301
|
Berg M, Søreide K. Genetic and epigenetic traits as biomarkers in colorectal cancer. Int J Mol Sci 2011; 12:9426-39. [PMID: 22272141 PMCID: PMC3257138 DOI: 10.3390/ijms12129426] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/28/2011] [Accepted: 12/07/2011] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer is a major health burden, and a leading cause of cancer-related deaths in industrialized countries. The steady improvements in surgery and chemotherapy have improved survival, but the ability to identify high- and low-risk patients is still somewhat poor. Molecular biology has, over the years, given insight into basic principles of colorectal cancer initiation and development. These findings include aberrations increasing risk of tumor development, genetic changes associated with the stepwise progression of the disease, and errors predicting response to a specific treatment. Potential biomarkers in colorectal cancer are extensively studied, and how the molecular aberrations relate to clinical features. Yet, little of this knowledge has been possible to transfer into clinical practice. In this review, an overview of colorectal cancer genetics will be given, as well as how aberrations found in this tumor type are proposed as biomarkers for risk prediction, as diagnostic tools, for prognosis or prediction of treatment outcome.
Collapse
Affiliation(s)
- Marianne Berg
- Department of Surgery, Stavanger University Hospital, P O Box 8100, N-4068 Stavanger, Norway
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +47-51-51-80-00; Fax: +47-51-88-08-95
| | - Kjetil Søreide
- Department of Surgery, Stavanger University Hospital, P O Box 8100, N-4068 Stavanger, Norway
- Department of Surgical Sciences, University of Bergen, 5021 Bergen, Norway; E-Mail:
| |
Collapse
|
302
|
Warren JD, Xiong W, Bunker AM, Vaughn CP, Furtado LV, Roberts WL, Fang JC, Samowitz WS, Heichman KA. Septin 9 methylated DNA is a sensitive and specific blood test for colorectal cancer. BMC Med 2011; 9:133. [PMID: 22168215 PMCID: PMC3271041 DOI: 10.1186/1741-7015-9-133] [Citation(s) in RCA: 308] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/14/2011] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND About half of Americans 50 to 75 years old do not follow recommended colorectal cancer (CRC) screening guidelines, leaving 40 million individuals unscreened. A simple blood test would increase screening compliance, promoting early detection and better patient outcomes. The objective of this study is to demonstrate the performance of an improved sensitivity blood-based Septin 9 (SEPT9) methylated DNA test for colorectal cancer. Study variables include clinical stage, tumor location and histologic grade. METHODS Plasma samples were collected from 50 untreated CRC patients at 3 institutions; 94 control samples were collected at 4 US institutions; samples were collected from 300 colonoscopy patients at 1 US clinic prior to endoscopy. SEPT9 methylated DNA concentration was tested in analytical specimens, plasma of known CRC cases, healthy control subjects, and plasma collected from colonoscopy patients. RESULTS The improved SEPT9 methylated DNA test was more sensitive than previously described methods; the test had an overall sensitivity for CRC of 90% (95% CI, 77.4% to 96.3%) and specificity of 88% (95% CI, 79.6% to 93.7%), detecting CRC in patients of all stages. For early stage cancer (I and II) the test was 87% (95% CI, 71.1% to 95.1%) sensitive. The test identified CRC from all regions, including proximal colon (for example, the cecum) and had a 12% false-positive rate. In a small prospective study, the SEPT9 test detected 12% of adenomas with a false-positive rate of 3%. CONCLUSIONS A sensitive blood-based CRC screening test using the SEPT9 biomarker specifically detects a majority of CRCs of all stages and colorectal locations. The test could be offered to individuals of average risk for CRC who are unwilling or unable to undergo colonscopy.
Collapse
Affiliation(s)
- Jorja D Warren
- New Technology Group, ARUP Laboratories, Inc., 500 Chipeta Way, Mail Code 209, Salt Lake City, UT 84108-1221, USA
| | - Wei Xiong
- New Technology Group, ARUP Laboratories, Inc., 500 Chipeta Way, Mail Code 209, Salt Lake City, UT 84108-1221, USA
| | - Ashley M Bunker
- ARUP Institute of Experimental Pathology, ARUP Laboratories, Inc., 500 Chipeta Way, Salt Lake City, UT 84108-1221, USA
| | - Cecily P Vaughn
- ARUP Institute of Experimental Pathology, ARUP Laboratories, Inc., 500 Chipeta Way, Salt Lake City, UT 84108-1221, USA
| | - Larissa V Furtado
- University of Utah Department of Pathology, ARUP Laboratories, Inc., 500 Chipeta Way, Salt Lake City, UT 84108-1221, USA
| | - William L Roberts
- University of Utah Department of Pathology, ARUP Laboratories, Inc., 500 Chipeta Way, Salt Lake City, UT 84108-1221, USA
| | - John C Fang
- Divison of Gastroenterology, University School of Utah Medicine, 30N 1900 E, Room 4R118, salt Lake City, UT 84132, USA
| | - Wade S Samowitz
- University of Utah Department of Pathology, ARUP Laboratories, Inc., 500 Chipeta Way, Salt Lake City, UT 84108-1221, USA
| | - Karen A Heichman
- New Technology Group, ARUP Laboratories, Inc., 500 Chipeta Way, Mail Code 209, Salt Lake City, UT 84108-1221, USA
- University of Utah Department of Pathology, ARUP Laboratories, Inc., 500 Chipeta Way, Salt Lake City, UT 84108-1221, USA
| |
Collapse
|
303
|
Jin H, Lee HC, Park SS, Jeong YS, Kim SY. Serum cancer biomarker discovery through analysis of gene expression data sets across multiple tumor and normal tissues. J Biomed Inform 2011; 44:1076-85. [DOI: 10.1016/j.jbi.2011.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 08/05/2011] [Accepted: 08/09/2011] [Indexed: 01/13/2023]
|
304
|
Cassinotti E, Melson J, Liggett T, Melnikov A, Yi Q, Replogle C, Mobarhan S, Boni L, Segato S, Levenson V. DNA methylation patterns in blood of patients with colorectal cancer and adenomatous colorectal polyps. Int J Cancer 2011; 131:1153-7. [PMID: 22020530 DOI: 10.1002/ijc.26484] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 09/15/2011] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) screening rates are currently suboptimal. Blood-based screening could improve rates of earlier detection for CRC and adenomatous colorectal polyps. In this study, we evaluated the feasibility of plasma-based detection of early CRC and adenomatous polyps using array-mediated analysis methylation profiling of 56 genes implicated in carcinogenesis. Methylation of 56 genes in patients with Stages I and II CRC (N=30) and those with adenomatous polyps (N=30) were compared with individuals who underwent colonoscopy and were found to have neither adenomatous changes nor CRC. Composite biomarkers were developed for adenomatous polyps and CRC, and their sensitivity and specificity was estimated using five-fold cross validation. Six promoters (CYCD2, HIC1, PAX 5, RASSF1A, RB1 and SRBC) were selected for the biomarker, which differentiated CRC patients and controls with 84% sensitivity and 68% specificity. Three promoters (HIC1, MDG1 and RASSF1A) were selected for the biomarker, which differentiated patients with adenomatous polyps and controls with sensitivity of 55% and specificity of 65%. Methylation profiling of plasma DNA can detect early CRC with significant accuracy and shows promise as a methodology to develop biomarkers for CRC screening.
Collapse
Affiliation(s)
- Elisa Cassinotti
- Department of Surgical Sciences, Minimally Invasive Surgery Research Center, University of Insubria, Varese, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
305
|
Jain S, Chang TT, Hamilton JP, Lin SY, Lin YJ, Evans AA, Selaru FM, Lin PW, Chen SH, Block TM, Hu CT, Song W, Meltzer SJ, Su YH. Methylation of the CpG sites only on the sense strand of the APC gene is specific for hepatocellular carcinoma. PLoS One 2011; 6:e26799. [PMID: 22073196 PMCID: PMC3206845 DOI: 10.1371/journal.pone.0026799] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 10/03/2011] [Indexed: 12/12/2022] Open
Abstract
Hypermethylation of the promoter of the tumor suppressor gene, adenomatous polyposis coli (APC), occurs in various malignancies, including hepatocellular carcinoma (HCC). However, reports on the specificity of the methylation of the APC gene for HCC have varied. To gain insight into how these variations occur, bisulfite PCR sequencing was performed to analyze the methylation status of both sense and antisense strands of the APC gene in samples of HCC tissue, matched adjacent non-HCC liver tissue, hepatitis, cirrhosis, and normal liver tissues. DNA derived from fetal liver and 12 nonhepatic normal tissue was also examined. These experiments revealed liver-specific, antisense strand-biased CpG methylation of the APC gene and suggested that, although methylation of the antisense strand of the APC gene exists in normal liver and other non-HCC disease liver tissue, methylation of the sense strand of the APC gene occurs predominantly in HCC. To determine the effect of the DNA strand on the specificity of the methylated APC gene as a biomarker for HCC detection, quantitative methylation-specific PCR assays for sense and antisense strand DNA were developed and performed on DNA isolated from HCC (n = 58), matched adjacent non-HCC (n = 58), cirrhosis (n = 41), and hepatitis (n = 39). Receiver operating characteristic curves were constructed. With the cutoff value set at the limit of detection, the specificity of sense and antisense strand methylation was 84% and 43%, respectively, and sensitivity was 67.2% and 72.4%, respectively. This result demonstrated that the identity of the methylated DNA strand impacted the specificity of APC for HCC detection. Interestingly, methylation of the sense strand of APC occurred in 40% of HCCs from patients with serum AFP levels less than 20 ng/mL, suggesting a potential role for APC as a biomarker to complement AFP in HCC screening.
