Design and experimental validation of OPERA_MET-A panel for deep methylation analysis by next generation sequencing

DNA methylation is the most recognized epigenetic mark that leads to a massive distortion in cancer cells. It has been observed that a large number of DNA aberrant methylation events occur simultaneously in a group of genes, thus providing a growth advantage to the cell in promoting cell differentiation and neoplastic transformation. Due to this reason, methylation profiles have been suggested as promising cancer biomarkers. Here, we designed and performed a first step of validation of a novel targeted next generation sequencing (NGS) panel for methylation analysis, which can simultaneously evaluate the methylation levels at CpG sites of multiple cancer-related genes. The OPERA_MET-A methylation panel was designed using the Ion AmpliSeq™ technology to amplify 155 regions with 125-175 bp mean length and covers a total of 1107 CpGs of 18 cancer-related genes. The performance of the panel was assessed by running commercially available fully methylated and unmethylated control human genomic DNA (gDNA) samples and a variable mixture of them. The libraries were run on Ion Torrent platform and the sequencing output was analyzed using the “methylation_analysis” plugin. DNA methylation calls on both Watson (W) and Crick (C) strands and methylated:unmethylated ratio for each CpG site were obtained. Cell lines, fresh frozen and formalin-fixed paraffin-embedded (FFPE) lung cancer tissues were tested. The OPERA_MET-A panel allows to run a minimum of 6 samples/530 chip to reach an observed mean target depth ≥2,500X (W and C strands) and an average number of mapped reads >750,000/sample. The conversion efficiency, determined by spiking-in unmethylated Lambda DNA into each sample before the bisulfite conversion process, was >97% for all samples. The observed percentage of global methylation for all CpGs was >95% and <5% for fully methylated and unmethylated gDNA samples, respectively, and the observed results for the variable mixtures were in agreement with what was expected. Methylation-specific NGS analysis represents a feasible method for a fast and multiplexed screening of cancer patients by a high-throughput approach. Moreover, it offers the opportunity to construct a more robust algorithm for disease prediction in cancer patients having a low quantity of biological material available.

Bilateral Brenner tumor with endometrial adenocarcinoma in a postmenopausal woman

Brenner tumor is a rare ovarian neoplasm which is generally monolateral, more rarely bilateral, and often associated with endometrial disorders related to oestrogenic production. However, there is no considerable evidence that the possible oestrogenic production of this tumor may be the cause of endometrial disorders. A case of bilateral Brenner tumor with endometrial adenocarcinoma in a postmenopausal woman is presented and the features are briefly discussed, with the conclusion that hormone-producing Brenner tumors may exert their promoter effect on the development of endometrial carcinoma causing an imbalance in the oestrogen and progesterone ratio rather than producing a large amount of oestrogen.

Alpha-fetoprotein production by pancreatic tumors exhibiting acinar cell differentiation: study of five cases, one arising in a mediastinal teratoma

Five cases of pancreatic neoplasms accompanied by production of alpha-fetoprotein (AFP) and serum elevation of this marker are presented, and the better-documented cases of this phenomenon from the literature are reviewed. Four of the cases originated in the orthotopic pancreas, whereas the fifth arose in the pancreatic component of a mediastinal teratoma. The patients were children or young adults. AFP production in pancreatic tumors is closely linked to acinar differentiation, most cases representing either pancreatoblastoma or acinar cell carcinoma. The distinction between these 2 tumors may be difficult because of the many morphologic and immunohistochemical features they share.