Histone post-translational modifications in frontal cortex from human donors with Alzheimer’s disease

Illarion V Turko,Kyle W Anderson

doi:10.1186/s12014-015-9098-1

Abstract

BackgroundAlzheimer’s disease (AD) is the sixth leading cause of death and the most costly disease in the US. Despite the enormous impact of AD, there are no treatments that delay onset or stop disease progression currently on the market. This is partly due to the complexity of the disease and the largely unknown pathogenesis of sporadic AD, which accounts for the vast majority of cases. Epigenetics has been implicated as a critical component to AD pathology and a potential “hot spot” for treatments. Histone post-translational modifications (PTMs) are a key element in epigenetic regulation of gene expression and are known to be associated with the pathology of numerous diseases. Investigation of histone PTMs can help elucidate AD pathology and identify targets for therapies.ResultsA multiple reaction monitoring mass spectrometry assay was used to measure changes in abundance of several histone PTMs in frontal cortex from human donors affected with AD (n = 6) and age-matched, normal donors (n = 6). Of the changes observed, notable decreases in methylation of H2B residue K108 by 25 % and H4 residue R55 by 35 % were measured and are likely associated with hydrogen bonding networks important for nucleosome stability. Additionally, a 91 % increase in ubiquitination of K120 on H2B was measured as well as an apparent loss in acetylation of the region near the N-terminus of H4. Our method of quantification was also determined to be precise and robust, signifying measured changes were representative of true biological differences between donors and sample groups.ConclusionWe are the first to report changes in methylation of H2B K108, methylation of H4 R55, and ubiquitination of H2B K120 in frontal cortex from human donors with AD. These notable PTM changes may be of great importance in elucidating the epigenetic mechanism of AD as it relates to disease pathology. Beyond the structural and functional impacts of the changes we have measured, the sites of altered PTMs may be used to identify enzymes responsible for their modulation, which could be used as prospective drug targets for highly specific AD therapies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12014-015-9098-1) contains supplementary material, which is available to authorized users.

Highlights

Alzheimer’s disease (AD) is the sixth leading cause of death and the most costly disease in the US
While dynamic exclusion was used during MS acquisition, data-dependent analysis benefits from having enrichment of the histone targets, when a histone post-translational modification (PTM) may be only a few percent of the total amount of the unmodified peptide
Histone PTMs that were found to be significantly different in AD frontal cortex were decreases in methylation of H2B K108 and H4 R55 and an increase in ubiquitination of H2B K120

Summary

Introduction

Alzheimer’s disease (AD) is the sixth leading cause of death and the most costly disease in the US. Histone post-translational modifications (PTMs) are a key element in epigenetic regulation of gene expression and are known to be associated with the pathology of numerous diseases. DNA is packaged into the eukaryotic nucleus as chromatin, a structure comprised of nucleosomes formed by 146 base pairs of DNA wrapped around an octamer of duplicates of histones H2A, H2B, H3, and H4. These histones are dynamically modified by post-translational modifications (PTMs), known as the “histone code”, which can Anderson and Turko Clin Proteom (2015) 12:26 methylation, phosphorylation, and ubiquitination. Phosphorylation is labile and typically lost during the relatively long post-mortem interval in human tissues and it is more appropriate to measure phosphorylation in animal models when the post-mortem interval is a few minutes [10]

Methods

Results

Conclusion