Collapse
Affiliation(s)
- Surbhi Jain
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Ting-Tsung Chang
- Department of Medicine, Infectious Diseases and Signaling Research Center, College of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - James P. Hamilton
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Selena Y. Lin
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yih-Jyh Lin
- Department of Surgery, National Cheng Kung University Hospital, Tainan, Taiwan, Republic of China
| | - Alison A. Evans
- School of Public Health, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Florin M. Selaru
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Pin- Wen Lin
- Department of Surgery, National Cheng Kung University Hospital, Tainan, Taiwan, Republic of China
| | - Shun-Hua Chen
- Department of Microbiology, Medical College, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Timothy M. Block
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Chi-Tan Hu
- Department of General Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, Republic of China
| | - Wei Song
- JBS Science Inc., Philadelphia, Pennsylvania, United States of America
| | - Stephen J. Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, United States of America
| | - Ying-Hsiu Su
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
306
|
Pawa N, Arulampalam T, Norton JD. Screening for colorectal cancer: established and emerging modalities. Nat Rev Gastroenterol Hepatol 2011; 8:711-22. [PMID: 22045159 DOI: 10.1038/nrgastro.2011.205] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It has been estimated that >95% of cases of colorectal cancer (CRC) would benefit from curative surgery if diagnosis was made at an early or premalignant polyp stage of disease. Over the past 10 years, most developed nation states have implemented mass population screening programs, which are typically targeted at the older (at-risk) age group (>50-60 years old). Conventional screening largely relies on periodic patient-centric investigation, particularly involving colonoscopy and flexible sigmoidoscopy, or else on the fecal occult blood test. These methods are compromised by either low cost-effectiveness or limited diagnostic accuracy. Advances in the development of diagnostic molecular markers for CRC have yielded an expanding list of potential new screening modalities based on investigations of patient stool (for colonocyte DNA mutations, epigenetic changes or microRNA expression) or blood specimens (for plasma DNA mutations, epigenetic changes, heteroplasmic mitochondrial DNA mutations, leukocyte transcriptome profile, plasma microRNA expression or protein and autoantibody expression). In this Review, we present a critical evaluation of the performance data and relative merits of these various new potential methods. None of these molecular diagnostic methods have yet been evaluated beyond the proof-of-principle and pilot-scale study stage and it could be some years before they replace existing methods for population screening in CRC.
Collapse
Affiliation(s)
- Nikhil Pawa
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | | | | |
Collapse
|
307
|
Bosch LJW, Carvalho B, Fijneman RJA, Jimenez CR, Pinedo HM, van Engeland M, Meijer GA. Molecular tests for colorectal cancer screening. Clin Colorectal Cancer 2011; 10:8-23. [PMID: 21609931 DOI: 10.3816/ccc.2011.n.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Detecting and removing high-risk adenomas and early colorectal cancer (CRC) can reduce mortality of this disease. The noninvasive fecal occult blood test (FOBT; guaiac-based or immunochemical) is widely used in screening programs and although effective, it leaves room for improvement in terms of test accuracy. Molecular tests are expected to be more sensitive, specific and informative than current detection tests, and are promising future tools for CRC screening. This review provides an overview of the performances of DNA, RNA, and protein markers for CRC detection in stool and blood. Most emphasis currently is on DNA and protein markers. Among DNA markers there is trend to move away from mutation markers in favor of methylation markers. The recent boost in proteomics research leads to many new candidate protein markers. Usually in small series, some markers show better performance than the present FOBT. Evaluation in large well-controlled randomized trials is the next step needed to take molecular markers for CRC screening to the next level and warrant implementation in a screening setting.
Collapse
Affiliation(s)
- Linda J W Bosch
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
308
|
Abstract
The past decade has highlighted the central role of epigenetic processes in cancer causation, progression and treatment. Next-generation sequencing is providing a window for visualizing the human epigenome and how it is altered in cancer. This view provides many surprises, including linking epigenetic abnormalities to mutations in genes that control DNA methylation, the packaging and the function of DNA in chromatin, and metabolism. Epigenetic alterations are leading candidates for the development of specific markers for cancer detection, diagnosis and prognosis. The enzymatic processes that control the epigenome present new opportunities for deriving therapeutic strategies designed to reverse transcriptional abnormalities that are inherent to the cancer epigenome.
Collapse
Affiliation(s)
- Stephen B. Baylin
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland 21231, USA
| | - Peter A. Jones
- The USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| |
Collapse
|
309
|
Zheng Y, Chen L, Li J, Yu B, Su L, Chen X, Yu Y, Yan M, Liu B, Zhu Z. Hypermethylated DNA as potential biomarkers for gastric cancer diagnosis. Clin Biochem 2011; 44:1405-11. [PMID: 21945024 DOI: 10.1016/j.clinbiochem.2011.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 08/31/2011] [Accepted: 09/04/2011] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To demonstrate the diagnostic significance of methylation, an important molecular event in gastric carcinogenesis. DESIGN AND METHODS We used methylation microarray to determine candidate genes, and performed MSP to evaluate the methylation status of them in tissues and sera. The effect of demethylation on mRNA expression was investigated by rt-PCR after gastric cancer cell lines were treated with 5-Aza-dC for 96 h. RESULTS In tissues and sera of gastric cancer patients, a higher prevalence of methylation was observed for BX141696, WT1, CYP26B1, and KCNA4, compared to healthy people (p<0.05, respectively). Detection of the methylation prevalence of KCNA4 and CYP26B1 together in serum demonstrated the good sensitivity (91.3%) and specificity (92.1%). After 5-Aza-dC treatment in gastric cancer cell lines, the mRNA expression level of these genes was restored. CONCLUSIONS This study underscores the potential application of measurement of serum DNA methylation of these genes, as promising tool for gastric cancer detection.
Collapse
Affiliation(s)
- Yanan Zheng
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
310
|
Tóth K, Galamb O, Spisák S, Wichmann B, Sipos F, Valcz G, Leiszter K, Molnár B, Tulassay Z. The influence of methylated septin 9 gene on RNA and protein level in colorectal cancer. Pathol Oncol Res 2011; 17:503-9. [PMID: 21267688 DOI: 10.1007/s12253-010-9338-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 11/22/2010] [Indexed: 02/05/2023]
Abstract
Colorectal cancer is one of the leading death causes in the world. Specificity and sensitivity of the present screening methods are unsuitable and their compliance is too low. Nowadays the most effective method is the colonoscopy, because it gives not only macroscopic diagnosis but therapeutic possibility as well, however the compliance of the patients is very low. Hence development of new diagnostic methods is needed. Altered expression of septin 9 was found in several tumor types including colorectal cancer. The aim of this study was to detect the methylation related mRNA and protein expression changes of septin 9 in colorectal adenoma-dysplasia-carcinoma sequence and to analyze its reversibility by demethylation treatment. Septin 9 protein expression showed significant difference between normal and colorectal cancer (CRC) samples (p < 0,001). According to biopsy microarray results, septin 9 mRNA expression decreased in the progression of colon neoplastic disease (p < 0,001). In laser microdissected epithelial cells, septin 9 significantly underexpressed in CRC compared to healthy controls (p < 0,001). The expression of septin9_v1 region was higher in the healthy samples, while septin9_v2, v4, v4*, v5 overexpression were detected in cancer epithelial cells compared to normal. The septin 9 mRNA and protein levels of HT29 cells increased after demethylation treatment. The increasing methylation of septin 9 gene during colorectal adenoma-dysplasia-carcinoma sequence progression is reflected in the decreasing mRNA and protein expression, especially in the epithelium. These changes can be reversed by demethylation agents converting this screening marker gene into therapeutic target.
