of Physiology, University of Toronto, Toronto, Canada.
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226
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Molnár B, Tóth K, Barták BK, Tulassay Z. Plasma methylated septin 9: a colorectal cancer screening marker. Expert Rev Mol Diagn 2014; 15:171-84. [PMID: 25429690 DOI: 10.1586/14737159.2015.975212] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Colorectal cancer (CRC) is a slow-developing cancer (10-15 years) with one of the highest frequencies in the world's population. Many countries have implemented various CRC screening programs, but have not achieved the desired compliance. Colonoscopy - considered the gold standard for CRC screening - has its limitations as well as the other techniques used, such as irrigoscopy, sigmoidoscopy, fecal blood and hemoglobin tests. The biomarker septin 9 has been found to be hypermethylated in nearly 100% of tissue neoplasia specimens and detected in circulating DNA fractions of CRC patients. A commercially available assay for septin 9 has been developed with moderate sensitivity (∼70%) and specificity (∼90%) and a second generation assay, Epi proColon 2.0 (Epigenomics AG), shows increased sensitivity (∼92%). The performance of the assay proved to be independent of tumor site and reaches a high sensitivity of 77%, even in early cancer stages (I and II). Furthermore, septin 9 was recently used in follow-up studies for detection of early recurrence of CRC. This article evaluates the opportunities, known limitations and future perspectives of the recently introduced Epi proColon(®) 2.0 test, which is based on the detection of aberrantly methylated DNA of the v2 region of the septin 9 gene in plasma.
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Affiliation(s)
- Béla Molnár
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
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227
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Abstract
Colorectal cancer (CRC) is the third most common non-skin cancer diagnosed in men and women in the USA and worldwide. While it has been clearly established that screening for CRC, using a variety of methods, is cost effective and has a significant impact on overall survival, screening rates have proven to be sub-optimal. It has been long conjectured that a simple blood-based test, with a specimen drawn at a routine doctor's office visit, would encourage those individuals who have refused or ignored screening recommendations to undergo screening. This article reviews the currently available blood-based screening tests for CRC, including the ColonSentry™ messenger RNA (mRNA) expression panel and the SEPT9 methylated DNA test, and explores newer biomarkers that are near clinical implementation. Also discussed are additional applications for blood-based CRC testing, such as assessing prognosis, disease surveillance, and expansion of screening tests to high-risk populations, such as the estimated 1.4 million individuals in the USA with inflammatory bowel disease.
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Affiliation(s)
- Karen A Heichman
- Oncology Technology Development and Licensing, ARUP Laboratories Inc., 500 Chipeta Way, Mail stop #209, Salt Lake City, UT, 84108, USA,
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228
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Serman L, Nikuseva Martic T, Serman A, Vranic S. Epigenetic alterations of the Wnt signaling pathway in cancer: a mini review. Bosn J Basic Med Sci 2014; 14:191-4. [PMID: 25428669 PMCID: PMC4333971 DOI: 10.17305/bjbms.2014.4.205] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 11/02/2014] [Indexed: 02/07/2023] Open
Abstract
Epigenetic mechanisms play a crucial role in cellular proliferation, migration and differentiation in both normal and neoplastic development. One of the key signaling pathways whose components are altered through the epigenetic mechanisms is the Wnt signaling pathway. In this review, we briefly discuss the key concepts of epigenetics and focus on the recent advances in the Wnt signaling pathway research and its potential diagnostic and therapeutic implications.
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Affiliation(s)
- Ljiljana Serman
- Department of Biology, School of Medicine, University of Zagreb.
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Yin LG, Zou ZQ, Zhao HY, Zhang CL, Shen JG, Qi L, Qi M, Xue ZQ. Analysis of tissue-specific differentially methylated genes with differential gene expression in non-small cell lung cancers. Mol Biol 2014. [DOI: 10.1134/s0026893314050185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Yang Z, Chen H, Huo L, Yang Z, Bai Y, Fan X, Ni B, Fang L, Hu J, Peng J, Wang L, Wang J. Epigenetic Inactivation and Tumor-Suppressor Behavior of NGFR in Human Colorectal Cancer. Mol Cancer Res 2014; 13:107-19. [PMID: 25244921 DOI: 10.1158/1541-7786.mcr-13-0247] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Zuli Yang
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University (Guangdong Gastrointestinal and Anal Hospital), Sun Yat-Sen University Guangzhou, P.R. China. Guangdong Institute of Gastroenterology, Guangzhou, P.R. China
| | - Hao Chen
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University (Guangdong Gastrointestinal and Anal Hospital), Sun Yat-Sen University Guangzhou, P.R. China
| | - Lijun Huo
- Department of Ophthalmology, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University Guangzhou, P.R. China
| | - Zihuan Yang
- Guangdong Institute of Gastroenterology, Guangzhou, P.R. China
| | - Yang Bai
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University (Guangdong Gastrointestinal and Anal Hospital), Sun Yat-Sen University Guangzhou, P.R. China
| | - Xinjuan Fan
- Guangdong Institute of Gastroenterology, Guangzhou, P.R. China
| | - Beibei Ni
- Guangdong Institute of Gastroenterology, Guangzhou, P.R. China
| | - Lekun Fang
- Guangdong Institute of Gastroenterology, Guangzhou, P.R. China
| | - Jun Hu
- Guangdong Institute of Gastroenterology, Guangzhou, P.R. China
| | - Junsheng Peng
- Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University (Guangdong Gastrointestinal and Anal Hospital), Sun Yat-Sen University Guangzhou, P.R. China
| | - Lei Wang
- Department of Colon and Rectum Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University (Guangdong Gastrointestinal and Anal Hospital), Sun Yat-Sen University Guangzhou, P.R. China.
