Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.

ABSTRACT: Cancer progression depends on both cell-intrinsic processes and interactions between different cell types. However, large-scale assessment of cell type composition and molecular profiles of individual cell types within tumors remains challenging. To address this, we developed epigenomic deconvolution (EDec), an in silico method that infers cell type composition of complex tissues as well as DNA methylation and gene transcription profiles of constituent cell types. By applying EDec to The Cancer Genome Atlas (TCGA) breast tumors, we detect changes in immune cell infiltration related to patient prognosis, and a striking change in stromal fibroblast-to-adipocyte ratio across breast cancer subtypes. Furthermore, we show that a less adipose stroma tends to display lower levels of mitochondrial

SUBMITTER: Onuchic V 

PROVIDER: S-EPMC5115176 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature