Search

Survival alleles at SNV level

Supplementary Figure 3

Somatic mutations and single nucleotide variants (SNVs) in paired tissue from cervical swabs, serum/plasma and urine from patient TG01

Supplementary Figure 1

Supplementary Figure 4

Supplementary Figure 2

Legends for Supplementary Figures 1-4

Methylation and mutation associations

Molecular alterations that contribute to long-term (LT) and short-term (ST) survival in ovarian high-grade serous carcinoma (HGSC) may be used as precision medicine biomarkers. DNA promoter methylation is an early event in tumorigenesis, which can be detected in blood and urine, making it a feasible companion biomarker to somatic mutations for early detection and targeted treatment workflows. We compared the methylation profile in 12 HGSC tissue samples to 30 fallopian tube epithelium samples, using the Infinium Human Methylation 450K Array. We also used 450K methylation arrays to compare methylation among HGSCs long-term survivors (more than 5 years) and short-term survivors (less than 3 years). We verified the array results using bisulfite sequencing and methylation-specific PCR (qMSP). in another cohort of HGSC patient samples (n = 35). Immunoblot and clonogenic assays after pharmacologic unmasking show that HIST1H2BB and MAGI2 promoter methylation downregulates mRNA expression levels in ovarian cancer cells. We then used qMSP in paired tissue, ascites, plasma/serum, vaginal swabs, and urine from a third cohort of patients with HGSC cancer (n = 85) to test the clinical potential of HIST1H2BB and MAGI2 in precision medicine workflows. We also performed next-generation exome sequencing of 50 frequently mutated in human cancer genes, using the Ion AmpliSeqCancer Hotspot Panel, to show that the somatic mutation profile found in tissue and plasma can be quantified in paired urine samples from patients with HGSC. Our results suggest that HIST1H2BB and MAGI2 have growth-suppressing roles and can be used as HGSC precision medicine biomarkers.

Somatic mutations and single nucleotide variants (SNVs) in paired tissue from cervical swabs, serum/plasma and urine from patient TG05

Introduction: Ovarian cancer (OC) is one of the most lethal diseases in the female population worldwide, being considered by 2020 the eighth most common type of cancer and the eighth cause of cancer death in that population. The most widely used chemotherapy treatment is based on the application of platinum based drugs, carboplatin (CBDCA) being one of the most common, in combination with taxanes and cisplatin. Unfortunately, a high percentage of the population relapses shortly after chemotherapy treatment, presenting a drug resistant phenotype. This phenotype reduces overall survival in patients with OC. In this context, various mechanisms have been investigated to understand and study these chemoresistant phenotypes. In the last decade, lncRNAs have been identified in multiple biological processes, including the development of drug-resistant phenotypes in malignant tumors, however, little is known about their role in carboplatin resistance in OC. This study seeks to characterize the effect of lncRNA expression on the chemoresistant phenotype and its potential molecular mechanism involved. Materials and Methods: Ovarian cancer cell lines corresponding to: A2780-R-CBDCA, A2780-P, UCI-101, OVCAR3 and SKOV3 were used. Drug susceptibility assays were performed using MTT. Relative expression was performed via RTqPCR. RNAseq was performed on a CBDCA resistance model in vitro using the Illumina HiSeq 4000 platform. Gene Ontology (GO) was analyzed using ClueGO. Gene set enrichment analysis (GSEA) was performed to define enriched biological pathways. Triplexator was used to predict the triplex forming oligonucleotides (TFO) and triplex target sites (TTS) that may be involved in the formation of RNA-DNA triplexes. Results: RNAseq analysis showed 156 differentially expressed protein coding genes (DEGs). The most enriched and deregulated signaling pathway was Wnt/β-catenin. In this context, several regulators of this pathway were found to be altered, including sFRP1, sFRP4, PCDHB6, CTNNA2, DACT1, PCDHB6, WNT3A, and CER1. In addition, 17 lncRNAs involved in CDBCA resistance were found to be deregulated. In this sense, MNX1-AS1 showed high levels of expression in CBDCA resistant cell lines. Interestingly, it has been shown that MNX1-AS1 has the ability to form a triplex with the PCDHB6 gene, which is a tumor suppressor gene and whose expression was found to be decreased in CBDCA resistant cell lines. Conclusions: Our results indicate that MNX1-AS1 expression could contribute to the modulation of platinum drug resistance through regulation of PCDHB6 expression via triplexes formation in OC. This finding could explain a new mechanism in CBDCA resistance in OC. Citation Format: Tamara Alejandra Viscarra Alvarez, Kurt Leopoldo Buchegger Mena, Daniela Inés León Garrido, Carmen Gloria Ili Gangas, Jorge Sapunar Zenteno, Marcela Berrios Flores, Ramón Silva Pezoa, Sindy Paola Cabarca Barreto, Priscilla Brebi Mieville. New potential mechanism of mnx1-as1 in the regulation of the carboplatin chemoresistant phenotype in ovarian cancer cell lines. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3895.