| | - Jianping Wang
- Guangdong Institute of Gastroenterology, Guangzhou, P.R. China. Department of Colon and Rectum Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University (Guangdong Gastrointestinal and Anal Hospital), Sun Yat-Sen University Guangzhou, P.R. China.
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231
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Discovery and validation of new potential biomarkers for early detection of colon cancer. PLoS One 2014; 9:e106748. [PMID: 25215506 PMCID: PMC4162553 DOI: 10.1371/journal.pone.0106748] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/01/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Accurate detection of characteristic proteins secreted by colon cancer tumor cells in biological fluids could serve as a biomarker for the disease. The aim of the present study was to identify and validate new serum biomarkers and demonstrate their potential usefulness for early diagnosis of colon cancer. METHODS The study was organized in three sequential phases: 1) biomarker discovery, 2) technical and biological validation, and 3) proof of concept to test the potential clinical use of selected biomarkers. A prioritized subset of the differentially-expressed genes between tissue types (50 colon mucosa from cancer-free individuals and 100 normal-tumor pairs from colon cancer patients) was validated and further tested in a series of serum samples from 80 colon cancer cases, 23 patients with adenoma and 77 cancer-free controls. RESULTS In the discovery phase, 505 unique candidate biomarkers were identified, with highly significant results and high capacity to discriminate between the different tissue types. After a subsequent prioritization, all tested genes (N = 23) were successfully validated in tissue, and one of them, COL10A1, showed relevant differences in serum protein levels between controls, patients with adenoma (p = 0.0083) and colon cancer cases (p = 3.2e-6). CONCLUSION We present a sequential process for the identification and further validation of biomarkers for early detection of colon cancer that identifies COL10A1 protein levels in serum as a potential diagnostic candidate to detect both adenoma lesions and tumor. IMPACT The use of a cheap serum test for colon cancer screening should improve its participation rates and contribute to decrease the burden of this disease.
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232
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Connolly D, Hoang HG, Adler E, Tazearslan C, Simmons N, Bernard VV, Castaldi M, Oktay MH, Montagna C. Septin 9 amplification and isoform-specific expression in peritumoral and tumor breast tissue. Biol Chem 2014; 395:157-67. [PMID: 24127542 DOI: 10.1515/hsz-2013-0247] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/09/2013] [Indexed: 12/31/2022]
Abstract
Septins are a large family of GTP-binding proteins abnormally expressed in many solid tumors. Septin 9 (SEPT9) in particular has been found overexpressed in diverse human tumors including breast, head and neck, ovarian, endometrial, kidney, and pancreatic cancer. Although we previously reported SEPT9 amplification in breast cancer, we now show specifically that high-grade breast carcinomas, the subtype with worst clinical outcome, exhibit a significant increase in SEPT9 copy number when compared with other tumor grades. We also present, for the first time, a sensitive and quantitative measure of seven (SEPT9_v1 through SEPT9_v7) isoform variant mRNA levels in mammary epithelial cells. SEPT9_v1, SEPT9_v3, SEPT9_v6, and SEPT9_v7 isoforms were expressed at the highest levels followed by SEPT9_v2 and SEPT9_v5, whereas SEPT9_v4 was almost undetectable. Although most of the isoforms were upregulated in primary tumor tissues relative to the patient-matched peritumoral tissues, SEPT9_v4 remained the lowest expressing isoform. This comprehensive analysis of SEPT9 provides substantial evidence for increased SEPT9 expression as a consequence of genomic amplification and is the first study to profile SEPT9_v1 through SEPT9_v7 isoform-specific mRNA expression in tumor and nontumor tissues from patients with breast cancer.
