title: Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples.
abstract: Epigenetic alterations in the pattern of DNA and histone modifications play a crucial role in cancer development. 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. Here, we present a methodology [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. 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.
authors.affiliation: Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61032 Fano, Italy. mirco.fanelli@uniurb.it
authors.forename: Mirco
authors.initials: M
authors.lastname: Fanelli
authors.forename: Stefano
authors.initials: S
authors.lastname: Amatori
authors.forename: Iros
authors.initials: I
authors.lastname: Barozzi
authors.forename: Matias
authors.initials: M
authors.lastname: Soncini
authors.forename: Roberto
authors.initials: R
authors.lastname: Dal Zuffo
authors.forename: Gabriele
authors.initials: G
authors.lastname: Bucci
authors.forename: Maria
authors.initials: M
authors.lastname: Capra
authors.forename: Micaela
authors.initials: M
authors.lastname: Quarto
authors.forename: Gaetano Ivan
authors.initials: GI
authors.lastname: Dellino
authors.forename: Ciro
authors.initials: C
authors.lastname: Mercurio
authors.forename: Myriam
authors.initials: M
authors.lastname: Alcalay
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Viale
authors.forename: Pier Giuseppe
authors.initials: PG
authors.lastname: Pelicci
authors.forename: Saverio
authors.initials: S
authors.lastname: Minucci
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D057890:Epigenomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics / Q000473:pathology; D011499:Protein Processing, Post-Translational; D017422:Sequence Analysis, DNA / Q000379:methods*; D016707:Tissue Fixation / Q000379:methods