Open facility of functional genomics aimed at disclosing late-onset Alzheimer's disease epigenetic mechanisms and biomarkers

BACKGROUND: Epigenetic signals are fundamental in regulating neuronal functions (Sweatt JD, 2013) and have been proposed as biomarkers of AD (Klein HU et al, 2019). Advances in genomic technologies endorse genome wide studies of the histone code of aging and diseases, including LOAD in animal models or patients (Nativio R et al. 2020). Up to date technology includes our recently developed pipeline that allows the identification of the distribution of most common histone marks by chromatin immunoprecipitation and throughput sequencing (Amatori S et al, 2018). Here we present the activity of our open facility involved in the identification of AD histone signature. METHOD: As reported in Figure 1, human or mouse brain biopsies or PBMC are collected from clinical centers and research labs as FFPE, frozen or fresh material. Chromatin is extracted, fragmented and immunoprecipitated for different marks, particularly those linked to transcription. A fraction of each original sample is reserved for RNA extraction to perform gene expression analysis by RNA-seq technology. Illumina sequencing is carried out and multi-omics analysis is conducted. RESULT: We present the study of H3K4me3 signature in human cortexes from Oxford BioBank starting from 10-20 mg of frozen tissues. Bioinformatic analysis revealed that profile obtained from AD brain (Braak staging = 5-6) could be discerned from those of normal brain (Braak index= 1-2) using a PCA plot. Moreover, TSS analysis revealed a strong difference in the signal between the two groups which correlates with an overall downregulation of multiple pathways in the group with severe dementia compared to the control. CONCLUSION: Our protocol allows us to discern patients with severe dementia from healthy people, identifying differences in H3K4me3 profile. Next goal will be to analyse more histone marks and to intersect these data with gene expression. Moreover, being open to world-wide collaborations, we are starting to process human PBMC samples from Lee-Way Neuropathology Lab (UC Davis) with the final goal to correlate the epigenetic signature of AD brains with the expression profile in PBMC from AD patients.