Introduction: Ovarian cancer is one of the most lethal diseases in the female population worldwide. Indeed, the survival rate of ovarian cancer is very low when diagnosed lately and the success rate of current chemotherapy regimens is not very efficient. One of the main chemotherapy treatment regimens is the use of platinum drugs, specifically carboplatin (CBDCA). Nevertheless, one of the main reasons for this low success rate is the acquired chemoresistance of these cancers during their progression. The mechanisms responsible for this chemoresistance are numerous, including efflux pumps, repair mechanisms, survival pathways and tumor suppressors. In the last decade, lncRNAs have been identified as a new element responsible in the regulation of chemoresistant phenotype since they have been linked to multiple biological processes and acting in combination with other mechanism involved in chemoresistant. However, little is known about their role in carboplatin resistance in OC. This study seeks to characterize the effect of lncRNA expression on the chemoresistant phenotype and its correlation with the hyperactivation of drug efflux pumps. Materials and Methods: Ovarian cancer cell lines A2780-R-CBDCA, A2780-P, UCI-101, OVCAR3 and SKOV3 were used in this study. Chemosensitivity to carboplatin was measured by MTT Assay in 96-well plates after 24, 48 and 72h treatment for determinating IC50 values. Relative expression of MNX1-AS1 associated with CBDCA-resistant phenotype and efflux pumps were evaluated by qRT-PCR. Results: It was observed that A2780-R-CBDCA, SKOV3 and OVCAR3 cell lines presented the highest resistance indices in contrast to UCI-101 and A2780-P, which turned out to be highly sensitive to treatment with CBDCA. The relative expression of MNX1-AS1 was found elevated in those lines that presented higher levels of resistance to the drug, while in those more sensitive to treatment, the expression of MNX1-AS1 was found to be decreased. On the other hand, the expression levels of the ABCB1 and ABCC1 efflux pumps showed contradictory results in relation to their expression compared to the resistance index shown in each cell line. Mainly, it could be observed that ABCB1 presented a decreased expression in A2780-R-CBDCA, while ABCC1 was found to be increased in the same line. Conclusion: Our results indicate that the expression of MNX1-AS1 could contribute to the development or maintenance of a chemoresistant phenotype to platinum drugs. Meanwhile, the effect of the expression of MNX1-AS1 on the efflux pumps is not yet possible to relate as a modulator of its hyperactivation. However, their potential participation in this mechanism is not ruled out and new analyzes are necessary to rule out this possible relationship. Citation Format: Kurt Buchegger Mena, Tamara Viscarra Alvarez, Daniela León Garrido, Ramón Silva Pezoa, Carmen Ili Gangas, Sindy Cabarca Barreto, Marcela Berrios Flores, Jorge Sapunar Zenteno, Priscilla Brebi Mieville. MNX1-AS1 expression is positively correlates with expression of drug efflux pumps in ovarian cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3897.

