Consortium to Infer Regulatory Circuits and Uncover Innovative Therapeutic Strategies—Production Group


Alzheimer’s disease is a devastating neurodegenerative disorder affecting 1 in 3 dying seniors and costing $236 billion annually in the United States alone. Its prevalence is increasing rapidly in an aging population, and there currently is no cure. Recent genetic studies provide new hope for therapeutic avenues, but translating genetic results into therapeutics has been remarkably difficult, due primarily to the fact that most genetic mutations do not alter protein function directly, but instead affect the expression of nearby genes in subtle ways.

Here, we seek to overcome this limitation by directly profiling changes in the circuitry of neurons and other brain cell types during Alzheimer’s disease, and how genetic variants are affecting that circuitry. In the first funding period of the award, we generated thousands of transcriptional and epigenomic maps of gene expression and control region activity across individuals at single-cell resolution. We integrated the resulting datasets to decipher the mechanistic basis of genetic variants associated with disease, and to discover new therapeutic targets, and the pathways and cell types where they act.

In the next period of the award, we expand these studies with a spatiotemporal single-cell map of disease progression across brain regions and disease stages, detailed analyses of genetic effects by APOE and other strong-effect variants on gene expression at single-cell resolution, a high-resolution characterization of microglia subtypes, and integration of common, rare and somatic mutations to predict target genes, regulatory regions and regulators, which we systematically perturb using highly parallel reporter assays.

Funding to Date





Manolis Kellis, Ph.D.

Li-Huei Tsai, Ph.D.