Collapse
Affiliation(s)
- Kinga Tóth
- Semmelweis University, 2nd Department of Internal Medicine, Budapest, Hungary.
| | | | | | | | | | | | | | | | | |
Collapse
|
311
|
Lind GE, Danielsen SA, Ahlquist T, Merok MA, Andresen K, Skotheim RI, Hektoen M, Rognum TO, Meling GI, Hoff G, Bretthauer M, Thiis-Evensen E, Nesbakken A, Lothe RA. Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas. Mol Cancer 2011; 10:85. [PMID: 21777459 PMCID: PMC3166273 DOI: 10.1186/1476-4598-10-85] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 07/21/2011] [Indexed: 12/16/2022] Open
Abstract
Background The presence of cancer-specific DNA methylation patterns in epithelial colorectal cells in human feces provides the prospect of a simple, non-invasive screening test for colorectal cancer and its precursor, the adenoma. This study investigates a panel of epigenetic markers for the detection of colorectal cancer and adenomas. Methods Candidate biomarkers were subjected to quantitative methylation analysis in test sets of tissue samples from colorectal cancers, adenomas, and normal colonic mucosa. All findings were verified in independent clinical validation series. A total of 523 human samples were included in the study. Receiver operating characteristic (ROC) curve analysis was used to evaluate the performance of the biomarker panel. Results Promoter hypermethylation of the genes CNRIP1, FBN1, INA, MAL, SNCA, and SPG20 was frequent in both colorectal cancers (65-94%) and adenomas (35-91%), whereas normal mucosa samples were rarely (0-5%) methylated. The combined sensitivity of at least two positives among the six markers was 94% for colorectal cancers and 93% for adenoma samples, with a specificity of 98%. The resulting areas under the ROC curve were 0.984 for cancers and 0.968 for adenomas versus normal mucosa. Conclusions The novel epigenetic marker panel shows very high sensitivity and specificity for both colorectal cancers and adenomas. Our findings suggest this biomarker panel to be highly suitable for early tumor detection.
Collapse
Affiliation(s)
- Guro E Lind
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
312
|
Connolly D, Abdesselam I, Verdier-Pinard P, Montagna C. Septin roles in tumorigenesis. Biol Chem 2011; 392:725-38. [PMID: 21740328 DOI: 10.1515/bc.2011.073] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Septins are a family of cytoskeleton related proteins consisting of 14 members that associate and interact with actin and tubulin. From yeast to humans, septins maintain a conserved role in cytokinesis and they are also involved in a variety of other cellular functions including chromosome segregation, DNA repair, migration and apoptosis. Tumorigenesis entails major alterations in these processes. A substantial body of literature reveals that septins are overexpressed, downregulated or generate chimeric proteins with MLL in a plethora of solid tumors and in hematological malignancies. Thus, members of this gene family are emerging as key players in tumorigenesis. The analysis of septins during cancer initiation and progression is challenged by the presence of many family members and by their potential to produce numerous isoforms. However, the development and application of advanced technologies is allowing for a more detailed analysis of septins during tumorigenesis. Specifically, such applications have led to the establishment and validation of SEPT9 as a biomarker for the early detection of colorectal cancer. This review summarizes the current knowledge on the role of septins in tumorigenesis, emphasizing their significance and supporting their use as potential biomarkers in various cancer types.
Collapse
Affiliation(s)
- Diana Connolly
- Department of Genetics, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
| | | | | | | |
Collapse
|
313
|
Herbst A, Rahmig K, Stieber P, Philipp A, Jung A, Ofner A, Crispin A, Neumann J, Lamerz R, Kolligs FT. Methylation of NEUROG1 in serum is a sensitive marker for the detection of early colorectal cancer. Am J Gastroenterol 2011; 106:1110-8. [PMID: 21326223 DOI: 10.1038/ajg.2011.6] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Colorectal cancer is the third most common cancer and a major cause of cancer-related deaths. Early detection of colonic lesions can reduce the incidence and mortality of colorectal cancer. Colonoscopy is the screening test for colorectal cancer with the highest efficacy, but its acceptance in the general public is rather low. To identify suitable tumor-derived markers that could detect colorectal cancer in blood samples, we analyzed the methylation status of a panel of genes in sera of affected patients. METHODS Using methylation-specific quantitative PCR, we analyzed the methylation of ten marker genes in sera of healthy individuals and patients with colorectal cancer. RESULTS Only HLTF, HPP1/TPEF, and NEUROG1 DNA methylation was detectable in at least 50% of patients with colorectal cancers. Whereas HLTF and HPP1/TPEF preferentially detected advanced and metastasized colorectal cancers, NEUROG1 methylation was detectable in UICC stages I-IV at a similar rate. Compared with other methylation markers, such as ALX4, SEPT9, and vimentin, NEUROG1 shows a higher sensitivity for colorectal cancer at UICC stages I and II. At a specificity of 91%, NEUROG1 reached a sensitivity of 61% (confidence interval, 50.4-70.6%) for the detection of colorectal cancers. Furthermore, detection of NEUROG1 methylation was independent of age and gender. CONCLUSIONS Methylation of the NEUROG1 gene is frequently found in sera of patients with colorectal cancers independent of tumor stage. The quantitative detection of NEUROG1 DNA methylation in serum is a suitable approach for the non-invasive screening for asymptomatic colorectal cancer.
Collapse
Affiliation(s)
- Andreas Herbst
- Department of Medicine II, University of Munich, Munich, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
314
|
Yamamoto N, Nakayama T, Kajita M, Miyake T, Iwamoto T, Kim SJ, Sakai A, Ishihara H, Tamaki Y, Noguchi S. Detection of aberrant promoter methylation of GSTP1, RASSF1A, and RARβ2 in serum DNA of patients with breast cancer by a newly established one-step methylation-specific PCR assay. Breast Cancer Res Treat 2011; 132:165-73. [PMID: 21594664 DOI: 10.1007/s10549-011-1575-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 05/06/2011] [Indexed: 12/31/2022]
Abstract
Aberrant promoter methylation of genes is a common molecular event in breast cancer. Thus, DNA methylation analysis is expected to be a new tool for cancer diagnosis. In this article, we have established a new, high-performance DNA methylation assay, the one-step methylation-specific polymerase chain reaction (OS-MSP) assay, which is optimized for analyzing gene methylation in serum DNA. The OS-MSP assay is designed to detect aberrant promoter methylation of GSTP1, RASSF1A, and RARβ2 genes in serum DNA. Moreover, two quality control markers were designed for monitoring the bisulfite conversion efficiency and measuring the DNA content in the serum. Serum samples were collected from patients with primary (n = 101, stages I-III) and metastatic breast cancers (n = 58) as well as from healthy controls (n = 87). If methylation of at least one of the three genes was observed, the OS-MSP assay was considered positive. The sensitivity of this assay was significantly higher than that of the assay involving conventional tumor markers (CEA and/or CA15-3) for stages I (24 vs. 8%) and II (26 vs. 8%) breast cancer and similar to that of the assay involving the conventional tumor markers for stage III (18 vs. 19%) and metastatic breast cancers (55 vs. 59%). The results of the OS-MSP assay and those of the assay involving CEA and/or CA15-3 seemed to compensate for each other because sensitivity of these assays increased to 78% when used in combination for metastatic breast cancer. In conclusion, we have developed a new OS-MSP assay with improved sensitivity and convenience; thus, this assay is more suitable for detecting aberrant promoter methylation in serum DNA. Moreover, the combination of the OS-MSP assay and the assay involving CEA and/or CA15-3 is promising for enhancing the sensitivity of diagnosis of metastatic breast cancer.
Collapse
Affiliation(s)
- Noriaki Yamamoto
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
315
|
van Vlodrop IJH, Niessen HEC, Derks S, Baldewijns MMLL, van Criekinge W, Herman JG, van Engeland M. Analysis of promoter CpG island hypermethylation in cancer: location, location, location! Clin Cancer Res 2011; 17:4225-31. [PMID: 21558408 DOI: 10.1158/1078-0432.ccr-10-3394] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The genetic and epigenetic alterations that underlie cancer pathogenesis are rapidly being identified. This provides novel insights in tumor biology as well as in potential cancer biomarkers. The somatic mutations in cancer genes that have been implemented in clinical practice are well defined and very specific. For epigenetic alterations, and more specifically aberrant methylation of promoter CpG islands, evidence is emerging that these markers could be used for the early detection of cancer as well as prediction of prognosis and response to therapy. However, the exact location of biologically and clinically relevant hypermethylation has not been identified for the majority of methylation markers. The most widely used approaches to analyze DNA methylation are based on primer- and probe-based assays that provide information for a limited number of CpG dinucleotides and thus for only part of the information available in a given CpG island. Validation of the current data and implementation of hypermethylation markers in clinical practice require a more comprehensive and critical evaluation of DNA methylation and limitations of the techniques currently used in methylation marker research. Here, we discuss the emerging evidence on the importance of the location of CpG dinucleotide hypermethylation in relation to gene expression and associations with clinicopathologic characteristics in cancer.
Collapse
Affiliation(s)
- Iris J H van Vlodrop
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
316
|
Franklin TB, Mansuy IM. The involvement of epigenetic defects in mental retardation. Neurobiol Learn Mem 2011; 96:61-7. [PMID: 21549207 DOI: 10.1016/j.nlm.2011.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/17/2011] [Accepted: 04/08/2011] [Indexed: 01/22/2023]
Abstract
Mental retardation is a group of cognitive disorders with a significant worldwide prevalence rate. This high rate, together with the considerable familial and societal burden resulting from these disorders, makes it an important focus for prevention and intervention. While the diseases associated with mental retardation are diverse, a significant number are linked with disruptions in epigenetic mechanisms, mainly due to loss-of-function mutations in genes that are key components of the epigenetic machinery. Additionally, several disorders classed as imprinting syndromes are associated with mental retardation. This review will discuss the epigenetic abnormalities associated with mental retardation, and will highlight their importance for diagnosis, treatment, and prevention of these disorders.
Collapse
Affiliation(s)
- Tamara B Franklin
- Brain Research Institute, Swiss Federal Institute of Technology, Zurich, Switzerland.
| | | |
Collapse
|
317
|
Tao S, Hundt S, Haug U, Brenner H. Sensitivity estimates of blood-based tests for colorectal cancer detection: impact of overrepresentation of advanced stage disease. Am J Gastroenterol 2011; 106:242-53. [PMID: 20959816 DOI: 10.1038/ajg.2010.393] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A large number of blood-based markers have been proposed for early detection of colorectal cancer (CRC). Their sensitivity for detecting CRC has mostly been evaluated in clinical settings, and found to be higher in more advanced stages compared with earlier stages of the disease. The aim of this study is to estimate the overall sensitivity of blood-based markers expected in screening settings, where the proportion of advanced stages is typically lower than in clinical settings. A systematic literature review was performed on studies evaluating sensitivity and specificity of blood-based markers for early detection of CRC. For each study, overall sensitivity expected in screening settings was estimated by weighting stage-specific sensitivities according to the stage distribution of CRC expected in the screening setting. The latter was derived from 12,605 CRC cases diagnosed in the German screening colonoscopy program during 2003-2007. Overall, 73 studies evaluating 55 blood-based markers were identified. Adjusted sensitivity was lower than reported sensitivity in 120 (90%) evaluations of different markers. Median absolute reduction in sensitivity after adjustment was 9.0% (interquartile range: 4.0-13.0) units, whereas median relative reduction was 19.5% (interquartile range: 11.3-33.3%). Blood-based markers for CRC detection reported from clinical settings showed higher sensitivities than expected in the screening setting in most cases, mainly due to substantially higher proportions of advanced stage cancers. Adjustment of sensitivity to the stage distribution expected in the screening setting is crucial to obtain realistic and comparable estimates of sensitivities.
Collapse
Affiliation(s)
- Sha Tao
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | | | | | | |
Collapse
|
318
|
Zhang XM, Guo MZ. The value of epigenetic markers in esophageal cancer. ACTA ACUST UNITED AC 2010; 4:378-84. [PMID: 21107750 DOI: 10.1007/s11684-010-0230-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 10/10/2010] [Indexed: 12/12/2022]
Abstract
Developing esophageal cancer is a multi-step process that begins with the accumulation of genetic and epigenetic alterations, and leads to the activation of oncogenes and the inactivation or loss of tumor suppressor genes (TSG). In addition to genetic alteration, epigenetic modifications, and in particular DNA methylation, are recognized as a common molecular alteration in human tumors. In esophageal cancer, aberrant methylation of promoter regions occurs not only in advanced cancer, but also in premalignant lesions. DNA methylation is related to survival time and sensitivity of chemoradiotherapy. This review is mainly focused on epigenetic changes in esophageal cancer and the value of early detection for patient prognosis, treatment choices, and potential targeting therapy.
Collapse
Affiliation(s)
- Xiao-Mei Zhang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, 100853, China
| | | |
Collapse
|
319
|
Kraus S, Goel A, Arber N. Blood-based peptide, genetic, and epigenetic biomarkers for diagnosing gastrointestinal cancers. ACTA ACUST UNITED AC 2010; 4:459-71. [DOI: 10.1517/17530059.2010.532208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
320
|
A novel method for sensitive and specific detection of DNA methylation biomarkers based on DNA restriction during PCR cycling. Biotechniques 2010; 47:737-44. [PMID: 19852759 DOI: 10.2144/000113208] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA methylation is an important epigenetic mechanism involved in fundamental biological processes such as development, imprinting, and carcino-genesis. For these reasons, DNA methylation represents a valuable source for cancer biomarkers. Methods for the sensitive and specific detection of methylated DNA are a prerequisite for the implementation of DNA biomarkers into clinical routine when early detection based on the analysis of body fluids is desired. Here, a novel technique is presented for the detection of DNA methylation biomarkers, based on real-time PCR of bisulfite-treated template with enzymatic digestion of background DNA during amplification using the heat-stable enzyme Tsp509I. An assay for the lung cancer methylation biomarker BARHL2 was used to show clinical and analytical performance of the method in comparison with methylation-specific PCR technology. Both technologies showed comparable performance when analyzing technical DNA mixtures and bronchial lavage samples from 75 patients suspected of having lung cancer. The results demonstrate that the approach is useful for sensitive and specific detection of a few copies of methylated DNA in samples with a high background of unmethylated DNA, such as in clinical samples from body fluids.
Collapse
|
321
|
Development of a multiplex MethyLight assay for the detection of multigene methylation in human colorectal cancer. ACTA ACUST UNITED AC 2010; 202:1-10. [PMID: 20804913 DOI: 10.1016/j.cancergencyto.2010.05.018] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 05/19/2010] [Accepted: 05/28/2010] [Indexed: 02/06/2023]
Abstract
In peripheral blood, cell-free methylated DNA has been reported to be a useful biomarker of noninvasive blood screening for the detection of colorectal cancer (CRC), including the genes ALX homeobox 4 (ALX4), septin 9 (SEPT9), or transmembrane protein with EGF-like, and two follistatin-like domains 2 (TMEFF2). Here we report a multiplex MethyLight polymerase chain reaction (PCR) assay that simultaneously detected the methylation status of ALX4, SEPT9, and TMEFF2, as well as quantifying methylation level of these genes in a total of 127 fresh tissue samples and 182 peripheral blood samples from CRC patients. Using the multiplex MethyLight assay, methylated ALX4, SEPT9, and TMEFF2 occurred in 56, 78, and 75% of CRC tissue samples and in 48, 75, and 71% of peripheral blood samples from CRC patients. The sensitivities of the combined study using the three genes as biomarkers for the detection of CRC in primary tissues and peripheral blood samples were 84 and 81%, with specificities of 87 and 90%, respectively. Combining the specificity of real-time PCR, the high throughput of multiplex PCR, and the high sensitivity of multigene detection, this multiplex MethyLight PCR assay may allow for future screening programs with large-scale noninvasive blood testing for early-stage CRC.
Collapse
|
322
|
Abstract
DNA methylation is a key component of mammalian gene regulation and the most classical example of an epigenetic mark. DNA methylation patterns are mitotically heritable and stable over time, but they undergo considerable changes in response to cell differentiation, diseases and environmental influences. Several methods have been developed for DNA methylation profiling on a genomic scale. Here, we benchmark four of these methods on two sample pairs, comparing their accuracy and power to detect DNA methylation differences. The results show that all evaluated methods (MeDIP-seq: methylated DNA immunoprecipitation, MethylCap-seq: methylated DNA capture by affinity purification, RRBS: reduced representation bisulfite sequencing, and the Infinium HumanMethylation27 assay) produce accurate DNA methylation data. However, these methods differ in their ability to detect differentially methylated regions between pairs of samples. We highlight strengths and weaknesses of the four methods and give practical recommendations for the design of epigenomic case-control studies.
Collapse
|
323
|
Tanaka T, Tanaka M, Tanaka T, Ishigamori R. Biomarkers for colorectal cancer. Int J Mol Sci 2010; 11:3209-25. [PMID: 20957089 PMCID: PMC2956090 DOI: 10.3390/ijms11093209] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/02/2010] [Accepted: 09/03/2010] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common epithelial malignancy in the world. Since CRC develops slowly from removable precancerous lesions, detection of the lesion at an early stage by regular health examinations can reduce the incidence and mortality of this malignancy. Colonoscopy significantly improves the detection rate of CRC, but the examination is expensive and inconvenient. Therefore, we need novel biomarkers that are non-invasive to enable us to detect CRC quite early. A number of validation studies have been conducted to evaluate genetic, epigenetic or protein markers for identification in the stool and/or serum. Currently, the fecal occult blood test is the most widely used method of screening for CRC. However, advances in genomics and proteomics will lead to the discovery of novel non-invasive biomarkers.
