Methylome remodeling in regional breast cancer metastasis [expression]

We sought to characterize methylome remodeling during regional metastasis. We profiled the DNA methylome (n=44) and transcriptome (n=36) of matched primary breast tumors and regional metastases. All paired samples (n = 88) were obtained following surgical resection at the MSKCC as part of routine clinical care, and snap frozen. Tumors were obtained in accordance with Institutional Review Board policies at the MSKCC. Each sample was examined histologically by a breast pathologist and microdissected to achieve >70% tumor cell content. Genomic DNA or RNA was extracted using the DNeasy kit (Qiagen) or RNeasy Kit (Qiagen) as per the manufacturer’s instructions. Expression analysis of tumors was performed using the Affymetrics U133 2.0 microarray (Affymetrix). Affymetrix CEL files were imported into the Partek Genomics Suite 6.1 (Partek), using RMA normalization.