Profiling the Epigenetic Landscape of the Tumor Microenvironment Using Chromatin Immunoprecipitation Sequencing

Abstract

Cancer cells within a tumor exhibit phenotypic plasticity that allows adaptation and survival in hostile tumor microenvironments. Reprogramming of epigenetic landscapes can support tumor progression within a specific microenvironment by influencing chromatin accessibility and modulating cell identity. The profiling of epigenetic landscapes within various tumor cell populations has significantly improved our understanding of tumor progression and plasticity. This protocol describes an integrated approach using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) optimized to profile genome-wide post-translational modifications of histone tails in tumors. Essential tools amenable to ChIP-seq to isolate tumor cell populations of interest from the tumor microenvironment are also presented to provide a comprehensive approach to perform heterogeneous epigenetic landscape profiling of the tumor microenvironment.

Keywords: Cell isolation; Chromatin immunoprecipitation followed by sequencing; Epigenetic heterogeneity; Epigenetic profiling; Phenotypic plasticity; Regional tumor microdissection; Single-cell tumor dissociation; Tumor microenvironment.