Collapse
Affiliation(s)
- Takuji Tanaka
- The Tohkai Cytopathology Institute: Cancer Research and Prevention (TCI-CaRP), 5-1-2 Minami- Uzura, Gifu 500-8285, Japan
- Department Oncologic Pathology, Kanazawa Medical University, 1-1 daigaku, Uchinada Ishikawa 920-0293, Japan
- *Author to whom correspondence should be addressed; E-Mail: or ; Tel.: +81-58-273-4399; Fax: +81-58-273-4392
| | - Mayu Tanaka
- Department of Pharmacy, Kinjo Gakuin University of Pharmacy, Moriyama-Ku, Nagoya, Aichi 463-8521, Japan
| | - Takahiro Tanaka
- Department of Physical Therapy, Kansai University of Health Sciences, Kumatori-Machi, Sennan-Gun, Osaka 590-0482, Japan; E-Mail:
| | - Rikako Ishigamori
- Cancer Prevention Basic Research Project, National Cancer Center Research Institute, Tokyo 104-0045, Japan; E-Mail:
| |
Collapse
|
324
|
Wild N, Andres H, Rollinger W, Krause F, Dilba P, Tacke M, Karl J. A combination of serum markers for the early detection of colorectal cancer. Clin Cancer Res 2010; 16:6111-21. [PMID: 20798228 DOI: 10.1158/1078-0432.ccr-10-0119] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE Fecal occult blood testing is recommended as first-line screening to detect colorectal cancer (CRC). We evaluated markers and marker combinations in serum as an alternative to improve the detection of CRC. EXPERIMENTAL DESIGN Using penalized logistic regression, 6 markers were selected for evaluation in 1,027 samples (301 CRC patients, 143 patients with adenoma, 266 controls, 141 disease controls, and 176 patients with other cancer). The diagnostic performance of each marker and of marker combinations was assessed. RESULTS To detect CRC from serum samples, we tested 22 biomarkers. Six markers were selected for a marker combination, including the known tumor markers CEA (carcinoembryonic antigen) and CYFRA 21-1 as well as novel markers or markers that are less routinely used for the detection of CRC: ferritin, osteopontin (OPN), anti-p53, and seprase. CEA showed the best sensitivity at 95% specificity with 43.9%, followed by seprase (42.4%), CYFRA 21-1 (35.5%), OPN (30.2%), ferritin (23.9%), and anti-p53 (20.0%). A combination of these markers gave 69.6% sensitivity at 95% specificity and 58.7% at 98% specificity. Focusing on International Union against Cancer (UICC) stages 0-III reduced the sensitivity slightly to 68.0% and 53.3%, respectively. In a subcollective, with matched stool samples (75 CRC cases and 234 controls), the sensitivity of the marker combination was comparable with fecal immunochemical testing (FIT) with 82.4% and 68.9% versus 81.8% and 72.7% at 95% and 98% specificity, respectively. CONCLUSIONS The performance of the serum marker combination is comparable with FIT. This provides a novel tool for CRC screening to trigger a follow-up colonoscopy for a final diagnosis.
Collapse
Affiliation(s)
- Norbert Wild
- Department of New Technologies, Roche Diagnostics GmbH, Penzberg, Germany.
| | | | | | | | | | | | | |
Collapse
|
325
|
Abstract
After the completion of the human genome, a need was identified by scientists to look for a functional map of the human genome. Epigenomics provided functional characteristics of genes identified in the genome. Epigenetics is the alteration in gene expression (function) without changing the nucleotide sequence. Both activation and inactivation of cancer-associated genes can occur by epigenetic mechanisms. The major players in epigenetic mechanisms of gene regulation are DNA methylation, histone deacetylation, chromatin remodeling, small noncoding RNA expression and gene imprinting. In the last few years, epigenetic mechanisms have been studied in a number of tumor types and epigenetic markers have been identified that are suitable for cancer detection, diagnosis, follow-up of treatment and screening high-risk populations. One interesting aspect of epigenetics is the reactivation of genes by successful reversion of some epigenetic changes using chemicals. The reversibility of epigenetic aberrations has made them attractive targets for cancer treatment with modulators that demethylate DNA and inhibit histone deacetylases, leading to the reactivation of silenced genes. In this article, we have described the current status of this powerful science and discussed the challenges in the clinical fields where epigenetic approaches in cancer are applied.
Collapse
Affiliation(s)
- Hirendra Nath Banerjee
- Department of Biology, Campus Box 930, Elizabeth City State University, 1704 Weeksville Road, Elizabeth City, NC 27909, USA.
| | | |
Collapse
|
326
|
Tierling S, Schuster M, Tetzner R, Walter J. A combined HM-PCR/SNuPE method for high sensitive detection of rare DNA methylation. Epigenetics Chromatin 2010; 3:12. [PMID: 20525169 PMCID: PMC2887863 DOI: 10.1186/1756-8935-3-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 06/02/2010] [Indexed: 02/06/2023] Open
Abstract
Background DNA methylation changes are widely used as early molecular markers in cancer detection. Sensitive detection and classification of rare methylation changes in DNA extracted from circulating body fluids or complex tissue samples is crucial for the understanding of tumor etiology, clinical diagnosis and treatment. In this paper, we describe a combined method to monitor the presence of methylated tumor DNA in an excess of unmethylated background DNA of non-tumorous cells. The method combines heavy methyl-PCR, which favors preferential amplification of methylated marker sequence from bisulfite-treated DNA with a methylation-specific single nucleotide primer extension monitored by ion-pair, reversed-phase, high-performance liquid chromatography separation. Results This combined method allows detection of 14 pg (that is, four to five genomic copies) of methylated chromosomal DNA in a 2000-fold excess (that is, 50 ng) of unmethylated chromosomal background, with an analytical sensitivity of > 90%. We outline a detailed protocol for the combined assay on two examples of known cancer markers (SEPT9 and TMEFF2) and discuss general aspects of assay design and data interpretation. Finally, we provide an application example for rapid testing on tumor methylation in plasma DNA derived from a small cohort of patients with colorectal cancer. Conclusion The method allows unambiguous detection of rare DNA methylation, for example in body fluid or DNA isolates from cells or tissues, with very high sensitivity and accuracy. The application combines standard technologies and can easily be adapted to any target region of interest. It does not require costly reagents and can be used for routine screening of many samples.
Collapse
|
327
|
Molecular detection of colorectal neoplasia. Gastroenterology 2010; 138:2127-39. [PMID: 20420950 DOI: 10.1053/j.gastro.2010.01.055] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 01/12/2010] [Accepted: 01/20/2010] [Indexed: 02/06/2023]
Abstract
A variety of noninvasive molecular approaches to colorectal cancer screening are emerging with potential to improve screening effectiveness and user-friendliness. These approaches are based on the sensitive assay of molecular markers in stool, blood, and urine samples. New methods, especially next generation stool-based tests, have been shown to detect both colorectal cancers and precancerous lesions with high accuracy. Validation of these technologies in average-risk populations are needed to establish their role for general colorectal cancer screening. This review addresses the biological rationale, technical advances, recent clinical performance data, and remaining issues with molecular screening for colorectal cancer.
Collapse
|
328
|
Abstract
Colorectal cancer (CRC) arises as a consequence of the accumulation of genetic and epigenetic alterations in colonic epithelial cells during neoplastic transformation. Epigenetic modifications, particularly DNA methylation in selected gene promoters, are recognized as common molecular alterations in human tumors. Substantial efforts have been made to determine the cause and role of aberrant DNA methylation ("epigenomic instability") in colon carcinogenesis. In the colon, aberrant DNA methylation arises in tumor-adjacent, normal-appearing mucosa. Aberrant methylation also contributes to later stages of colon carcinogenesis through simultaneous methylation in key specific genes that alter specific oncogenic pathways. Hypermethylation of several gene clusters has been termed CpG island methylator phenotype and appears to define a subgroup of colon cancer distinctly characterized by pathological, clinical, and molecular features. DNA methylation of multiple promoters may serve as a biomarker for early detection in stool and blood DNA and as a tool for monitoring patients with CRC. DNA methylation patterns may also be predictors of metastatic or aggressive CRC. Therefore, the aim of this review is to understand DNA methylation as a driving force in colorectal neoplasia and its emerging value as a molecular marker in the clinic.
