APOE deficiency impacts neural differentiation and cholesterol biosynthesis in human iPSC-derived cerebral organoids

Abstract

The apolipoprotein E (APOE) gene is the strongest genetic risk factor for Alzheimer's disease (AD); however, how it modulates brain homeostasis is not clear. The apoE protein is a major lipid carrier in the brain transporting lipids such as cholesterol among different brain cell types. Here, we show that APOE deficiency in human iPSC-derived cerebral organoids impacts brain lipid homeostasis by modulating multiple cellular and molecular pathways. Molecular profiling through single cell RNA-sequencing revealed that APOE deficiency leads to changes in cellular composition of isogenic cerebral organoids likely by modulating the EIF2 signaling pathway as these events were alleviated by the treatment of a pathway inhibitor ISRIB. APOE deletion also leads to activation of the Wnt/β-catenin signaling pathway with concomitant decrease of SFRP1 expression in glia cells. Importantly, the critical role of apoE in cell type-specific lipid homeostasis was observed upon APOE deletion in cerebral organoids with a specific upregulation of cholesterol biosynthesis in excitatory neurons and excessive lipid accumulation in astrocytes. Relevant to human AD, APOE4 cerebral organoids show altered neurogenesis and cholesterol metabolism compared to those with APOE3. Our work demonstrates critical roles of apoE in brain homeostasis and offers critical insights into the APOE4-related pathogenic mechanisms.

Proteins linking APOE ɛ4 with Alzheimer's disease

“…SFRP1 is an inhibitor of disintegrin and metalloproteinase domain‐containing protein 10 (ADAM10), 47,48 which is a part of α‐secretase, which provides an alternative processing pathway for amyloid precursor proteins yielding less toxic soluble amyloid precursor protein α rather than Aβ. In addition, lower levels of SFRP1 were observed in brain organelles derived from APOE ‐deficient stem cells 49 . We hypothesize that higher levels of SFRP1 associated with APOE ɛ4 result in the production of more Aβ as a result of inhibiting α‐secretase.…”

Myelin organoids for the study of Alzheimer's disease

“…The roles of genetic risk factors for AD in myelin homeostasis can be defined by deriving genetically engineered myelinoids that express genetic risk variants, such as APOE4 (Figure 1B). As a transporter of cholesterol, ApoE plays an important role in the recycling of myelin lipids and in myelin repair; notably, neurons and astrocytes exhibit dysregulated cholesterol biosynthesis and accumulate cholesterol in APOE4 brain organoids (Zhao et al, 2023). Therefore, myelinoids with different ApoE isoforms can be used to characterize how each isoform affects lipid metabolism and myelination that require coordinated interactions and metabolite exchange between different brain cell types.…”

KDM4C promotes mouse hippocampal neural stem cell proliferation through modulating ApoE expression

“…13,14 In induced pluripotent stem cell (iPSC)-derived cerebral organoids, the absence of ApoE leads to a downregulation of genes associated with neurogenesis, subsequently hindering cell proliferation. 15 Remarkably, ApoE expression during postnatal development is crucial for maintaining the hippocampus NSC pool, and its absence dysregulates progenitor cell behavior, leading to long-term depletion of the stem cell pool. 16 This study aimed to investigate the role of KDM4C in regulating the proliferation of hippocampal NSCs and to elucidate the underlying regulatory mechanisms.…”

“…ApoE serves as a secreted factor from mouse NSCs capable of stimulating neurosphere formation, proliferation, and survival 13,14 . In induced pluripotent stem cell (iPSC)‐derived cerebral organoids, the absence of ApoE leads to a downregulation of genes associated with neurogenesis, subsequently hindering cell proliferation 15 . Remarkably, ApoE expression during postnatal development is crucial for maintaining the hippocampus NSC pool, and its absence dysregulates progenitor cell behavior, leading to long‐term depletion of the stem cell pool 16 …”