Recent advances in mass spectrometry analysis of histone post-translational modifications: potential clinical impact of the PAT-H-MS approach

SUMMARY

Histone post-translational modifications (hPTMs) contribute to the regulation of gene expression and increasing evidence links them to the development of various pathologies, highlighting their potential as biomarkers for prognostic, diagnostic and therapeutic applications. Mass spectrometry (MS) has emerged as a powerful analytical tool for hPTM analysis, which has also been applied to the analysis of epigenetic aberrations in diseases. However, the potential offered by the MS-based hPTM analysis of clinical samples for epigenetic biomarker discovery has been left largely unexploited. This article summarizes the contribution of MS-based approaches to clinical epigenetics, with a special focus on the PAThology tissue analysis of Histones by Mass Spectrometry (PAT-H-MS) approach – which represents the first application of MS-based hPTM analysis to formalin-fixed paraffin-embedded clinical samples – discussing its strengths and limitations, as well as possible implementations.

KEYWORDS:

• Biomarker
• histone post-translational modifications
• epigenetics
• mass spectrometry
• proteomics
• breast cancer
• formalin-fixed paraffin-embedded tissues
• PAT-H-MS

Financial & competing interests disclosure

T Bonaldi’s research group is supported by grants from the Italian Association for Cancer Research (AIRC), the Italian Ministry of Health and the CNR-EPIGEN flagship project.

Key issues

• Aberrant hPTM patterns have been increasingly linked with pathological states and epigenetic biomarkers could be useful for prognostic, diagnostic and therapeutical purposes.

• MS has become an invaluable tool to analyze hPTMs, thanks to its accuracy, its unbiased nature, and its ability to quantify modifications and detect their combinations.

• MS-based hPTM analysis has been applied to the discovery of epigenetic biomarkers, but the potential offered by the analysis of clinical samples has been left unexploited.

• Although FFPE archives represent an invaluable source of samples linked with clinical information, the proteomics analysis of FFPE specimens had been hindered until recently by technical limitations.

• The PAT-H-MS approach allows for the first time the identification and quantitation of 24 differentially modified histone H3 peptides from FFPE tissues.

• The analysis of breast cancer human samples belonging to different breast cancer subtypes revealed possible hPTM marks that distinguish them.

• Future implementations of the PAT-H-MS, including expansion of the number analyzable peptides from other histones and of the storage time frame, as well as coupling with alternative platforms for hPTM analysis, will be crucial to fully exploit the power of this technique.