Histone post-translational modification analysis from low-abundance clinical samples

We streamlined the protein extraction procedure from low-amount clinical samples and tested and implemented different in-gel digestion strategies, obtaining a protocol that allows the analysis of the most common histone PTMs from laser microdissected tissue areas containing as low as 1000 cells. We then applied this protocol to breast cancer patient tissue sections in two proof-of-concept experiments, identifying differences in histone marks in heterogeneous regions selected by either morphological evaluation or MALDI-imaging profiling. These results demonstrate that analyzing histone PTMs from very small tissue areas and detecting differences from adjacent tumor regions is technically feasible, opening the way for the investigation of epigenetic features in the context of tissue and tumor heterogeneity.