DNA and RNA deep sequencing and epigenetic characterization of two kindred cases affected by slow and fast decline dementia

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AbstractBackgroundGenetics, transcriptomic and epigenetics play an important interplay in influencing the clinical picture and the final diagnosis of patients affected by neurodegenerative diseases. Clinical diagnosis is often inaccurate compared to the neuropathological one, which remains the gold standard for neurodegenerative disease diagnosis so far. For this reason, it becomes necessary to strengthener molecular efforts to sustain clinical diagnosis. Here, we present the molecular characterization of two kindred cases (mother and son) initially diagnosed as slow and fast dementia and, after post‐mortem neuropathological examination, classified as Alzheimer’s Disease (AD) and Dementia with Lewy Body (DLB) respectively.MethodA customized panel of over 6000 genes associated to mendelian disorders and to inherited neurodegenerative diseases was sequenced by NGS (SureSelectQXT Target Enrichment, Agilent Technology) on peripheral blood DNA of the two patients. Total RNA from hippocampus, parietal lobe, substantia nigra and basal ganglia was extracted and RNA‐Seq analysis was run (SENSE Total RNA‐Seq, Lexogen). Differentially Expressed Genes (DEGs) were identified via R package DESeq2. Kegg pathway and Gene Ontology (GO) analyses for biological processes were made using enrichR. AlphaLisa analysis was performed on brain homogenates to investigate the dimethylation status of Histone 3 Lysine 9 (H3‐K9) and Histone 3 Lysine 4 (H3‐K4) and the acetylation status of H3‐K9.ResultSeven variants were found to be shared by patients (Table 1), while six variants were present only in the son and (Table 2). DEGs analysis revealed a dysregulation in the mother’s hippocampus and in the son’s substantia nigra, with a 10‐fold higher number of DEGs. GO analyses highlighted a deregulation in the epigenetic landscape. In particular, the substantia nigra of the son resulted hypomethylated and hyperacetylated respectively in the H3‐K9 residue, while the mother resulted globally hypermethylated in all the brain areas analysed at the H3‐K9 and H3‐K4 residues.ConclusionWe identified genetic factors that may explain the AD and the DBL phenotypes and DEGs in AD‐ and DBL‐specific brain areas involved in the epigenetic spectrum. Our investigation highlighted either the importance of DNA and RNA sequencing and the relevance to study the epigetic lanscape to support differential diagnoses of complex neurodegenerative pathologies.