PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples

Roberta Noberini, Rémi Longuespée, Cristina Richichi, Giancarlo Pruneri, Mark Kriegsmann, Giuliana Pelicci, Tiziana Bonaldi

Research output: Contribution to journalArticlepeer-review


Background: Aberrations in histone post-translational modifications (hPTMs) have been linked with various pathologies, including cancer, and could not only represent useful biomarkers but also suggest possible targetable epigenetic mechanisms. We have recently developed an approach, termed pathology tissue analysis of histones by mass spectrometry (PAT-H-MS), that allows performing a comprehensive and quantitative analysis of histone PTMs from formalin-fixed paraffin-embedded pathology samples. Despite its great potential, the application of this technique is limited by tissue heterogeneity. Methods: In this study, we further implemented the PAT-H-MS approach by coupling it with techniques aimed at reducing sample heterogeneity and selecting specific portions or cell populations within the samples, such as manual macrodissection and laser microdissection (LMD). Results: When applied to the analysis of a small set of breast cancer samples, LMD-PAT-H-MS allowed detecting more marked changes between luminal A-like and triple negative patients as compared with the classical approach. These changes included not only the already known H3 K27me3 and K9me3 marks, but also H3 K36me1, which was found increased in triple negative samples and validated on a larger cohort of patients, and could represent a potential novel marker distinguishing breast cancer subtypes. Conclusions: These results show the feasibility of applying techniques to reduce sample heterogeneity, including laser microdissection, to the PAT-H-MS protocol, providing new tools in clinical epigenetics and opening new avenues for the comprehensive analysis of histone post-translational modifications in selected cell populations.

Original languageEnglish
Article number69
JournalClinical Epigenetics
Issue number1
Publication statusPublished - Jul 11 2017


  • Epigenetic marker
  • Formalin-fixed paraffin embedded
  • Histone post-translational modifications
  • Laser microdissection
  • Mass spectrometry
  • PAT-H-MS
  • Proteomics

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Developmental Biology
  • Genetics(clinical)


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