Leveraging iPSC technology to understand neuro-immune responses to SARS-CoV-2 variants

PROJECT SUMMARY The COVID-19 pandemic has led to significant morbidity and mortality globally. While vaccination has dramatically reduced incidence of severe COVID-19 cases, SARS-CoV-2 continues to circulate with new variants arising. Importantly, even mild COVID-19 can lead to long term consequences termed post-acute sequelae of SARS-CoV-2 infection (PASC) or "Long COVID". The current proposal will use innovative stem cell technology to study mechanisms underlying neurological and psychiatric symptoms of PASC. Neuroinflammation, including microglial activation, is a hallmark of PASC and cell line models have demonstrated that SARS-CoV-2 or SARS- CoV-2 proteins can induce pro-inflammatory responses in microglia. What remains unknown, however, are the specific cellular and molecular mechanisms by which SARS-CoV-2 affects microglial-neuronal crosstalk. Here, we will generate microglia and 3D brain organoids from human induced pluripotent stem cells (iPSC) which are clinically relevant models to study neuroimmune interactions. Our preliminary data indicate that SARS-CoV-2 can enter but not efficiently replicate in human microglia. We did, however, observe significant transcriptional remodeling following SARS-CoV-2 exposure involving inflammatory, antiviral, and metabolic pathways. Interestingly, these responses were strain-specific with the strongest changes observed after SARS-CoV-2 Washington (root-lineage strain) stimulation and more moderate responses to Delta and Omicron variants. In the current project, we aim to further elucidate molecular mechanism of PASC-related neuroinflammation. Specifically, we will perform multi-omic and functional characterization of SARS-CoV-2 infected microglia and cross-reference these signatures with molecular markers observed in PASC (Aim 1). We will further generate microglia-incorporated brain organoids and study the impact of SARS-CoV-2 on microglia-neuronal communication as well as neuronal activity (Aim 2). Taken together, the proposed experiments will provide an important proof of principle for the use of stem cell technology to reveal molecular characteristics of microglial responses to SARS-CoV-2 and variants, shedding new light on pathogenic mechanisms underlying Neuro-PASC and providing a platform for future drug development.