title: Pathology Tissue-quantitative Mass Spectrometry Analysis to Profile Histone Post-translational Modification Patterns in Patient Samples.
abstract: Histone post-translational modifications (hPTMs) generate a complex combinatorial code that has been implicated with various pathologies, including cancer. Dissecting such a code in physiological and diseased states may be exploited for epigenetic biomarker discovery, but hPTM analysis in clinical samples has been hindered by technical limitations. Here, we developed a method (PAThology tissue analysis of Histones by Mass Spectrometry - PAT-H-MS) that allows to perform a comprehensive, unbiased and quantitative MS-analysis of hPTM patterns on formalin-fixed paraffin-embedded (FFPE) samples. In pairwise comparisons, histone extracted from formalin-fixed paraffin-embedded tissues showed patterns similar to fresh frozen samples for 24 differentially modified peptides from histone H3. In addition, when coupled with a histone-focused version of the super-SILAC approach, this method allows the accurate quantification of modification changes among breast cancer patient samples. As an initial application of the PAThology tissue analysis of Histones by Mass Spectrometry method, we analyzed breast cancer samples, revealing significant changes in histone H3 methylation patterns among Luminal A-like and Triple Negative disease subtypes. These results pave the way for retrospective epigenetic studies that combine the power of MS-based hPTM analysis with the extensive clinical information associated with formalin-fixed paraffin-embedded archives.
authors.affiliation: From the ‡Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy;
authors.forename: Roberta
authors.initials: R
authors.lastname: Noberini
authors.affiliation: §Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano;
authors.forename: Andrea
authors.initials: A
authors.lastname: Uggetti
authors.affiliation: §Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano; ¶School of Medicine, University of Milan, 20122 Milan, Italy;
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Pruneri
authors.affiliation: ‖Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; **Drug Development Program, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; ‡‡Department of Bioscience, University of Milan, 20133 Milan, Italy.
authors.forename: Saverio
authors.initials: S
authors.lastname: Minucci
authors.affiliation: ‖Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; tiziana.bonaldi@ieo.eu.
authors.forename: Tiziana
authors.identifier: http://orcid.org/0000-0003-3556-1265
authors.initials: T
authors.lastname: Bonaldi
mesh_terms: D000818:Animals; D001943:Breast Neoplasms / Q000378:metabolism / Q000473:pathology*; D018270:Carcinoma, Ductal, Breast / Q000378:metabolism / Q000473:pathology*; D045744:Cell Line, Tumor; D005260:Female; D006657:Histones / Q000378:metabolism*; D006801:Humans; D015473:Leukemia, Promyelocytic, Acute / Q000378:metabolism / Q000473:pathology*; D008745:Methylation; D051379:Mice; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods*; D016707:Tissue Fixation
chemical_list: D006657:Histones