Additional file 3: Table S1. of Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways

All ovarian cancer cell lines and their culture conditions. (XLSX 13 kb

Additional file 1: Figure S1. of Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways

a Clinicopathological features of transplanted HGSOC tumors. b Representation of patients and their corresponding PDX tumor samples used in this study. c All preprocessing of 450 K data of each sample. d DNA methylation level of each sample type according to HIL CpG classes [38] for PDX-36, -37, and -56 for all generation tumors (F0, F1, F2, and F3), p < 0.01. e Global distribution of 450 K methylation probes of the raw data of PDX-36, -37, and -56 for all generation tumors (F0, F1, F2, and F3). f Validation of global methylation using bisulfite pyrosequencing of ALU-Yb8 in PDX samples. Each bar represents average methylation (%) ± SD of five CpG sites for ALU-Yb8 in the indicated PDX samples. g Correlation heat map of PDX-36 biological replicates (n = 3) of generation F3 based on their genome-wide CpGs β values. Pearson correlation coefficients are shown in each heatmap box. (PDF 620 kb

Antibody-Free LC-MS/MS Quantification of rhTRAIL in Human and Mouse Serum

The major challenge in targeted protein quantification by LC-MS/MS in serum lies in the complexity of the biological matrix with regard to the wide diversity of proteins and their extremely large dynamic concentration range. In this study, an LC-MS/MS method was developed for the simultaneous quantification of the 60-kDa biopharmaceutical proteins recombinant human tumor necrosis factor-related apoptosis-inducing ligand wild type (rhTRAIL^WT) and its death receptor 4 (DR4)-specific variant rhTRAIL^4C7 in human and mouse serum. Selective enrichment of TRAIL was accomplished by immobilized metal affinity chromatography (IMAC), which was followed by tryptic digestion of the enriched sample and quantification of a suitable signature peptide. For absolute quantification, ¹⁵N-metabolically labeled internal standards of rhTRAIL^WT and rhTRAIL^4C7 were used. Since the signature peptides that provided the highest sensitivity and allowed discrimination between rhTRAIL^WT and rhTRAIL^4C7 contained methionine residues, we oxidized these quantitatively to their sulfoxides by the addition of 0.25% (w/w) hydrogen peroxide. The final method has a lower limit of quantification of 20 ng/mL (ca. 350 pM) and was fully validated according to current international guidelines for bioanalysis. To show the applicability of the LC-MS/MS method for pharmacokinetic studies, we quantified rhTRAIL^WT and rhTRAIL^4C7 simultaneously in serum from mice injected intraperitoneally at a dose of 5 mg/kg for each protein. This is the first time that two variants of rhTRAIL differing by only a few amino acids have been analyzed simultaneously in serum, an approach that is not possible by conventional enzyme-linked immuno-sorbent assay (ELISA) analysis