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IGFBP3 methylation is a novel diagnostic and predictive biomarker in colorectal cancer. PLoS One 2014; 9:e104285. [PMID: 25127039 PMCID: PMC4134211 DOI: 10.1371/journal.pone.0104285] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/07/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND AIM Aberrant hypermethylation of cancer-related genes has emerged as a promising strategy for the development of diagnostic, prognostic and predictive biomarkers in human cancer, including colorectal cancer (CRC). The aim of this study was to perform a systematic and comprehensive analysis of a panel of CRC-specific genes as potential diagnostic, prognostic and predictive biomarkers in a large, population-based CRC cohort. PATIENTS AND METHODS Methylation status of the SEPT9, TWIST1, IGFBP3, GAS7, ALX4 and miR137 genes was studied by quantitative bisulfite pyrosequencing in a population-based cohort of 425 CRC patients. RESULTS Methylation levels of all genes analyzed were significantly higher in tumor tissues compared to normal mucosa (p<0.0001); however, cancer-associated hypermethylation was most frequently observed for miR137 (86.7%) and IGFBP3 (83%) in CRC patients. Methylation analysis using the combination of these two genes demonstrated greatest accuracy for the identification of colonic tumors (sensitivity 95.5%; specificity 90.5%). Low levels of IGFBP3 promoter methylation emerged as an independent risk factor for predicting poor disease free survival in stage II and III CRC patients (HR = 0.49, 95% CI: 0.28-0.85, p = 0.01). Our results also suggest that stage II & III CRC patients with high levels of IGFBP3 methylation do not benefit from adjuvant 5FU-based chemotherapy. CONCLUSION By analyzing a large, population-based CRC cohort, we demonstrate the potential clinical significance of miR137 and IGFBP3 hypermethylation as promising diagnostic biomarkers in CRC. Our data also revealed that IGFBP3 hypermethylation may serve as an independent prognostic and predictive biomarker in stage II and III CRC patients.
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234
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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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235
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Abstract
Pancreatic cancer is one of the worst prognostic cancers because of the late diagnosis and the absence of effective treatment. Within all subtypes of this disease, ductal adenocarcinoma has the shortest survival time. In recent years, global genomics profiling allowed the identification of hundreds of genes that are perturbed in pancreatic cancer. The integration of different omics sources in the study of pancreatic cancer has revealed several molecular mechanisms, indicating the complex history of its development. However, validation of these genes as biomarkers for early diagnosis, prognosis or treatment efficacy is still incomplete but should lead to new approaches for the treatment of the disease in the future.
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Affiliation(s)
- Christian Pilarsky
- Department of Vascular-, Thoracic and Visceral Surgery, University Hospital Dresden, Technische Universit?t Dresden, Fetscherstr. 74, Dresden 01307, Germany.
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Shah R, Jones E, Vidart V, Kuppen PJK, Conti JA, Francis NK. Biomarkers for early detection of colorectal cancer and polyps: systematic review. Cancer Epidemiol Biomarkers Prev 2014; 23:1712-28. [PMID: 25004920 DOI: 10.1158/1055-9965.epi-14-0412] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
There is growing interest in early detection of colorectal cancer as current screening modalities lack compliance and specificity. This study systematically reviewed the literature to identify biomarkers for early detection of colorectal cancer and polyps. Literature searches were conducted for relevant papers since 2007. Human studies reporting on early detection of colorectal cancer and polyps using biomarkers were included. Methodologic quality was evaluated, and sensitivity, specificity, and the positive predictive value (PPV) were reported. The search strategy identified 3,348 abstracts. A total of 44 papers, examining 67 different tumor markers, were included. Overall sensitivities for colorectal cancer detection by fecal DNA markers ranged from 53% to 87%. Combining fecal DNA markers increased the sensitivity of colorectal cancer and adenoma detection. Canine scent detection had a sensitivity of detecting colorectal cancer of 99% and specificity of 97%. The PPV of immunochemical fecal occult blood test (iFOBT) is 1.26%, compared with 0.31% for the current screening method of guaiac fecal occult blood test (gFOBT). A panel of serum protein biomarkers provides a sensitivity and specificity above 85% for all stages of colorectal cancer, and a PPV of 0.72%. Combinations of fecal and serum biomarkers produce higher sensitivities, specificities, and PPVs for early detection of colorectal cancer and adenomas. Further research is required to validate these biomarkers in a well-structured population-based study.
