Pathology tissue–chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples

Epigenetic alterations in the pattern of DNA and histone modifications (such as DNA methylation, histone methylation, histone acetylation, etc.) play a crucial role in cancer development. Pathological changes in DNA methylation and in the combinatorial patterns of histone post- translational modifications (PTMs) have a profound impact on gene expression and other nuclear events, driving inappropriate proliferation of cancer cells. Analysis of patient samples, however, is hampered by technical limitations in the study of chromatin structure from pathology archives that usually consist of heavily fixed, paraffin-embedded material (FFPE-tissues). Here, we present a new experimental aprroach [pathology tissue-ChIP (PAT-ChIP)] to extract and immunoprecipitate chromatin from paraffin-embedded patient samples up to several years old. In a pairwise comparison with canonical ChIP, PAT-ChIP showed a high reproducibility of results for several histone marks and an identical ability to detect dynamic changes in chromatin structure upon pharmacological treatment. Interestingly, the PAT-ChIP procedure has been successfully employed in the immunoselection of a chromatin-related protein (such as RNA polymerase II) instead the canonical histone marks. New technologies are beginning to allow global analyses of the epigenetic profile of the genome (the so-called “epigenome”), which have revealed at an unprecedented resolution the position of both DNA and histone modifications and dramatically extended our understanding of the structural determinants of the epigenome. These technologies, based on massively parallel sequencing of DNA fragments, are being applied systematically to the study of the epigenome in model cell lines. Finally, we showed that PAT-ChIP can be coupled with high-throughput sequencing (PAT-ChIP-Seq) for the genome-wide analysis of distinct chromatin modifications. PAT-ChIP therefore represents a versatile procedure and diagnostic tool for the analysis of epigenetic alterations in cancer and potentially other diseases.