Molecular alterations that contribute to long-term (LT) and short-term (ST) survival in ovarian high-grade serous carcinoma (HGSC) may be used as precision medicine biomarkers. DNA promoter methylation is an early event in tumorigenesis, which can be detected in blood and urine, making it a feasible companion biomarker to somatic mutations for early detection and targeted treatment workflows. We compared the methylation profile in 12 HGSC tissue samples to 30 fallopian tube epithelium samples, using the Infinium Human Methylation 450K Array. We also used 450K methylation arrays to compare methylation among HGSCs long-term survivors (more than 5 years) and short-term survivors (less than 3 years). We verified the array results using bisulfite sequencing and methylation-specific PCR (qMSP). in another cohort of HGSC patient samples (n = 35). Immunoblot and clonogenic assays after pharmacologic unmasking show that HIST1H2BB and MAGI2 promoter methylation downregulates mRNA expression levels in ovarian cancer cells. We then used qMSP in paired tissue, ascites, plasma/serum, vaginal swabs, and urine from a third cohort of patients with HGSC cancer (n = 85) to test the clinical potential of HIST1H2BB and MAGI2 in precision medicine workflows. We also performed next-generation exome sequencing of 50 frequently mutated in human cancer genes, using the Ion AmpliSeqCancer Hotspot Panel, to show that the somatic mutation profile found in tissue and plasma can be quantified in paired urine samples from patients with HGSC. Our results suggest that HIST1H2BB and MAGI2 have growth-suppressing roles and can be used as HGSC precision medicine biomarkers.

ABSTRACT Aim: The aim of the study was to evaluate the use of global and gene-specific DNA methylation changes as potential biomarkers for gallbladder cancer (GBC) in a cohort from Chile. Material & methods: DNA methylation was analyzed through an ELISA-based technique and quantitative methylation-specific PCR. Results: Global DNA Methylation Index (p = 0.02) and promoter methylation of SSBP2 (p = 0.01) and ESR1 (p = 0.05) were significantly different in GBC when compared with cholecystitis. Receiver curve operator analysis revealed promoter methylation of APC, CDKN2A, ESR1, PGP9.5 and SSBP2, together with the Global DNA Methylation Index, had 71% sensitivity, 95% specificity, a 0.97 area under the curve and a positive predictive value of 90%. Conclusion: Global and gene-specific DNA methylation may be useful biomarkers for GBC clinical assessment.

Methylation alterations of CpG islands, CpG island shores and first exons are key events in the formation and progression of human cancer, and an increasing number of differentially methylated regions and genes have been identified in breast cancer. Recent studies of the breast cancer methylome using deep sequencing and microarray platforms are providing a novel insight on the different roles aberrant methylation plays in molecular subtypes of breast cancer. Accumulating evidence from a subset of studies suggests that promoter methylation of tumor-suppressor genes associated with breast cancer can be quantified in circulating DNA. However, there is a paucity of studies that examine the combined presence of genetic and epigenetic alterations associated with breast cancer using blood-based assays. Dysregulation of DNA repair capacity (DRC) is a genetic risk factor for breast cancer that has been measured in lymphocytes. We isolated plasma DNA from 340 participants in a breast cancer case control project to study promoter methylation levels of five genes previously shown to be associated with breast cancer in frozen tissue and in cell line DNA: MAL, KIF1A, FKBP4, VGF and OGDHL. Methylation of at least one gene was found in 49% of the cases compared to 20% of the controls. Three of the four genes had receiver characteristic operator curve values of ≥ 0.50: MAL (0.64), KIF1A (0.51) and OGDHL (0.53). KIF1A promoter methylation was associated with breast cancer and inversely associated with DRC. This is the first evidence of a significant association between genetic and epigenetic alterations in breast cancer using blood-based tests. The potential diagnostic utility of these biomarkers and their relevance for breast cancer risk prediction should be examined in larger cohorts.

// Francesca Pirini 1, * , Sassan Noazin 2, * , Martha H. Jahuira-Arias 3, 4, * , Sebastian Rodriguez-Torres 3 , Leah Friess 3 , Christina Michailidi 3 , Jaime Cok 5 , Juan Combe 6 , Gloria Vargas 7 , William Prado 8 , Ethan Soudry 3 , Jimena Perez 3 , Tikki Yudin 3 , Andrea Mancinelli 3 , Helen Unger 3 , Carmen Ili-Gangas 9, 10 , Priscilla Brebi-Mieville 9, 10 , Douglas E. Berg 11, 12 , Masamichi Hayashi 3, 13 , David Sidransky 3 , Robert H. Gilman 2, 4 , Rafael Guerrero-Preston 3, 14 1 Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy 2 The Johns Hopkins University, Bloomberg School of Public Health, Department of International Health, Baltimore, MD, USA 3 The Johns Hopkins University, School of Medicine, Otolaryngology Department, Head and Neck Cancer Research Division, Baltimore, MD, USA 4 Universidad Peruana Cayetano Heredia, Lima, Peru 5 Hospital Nacional Cayetano Heredia, Pathology Department, Lima, Peru 6 Instituto Nacional de Enfermedades Neoplasicas, Gastroenterology Department, Lima, Peru 7 Hospital Nacional Arzobispo Loayza, Gastroenterology Department, Lima, Peru 8 Hospital Nacional Dos de Mayo, Gastroenterology Department, Lima, Peru 9 Laboratory of Molecular Pathology, Department of Pathological Anatomy, School of Medicine, Universidad de La Frontera, Temuco, Chile 10 Center of Excellence in Translational Medicine - Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco, Chile 11 Washington University Medical School, Department of Molecular Microbiology, St Louis, MO, USA 12 University of California San Diego, Department of Medicine, La Jolla, CA, USA 13 Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan 14 University of Puerto Rico School of Medicine, Department of Obstetrics and Gynecology, San Juan, Puerto Rico * These authors equally contributed to this work Correspondence to: Rafael Guerrero-Preston, email: rafael.guerrero@upr.edu Robert H. Gilman, email: rgilman1@jhmi.edu Keywords: translational epigenomics, global DNA methylation index, epigenome-wide DNA methylation analysis, IRF4, ELMO1 Received: January 09, 2017 Accepted: February 24, 2017 Published: March 16, 2017 ABSTRACT Clinically useful molecular tools to triage gastric cancer patients are not currently available. We aimed to develop a molecular tool to predict gastric cancer risk in endoscopy-driven biopsies obtained from high-risk gastric cancer clinics in low resource settings. We discovered and validated a DNA methylation biomarker panel in endoscopic samples obtained from 362 patients seen between 2004 and 2009 in three high-risk gastric cancer clinics in Lima, Peru, and validated it in 306 samples from the Cancer Genome Atlas project (“TCGA”). Global, epigenome wide and gene-specific DNA methylation analyses were used in a Phase I Biomarker Development Trial to identify a continuous biomarker panel that combines a Global DNA Methylation Index (GDMI) and promoter DNA methylation levels of IRF4, ELMO1, CLIP4 and MSC . We observed an inverse association between the GDMI and histological progression to gastric cancer, when comparing gastritis patients without metaplasia (mean = 5.74, 95% CI, 4.97−6.50), gastritis patients with metaplasia (mean = 4.81, 95% CI, 3.77−5.84), and gastric cancer cases (mean = 3.38, 95% CI, 2.82−3.94), respectively ( p 4 are useful molecular tools for gastric cancer risk stratification in endoscopic biopsies.

Differentially methylated oral squamous cell carcinoma (OSCC) biomarkers, identified in vitro and validated in well-characterized surgical specimens, have shown poor clinical correlation in cohorts with different risk profiles. To overcome this lack of relevance, we used the HumanMethylation27 BeadChip, publicly available methylation and expression array data, and quantitative methylation specific PCR to uncover differential methylation in OSCC clinical samples with heterogeneous risk profiles. A two stage design consisting of discovery and prevalence screens was used to identify differential promoter methylation and deregulated pathways in patients diagnosed with OSCC and head and neck squamous cell carcinoma. Promoter methylation of KIF1A (κ = 0.64), HOXA9 (κ = 0.60), NID2 (κ = 0.60), and EDNRB (κ = 0.60) had a moderate to substantial agreement with clinical diagnosis in the discovery screen. HOXA9 had 68% sensitivity, 100% specificity, and a 0.81 Area Under the Curve (AUC). NID2 had 71% sensitivity, 100% specificity, and a 0.79 AUC. In the prevalence screen, HOXA9 (κ = 0.82) and NID2 (κ = 0.80) had an almost perfect agreement with histologic diagnosis. HOXA9 had 85% sensitivity, 97% specificity, and a 0.95 AUC. NID2 had 87% sensitivity, 95% specificity, and a 0.91 AUC. A HOXA9 and NID2 gene panel had 94% sensitivity, 97% specificity, and a 0.97 AUC. In saliva, from OSCC cases and controls, HOXA9 had 75% sensitivity, 53% specificity, and a 0.75 AUC. NID2 had 87% sensitivity, 21% specificity, and a 0.73 AUC. This phase I Biomarker Development Trial identified a panel of differentially methylated genes in normal and OSCC clinical samples from patients with heterogeneous risk profiles. This panel may be useful for early detection and cancer prevention studies. Cancer Prev Res; 4(7); 1061–72. ©2011 AACR.