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Affiliation(s)
- Reena Shah
- Yeovil District Hospital NHS Trust, Yeovil, United Kingdom.
| | - Emma Jones
- University of Leicester, Leicester, United Kingdom
| | | | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Centre, Leiden, the Netherlands
| | - John A Conti
- Portsmouth Hospital NHS Trust, Portsmouth, United Kingdom. University of Southampton, Southampton, United Kingdom
| | - Nader K Francis
- Yeovil District Hospital NHS Trust, Yeovil, United Kingdom. University of Bristol, Bristol, United Kingdom
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237
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Reimers MS, Engels CC, Kuppen PJK, van de Velde CJH, Liefers GJ. How does genome sequencing impact surgery? Nat Rev Clin Oncol 2014; 11:610-8. [PMID: 24958181 DOI: 10.1038/nrclinonc.2014.101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cancer is a leading cause of death worldwide. Great efforts are dedicated to the development of prognostic and predictive biomarkers to improve diagnosis and achieve optimal treatment selection, thereby, introducing precision medicine in the multimodality treatment of cancer. Genomic aberrations are the basis of tumour development, representing excellent candidates for the development of promising clinical biomarkers. Over the past decade, single-gene mutations and genomic profiling have been increasingly used in multidisciplinary consultations for risk-assessment and treatment planning for patients with cancer. We discuss the impact of such genetic-based information on surgical decision-making. Single-gene mutations have already influenced surgical decision-making in breast, colorectal and thyroid cancer. However, the direct impact of genomic profiling on surgical care has not yet been fully established. We discuss the direct and indirect influences of genomic profiling on surgery, and analyse the limitations and unresolved issues of a genotypic-approach to the surgical management of cancer.
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Affiliation(s)
- Marlies S Reimers
- Department of Surgery, Leiden University Medical Centre, PO Box 9600, 2300 RC Leiden, Netherlands
| | - Charla C Engels
- Department of Surgery, Leiden University Medical Centre, PO Box 9600, 2300 RC Leiden, Netherlands
| | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Centre, PO Box 9600, 2300 RC Leiden, Netherlands
| | | | - Gerrit J Liefers
- Department of Surgery, Leiden University Medical Centre, PO Box 9600, 2300 RC Leiden, Netherlands
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238
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DNA methylation ratio variability may impede clinical application of cancer diagnostic markers. Anal Bioanal Chem 2014; 406:6529-37. [DOI: 10.1007/s00216-014-7914-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 01/22/2023]
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239
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Potter NT, Hurban P, White MN, Whitlock KD, Lofton-Day CE, Tetzner R, Koenig T, Quigley NB, Weiss G. Validation of a real-time PCR-based qualitative assay for the detection of methylated SEPT9 DNA in human plasma. Clin Chem 2014; 60:1183-91. [PMID: 24938752 DOI: 10.1373/clinchem.2013.221044] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Epi proColon® is a new blood-based colorectal cancer (CRC) screening test designed to determine the methylation status of a promoter region of the SEPT9 (septin 9) gene in cell-free DNA isolated from plasma. We describe the analytical and clinical performance of the test. METHODS Analytical performance at 4 testing laboratories included determination of limit of detection, precision, and reproducibility of the SEPT9 test. Clinical performance was evaluated in a prospective study by use of samples (n = 1544) from subjects enrolled in the PRESEPT clinical trial. Results were analyzed by comparison with colonoscopy, the reference standard. RESULTS The limit of detection for methylated SEPT9 DNA was 7.8 pg/mL (95% CI 6-11 pg/mL) corresponding to <2 genome copies of methylated SEPT9 per milliliter of plasma. In the prospective clinical trial, sensitivity for all stages of CRC was 68% (95% CI 53%-80%) and for stage I-III CRC, 64% (48%-77%). Adjusted specificity, on the basis of negative colonoscopy findings, was 80.0% (78%-82%). SIGNIFICANCE The Epi proColon test is a simple, real-time PCR-based assay for the detection of methylated SEPT9 DNA in blood that may provide a noninvasive CRC screening alternative for people noncompliant with current CRC screening guidelines.
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Affiliation(s)
| | | | - Mary N White
- Molecular Pathology Laboratory Network, Maryville TN
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Abstract
DNA methylation is a significant regulator of gene expression, and its role in carcinogenesis recently has been a subject of remarkable interest. The aim of this review is to analyze the mechanism and cell regulatory effects of both hypo- and hyper-DNA methylation on cancer. In this review, we report new developments and their implications regarding the effects of DNA methylation on cancer development. Indeed, alteration of the pattern of DNA methylation has been a constant finding in cancer cells of the same type and differences in the pattern of DNA methylation not only occur in a variety of tumor types, but also in developmental processes Furthermore, the pattern of histone modification appears to be a predicator of the risk of recurrence of human cancers. It is well known that hypermethylation represses transcription of the promoter sections of tumor-suppressor genes leading to gene silencing. However, hypomethylation also has been identified as a cause of oncogenesis. Furthermore, experiments concerning the mechanism of methylation and its control have led to the discovery of many regulatory enzymes and proteins. This review reports on methods developed for the detection of 5-hydroxymethylcytosine methylation at the 5-methylcytosine of protein domains in the CpG context compared to non-methylated DNA, histone modification, and microRNA change.
