Mass spectrometry-based profiling of histone posttranslational modifications in human uveal melanoma tissue

Abstract

Purpose : Epigenetic mechanisms and alterations in uveal melanoma (UM) development are still not well understood. We recently demonstrated the presence of different patterns of histone posttranslational modifications (hPTMs) - which are epigenetic features involved in gene expression regulation at the level of transcription - between uveal melanocytes and UM cell lines, as well as between UM cell lines with a different prognostic profile. In this pilot study, hPTMs were profiled by a quantitative mass spectrometry (MS) approach in UM formalin-fixed paraffin-embedded (FFPE) tissues and regular choroid from enucleated eyes, in order to gain a deeper insight into the prognostic relevance of these molecular markers for UM.

Methods : FFPE tissue of UM (n=24) and regular choroid (n=4) from enucleated eyes were analyzed by quantitative MS which allowed profiling 48 different histone modifications linked to different functional states of chromatin. The UMs were analyzed according to the TNM classification (T2: n=8, T3: n=13, T4: n=3; G1: n=5, G2: n=12, G3: n=7), as well as the G-protein and BAP1 mutation status (available for 18 specimens).

Results : The analysis revealed significant differences between the control uvea and the tumor tissue, in particular for H3K27 methylation which was decreased in the tumor tissue. Regarding the T stage, a decrease of several acetylated peptides of both histone 3 and histone 4 was associated with an increasing T stage. Differences between tumors with a BAP1 wildtype and a BAP1 mutation were also identified, revealing variations similar to the T stage results.

Conclusions : The results indicate the presence of different hPTM patterns allowing to distinguish between control uvea and UM tissue. Potential prognostically-relevant hPTM were also identified. There were also similarities to the previously analyzed UM cell lines. Since this is only a preliminary study, further analyses are needed to confirm these findings in a larger cohort. However, our findings suggest the presence of epigenetic alterations in UM warranting further investigation in order to identify potential novel targets (e.g. histone modifying enzymes) to tackle this tumor and its metastasis with epigenetic drugs.

This abstract was presented at the 2023 ARVO Annual Meeting, held in New Orleans, LA, April 23-27, 2023.