Environmental exposures in utero may alter the epigenome, thus impacting chromosomal stability and gene expression. We hypothesized that in utero exposures to maternal smoking and perfluoroalkyl compounds (PFCs) are associated with global DNA hypomethylation in umbilical cord serum. Our objective was to determine if global DNA methylation could be used as a biomarker of in utero exposures to maternal smoking and PFCs. Using an ELISA-based method, global DNA methylation was quantified in umbilical cord serum from 30 newborns with high (>10 ng/ml, mean 123.8 ng/ml), low (range 1–10 ng/ml, mean 1.6 ng/ml) and very low (

MicroRNAs (miRNAs) are defined as small non-coding RNAs ~22 nt in length. They regulate gene expression at a post-transcriptional level through complementary base pairing with the target mRNA, leading to mRNA degradation and therefore blocking translation. In the last decade, the dysfunction of miRNAs has been related to the development and progression of many diseases. Currently, researchers need a method to identify precisely the miRNA targets, prior to applying experimental approaches that allow a better functional characterization of miRNAs in biological processes and can thus predict their effects. Computational prediction tools provide a rapid method to identify putative miRNA targets. However, since a large number of tools for the prediction of miRNA:mRNA interactions have been developed, all with different algorithms, the biological researcher sometimes does not know which is the best choice for his study and many times does not understand the bioinformatic basis of these tools. This review describes the biological fundamentals of these prediction tools, characterizes the main sequence-based algorithms, and offers some insights into their uses by biologists.

The methylated DNA immunoprecipitation method (MeDIP) is a genome-wide, high-resolution approach that detects DNA methylation with oligonucleotide tiling arrays or high throughput sequencing platforms. A simplified high-throughput MeDIP assay will enable translational research studies in clinics and populations, which will greatly enhance our understanding of the human methylome. We compared three commercial kits, MagMeDIP Kit TM (Diagenode), Methylated-DNA IP Kit (Zymo Research) and Methylamp (TM) Methylated DNA Capture Kit (Epigentek), in order to identify which one has better reliability and sensitivity for genomic DNA enrichment. Each kit was used to enrich two samples, one from fresh tissue and one from a cell line, with two different DNA amounts. The enrichment efficiency of each kit was evaluated by agarose gel band intensity after Nco I digestion and by reaction yield of methylated DNA. A successful enrichment is expected to have a 1:4 to 10:1 conversion ratio and a yield of 80% or higher. We also evaluated the hybridization efficiency to genome-wide methylation arrays in a separate cohort of tissue samples. We observed that the MagMeDIP kit had the highest yield for the two DNA amounts and for both the tissue and cell line samples, as well as for the positive control. In addition, the DNA was successfully enriched from a 1:4 to 10:1 ratio. Therefore, the MagMeDIP kit is a useful research tool that will enable clinical and public health genome-wide DNA methylation studies.

Background: Most genome-wide methylation studies have focused on technology to profile and identify therapeutic biomarkers in HCC. However, attempts to integrate these technologies to clinical and population based studies are still lacking. Objective: Our aim was to identify existing methylation profiling technologies that can be used in translational epigenomic efforts. Methods: We examined Quantitative Methylation specific PCR, oligonucleotide methylation tiling arrays (MeDIP-chip), and Methylation BeadChip arrays and their ability to distinguish between HHC cases and controls, a key goal in Phase I biomarker development trials. Scatterplots, histograms and heat maps of genome-wide DNA methylation array data were used to provide a snapshot of the differences in methylation patterns between tumor and normal samples. Results: The representative tumor sample had a lower methylation score median and less significant genome-wide methylated probes (1,503) than either normal liver tissue samples (2,585 and 2,2887 respectively). RASSF1A and B4GALT1 had a sensitivity of 52%, a specificity of 100% and an AUC of 0.73 (RASSF1A) and 0.75 (B4GALT1). SSBP2 had a sensitivity of 38%, a specificity of 100% and an AUC of 0.58. A panel combining these genes with HCC risk factors had a sensitivity of 87%, a specificity of 100% and an AUC of 0.91. Conclusions: We have shown that genome-wide and gene-specific methylation platforms, which interrogate gene promoter regions, can be used to examine novel biomarkers and differentiate HCC from normal liver tissue. Additional studies will confirm the value of using methylation-profiling technologies to evaluate these new markers as we move forward. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3172. doi:10.1158/1538-7445.AM2011-3172

