An Epigenetic Marker Panel for Detection of Lung Cancer Using Cell-Free Serum DNA

Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
Clinical Cancer Research (Impact Factor: 8.72). 05/2011; 17(13):4494-503. DOI: 10.1158/1078-0432.CCR-10-3436
Source: PubMed


We investigated the feasibility of detecting aberrant DNA methylation of some novel and known genes in the serum of lung cancer patients.
To determine the analytic sensitivity, we examined the tumor and the matched serum DNA for aberrant methylation of 15 gene promoters from 10 patients with primary lung tumors by using quantitative methylation-specific PCR. We then tested this 15-gene set to identify the more useful DNA methylation changes in the serum of a limited number of lung cancer patients and controls. In an independent set, we tested the six most promising genes (APC, CDH1, MGMT, DCC, RASSF1A, and AIM1) for further elucidation of the diagnostic application of this panel of markers.
Promoter hypermethylation of at least one of the genes studied was detected in all 10 lung primary tumors. In majority of cases, aberrant methylation in serum DNA was accompanied by methylation in the matched tumor samples. In the independent set, using a single gene that had 100% specificity (DCC), 35.5% (95% CI: 25-47) of the 76 lung cancer patients were correctly identified. For patients without methylated DCC, addition of a logistic regression score that was based on the five remaining genes improved sensitivity from 35.5% to 75% (95% CI: 64-84) but decreased the specificity from 100% to 73% (95% CI: 54-88).
This approach needs to be evaluated in a larger test set to determine the role of this gene set in early detection and surveillance of lung cancer.

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Available from: Andre Carvalho, Jan 27, 2014
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    • "Using similar methodology, the influence on meta-regression was determined by omitting one study each time to explore heterogeneity sources. The sample type of tissue or serum would be one of the heterogeneity sources (P < 0.026) when Begum et al. ([12], US) were removed from the meta studies; likewise, the proportion of stage I and aim of the study would become the heterogeneity source when Lin et al. ([17], China), Zhang et al. ([27], China) or Yanagawa et al. ([26], Japan) was removed (P-values were 0.0046, 0.029 and 0.039 respectively). This analysis suggested the above factors should be considered in a future case-control association study. "
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    03/2014; 6(1):5. DOI:10.1186/1868-7083-6-5
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    • "Some of these are as follows: 34 miRNA signatures [6], expression profiles of 11 miRNAs (miR-106a, miR-15b, miR-27b, miR-142-3p, miR-26b, miR-182, miR-126, let7g, let-7i and miR-30e-5p) from serum [7], 7 miRNA signatures [8], overexpression of six snoRNAs [9], and expression of 3 miRs (miR-205, miR-210 and miR-708) in sputum [10]. Additional signatures and markers have also been reported from the plasma proteome [11,12], the salivary proteome [13], the serum epigenome [14], sputum-based genomics [15], and blood-based gene expression studies [16]. However, none of these have progressed sufficiently to provide the necessary specificity and sensitivity required for clinical implementation. "
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    ABSTRACT: Lung cancer accounts for the highest number of cancer-related deaths worldwide. Early diagnosis significantly increases the disease-free survival rate and a large amount of effort has been expended in screening trials and the development of early molecular diagnostics. However, a gold standard diagnostic strategy is not yet available. Here, based on miRNA expression profile in lung cancer and using a novel in silico reverse-transcriptomics approach, followed by analysis of the interactome; we have identified potential transcription factor (TF) markers that would facilitate diagnosis of subtype specific lung cancer. A subset of seven TF markers has been used in a microarray screen and was then validated by blood-based qPCR using stage-II and IV non-small cell lung carcinomas (NSCLC). Our results suggest that overexpression of HMGA1, E2F6, IRF1, and TFDP1 and downregulation or no expression of SUV39H1, RBL1, and HNRPD in blood is suitable for diagnosis of lung adenocarcinoma and squamous cell carcinoma sub-types of NSCLC. Here, E2F6 was, for the first time, found to be upregulated in NSCLC blood samples. The miRNA-TF-miRNA interaction based molecular mechanisms of these seven markers in NSCLC revealed that HMGA1 and TFDP1 play vital roles in lung cancer tumorigenesis. The strategy developed in this work is applicable to any other cancer or disease and can assist in the identification of potential biomarkers.
    BMC Genomics 10/2013; DOI:10.1186/1471-2164-14-S6-S5 · 3.99 Impact Factor
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    • "Other genes with aberrant methylation in serum DNA have been found to associate with lung cancer risk, including TMEFF2[68], RUNX3[69] and CDH13 [70], suggesting that many genes in the serum could signify lung cancer risk and that a larger profile of aberrant methylation could produce a more accurate biomarker for lung cancer risk. The work by Begum et al. [71], who looked at methylation profiles of a slightly larger set of 15 genes and then selected the six most sensitive and specific genes for predicting lung cancer risk (APC, CDH1, MGMT, DCC, RASSF1A and AIM1), clearly shows evidence that a more global methylome approach could lead to a more sensitive (75%) and specific (73%) biomarker of lung cancer risk from serum DNA [71]. Methylation events in plasma, specifically in CDKN2A, MGMT and RASSF1A[61], as well as in peripheral blood leukocytes [58] and lymphocytes [72,73], are promising less invasive sites for assessing lung cancer risk through measuring DNA methylation differences. "
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    ABSTRACT: Lung cancer is the leading cause of cancer death worldwide in part due to our inability to identify which smokers are at highest risk and the lack of effective tools to detect the disease at its earliest and potentially curable stage. Recent results from the National Lung Screening Trial have shown that annual screening of high-risk smokers with low-dose helical computed tomography of the chest can reduce lung cancer mortality. However, molecular biomarkers are needed to identify which current and former smokers would benefit most from annual computed tomography scan screening in order to reduce the costs and morbidity associated with this procedure. Additionally, there is an urgent clinical need to develop biomarkers that can distinguish benign from malignant lesions found on computed tomography of the chest given its very high false positive rate. This review highlights recent genetic, transcriptomic and epigenomic biomarkers that are emerging as tools for the early detection of lung cancer both in the diagnostic and screening setting.
    BMC Medicine 07/2013; 11(1):168. DOI:10.1186/1741-7015-11-168 · 7.25 Impact Factor
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