Integrative Resource to Develop Translational Strategies to Promote Longevity. Translating information about genetic variants that are associated with a phenotype, such as longevity or a disease such as AD, into insights about drug targets for those phenotypes is far from trivial. The NIA-funded ?Longevity Genomics? project (LGp; U24AG051129 titled ?Integrative Resource to Develop Translational Strategies to Promote Longevity?) is developing computational and bioinformatics infrastructure to facilitate the translation of genetic variants associated with longevity into drug targets. This infrastructure can easily be exploited with other phenotypes and diseases. We propose leveraging some of the techniques and infrastructure being developed in the LGp to explore the transcriptional landscape of cells engineered to harbor specific variants associated with AD. These studies will lead to insights into drugs that might combat AD, and their results will be made available through the LGp project website as proof-of-concept studies. Essentially, we will create human induced pluripotent stem cells (hiPSCs) harboring three variants known to cause AD in the amyloid precursor protein (APP) and presenilin (PSEN or PS) genes. We will also use genome editing techniques to create isogenic control cells (though two of the three AD variants will use them same control cells). We will then differentiate these hiPSCs into cerebrocortical neurons, including both inhibitory and excitatory neurons, and also create organoids for harvesting individual cells. These cells will be identified through the interrogation of specific biomarkers and electrophysiological evaluations. A subset of these cells will be phenotyped in a wide variety of ways, including assessments for aberrant electrical activity, synaptic damage, and neuronal cell injury. We will then perform single cell RNA-sequencing for the cells made for each condition (i.e., [3 mutant sets of cells + 2 control sets] x 2 cell types: inhibitory and excitatory = 10 conditions). We will do this for two time points: as the neurons are developing in vitro (at 2 weeks) and after they become mature neurons (at 6 weeks) to insure that our phenotypes are not developmental in nature, for a total a 20 conditions. Each of these conditions will be pursued in duplicate for quality control purposes, for a grand total of 40 conditions. We will then explore gene expression differences between cells harboring the AD-associated variants and the controls that might be amenable to pharmacological modulation. We will also correlate, at the condition level, average gene expression levels with cell condition-specific phenotypes. We will leverage chemoinformatics techniques and the connectivity map (CMap) to search for drugs that target the genes exhibiting differences in the cells carrying the AD-associated variants. Relevant analyses will exploit statistical models for mediation analyses, CMap interrogation methods, and chemoinformatic tools being developed by the LGp. !
There is a dire need for new Alzheimer's disease (AD) treatments, as traditional strategies for identifying drugs and drug targets have not yielded new drugs. We will leverage state-of-the-field stem cell technologies, genome editing techniques, single cell sequencing assays and novel data analysis tools to identify drug targets in cells obtained from individuals known to carry AD-related genetic mutations. We will study the targets emerging from these studies with analysis tools developed as part of a previously funded consortium effort and hope to set precedents for how genetic studies can lead to promising drugs for AD.
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