Introduction: Panels of hypermethylated genes have been proposed as diagnostic markers in primary head and neck squamous cell carcinoma using a pharmacological unmasking expression microarray approach. Such experiments are performed in cancer cell lines, mostly with poor relevance when extrapolating to primary cancers. Objective: To overcome this lack of relevance we used two unbiased genome-wide DNA methylation platforms that represent 28K CpG Islands and the promoter regions of 14K-17K genes to identify hypermethylated genes in Oral Squamous Cell Carcinoma (OSCC), which also exhibited downregulated expression in the Gene Expression Omnibus (GEO) repository. Methods: DNA isolated from normal, premalignant lesions and squamous cell carcinoma lesions of the oral cavity was: a) bisulfite treated and hybridized to Infinium arrays; b) enriched with Methylated DNA Immunoprecipitation (MeDIP) and hybridized to Nimblegen 385K tiling arrays. Bioinformatics strategies were used for background correction, array normalization and data analysis of differentially methylated genomic regions between tumor and normal tissue. Genes identified as hypermethylated in cancer with methylation platforms were cross-validated against expression profiles published in the GEO public data repository. Quantitative Methylation Specific PCR (QMSP) was then used to validate candidate genes that were both, hypermethylated and downregulated in cancer. Results: The two unbiased microarray platforms were successful in identifying three novel genes hypermethylated and down regulated in OSCC: MCAM, EDNRB and CALCA. EDNRB, MCAM and CALCA expression was downregulated in HNSCC when compared to normal tissue. A twofold or higher downregulated expression was seen for EDNRB (59%) than for MCAM (55%) and CALCA (55%). The sensitivity of each gene was higher for EDNRB (82%) than for MCAM (60%) and CALCA (76%). The specificity was also higher for EDNRB (86%) than for CALCA (71%), and MCAM (57%). KIF1a had both high sensitivity (82%) and specificity (86%) but there was no expression data in HNSCC available for this gene in the GEO repository. The Receiver Characteristic Operator Curves (ROC) for individual genes revealed area under the curve values (AUC) for: EDNRB (0.88), CALCA (0.85), KIF1a (0.84), and MCAM (0.61). Methylation of three genes was found in 71% of tumor and 0% of normal tissue. Methylation of two genes was found in 82% of tumor and 29% of normal tissue. Conclusion: We successfully demonstrated that unbiased genome-wide methylation arrays paired with publicly available expression data identify panels of relevant hypermethylated genes in primary OSCC. MCAM, KIF1a, EDNRB and CALCA were identified as hypermethylated in OSSC tumor tissue, when compared to normal tissue. These results should be validated in a Phase II Biomarker Development Study. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2924.

The majority of the epigenomic reports in hepatocellular carcinoma have focused on identifying novel differentially methylated drivers or passengers of the oncogenic process. Few reports have considered the technologies in place for clinical translation of newly identified biomarkers. The aim of this study was to identify epigenomic technologies that need only a small number of samples to discriminate HCC from non-HCC tissue, a basic requirement for biomarker development trials. To assess that potential, we used quantitative Methylation Specific PCR, oligonucleotide tiling arrays, and Methylation BeadChip assays. Concurrent global DNA hypomethylation, gene-specific hypermethylation, and chromatin alterations were observed as a hallmark of HCC. A global loss of promoter methylation was observed in HCC with the Illumina BeadChip assays and the Nimblegen oligonucleotide arrays. HCC samples had lower median methylation peak scores and a reduced number of significant promoter-wide methylated probes. Promoter hypermethylation ofRASSF1A,SSBP2, andB4GALT1quantified by qMSP had a sensitivity ranging from 38% to 52%, a specificity of 100%, and an AUC from 0.58 to 0.75. A panel combining these genes with HCC risk factors had a sensitivity of 87%, a specificity of 100%, and an AUC of 0.91.