Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples

Background: Increasing evidence linking epigenetic mechanisms and diferent diseases, including cancer, has prompted in the last 15 years the investigation of histone post-translational modifcations (PTMs) in clinical samples. Methods allowing the isolation of histones from patient samples followed by the accurate and comprehensive quantifcation of their PTMs by mass spectrometry (MS) have been developed. However, the applicability of these methods is limited by the requirement for substantial amounts of material. Results: To address this issue, in this study we streamlined the protein extraction procedure from low-amount clinical samples and tested and implemented diferent in-gel digestion strategies, obtaining a protocol that allows the MSbased analysis of the most common histone PTMs from laser microdissected tissue areas containing as low as 1000 cells, an amount approximately 500 times lower than what is required by available methods. We then applied this protocol to breast cancer patient laser microdissected tissues in two proof-of-concept experiments, identifying diferences in histone marks in heterogeneous regions selected by either morphological evaluation or MALDI MS imaging. Conclusions: These results demonstrate that analyzing histone PTMs from very small tissue areas and detecting diferences from adjacent tumor regions is technically feasible. Our method opens the way for spatial epi-proteomics, namely the investigation of epigenetic features in the context of tissue and tumor heterogeneity, which will be instrumental for the identifcation of novel epigenetic biomarkers and aberrant epigenetic mechanisms.