Supplementary Material for: Modest neurodevelopment impacts of APOE4 in a human brain organoid model of low-grade SARS-CoV-2 infection

Introduction: The long-term neurological consequences of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, are an area of growing concern, particularly for prenatally exposed individuals. Prior research has shown that APOE4, the leading genetic risk factor for late-onset Alzheimer’s disease, is associated with increased COVID-19 severity and enhanced SARS-CoV-2 neurotropism. However, whether the interaction between APOE4 and SARS-CoV-2 infection leads to adverse neurodevelopmental outcomes remains unclear. Using human induced pluripotent stem cell derived cortical and ganglionic eminence organoids (COs and GEOs) to model neurodevelopment, we have previously reported that SARS-CoV-2 preferentially infects glial cells, and that APOE4 promotes gliogenesis in COs and accelerates GABAergic neuron differentiation in GEOs. Here, we build upon our previous work by using COs and GEOs to examine how APOE4 modifies cellular responses to SARS-CoV-2 during late gestational development. Methods: Using low viral titers to better mimic natural infection, COs and GEOs were infected at 220-270 DIV, aligning with the third trimester, and were analyzed 7 days post infection. Results: We observed region-specific, APOE4-dependent changes. In infected COs, APOE4 elevated immature astrocyte marker, suggesting a genotype-dependent glial response. Additionally, infected GEOs exhibited reduced marker expression for mature neurons within both genotypes. Notably, APOE4 and infection interacted to modulate immature neuron expression in a region-specific manner. Conclusion: Taken together, this study suggests that APOE4 modulates region-specific responses to low-grade SARS-CoV-2 infection, underscoring the importance of exploring how genetic risk factors alter neurodevelopmental vulnerability to prenatal viral infection.