Differential expression and differential coexpression analyses revealed altered gene expressions and pathways in atypical Alzheimer’s Disease sub‐cohort brains

Abstract

AbstractBackgroundIn the Alzheimer’s disease (AD) brain, the hyperphosphorylated tau protein forms neurofibrillary tangles (NFTs), which extent usually matches the dementia severity. However, for some patients, this is not the case. which we name them as asymptomatic AD (AsymAD, heavy NFTs but relatively normal cognition) and Low‐NFT AD (light NFT but severe dementia). We aim to characterize these two subtypes’ transcriptome and proteome, to understand the role of tauopathy in the AD etiology and identify resilient/vulnerable factors contributing to the cognitive decline as well as the potential drug targets for the precision treatment of AD.MethodWe performed differential analyses on both RNA and protein expression data from the atypical groups of two separate datasets ROSMAP and MSBB, using typical AD sub‐cohort as reference. In addition, highly correlated gene/protein co‐expression network modules were mined for each of the four datasets. Enrichment analysis identified biological processes and functions associated with the differentially expressed genes (DEGs) and co‐expressed modules.ResultFive DEG targets were tested in human AsymAD samples and compared with age‐matched controls and typical AD. Using western blot and qRT‐PCR, we confirmed the altered gene expressions in PSCK1 which is related to vesicle trafficking and neuron secretory pathway. Moreover, oppositely regulated pathways were identified for the two subtypes, such as oxidative phosphorylation pathway, neuron CREB signaling, necroptosis signaling pathway. Coexpression analysis also revealed that several coexpressed modules have significant altered expressions in the atypical AD subtypes as compared to typical AD group and are correlated with the disease severeness. For example, the protein modules from both ROSMAP and MSBB, which are enriched with mitochondrial functions and negatively correlated with disease severeness, are significantly elevated in Asym AD group than that of the typical AD or Low‐tau AD group.ConclusionWe have identified several altered pathways and genes that potentially render neuron protection or vulnerability. Identifying key factors in such uncoupling between tauopathy and cognitive impairment will not only improve precision medicine in AD, but also provide insights to prevent or slow down cognitive decline during AD progression. Further validations in Drosophila will elucidate their roles in the pathology or disease progression.