Preclinical Modeling of Neural Regulatory Networks in Baboon Epilepsy

PROJECT SUMMARY
Genetic generalized epilepsies (GGE) are the major subtype of epilepsy syndromes, accounting for about 40%
of U.S. cases. Contrary to popular belief, over one-third of GGE cases that persist into adulthood live with
uncontrolled seizure activity and neurocognitive impairments, negatively impacting quality of life and leading to
higher-than-expected risk of death. Despite the urgent need for new treatment options, development of effective
anti-seizure medications has largely stalled over the past decade, as research is mainly centered on rodent
models that fail to manifest the complex symptomology and recapitulate the polygenic etiology that underlies
human GGE. As such, alternative approaches are needed to advance the field of epilepsy research, including
animal models that are more congruent to the human condition. The baboon represents one such alternative, as
it resembles humans more closely than rodent strains – genetically, physiologically, and (neuroanatomically) –
and presents naturally occurring, highly heritable GGE, with strong electroclinical similarities with human
epilepsy. Our primary objective in this study is to robustly characterize the genetic and transcriptomic architecture
of epilepsy in baboons and develop an in vitro model, based on induced pluripotent stem cell (iPSC)-derived
cerebral organoids, that recapitulates molecular signatures observed in human epilepsy.
We will achieve this through the following integrated aims: (1) identify epilepsy-risk variants across the baboon
genome, including targeted examinations of human candidate gene homologs, and characterize biological
pathways enriched with potential risk genes; (2) quantify gene and miRNA expression levels in epileptic and
healthy baboon brains through single nuclei RNA sequencing (snRNA-Seq) and identify genetic-transcriptomic
associations involving risk variants, such as our recently implicated RBFOX1, as well as wider perturbations in
co-expression networks; and (3) generate primary and CRISPR-edited isogenic cerebral organoids derived from
epileptic and healthy baboons to assess the effect of RBFOX1 perturbations on the transcriptional landscape
and synaptic function, and explore potential mechanisms for restoration of synaptic function in epilepsy. The
results of this study will be the first necessary step in establishing a novel in vivo and in vitro preclinical platform
for therapeutic discovery that is based on non-human organoids. With a high incidence of new GGE cases in
our studied baboon colony, large-scale investigations can be initiated and maintained, allowing for a vertically
integrated pipeline from epileptic animal to manipulated organoid systems that can interrogate the etiological
architecture of epilepsy from a multi-omic perspective. This includes whole genome sequencing, snRNA-Seq,
epigenomic and proteomic profiling, neuroimaging, and electroencephalography, as well as more invasive
investigations of the epileptic brain that are not feasible or are limited in human cohorts, creating a unique
research platform that can inform, complement, and support findings from human-based epilepsy studies.

Grant Number: 1R56NS135399-01
NIH Institute/Center: NIH
Principal Investigator: Melanie Carless