APOE4 impacts cortical neurodevelopment and alters network formation in human brain organoids

Apolipoprotein E4 (APOE4) is the leading genetic risk factor for Alzheimer’s disease. While most studies examine the role of APOE4 in aging, APOE4 causes persistent changes in brain structure as early as infancy and is associated with altered functional connectivity that extends beyond adolescence. Here, we used human induced pluripotent stem cell (iPSC) derived cortical and ganglionic eminence organoids (COs and GEOs) to examine APOE4’s influence during cortical development of excitatory and inhibitory neurons. We show that APOE4 reduced cortical neurons and increased glia by promoting gliogenic transcriptional programs. In contrast, increased proliferation and differentiation of GABAergic progenitors resulted in early and persistent increases in GABAergic neurons. Multi-electrode array recordings in assembloids revealed that APOE4 disrupted neural network function resulting in heightened excitability and synchronicity. Together, our data provides new insights on how APOE4 influences cortical neurodevelopmental processes and network formation. To investigate the neurodevelopmental role of APOE4, we performed bulk RNA-sequencing APOE4 and APOE3 organoids. 2 isogenic iPSC pairs were used. Isogenic female line was derived from APOE3/3 healthy control converted to APOE4/4, and male isogenic line was derived from APOE4/4 alzheimer’s disease male converted to APOE3/3. Each line, 2 APOE3/3 and 2 APOE4/4, were used to generate cortical and ganglionic eminence organoids (COs and GEOs, respectively), undergoing 2 independent replicates. We harvest mRNA at two time points (days in vitro, DIV) 30 and 120 for RNAseq. 4 different comparisons, which we call conditions, were made (COs and GEOs, at both 30 and 120 DIV). For example, samples collected for 1 condition, COs at 30 DIV: 1 sample was collected x 2 replicates for each iPSC line. This results in 2 APOE3/3 samples, 2 APOE4/4 samples for each iPSC line, resulting in 4 APOE3/3 and 4 APOE4/4 samples total (2 iPSC line pairs) for this condition. All samples were ran at the same time. For all 4 conditions, 16 APOE3/3 samples, 16 APOE4/4 samples were collected for a total of 32 samples.