Collapse
Affiliation(s)
- Myoung Sook Kim
- Department of Otolaryngology, Head and Neck Surgery, The Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB II-5M, Baltimore, MD, 21231, USA
| | | | | |
Collapse
|
329
|
Peterson EA, Petty EM. Conquering the complex world of human septins: implications for health and disease. Clin Genet 2010; 77:511-24. [PMID: 20236126 DOI: 10.1111/j.1399-0004.2010.01392.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Septins are highly conserved filamentous proteins first characterized in budding yeast and subsequently identified in must eukaryotes. Septins can bind and hydrolyze GTP, which is intrinsically related to their formation of septin hexamers and functional protein interactions. The human septin family is composed of 14 loci, SEPT1-SEPT14, which encode dozens of different septin proteins. Their central GTPase and polybasic domain regions are highly conserved but they diverge in their N-terminus and/or C-terminus. The mechanism by which the different isoforms are generated is not yet well understood, but one can hypothesize that the use of different promoters and/or alternative splicing could give rise to these variants. Septins perform diverse cellular functions according to tissue expression and their interacting partners. Functions identified to date include cell division, chromosome segregation, protein scaffolding, cellular polarity, motility, membrane dynamics, vesicle trafficking, exocytosis, apoptosis, and DNA damage response. Their expression is tightly regulated to maintain proper filament assembly and normal cellular functions. Alterations of these proteins, by mutation or expression changes, have been associated with a variety of cancers and neurological diseases. The association of septins with cancer results from alterations of expression in solid tumors or translocations in leukemias [mixed lineage leukemia (MLL)]. Expression changes in septins have also been associated with neurological conditions such as Alzheimer's and Parkinson's disease, as well as retinopathies, hepatitis C, spermatogenesis and Listeria infection. Pathogenic mutations of SEPT9 were identified in the autosomal dominant neurological disorder hereditary neuralgic amyotrophy (HNA). Human septin research over the past decade has established their importance in cell biology and human disease. Further functional characterization of septins is crucial to our understanding of their possible diagnostic, prognostic, and therapeutic applications.
Collapse
Affiliation(s)
- E A Peterson
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | | |
Collapse
|
330
|
Quintero E, Gimeno-García AZ, Salido E. Blood Tests for Early Detection of Colorectal Cancer. CURRENT COLORECTAL CANCER REPORTS 2010. [DOI: 10.1007/s11888-009-0039-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
331
|
|
332
|
Deng D, Liu Z, Du Y. Epigenetic alterations as cancer diagnostic, prognostic, and predictive biomarkers. ADVANCES IN GENETICS 2010; 71:125-76. [PMID: 20933128 DOI: 10.1016/b978-0-12-380864-6.00005-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Alterations of DNA methylation and transcription of microRNAs (miRNAs) are very stable phenomena in tissues and body fluids and suitable for sensitive detection. These advantages enable us to translate some important discoveries on epigenetic oncology into biomarkers for control of cancer. A few promising epigenetic biomarkers are emerging. Clinical trials using methylated CpG islands of p16, Septin9, and MGMT as biomarkers are carried out for predication of cancer development, diagnosis, and chemosensitivity. Circulating miRNAs are promising biomarkers, too. Breakthroughs in the past decade imply that epigenetic biomarkers may be useful in reducing the burden of cancer.
Collapse
Affiliation(s)
- Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry ofEducation), Peking University School of Oncology, Beijing Cancer Hospitaland Institute, Fu-Cheng-Lu, Haidian District, Beijing, 100142, PR China
| | | | | |
Collapse
|
333
|
|
334
|
Tainsky MA. Genomic and proteomic biomarkers for cancer: a multitude of opportunities. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1796:176-93. [PMID: 19406210 PMCID: PMC2752479 DOI: 10.1016/j.bbcan.2009.04.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 04/14/2009] [Accepted: 04/21/2009] [Indexed: 02/06/2023]
Abstract
Biomarkers are molecular indicators of a biological status, and as biochemical species can be assayed to evaluate the presence of cancer and therapeutic interventions. Through a variety of mechanisms cancer cells provide the biomarker material for their own detection. Biomarkers may be detectable in the blood, other body fluids, or tissues. The expectation is that the level of an informative biomarker is related to the specific type of disease present in the body. Biomarkers have potential both as diagnostic indicators and monitors of the effectiveness of clinical interventions. Biomarkers are also able to stratify cancer patients to the most appropriate treatment. Effective biomarkers for the early detection of cancer should provide a patient with a better outcome which in turn will translate into more efficient delivery of healthcare. Technologies for the early detection of cancer have resulted in reductions in disease-associated mortalities from cancers that are otherwise deadly if allowed to progress. Such screening technologies have proven that early detection will decrease the morbidity and mortality from cancer. An emerging theme in biomarker research is the expectation that panels of biomarker analytes rather than single markers will be needed to have sufficient sensitivity and specificity for the presymptomatic detection of cancer. Biomarkers may provide prognostic information of disease enabling interventions using targeted therapeutic agents as well as course-corrections in cancer treatment. Novel genomic, proteomic and metabolomic technologies are being used to discover and validate tumor biomarkers individually and in panels.
Collapse
Affiliation(s)
- Michael A Tainsky
- Program in Molecular Biology and Genetics, Barbara Ann Karmanos Cancer Institute, Department of Pathology, Wayne State University School of Medicine, USA.
| |
Collapse
|
335
|
Kondratova VN, Botezatu IV, Shelepov VP, Lichtenstein AV. Isotachophoresis of nucleic acids in agarose gel rods. BIOCHEMISTRY (MOSCOW) 2009; 74:1285-8. [DOI: 10.1134/s0006297909110169] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
336
|
Payne SR, Serth J, Schostak M, Kamradt J, Strauss A, Thelen P, Model F, Day JK, Liebenberg V, Morotti A, Yamamura S, Lograsso J, Sledziewski A, Semjonow A. DNA methylation biomarkers of prostate cancer: confirmation of candidates and evidence urine is the most sensitive body fluid for non-invasive detection. Prostate 2009; 69:1257-69. [PMID: 19459176 DOI: 10.1002/pros.20967] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND A prostate cancer (PCa) biomarker with improved specificity relative to PSA is a public health priority. Hypermethylated DNA can be detected in body fluids from PCa patients and may be a useful biomarker, although clinical performance varies between studies. We investigated the performance of candidate PCa DNA methylation biomarkers identified through a genome-wide search. METHODS Real-time PCR was used to measure four DNA methylation biomarkers: GSTP1 and three previously unreported candidates associated with the genes RASSF2, HIST1H4K, and TFAP2E in sodium bisulfite-modified DNA. Matched plasma and urine collected prospectively from 142 patients referred for prostate biopsy and 50 young asymptomatic males were analyzed. RESULTS Analysis of all biomarkers in urine DNA significantly discriminated PCa from biopsy negative patients. The biomarkers discriminated PCa from biopsy negative patients with AUCs ranging from 0.64 for HIST1H4K (95% CI 0.55-0.72, P < 0.00001) to 0.69 for GSTP1 (95% CI 0.60-0.77, P < 0.00001). All biomarkers showed minimal correlation with PSA. Multivariate analysis did not yield a panel that significantly improved performance over that of single biomarkers. All biomarkers showed greater sensitivity for PCa in urine than in plasma DNA. CONCLUSIONS Analysis of the biomarkers in urine DNA significantly discriminated PCa from biopsy negative patients. The biomarkers provided information independent of PSA and may warrant inclusion in nomograms for predicting prostate biopsy outcome. The biomarkers' PCa sensitivity was greater for urine than plasma DNA. The biomarker performances in urine DNA should next be validated in formal training and test studies.
Collapse
|
337
|
Kimura N, Moribe T, Iizuka N, Miura T, Tamatsukuri S, Ishitsuka H, Hamamoto Y, Oka M. Rapid and quantitative detection of CpG-methylation status using TaqMan PCR combined with methyl-binding-domain polypeptide. Clin Biochem 2009; 42:1113-22. [DOI: 10.1016/j.clinbiochem.2009.03.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 02/24/2009] [Accepted: 03/15/2009] [Indexed: 12/31/2022]
|
338
|
Radpour R, Kohler C, Haghighi MM, Fan AXC, Holzgreve W, Zhong XY. Methylation profiles of 22 candidate genes in breast cancer using high-throughput MALDI-TOF mass array. Oncogene 2009; 28:2969-78. [PMID: 19503099 DOI: 10.1038/onc.2009.149] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Alterations of DNA methylation patterns have been suggested as biomarkers for diagnostics and therapy of cancers. Every novel discovery in the epigenetic landscape and every development of an improved approach for accurate analysis of the events may offer new opportunity for the management of patients. Using a novel high-throughput mass spectrometry on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) silico-chips, we determined semiquantitative methylation changes of 22 candidate genes in breast cancer tissues. For the first time we analysed the methylation status of a total of 42 528 CpG dinucleotides on 22 genes in 96 different paraffin-embedded tissues (48 breast cancerous tissues and 48 paired normal tissues). A two-way hierarchical cluster analysis was used to classify methylation profiles. In this study, 10 hypermethylated genes (APC, BIN1, BMP6, BRCA1, CST6, ESRb, GSTP1, P16, P21 and TIMP3) were identified to distinguish between cancerous and normal tissues according to the extent of methylation. Individual assessment of the methylation status for each CpG dinucleotide indicated that cytosine hypermethylation in the cancerous tissue samples was mostly located near the consensus sequences of the transcription factor binding sites. These hypermethylated genes may serve as biomarkers for clinical molecular diagnosis and targeted treatments of patients with breast cancer.
