Endogenous barcoding to determine complex dynamics of adult neurogenesis in aging and Alzheimer's disease

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ABSTRACT New neurons in the adult human and animal hippocampus have been implicated in several cognitive functions. These functions are profoundly impaired by the loss or insufficient production of new neurons. Neurons are produced after a prolonged series of transitions including the activation, proliferation, elimination, and differentiation of neural stem cells and their progeny. Competing hypotheses have been proposed to describe how these steps are executed. These hypotheses imply divergent, sometimes contradicting, blueprints of the transitions from stem cells to neurons, as well as different outcomes when these blueprints are perturbed by aging or disease. Alzheimer's disease (AD) has a dramatic adverse effect on hippocampal neurogenesis in humans and in animal models, and this decrease is thought to be directly linked to the cognitive dysfunction observed in AD. Identifying the changes in neurogenesis induced by AD and differentiating them from the changes induced by aging may reveal new means of mitigating or even reversing AD-associated cognitive impartment. This goal is challenging not only because of the complexity of the system, but also because of the limitations inherent in currently available approaches for tracing stem cells and their progeny. We have recently developed a novel approach of endogenous barcoding to determine the lineage trajectory and differentiation trajectories of neural stem cells in the adult mouse brain. In addition, we have developed a new technique for combinatorial multitag labeling of subpopulations of dividing stem cells and their progeny. Now we propose applying these new approaches to identify the changes that AD and aging induce in the basic scheme of neural stem cell division and differentiation and to examine how those changes can be mitigated. In our first specific aim, we will introduce the Polylox barcode cassette and related genes into the genome of mouse models of AD, apply recombination-induced endogenous barcoding, and perform barcode analysis integrated with single-cell transcriptome analysis as a novel approach for determining the division, differentiation, and lineages of individual neural stem cells, as well as the changes inflicted by AD and aging. In our second aim, we will apply our new technique of multitag labeling of dividing cells to further determine the dynamics of adult neurogenesis and perturbations introduced by AD and aging. Together, these approaches will provide a new means of dissecting the perturbations in neurogenesis provoked by aging and AD. Finally, in our third aim, we will determine how these changes are modified by drugs used in different therapy modalities, using them here as experimental instruments for further revealing the AD- and aging-induced changes.