Transcriptomics-based identification of cell type specific host genes and gene networks perturbed by HSV-1 in cerebral organoids. - PROJECT SUMMARY/ABSTRACT Herpesviruses such as herpes simplex virus 1 (HSV-1) had been associated with increased risk for Alzheimer’s Disease (AD) through several seminal clinical, molecular and epidemiological studies. Building on top of the foundation established by these research, two seminal papers reported in Neuron 2018 that molecular gene networks implicating herpesviruses, such as HHV-6A, HHV-7 and HSV-1, were enriched in preclinical AD brains. Furthermore, it was shown that HSV-1 infection led to amyloidosis of Amyloid beta (Aβ). Since then, our team has been creating and developing novel resources, technologies and collaborations, to systematically address the role of pathogens (e.g. HSV-1) in AD and AD-related dementias. More specifically, we used recent human in-vitro induced pluripotent stem cell (iPSC) based models (e.g. cerebral organoids, cOrgs), combined with large-scale omics data from human samples (post-mortem brains and CSF antigen profiling) to identify transcriptomic perturbations by HSV-1 and their association with AD-associated genes. Given the importance of precision medicine, we will also like to understand if AD-associated host genetics (e.g. APOE e4) play a role to exacerbate the cell type specific transcriptomic perturbations by HSV-1 in cOrgs. Using recent spatial single-cell RNA sequencing (scRNA-seq) technologies and methods in Aims 1-2, we will also like to directly evaluate if there are cell types in cOrgs and post-mortem brains targeted by HSV-1 and other herpesviruses or cell type co-localization differences and cell type specific gene networks that are critical for AD subtype and outcome analyses. We aim to understand if AD-associated host genetics might play a role to exacerbate these cell type specific perturbations by HSV-1 in cOrgs and the effects of acyclovir (ACV) treatment in reversing AD-associated cell type specific gene networks and pathways. We have also established high-throughput, scalable and quantitative non-transcriptomics based assays (ELISA and flow cytometry) to quantify AD-associated readouts (secreted Ab42/40/38 and intracellular Ab42 and phosphorylated Tau-Thr212) to validate our results from the transcriptomics based approaches in Aim 3. These AD-associated readouts, coupled with the use of flow cytometry results from cell type specific antibody markers, will enable us to dissect the contribution of cell types to AD and illuminate molecular mechanisms on how herpesviruses can contribute to AD pathogenesis or disease progression. Finally, in Aim 4, we propose to perform data integration of the multi-transcriptomics datasets from human cOrgs and post-mortem brains with flow cytometry data, as well as previously published large-scale datasets from post-mortem brains of AD patients, to estimate the population prevalence of AD patient subtypes whose etiology may be triggered by herpesviral infections and who may benefit from early anti-herpetic treatment. Our research has broad implications to pave the path for future research and development into precision medicine for a subset of AD patients whose pathogenesis might arise from herpesviruses.
