Alzheimer's disease master regulators analysis: search for potential molecular targets and drug repositioning candidates

• Published in: Alzheimer's research & therapy Vol. 10; no. 1; p. 59
• Main Authors: Vargas, D M, De Bastiani, M A, Zimmer, E R, Klamt, F
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 23-06-2018; BioMed Central; BMC
• Subjects: Alzheimer Disease - metabolism; Alzheimer Disease - pathology; Alzheimer's disease; Antibiotics; Brain Mapping; Brain research; Care and treatment; Dementia; Drug repositioning; Drug Repositioning - methods; Drug therapy; Female; Gene expression; Gene Expression Regulation - physiology; Gene Regulatory Networks; Genetic aspects; Genomes; Growth factors; Hippocampus; Hippocampus - metabolism; Hippocampus - pathology; Humans; Male; Master regulators; Molecular targeted therapy; Pathology; Reverse engineering; Transcription factors; Transcriptional regulatory network reconstruction; United States > US; Drug repositioning; Transcription factors; Transcriptional regulatory network reconstruction; Alzheimer’s disease; Hippocampus; Master regulators
• ISSN: 1758-9193; 1758-9193
• DOI: 10.1186/s13195-018-0394-7

Alzheimer's disease (AD) is a multifactorial and complex neuropathology that involves impairment of many intricate molecular mechanisms. Despite recent advances, AD pathophysiological characterization remains incomplete, which hampers the development of effective treatments. In fact, currently, there are no effective pharmacological treatments for AD. Integrative strategies such as transcription regulatory network and master regulator analyses exemplify promising new approaches to study complex diseases and may help in the identification of potential pharmacological targets.
In this study, we used transcription regulatory network and master regulator analyses on transcriptomic data of human hippocampus to identify transcription factors (TFs) that can potentially act as master regulators in AD. All expression profiles were obtained from the Gene Expression Omnibus database using the GEOquery package. A normal hippocampus transcription factor-centered regulatory network was reconstructed using the ARACNe algorithm. Master regulator analysis and two-tail gene set enrichment analysis were employed to evaluate the inferred regulatory units in AD case-control studies. Finally, we used a connectivity map adaptation to prospect new potential therapeutic interventions by drug repurposing.
We identified TFs with already reported involvement in AD, such as ATF2 and PARK2, as well as possible new targets for future investigations, such as CNOT7, CSRNP2, SLC30A9, and TSC22D1. Furthermore, Connectivity Map Analysis adaptation suggested the repositioning of six FDA-approved drugs that can potentially modulate master regulator candidate regulatory units (Cefuroxime, Cyproterone, Dydrogesterone, Metrizamide, Trimethadione, and Vorinostat).
Using a transcription factor-centered regulatory network reconstruction we were able to identify several potential molecular targets and six drug candidates for repositioning in AD. Our study provides further support for the use of bioinformatics tools as exploratory strategies in neurodegenerative diseases research, and also provides new perspectives on molecular targets and drug therapies for future investigation and validation in AD.