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241
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Johnson DA, Barclay RL, Mergener K, Weiss G, König T, Beck J, Potter NT. Plasma Septin9 versus fecal immunochemical testing for colorectal cancer screening: a prospective multicenter study. PLoS One 2014; 9:e98238. [PMID: 24901436 PMCID: PMC4046970 DOI: 10.1371/journal.pone.0098238] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/30/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Screening improves outcomes related to colorectal cancer (CRC); however, suboptimal participation for available screening tests limits the full benefits of screening. Non-invasive screening using a blood based assay may potentially help reach the unscreened population. OBJECTIVE To compare the performance of a new Septin9 DNA methylation based blood test with a fecal immunochemical test (FIT) for CRC screening. DESIGN In this trial, fecal and blood samples were obtained from enrolled patients. To compare test sensitivity for CRC, patients with screening identified colorectal cancer (n = 102) were enrolled and provided samples prior to surgery. To compare test specificity patients were enrolled prospectively (n = 199) and provided samples prior to bowel preparation for screening colonoscopy. MEASUREMENTS Plasma and fecal samples were analyzed using the Epi proColon and OC Fit-Check tests respectively. RESULTS For all samples, sensitivity for CRC detection was 73.3% (95% CI 63.9-80.9%) and 68.0% (95% CI 58.2-76.5%) for Septin9 and FIT, respectively. Specificity of the Epi proColon test was 81.5% (95% CI 75.5-86.3%) compared with 97.4% (95% CI 94.1-98.9%) for FIT. For paired samples, the sensitivity of the Epi proColon test (72.2% -95% CI 62.5-80.1%) was shown to be statistically non-inferior to FIT (68.0%-95% CI 58.2-76.5%). When test results for Epi proColon and FIT were combined, CRC detection was 88.7% at a specificity of 78.8%. CONCLUSIONS At a sensitivity of 72%, the Epi proColon test is non- inferior to FIT for CRC detection, although at a lower specificity. With negative predictive values of 99.8%, both methods are identical in confirming the absence of CRC. TRIAL REGISTRATION ClinicalTrials.gov NCT01580540.
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Affiliation(s)
- David A. Johnson
- Gastroenterology Division, Eastern VA Medical School, Norfolk, Virginia, United States of America
| | - Robert L. Barclay
- Rockford Gastroenterology Associates, Ltd., Rockford, Illinois, United States of America
| | - Klaus Mergener
- Digestive Health Specialists, Tacoma, Washington, United States of America
| | | | | | | | - Nicholas T. Potter
- Molecular Pathology Laboratory Network, Inc., Maryville, Tennessee, United States of America
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242
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Ladabaum U, Alvarez-Osorio L, Rösch T, Brueggenjuergen B. Cost-effectiveness of colorectal cancer screening in Germany: current endoscopic and fecal testing strategies versus plasma methylated Septin 9 DNA. Endosc Int Open 2014; 2:E96-E104. [PMID: 26135268 PMCID: PMC4440365 DOI: 10.1055/s-0034-1377182] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/17/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND AND STUDY AIMS Colorectal cancer (CRC) screening strategies in Germany include guaiac-based fecal occult blood testing (gFOBT) starting at age 50 and a switch to colonoscopy at age 55 or continued gFOBT testing, but screening utilization is limited. Blood-based biomarkers, such as methylated Septin 9 DNA ( (m) SEPT9), may improve screening rates. We performed a cost-effectiveness analysis of current and emerging CRC screening strategies in Germany. METHODS Using a validated Markov model, we compared annual gFOBT for ages 50 through 54 followed by biennial testing until age 75 (FOBT) or by colonoscopy at ages 55 and 65 (FOBT/COLO 55,65), substitution of fecal immunochemical testing (FIT) for gFOBT (FIT, FIT/COLO 55,65), and annual or biennial plasma (m) SEPT9 testing. We also considered persons who utilize only colonoscopy and varied age at colonoscopy utilization. RESULTS The current strategies were more effective and less costly than no screening. FIT was more effective and less costly than (m) SEPT9 testing. FIT/COLO 55,65 cost €12 200 per quality-adjusted life-years gained in comparison with FIT. (m) SEPT9-based screening was cost-effective in comparison with no screening but was dominated by other cost-saving strategies. Differential screening utilization and adherence greatly affected incremental results between strategies. In probabilistic analyses, FIT was preferred in 49 % and FIT/COLO 55,65 in 47 % of iterations. CONCLUSION Currently available CRC screening strategies in Germany, including hybrid fecal testing/colonoscopy, are likely to be cost-saving. Current strategies appear superior to (m) SEPT9-based screening. The impact of blood-based biomarkers is likely to depend on utilization and adherence as much as on test performance characteristics and cost.
