Cell Type-Specific Alternative polyadenylation of mRNA in Alzheimer's disease

Project summary Alzheimer’s disease (AD) is the most common, slowly progressing neurodegenerative disease, resulting in de- mentia and eventually death. More than six million Americans are affected by AD and more than 50 million people suffer with dementia worldwide. The pathology of AD is characterized by an increased production and

reduced clearance of extracellular amyloid-β (Aβ) within the affected brain regions. Aβ accumulation leads to subsequent increase of hyperphosphorylated intraneuronal tau, which is followed by synaptic impairment, neu- roinflammation, functional neural changes, and ultimately neuronal death. AD symptoms progress from mild

memory loss to severe cognitive and executive impairment at the latest stages of the disease. Identifying mo- lecular mechanisms influencing disease related protein pathways and networks is of ultimate importance to broaden the understanding of the complexity of AD and to advance the development of therapeutics. Gene ex-

pression studies in human subjects and animal models identified many changes in RNA abundance associated with the development and complexity of AD. However, the full spectrum of AD-associated gene expression regulation in a cell type-specific pattern is still not well understood. Here, we will examine alternative polyad-

enylation (APA) of mRNAs and how it results in downstream functional changes leading to AD. In affected mRNAs, APA regulates both the functional diversity of open reading frames (ORFs), which alters the functional protein produced, and the length of mRNA 3¢ untranslated regions (UTRs), which controls the stability, transla-

tion, and localization of transcripts within the cell. APA is most apparent in astrocytes, where we identified a profound shortening of ORFs and UTRs of many key mRNAs involved in the etiology of AD. We propose that such shortening in a cell type-specific manner contributes to the pathology of AD by modulating the production,

removal, and toxicity of Aβ in addition to global changes of neural cell physiology. The goals of this project are two-fold: 1) To identify APA genes and pathways associated with the underlying pathology of AD using our computational pipeline by interrogating existing AD-related single nucleus RNA-Seq datasets; and 2) To vali-

date our findings on prioritized APA genes in the prefrontal cortex of Alzheimer’s disease and non-symptomatic donors using RNAscope in situ hybridization technology. Successful completion of this research project will provide insight into the understanding of the molecular mechanisms underlying the development and contrib-

uting to progression of AD. It will also provide the foundation to advance innovative pharmacological interven- tions. Finally, these results will build a foundation for analysis of numerous existing and future high-throughput sequencing datasets to study the role of APA in not only AD but also additional neurodegenerative disorders.