Epigenome analysis of MTHFD2 as a biomarker for decitabine response in MDA-MB-231 tumours

Genome-wide DNA methylation profiling of MDA-MB-231 tumours with or without MTHFD2 knockdown and decitabine treatment. The Illimuna Infinium MethylationEPIC DNA Beadchip v-1-0 B3 was used to obtain DNA methylation performed by The Centre for Applied Genomics in Toronto, Canada. Samples from 24 MDA-MB-231 tumours with or without MTHFD2 knockdown were implanted into NOD-SCID mice that received either control PBS or decitabine treatment were analysed. The tumours had either scramble control lentiviral vector or shRNA knockdown. There were two shRNA clones, labeled shRNA 1 or 2. Eight samples from each clone were submitted, with four each of PBS control or decitabine-treated tumours. Bisulphite converted DNA from the 24 samples were hybridized to the Illumina Infinium MethylationEPIC Beadchip v-1-0 B3.