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Affiliation(s)
- Uri Ladabaum
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA,Corresponding author Uri Ladabaum, MD, MS Division of Gastroenterology and Hepatology, Department of MedicineStanford University School of Medicine300 Pasteur Drive, Always Bldg Room M211Stanford, CA, USA 94305-5187+1-650-723-5488
| | | | - Thomas Rösch
- Charité Medical University of Berlin, Virchow Clinic Campus, Berlin, Germany
| | - Bernd Brueggenjuergen
- Boston Healthcare Associates International GmbH, Berlin, Germany ,Steinbeis University, Berlin, Germany
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243
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Levenson V, Mori Y. The era of personalized medicine: mechanistic or correlative biomarkers? Per Med 2014; 11:361-364. [PMID: 29783484 DOI: 10.2217/pme.14.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Victor Levenson
- CatholicHealth Initiatives Center for Translational Research, 801 West Baltimore Street, Ste 302, Baltimore, MD 21201, USA
| | - Yuriko Mori
- CatholicHealth Initiatives Center for Translational Research, 801 West Baltimore Street, Ste 302, Baltimore, MD 21201, USA
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Takane K, Midorikawa Y, Yagi K, Sakai A, Aburatani H, Takayama T, Kaneda A. Aberrant promoter methylation of PPP1R3C and EFHD1 in plasma of colorectal cancer patients. Cancer Med 2014; 3:1235-45. [PMID: 24861485 PMCID: PMC4302673 DOI: 10.1002/cam4.273] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/17/2014] [Accepted: 04/23/2014] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a common epigenetic alteration involved in colorectal cancer (CRC). In our previous study, we performed methylated DNA immunoprecipitation-on-chip analysis combined with gene re-expression analysis by 5-aza-2′-deoxycytidine treatment, to identify methylation genes in CRC genome widely. Among these genes, 12 genes showed aberrant hypermethylation frequently in >75% of 149 CRC samples but did not in normal samples. In this study, we aim to find out any of these methylation genes to be utilized for CRC detection using plasma DNA samples. Primers for methylation-specific PCR and pyrosequencing were designed for seven of the 12 genes. Among them, PPP1R3C and EFHD1 were rarely hypermethylated in peripheral blood cells, but frequently hypermethylated in 24 CRC tissue samples and their corresponding plasma samples. In plasma samples, PPP1R3C was methylated in 81% (97/120) of CRC patients, but only in 19% (18/96) of noncancer patients (P = 6 × 10−20, Fisher's exact test). In combined analysis with EFHD1, both genes were methylated in 53% (64/120) of CRC patients, but only in 4% (4/96) of noncancer patients (P = 2 × 10−16), giving high specificity of 96%. At least one of the two genes was methylated in 90% (108/120) of CRC patients, and 36% (35/96) of control patients, giving high sensitivity of 90%. Compared with low sensitivity of carcinoembryonic antigen (17% at stage I, 40% at stage II) and CA19-9 (0% at stage I, 13% at stage II) for early-stage CRCs, sensitivity of aberrant methylation was significantly higher: PPP1R3C methylation at 92% (11/12) for stage I and 77% (23/30) for stage II, and methylation of at least one gene at 100% (12/12) for stage I and 87% (26/30) for stage II. PPP1R3C methylation or its combined use of EFHD1 methylation was highly positive in CRC plasma samples, and they might be useful in detection of CRC, especially for early-stage CRCs.
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Affiliation(s)
- Kiyoko Takane
- Department of Digestive Surgery and Pathology, Nihon University School of Medicine, Tokyo, Japan; Department of Molecular Oncology, Graduate school of Medicine, Chiba University, Chiba, Japan
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McNally B, Linder M, Valdes R. Epigenetic primer for diagnostic applications: a window into personalized medicine. Per Med 2014; 11:323-337. [DOI: 10.2217/pme.14.21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetic testing, primarily in the form of DNA methylation analysis, is currently being used in healthcare settings to help identify and manage disease conditions and to develop and select drugs that specifically target epigenetic machinery. Yet, the clinical application of epigenetic analysis is still in its infancy. With a number of large-scale national and international epigenomic consortia projects in progress to identify tissue-specific epigenomes in normal and disease conditions, we are now poised for a new era of understanding disease processes based upon genetic changes that do not involve alterations to the DNA sequence. The developing epigenetic knowledge base will significantly advance the practice of personalized medicine and precision therapeutics. In this article, we provide a primer on the fundamentals of epigenetics with an emphasis on DNA methylation and review the prospective uses of epigenetic testing in advancing healthcare.
