Novel Methylation Biomarker Panel for the Early Detection of Pancreatic Cancer

Abstract

Purpose Pancreatic cancer is the fourth leading cause of cancer deaths and there currently is no reliable modality for the early detection of this disease. Here we identify cancer-specific promoter DNA methylation of BNC1 and ADAMTS1 as a promising biomarker detection strategy meriting investigation in pancreatic cancer. Experimental Design We used a genome-wide pharmacologic transcriptome approach to identify novel cancer-specific DNA methylation alterations in pancreatic cancer cell lines. Of 8 promising genes, we focused our studies on BNC1 and ADAMTS1 for further downstream analysis including methylation and expression. We used a nanoparticle-enabled MOB (Methylation On Beads) technology to detect early stage pancreatic cancers by analyzing DNA methylation in patient serum. Results We identified 2 novel genes, BNC1 (92%) and ADAMTS1, (68%) that showed a high frequency of methylation in pancreas cancers (n=143), up to 100% in PanIN-3 and 97% in Stage I invasive cancers. Using the nanoparticle-enabled MOB technology, these alterations could be detected in serum samples (n=42) from pancreas cancer patients, with a sensitivity for BNC1 of 79% (95%CI:66-91%) and for ADAMTS1 of 48% (95%CI:33-63%), while specificity was 89% for BNC1 (95%CI:76-100%) and 92% for ADAMTS1 (95%CI:82-100%). Overall sensitivity using both markers is 81% (95%CI:69-93%) and specificity is 85% (95%CI:71-99%). Conclusions Promoter DNA methylation of BNC1 and ADAMTS1 are potential biomarkers to detect early stage pancreatic cancers. Assaying the promoter methylation status of these genes in circulating DNA from serum is a promising strategy for early detection of pancreatic cancer and has the potential to improve mortality from this disease.

Cell-free DNA promoter hypermethylation in plasma as a diagnostic marker for pancreatic adenocarcinoma

“…Cell-free DNA hypermethylation of BMP3 , MESTv2 , SST , TFPI2 , TAC1 , ALX4 , HIC1 , SFRP2 , SEPT9v2 and WNT5A has not previously been described in the literature in relation to pancreatic cancer. Yi et al described BNC1 hypermethylation to have a sensitivity of 79% and a specificity of 89% when comparing pancreatic cancer and healthy individuals [17]. We found BNC1 to be hypermethylated in only 36% of pancreatic cancer patients with a specificity of 94%.…”

“…This approach was used, to evaluate the overall diagnostic performance of genes which previously had been examined separately as diagnostic markers for pancreatic cancer. The panel was composed of genes previously detected as hypermethylated in plasma/serum and tumour tissue in relation to pancreatic adenocarcinoma ( BNC1 [17, 24, 25], NPTX2 [4, 24–26], PENK [4, 14, 25], CDKN2A [4, 26, 27], RASSF1A [4, 24, 27], SFRP1 ( SARP2 ) [4, 25], APC [24, 27], BRCA1 [28, 29], CDKN2B [28, 30], ESR1 [25, 28], MGMT [24, 28], MLH1 [28, 31] and RARB [28, 32]), genes earlier found to be hypermethylated in pancreatic juice or tumour tissue from patients with pancreatic adenocarcinoma ( BMP3 [24], EYA2 [24], GSTP1 [29], HIC1 [25, 33], SFRP2 [24], TFPI2 [25], VIM [25], NEUROG1 [24, 25], TAC1 [24, 25], CHFR [24] and WNT5a [24, 25]) and genes found based on a pilot study on cell-free DNA hypermethylation in colorectal adenocarcinoma ( ALX4 , MESTv2 , SEPT9v2 and SST ). To our knowledge, this is the first study to examine cell-free DNA hypermethylation in a wide selection of genes by methylation-specific PCR in a large group of patients with either malignant or benign pancreatic disease.…”

“…These data have shown a significant difference in DNA hypermethylation between patients with pancreatic cancer and healthy controls [4, 17]. However, the studies had difficulties in differentiating between malignant and benign pancreatic disease [4].…”

Pancreatic Cancer Cell Fraction Estimation in a DNA Sample

“…Third, our present criterion for the isolation of fraction marker genes might have been too strict. Indeed, although BNC1, ADMTS1, and CD1D have been reported to be accurate in the detection of pancreatic cancers [37,38], these genes were excluded from the candidate marker genes in this study. Specifically, ADMTS1 showed a low incidence of methylation (β > 0.3) in the cancer tissues (0-2 of 22 tissues).…”

Extracting biomarkers of commitment to cancer development: potential role of vibrational spectroscopy in systems biology

“…These oligonucleotides are complimentary to genes on the array and allow the measurement of particular gene expression profiles with high sensitivity. This array is unable to predict and analyze unknown genes, as their sequences need to be known for the manufacture of the [219] PSA [220] Cyclooxygenasearachidonic acid metabolites [221] 2000 cell surface protein cluster in cancer [222] Ovarian BRCA1 BRCA2 mutations [223] CpG-island hypermethylation (BRCA1) [224] Prostasin [225] HE4 [226] Ca125 [227] Eosinophil-derived neurotoxin and COOHterminal osteopontin [228] Breast BRCA1 BRCA2 mutations [223] CpG-island hypermethylation (BRCA1, E-cadherin, TMS1 and estrogen receptor) [229] EpCAM, CD45 [230] Pancreatic Palladin mutation [231] BNC1 ADAMTS1 methylation [232] A1-antitrypsin Apolipoprotein A1 [233] Gastric PTEN mutation [234] CpG-island hypermethylation (hMLH1 and p14ARF) [235] miR-1, miR20a, miR-27a, miR-34 and miR-423-5p expression [236] Hepatocellular RASSF1A, SSBP2 and B4GALT1 hypermethylation [237] AFP-L3 [238] Colorectal CpG-island hypermethylation, hypermethylation of miRNAs (miR-124a) [239] p53 expression [239], EGFR-related KRAS [240], c-MET, b-catenin [241] CEA [242] Smaller number of combinational molecular phenotype cluster in cancer [167] Some of these biomarkers are currently in clinical practice. AFP: Alpha feto-protein; CEA: Carcino-embryonic antigen; PSA: Prostate specific antigen.…”