Transcriptome analysis identifies the role of Class I histone deacetylase in Alzheimer’s disease

Epigenetics modification is a process that does not change the sequence of deoxyribonucleic acid (DNA) in disease progression but can alter the genetic expression of the brain in Alzheimer’s disease (AD). In this study, we deployed the weighted gene co-expression network analysis (WGCNA) to explore the role of Class I histone deacetylases (HDACs) in AD, which included HDAC1, HDAC2, HDAC3, and HDAC8. The aim of the study was to find how Class I HDACs affected AD pathology by analyzing the Gene Expression Omnibus (GEO) microarray datasets GSE33000. We found that HDAC1 and HDAC8 were more highly expressed in the cortex of AD patients than in Controls, while HDAC2 and HDAC3 were lower expressed. By WGCNA analysis, we found the blue module was associated with HDAC1 and HDAC8, and the turquoise module was related to HDAC2 and HDAC3. Functional enrichment analysis revealed that the Wnt signaling pathway and synaptic plasticity played an important role in the modification of HDAC1 and HDAC8 while gap junction and cell-cell junction were involved in the regulation of HDAC2 and HDAC3 in the disease progression of AD. By Receiver Operating Characteristics (ROC) analysis, we concluded that HDAC1 might be the most probable diagnostic biomarker of Class I HDACs for AD. Our study provided a comprehensive understanding of Class I HDACs and provided new insight into the function of HDAC1 in AD disease progression.