Leveraging unbiased LC-MS analysis to identify histone post-translational modifications associated with age-related decline of learning and memory

Abstract Age-associated cognitive decline is a significant societal challenge, with several neurodegenerative diseases like Alzheimer’s disease becoming prevalent. Normal ageing is associated with several molecular, cellular, and metabolic hallmarks, including epigenetic mechanisms. In particular, dysregulation of post-translational modifications on histone tails is emerging as a mechanism associated with functional decline. The hippocampus is a region of the brain that is essential for the formation of episodic and spatial memories, which are particularly susceptible to age-related decline. In this perspective manuscript, we have used mass spectrometry as an unbiased method to profile histone tail post-translational modifications both at baseline and after contextual fear conditioning (CFC) from young and aged mouse hippocampi to identify age- and activity-dependent changes. Using this approach, we identify epigenetic marks not widely studied in ageing and in activity-induced learning. We propose a framework on how to integrate these epigenetic marks into current knowledge and discuss how to use this new analysis to formulate novel hypotheses that will broaden this field of ageing research. We believe that this work will be of interest to scientists, clinicians and the wider public by making a significant contribution to our understanding of the molecular mechanisms responsible for age-associated cognitive decline and by reporting the identification of new mechanisms to focus on. Competing Interest Statement SG is an employee of MSD (UK) Limited, London, UK and HK, SB, RG and AC are employees of Merck Sharp & Dohme LLC, a subsidiary of Merck & Co., Inc., Rahway, NJ, USA known as MSD outside of the US and Canada. SG, SB, RG and AC are shareholders of Merck & Co., Inc., Rahway, NJ, USA. The other authors declare no competing interests. Footnotes Declarations Ethics approval All work involving mice was conducted in accordance with the UK Animals Scientific Procedures Act 1986 (PIL I44558708), under the project licenses P8DC5B496//PP6246123 (Prof. Basson) and was approved by the King’s College London Animal Welfare and Ethical Review Board (AWERB). Availability of data and material All data analysed during this study are included in this published article as supplementary information Table 1 (processed data). Competing interests SG is an employee of MSD (UK) Limited, London, UK and HK, SB, RG and AC are employees of Merck Sharp & Dohme LLC, a subsidiary of Merck & Co., Inc., Rahway, NJ, USA known as MSD outside of the US and Canada. SG, SB, RG and AC are shareholders of Merck & Co., Inc., Rahway, NJ, USA. The other authors declare no competing interests. Funding This work was supported by the MRC DTP iCASE programme, King’s College London and MSD, to SUB & Medical Research Council grants MR/V013173/1 and MR/Y008170/1 to MAB. List of abbreviations - AD - Alzheimer’s disease - CBP - CREB-binding protein - CFC - contextual fear conditioning - DNA - Deoxyribonucleic acid - H2AX.K36ac - Histone 2A variant X lysine 36 acetylation - H3K4 - histone 3 lysine 4 trimethylation - Me1 - monomethylation - Me2 - dimethylation - Me3 - trimethylation - H3K9me - Histone 3 lysine 9 methylation - H3K14ac - Histone 3 lysine 14 acetylation - H3K27ac - Histone 3 lysine 27 acetylation - H3K27me - Histone 3 lysine 27 methylation - H3K36ac - Histone 3 lysine 36 acetylation - H3K56ac - Histone 3 lysine 56 acetylation - H3K122ac - Histone 3 lysine 122 acetylation - H3R2me - Histone 3 arginine 2 methylation - H4K16ac - Histone 4 lysine 16 acetylation - H4K20me - Histone 4 lysine 20 methylation - IR - Ionizing radiation - LC/MS - Liquid chromatography/mass spectrometry - LTM - Long-term memory - PTMs - post-translational modifications - RNA - Ribonucleic acid