Epigenetic profiling of docetaxel resistance in Breast Cancer

Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across 850000 CpGsites in nine different breast cancer PDX models. Docetaxel resistant and residual disease PDX models were also analyzed DNA was isoleted from frozen tumors of different TNBC PDX models sensitive to docetaxel and from docetaxel resistant-derived TNBC PDX models. DNA was quanitifed by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600ng of each sample was performed according to the manufacturer’s recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for the threecontrols that were converted simultaneously with the samples.4ul of bisulfite converted DNA were used to hybridize on Infinium MethylationEPIC BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intesities of the images were extracted with Minfi in Rstudio. Methylation score of each CpG is represented as beta value