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Affiliation(s)
| | - Mark Linder
- PGXL Laboratories, Louisville, KY 40202, USA
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, MDR Building, 511 S Flloyd Street, Room 222, Louisville KY 40292, USA
| | - Roland Valdes
- PGXL Laboratories, Louisville, KY 40202, USA
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, MDR Building, 511 S Flloyd Street, Room 222, Louisville KY 40292, USA
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246
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Church TR, Wandell M, Lofton-Day C, Mongin SJ, Burger M, Payne SR, Castaños-Vélez E, Blumenstein BA, Rösch T, Osborn N, Snover D, Day RW, Ransohoff DF. Prospective evaluation of methylated SEPT9 in plasma for detection of asymptomatic colorectal cancer. Gut 2014; 63:317-25. [PMID: 23408352 PMCID: PMC3913123 DOI: 10.1136/gutjnl-2012-304149] [Citation(s) in RCA: 524] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND As screening methods for colorectal cancer (CRC) are limited by uptake and adherence, further options are sought. A blood test might increase both, but none has yet been tested in a screening setting. OBJECTIVE We prospectively assessed the accuracy of circulating methylated SEPT9 DNA (mSEPT9) for detecting CRC in a screening population. DESIGN Asymptomatic individuals ≥50 years old scheduled for screening colonoscopy at 32 US and German clinics voluntarily gave blood plasma samples before colon preparation. Using a commercially available assay, three independent blinded laboratories assayed plasma DNA of all CRC cases and a stratified random sample of other subjects in duplicate real time PCRs. The primary outcomes measures were standardised for overall sensitivity and specificity estimates. RESULTS 7941 men (45%) and women (55%), mean age 60 years, enrolled. Results from 53 CRC cases and from 1457 subjects without CRC yielded a standardised sensitivity of 48.2% (95% CI 32.4% to 63.6%; crude rate 50.9%); for CRC stages I-IV, values were 35.0%, 63.0%, 46.0% and 77.4%, respectively. Specificity was 91.5% (95% CI 89.7% to 93.1%; crude rate 91.4%). Sensitivity for advanced adenomas was low (11.2%). CONCLUSIONS Our study using the blood based mSEPT9 test showed that CRC signal in blood can be detected in asymptomatic average risk individuals undergoing screening. However, the utility of the test for population screening for CRC will require improved sensitivity for detection of early cancers and advanced adenomas. CLINICAL TRIAL REGISTRATION NUMBER NCT00855348.
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Affiliation(s)
- Timothy Robert Church
- Department of Environmental Health Sciences, University of Minnesota School of Public Health, , Minneapolis, Minnesota, USA
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247
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Deb S, Fox SB. Molecular profiling in colorectal cancer: current state of play and future directions. COLORECTAL CANCER 2014. [DOI: 10.2217/crc.13.82] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SUMMARY In the era of molecular scientific discovery, there is a continuing gap between our growing scientific knowledge and its utility at the bedside. This phenomenon probably occurs more frequently in colorectal cancer than in other cancer streams, with thousands of scientific studies having produced only a handful of molecular interventions. This review examines our current practices of molecular profiling in colorectal cancer and the scientific research that may impact on this area in the future.
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Affiliation(s)
- Siddhartha Deb
- Department of Anatomical Pathology, Peter MacCallum Cancer Centre, East Melbourne 3002, Australia
- Department of Pathology, University of Melbourne, Parkville 3052, Australia
| | - Stephen B Fox
- Department of Pathology, University of Melbourne, Parkville 3052, Australia
- Department of Anatomical Pathology, Peter MacCallum Cancer Centre, East Melbourne 3002, Australia.