Collapse
Affiliation(s)
- R Radpour
- Laboratory for Prenatal Medicine and Gynecologic Oncology, Women's Hospital/Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | | | | | | |
Collapse
|
339
|
Tóth K, Galamb O, Spisák S, Wichmann B, Sipos F, Leiszter K, Molnár J, Molnár B, Tulassay Z. [Free circulating DNA based colorectal cancer screening from peripheral blood: the possibility of the methylated septin 9 gene marker]. Orv Hetil 2009; 150:969-77. [PMID: 19443305 DOI: 10.1556/oh.2009.28625] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA methylation acts in early tumorigenesis. Its detection is possible either from tissue, stool or peripheral blood. Septin 9 is a sensitive methylation marker, which has been studied in several cancers such as breast and ovarian tumors and in neurological or hematological diseases. Septin proteins have an important role from cytoskeleton organisation to development of embryonal pattern. Nowadays intensive researches are going on about the relation between the septin 9 gene hypermethylation and colorectal cancer development.
Collapse
Affiliation(s)
- Kinga Tóth
- Semmelweis Egyetem, Altalános Orvostudományi Kar, II. Belgyógyászati Klinika, Budapest.
| | | | | | | | | | | | | | | | | |
Collapse
|
340
|
Alternative splicing variants and DNA methylation status of BDNF in inbred chicken lines. Brain Res 2009; 1269:1-10. [DOI: 10.1016/j.brainres.2009.01.071] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2008] [Revised: 12/14/2008] [Accepted: 01/19/2009] [Indexed: 12/31/2022]
|
341
|
deVos T, Tetzner R, Model F, Weiss G, Schuster M, Distler J, Steiger KV, Grützmann R, Pilarsky C, Habermann JK, Fleshner PR, Oubre BM, Day R, Sledziewski AZ, Lofton-Day C. Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer. Clin Chem 2009; 55:1337-46. [PMID: 19406918 DOI: 10.1373/clinchem.2008.115808] [Citation(s) in RCA: 379] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND The presence of aberrantly methylated SEPT9 DNA in plasma is highly correlated with the occurrence of colorectal cancer. We report the development of a new SEPT9 biomarker assay and its validation in case-control studies. The development of such a minimally invasive blood-based test may help to reduce the current gap in screening coverage. METHODS A new SEPT9 DNA methylation assay was developed for plasma. The assay comprised plasma DNA extraction, bisulfite conversion of DNA, purification of bisulfite-converted DNA, quantification of converted DNA by real-time PCR, and measurement of SEPT9 methylation by real-time PCR. Performance of the SEPT9 assay was established in a study of 97 cases with verified colorectal cancer and 172 healthy controls as verified by colonoscopy. Performance based on predetermined algorithms was validated in an independent blinded study with 90 cases and 155 controls. RESULTS The SEPT9 assay workflow yielded 1.9 microg/L (CI 1.3-3.0) circulating plasma DNA following bisulfite conversion, a recovery of 45%-50% of genomic DNA, similar to yields in previous studies. The SEPT9 assay successfully identified 72% of cancers at a specificity of 93% in the training study and 68% of cancers at a specificity of 89% in the testing study. CONCLUSIONS Circulating methylated SEPT9 DNA, as measured in the new (m)SEPT9 assay, is a valuable biomarker for minimally invasive detection of colorectal cancer. The new assay is amenable to automation and standardized use in the clinical laboratory.
Collapse
Affiliation(s)
- Theo deVos
- Epigenomics Inc., Seattle, WA 98101, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
342
|
Mayor R, Casadomé L, Azuara D, Moreno V, Clark SJ, Capellà G, Peinado MA. Long-range epigenetic silencing at 2q14.2 affects most human colorectal cancers and may have application as a non-invasive biomarker of disease. Br J Cancer 2009; 100:1534-9. [PMID: 19384295 PMCID: PMC2696749 DOI: 10.1038/sj.bjc.6605045] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Large chromosomal regions can be suppressed in cancer cells as denoted by hypermethylation of neighbouring CpG islands and downregulation of most genes within the region. We have analysed the extent and prevalence of long-range epigenetic silencing at 2q14.2 (the first and best characterised example of coordinated epigenetic remodelling) and investigated its possible applicability as a non-invasive diagnostic marker of human colorectal cancer using different approaches and biological samples. Hypermethylation of at least one of the CpG islands analysed (EN1, SCTR, INHBB) occurred in most carcinomas (90%), with EN1 methylated in 73 and 40% of carcinomas and adenomas, respectively. Gene suppression was a common phenomenon in all the tumours analysed and affected both methylated and unmethylated genes. Detection of methylated EN1 using bisulfite treatment and melting curve (MC) analysis from stool DNA in patients and controls resulted in a predictive capacity of, 44% sensitivity in positive patients (27% of overall sensitivity) and 97% specificity. We conclude that epigenetic suppression along 2q14.2 is common to most colorectal cancers and the presence of a methylated EN1 CpG island in stool DNA might be used as biomarker of neoplastic disease.
Collapse
Affiliation(s)
- R Mayor
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC), Badalona, Catalonia, Spain
| | | | | | | | | | | | | |
Collapse
|
343
|
Lopez J, Percharde M, Coley HM, Webb A, Crook T. The context and potential of epigenetics in oncology. Br J Cancer 2009; 100:571-7. [PMID: 19223907 PMCID: PMC2653733 DOI: 10.1038/sj.bjc.6604930] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cancer has long been known to be a disease caused by alterations in the genetic blueprint of cells. In the past decade it has become evident that epigenetic processes have a function, at least equally important, in neoplasia. Epigenetics describes the mechanisms that result in heritable alterations in gene expression profiles without an accompanying change in DNA sequence. Genetics and epigenetics intricately interact in the pathogenesis of cancer (Esteller, 2007). In this review, we paint a broad picture of current understanding of epigenetic changes in cancer cells and reflect on the immense clinical potential of emerging knowledge of epigenetics in the diagnosis, prognostic assessment, treatment, and screening of cancer.
Collapse
Affiliation(s)
- J Lopez
- The Breakthrough Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | | | | | | | | |
Collapse
|
344
|
Ally MS, Al-Ghnaniem R, Pufulete M. The relationship between gene-specific DNA methylation in leukocytes and normal colorectal mucosa in subjects with and without colorectal tumors. Cancer Epidemiol Biomarkers Prev 2009; 18:922-8. [PMID: 19258481 DOI: 10.1158/1055-9965.epi-08-0703] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
CpG island methylation in the promoter regions of tumor suppressor genes has been shown to occur in normal colonic tissue and can distinguish between subjects with and without colorectal neoplasms. It is unclear whether this relationship exists in other tissues such as blood. We report the relationship between estrogen receptor gene (estrogen receptor alpha) methylation in leukocyte and normal colonic tissue DNA in subjects with and without colorectal neoplasia. DNA was extracted from frozen stored whole blood samples of 27 subjects with cancer, 30 with adenoma, 16 with hyperplastic polyps, and 57 disease-free subjects. DNA methylation in seven CpG sites close to the transcription start of estrogen receptor alpha was quantitated using pyrosequencing and expressed as a methylation index (average methylation across all CpG sites analyzed). Estrogen receptor alpha methylation in leukocyte DNA was compared with estrogen receptor alpha methylation in normal colonic mucosa DNA that had been previously determined in the same subjects. Estrogen receptor alpha was partially methylated (median, 4.3%; range, 0.0-12.6%) in leukocyte DNA in all subjects, with no significant difference between disease groups (P>0.05). Estrogen receptor alpha methylation in leukocytes was 60% lower than estrogen receptor alpha methylation in normal colonic tissue (P<0.001). Estrogen receptor alpha methylation in colonic tissue (P<0.001) and smoking (P=0.016) were determinants of estrogen receptor alpha methylation in leukocytes, independent of age, body mass index, gender, and disease status. In conclusion, there was a positive relationship between estrogen receptor alpha methylation in leukocytes and colonic tissue in subjects with and without colorectal tumors. However, unlike in colonic tissue, estrogen receptor alpha methylation in leukocytes was unable to distinguish between disease groups.