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248
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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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249
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Tóth K, Wasserkort R, Sipos F, Kalmár A, Wichmann B, Leiszter K, Valcz G, Juhász M, Miheller P, Patai ÁV, Tulassay Z, Molnár B. Detection of methylated septin 9 in tissue and plasma of colorectal patients with neoplasia and the relationship to the amount of circulating cell-free DNA. PLoS One 2014; 9:e115415. [PMID: 25526039 PMCID: PMC4272286 DOI: 10.1371/journal.pone.0115415] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 11/23/2014] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Determination of methylated Septin 9 (mSEPT9) in plasma has been shown to be a sensitive and specific biomarker for colorectal cancer (CRC). However, the relationship between methylated DNA in plasma and colon tissue of the same subjects has not been reported. METHODS Plasma and matching biopsy samples were collected from 24 patients with no evidence of disease (NED), 26 patients with adenoma and 34 patients with CRC. Following bisulfite conversion of DNA a commercial RT-PCR assay was used to determine the total amount of DNA in each sample and the fraction of mSEPT9 DNA. The Septin-9 protein was assessed using immunohistochemistry. RESULTS The percent of methylated reference (PMR) values for SEPT9 above a PMR threshold of 1% were detected in 4.2% (1/24) of NED, 100% (26/26) of adenoma and 97.1% (33/34) of CRC tissues. PMR differences between NED vs. adenoma and NED vs. CRC comparisons were significant (p<0.001). In matching plasma samples using a PMR cut-off level of 0.01%, SEPT9 methylation was 8.3% (2/24) of NED, 30.8% (8/26) of adenoma and 88.2% (30/34) of CRC. Significant PMR differences were observed between NED vs. CRC (p<0.01) and adenoma vs. CRC (p<0.01). Significant differences (p<0.01) were found in the amount of cfDNA (circulating cell-free DNA) between NED and CRC, and a modest correlation was observed between mSEPT9 concentration and cfDNA of cancer (R2 = 0.48). The level of Septin-9 protein in tissues was inversely correlated to mSEPT9 levels with abundant expression in normals, and diminished expression in adenomas and tumors. CONCLUSIONS Methylated SEPT9 was detected in all tissue samples. In plasma samples, elevated mSEPT9 values were detected in CRC, but not in adenomas. Tissue levels of mSEPT9 alone are not sufficient to predict mSEPT9 levels in plasma. Additional parameters including the amount of cfDNA in plasma appear to also play a role.
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Affiliation(s)
- Kinga Tóth
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- * E-mail:
| | | | - Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Katalin Leiszter
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Gábor Valcz
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Márk Juhász
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Pál Miheller
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Árpád V. Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Zsolt Tulassay
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Béla Molnár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
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Dietrich D, Jung M, Puetzer S, Leisse A, Holmes EE, Meller S, Uhl B, Schatz P, Ivascu C, Kristiansen G. Diagnostic and prognostic value of SHOX2 and SEPT9 DNA methylation and cytology in benign, paramalignant and malignant pleural effusions. PLoS One 2013; 8:e84225. [PMID: 24386354 PMCID: PMC3874014 DOI: 10.1371/journal.pone.0084225] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/20/2013] [Indexed: 02/06/2023] Open
Abstract
Pleural effusions (PE) are a common clinical problem. The discrimination between benign (BPE), malignant (MPE) and paramalignant (PPE) pleural effusions is highly important to ensure appropriate patient treatment. Today, cytology is the gold standard for diagnosing malignant pleural effusions. However, its sensitivity is limited due to the sometimes low abundance of tumor cells and the challenging assessment of cell morphology in cytological samples. This study aimed to develop and validate a diagnostic test, which allows for the highly specific detection of malignant cells in pleural effusions based on the DNA methylation biomarkers SHOX2 and SEPT9. A quantitative real-time PCR assay was developed which enabled the accurate and sensitive detection of SHOX2 and SEPT9 in PEs. Cytological and DNA methylation analyses were conducted in a case control study comprised of PEs from 114 patients (58 cases, 56 controls). Cytological analysis as well as SHOX2 and SEPT9 methylation resulted in 100% specificity. 21% of the cases were cytologically positive and 26% were SHOX2 or SEPT9 methylation positive. The combined analysis of cytology and DNA methylation resulted in an increase of 71% positively classified PEs from cancer patients as compared to cytological analysis alone. The absolute sensitivity of cytology and DNA methylation was not determinable due to the lack of an appropriate gold standard diagnostic for distinguishing between MPEs and PPEs. Therefore, it was unclear which PEs from cancer patients were malignant (containing tumor cells) and which PEs were paramalignant and resulted from benign conditions in cancer patients, respectively. Furthermore, DNA methylation analysis in PEs allowed the prognosis of the overall survival in cancer patients (Kaplan-Meier analysis, log rank test, p = 0.02 (SHOX2), p = 0.02 (SEPT9)). The developed test may be used as a diagnostic and prognostic adjunct to existing clinical and cytopathological investigations in patients with PEs of unclear etiology.
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Affiliation(s)
- Dimo Dietrich
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
- * E-mail:
| | - Maria Jung
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Svenja Puetzer
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Annette Leisse
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Emily Eva Holmes
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Sebastian Meller
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Barbara Uhl
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | | | - Claudia Ivascu
- Roche Pharma AG, Hematology/Oncology, Grenzach-Wyhlen, Germany
| | - Glen Kristiansen
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
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