Collapse
Affiliation(s)
- Mina Sarah Ally
- Diet and Gastrointestinal Health Group, Department of Nutrition and Dietetics, King's College London, Franklin Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | | | | |
Collapse
|
345
|
Wieczorek G, Asemissen A, Model F, Turbachova I, Floess S, Liebenberg V, Baron U, Stauch D, Kotsch K, Pratschke J, Hamann A, Loddenkemper C, Stein H, Volk HD, Hoffmüller U, Grützkau A, Mustea A, Huehn J, Scheibenbogen C, Olek S. Quantitative DNA methylation analysis of FOXP3 as a new method for counting regulatory T cells in peripheral blood and solid tissue. Cancer Res 2009; 69:599-608. [PMID: 19147574 DOI: 10.1158/0008-5472.can-08-2361] [Citation(s) in RCA: 258] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Regulatory T-cells (Treg) have been the focus of immunologic research due to their role in establishing tolerance for harmless antigens versus allowing immune responses against foes. Increased Treg frequencies measured by mRNA expression or protein synthesis of the Treg marker FOXP3 were found in various cancers, indicating that dysregulation of Treg levels contributes to tumor establishment. Furthermore, they constitute a key target of immunomodulatory therapies in cancer as well as transplantation settings. One core obstacle for understanding the role of Treg, thus far, is the inability of FOXP3 mRNA or protein detection methods to differentiate between Treg and activated T cells. These difficulties are aggravated by the technical demands of sample logistics and processing. Based on Treg-specific DNA demethylation within the FOXP3 locus, we present a novel method for monitoring Treg in human peripheral blood and solid tissues. We found that Treg numbers are significantly increased in the peripheral blood of patients with interleukin 2-treated melanoma and in formalin-fixed tissue from patients with lung and colon carcinomas. Conversely, we show that immunosuppressive therapy including therapeutic antibodies leads to a significant reduction of Treg from the peripheral blood of transplantation patients. In addition, Treg numbers are predictively elevated in the peripheral blood of patients with various solid tumors. Although our data generally correspond to data obtained with gene expression and protein-based methods, the results are less fluctuating and more specific to Treg. The assay presented here measures Treg robustly in blood and solid tissues regardless of conservation levels, promising fast screening of Treg in various clinical settings.
Collapse
|
346
|
Kim HJ, Yu MH, Kim H, Byun J, Lee C. Noninvasive molecular biomarkers for the detection of colorectal cancer. BMB Rep 2009; 41:685-92. [PMID: 18959813 DOI: 10.5483/bmbrep.2008.41.10.685] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common malignancy in the world. Because CRC develops slowly from removable precancerous lesions, detection of the disease at an early stage during regular health examinations can reduce both the incidence and mortality of the disease. Although sigmoidoscopy offers significant improvements in the detection rate of CRC, its diagnostic value is limited by its high costs and inconvenience. Therefore, there is a compelling need for the identification of noninvasive biomarkers that can enable earlier detection of CRC. Accordingly, many validation studies have been conducted to evaluate genetic, epigenetic or protein markers that can be detected in the stool or in serum. Currently, the fecal-occult blood test is the most widely used method of screening for CRC. However, advances in genomics and proteomics combined with developments in other relevant fields will lead to the discovery of novel non invasive biomarkers whose usefulness will be tested in larger validation studies. Here, noninvasive molecular biomarkers that are currently used in clinical settings and have the potential for use as CRC biomarkers are discussed.
Collapse
Affiliation(s)
- Hye-Jung Kim
- Life Sciences Division, Korea Institute of Science and Technology, Seoul, Korea
| | | | | | | | | |
Collapse
|
347
|
Duffy MJ, Napieralski R, Martens JWM, Span PN, Spyratos F, Sweep FCGJ, Brunner N, Foekens JA, Schmitt M. Methylated genes as new cancer biomarkers. Eur J Cancer 2009; 45:335-46. [PMID: 19138839 DOI: 10.1016/j.ejca.2008.12.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 12/05/2008] [Accepted: 12/12/2008] [Indexed: 01/22/2023]
Abstract
Aberrant hypermethylation of promoter regions in specific genes is a key event in the formation and progression of cancer. In at least some situations, these aberrant alterations occur early in the formation of malignancy and appear to be tumour specific. Multiple reports have suggested that measurement of the methylation status of the promoter regions of specific genes can aid early detection of cancer, determine prognosis and predict therapy responses. Promising DNA methylation biomarkers include the use of methylated GSTP1 for aiding the early diagnosis of prostate cancer, methylated PITX2 for predicting outcome in lymph node-negative breast cancer patients and methylated MGMT in predicting benefit from alkylating agents in patients with glioblastomas. However, prior to clinical utilisation, these findings require validation in prospective clinical studies. Furthermore, assays for measuring gene methylation need to be standardised, simplified and evaluated in external quality assurance programmes. It is concluded that methylated genes have the potential to provide a new generation of cancer biomarkers.
Collapse
Affiliation(s)
- M J Duffy
- Department of Pathology and Laboratory Medicine, Nuclear Medicine Laboratory, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
348
|
Ullah MF, Aatif M. The footprints of cancer development: Cancer biomarkers. Cancer Treat Rev 2008; 35:193-200. [PMID: 19062197 DOI: 10.1016/j.ctrv.2008.10.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 10/16/2008] [Accepted: 10/17/2008] [Indexed: 12/31/2022]
Abstract
Diagnostic detection and measurement of cancer disease progression are essential elements for successful cancer disease management. The early stages of cancer development carry the maximum potential for therapeutic interventions. However, these stages are often asymptomatic, leading to delayed diagnosis at the very advanced stages when effective treatments are unavailing. The application of biomarkers to cancer is leading the way because of the unique association of genomic changes in cancer cells with the disease process. They have the potential to not only help identify who will develop cancer but also to predict as to when the event is most likely to occur. In recent years, there has been an enormous effort to develop specific and sensitive biomarkers for precise and accurate screening, diagnosis, prognosis and monitoring of high risk cancer to assist with therapeutic decisions. The present article is a brief review of the emerging trends in the development of biomarkers for early detection and precise evaluation of cancer disease.
Collapse
Affiliation(s)
- Mohd Fahad Ullah
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, UP 202002, India
| | | |
Collapse
|
349
|
Sensitive detection of colorectal cancer in peripheral blood by septin 9 DNA methylation assay. PLoS One 2008; 3:e3759. [PMID: 19018278 PMCID: PMC2582436 DOI: 10.1371/journal.pone.0003759] [Citation(s) in RCA: 291] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 10/21/2008] [Indexed: 02/06/2023] Open
Abstract
Background Colorectal cancer (CRC) is the second leading cause of cancer deaths despite the fact that detection of this cancer in early stages results in over 90% survival rate. Currently less than 45% of at-risk individuals in the US are screened regularly, exposing a need for better screening tests. We performed two case-control studies to validate a blood-based test that identifies methylated DNA in plasma from all stages of CRC. Methodology/Principal Findings Using a PCR assay for analysis of Septin 9 (SEPT9) hypermethylation in DNA extracted from plasma, clinical performance was optimized on 354 samples (252 CRC, 102 controls) and validated in a blinded, independent study of 309 samples (126 CRC, 183 controls). 168 polyps and 411 additional disease controls were also evaluated. Based on the training study SEPT9-based classification detected 120/252 CRCs (48%) and 7/102 controls (7%). In the test study 73/126 CRCs (58%) and 18/183 control samples (10%) were positive for SEPT9 validating the training set results. Inclusion of an additional measurement replicate increased the sensitivity of the assay in the testing set to 72% (90/125 CRCs detected) while maintaining 90% specificity (19/183 for controls). Positive rates for plasmas from the other cancers (11/96) and non-cancerous conditions (41/315) were low. The rate of polyp detection (>1 cm) was ∼20%. Conclusions/Significance Analysis of SEPT9 DNA methylation in plasma represents a straightforward, minimally invasive method to detect all stages of CRC with potential to satisfy unmet needs for increased compliance in the screening population. Further clinical testing is warranted.
Collapse
|
350
|
Meng H, Murrelle EL, Li G. Identification of a small optimal subset of CpG sites as bio-markers from high-throughput DNA methylation profiles. BMC Bioinformatics 2008; 9:457. [PMID: 18954440 PMCID: PMC2613930 DOI: 10.1186/1471-2105-9-457] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 10/27/2008] [Indexed: 12/16/2022] Open
Abstract
Background DNA methylation patterns have been shown to significantly correlate with different tissue types and disease states. High-throughput methylation arrays enable large-scale DNA methylation analysis to identify informative DNA methylation biomarkers. The identification of disease-specific methylation signatures is of fundamental and practical interest for risk assessment, diagnosis, and prognosis of diseases. Results Using published high-throughput DNA methylation data, a two-stage feature selection method was developed to select a small optimal subset of DNA methylation features to precisely classify two sample groups. With this approach, a small number of CpG sites were highly sensitive and specific in distinguishing lung cancer tissue samples from normal lung tissue samples. Conclusion This study shows that it is feasible to identify DNA methylation biomarkers from high-throughput DNA methylation profiles and that a small number of signature CpG sites can suffice to classify two groups of samples. The computational method we developed in the study is efficient to identify signature CpG sites from disease samples with complex methylation patterns.
Collapse
Affiliation(s)
- Hailong Meng
- Scientific Division, ClearPoint Resources Inc., Richmond, VA 23219, USA.
| | | | | |
Collapse
|