APOE4 exacerbates synapse loss and neurodegeneration in Alzheimer’s disease patient iPSC-derived cerebral organoids

APOE4 is the strongest genetic risk factor associated with late-onset Alzheimer’s disease (AD). To address the underlying mechanism, we develop cerebral organoid models using induced pluripotent stem cells (iPSCs) with APOE ε3/ε3 or ε4/ε4 genotype from individuals with either normal cognition or AD dementia. Cerebral organoids from AD patients carrying APOE ε4/ε4 show greater apoptosis and decreased synaptic integrity. While AD patient-derived cerebral organoids have increased levels of Aβ and phosphorylated tau compared to healthy subject-derived cerebral organoids, APOE4 exacerbates tau pathology in both healthy subject-derived and AD patient-derived organoids. Transcriptomics analysis by RNA-sequencing reveals that cerebral organoids from AD patients are associated with an enhancement of stress granules and disrupted RNA metabolism. Importantly, isogenic conversion of APOE4 to APOE3 attenuates the APOE4-related phenotypes in cerebral organoids from AD patients. Together, our study using human iPSC-organoids recapitulates APOE4-related phenotypes and suggests APOE4-related degenerative pathways contributing to AD pathogenesis.


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Full scans of the gels and blots are available in Source data file. All relevant data are available from the corresponding author upon reasonable request. All the other data supporting the findings of this study are available within the article and its supplementary information files and from the corresponding author upon reasonable request. A reporting summary for this article is available as a Supplementary Information file.

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All studies must disclose on these points even when the disclosure is negative. Same experiments were replicated in second batch of cerebral organoid culture. All replications were consistent.
Samples were allocated in different experimental groups based on their APOE genotypes and AD disease status.
Antibodies used in our study have been highly cited in the filed and validated by multiple lab. We have focused on the citation lists as validation to support our claim. According to the manufacturer's website: The Cleaved Caspase 3 antibody (Cell Signaling Technologies, 9661) is reactive to human tissue, and has been cited in 3,488 publications for both immunostaining and western blots, including Velasco et al., 2019, which used this antibody on human brain organoids. The CTIP2 antibody (Abcam, ab18465) is reactive to human tissue, and has been cited in 295 publications, including Quadrato et al., 2017, which used this antibody on human brain organoids. The Nanog antibody (Cell Signaling, 4903) is reactive to human tissue, and has been cited in 159 publications, including Zhao et al., 2017, from our lab, which used this antibody for iPSC characterization. The TRA-1-60 antibody (Abcam, ab16288) is reactive to human tissue, and has been cited in 74 publications, including Zhao et al., 2017, from our lab, which used this antibody for iPSC characterization. The SSEA4 antibody (Abcam, ab16287) is reactive to human tissue, has been cited in 114 publications, including Zhao et al., 2017, from our lab, which used this antibody for iPSC characterization. The Sox17 antibody (Abcam, ab84990) is reactive to human tissue, and has been cited in 11 publications. The Brachyury antibody (R&D, AF2085) is reactive to human tissue, and has been cited in 68 publications. The Nestin antibody (Abcam, ab18102) is reactive to human tissue, has been cited in 9 publications. The Sox2 antibody (Abcam, ab97959) is reactive to human tissue, has been cited in 358 publications, Ballabio C et al. 2020, which used this antibody for cerebral organoid. The TUJ1 antibody (Abcam, ab78078) is reactive to human tissue, has been cited in 110 publications. The TUJ1 antibody (Sigma, T2200) is reactive to human tissue, has been cited in 291 publications. The SATB2 antibody (Abcam, ab34735) is reactive to human tissue, has been cited in 43 publications. The GFAP antibody (Millipore, MAB360) is reactive to human tissue, has been cited in 384 publications for both immunostaining and western blots. The AT8 antibody (Thermo Fisher Scientific, MN1020) is reactive to human tissue, has been cited in 600 publications for both immunostaining and western blots. The G3BP antibody (BD, 611126) is reactive to human tissue, has been cited in 2 publications. The Caspase-3 antibody (Cell Signaling Technology, 9662) is reactive to human tissue, has been cited in 2240 publications. The PSD95 antibody (Abcam, ab2723) is reactive to human tissue, has been cited in 106 publications. The Synaptophysin antibody (Abcam, ab8049) is reactive to human tissue, has been cited in 109 publications. The PHF-1 antibody (Abcam, ab184951, 1:1000) is reactive to human tissue, has been cited in 9 publications. The Tau5 antibody (Millipore, 577801) is reactive to human tissue, has been cited in 5 publications. The APP antibody (Thermo Fisher Scientific, 14-9749-82) is reactive to human tissue. Expression of APP was observed in in Mouse and Rat Brain, but not in the mouse and rat skeletal muscle in western blots. The EEA1 antibody (Cell Signaling Technology, 2411) is reactive to human tissue, has been cited in 73 publications. The LAMP1 antibody (Cell Signaling Technology, 9091) is reactive to human tissue, has been cited in 149 publications. The ERCC4 antibody (Fitzgerald, 10R-4026) is reactive to human tissue. In the website, western blots show bands in HEK293T cell lysates transfected with recombinant ERCC4 protein, but not in the empty vector group. The POLR3A antibody (Abcam, ab96328) is reactive to human tissue, has been cited in 8 publications.
The HSPA4 (Cell Signaling Technology, 3303) is reactive to human tissue, has been cited in 11 publications. The Cleaved Caspase 3 antibody (Cell Signaling Technologies, 9661) is reactive to human tissue, and has been cited in 3,488 publications for both immunostaining and western blots, including Velasco et al., 2019, which used this antibody on human brain organoids. The CTIP2 antibody (Abcam, ab18465) is reactive to human tissue, and has been cited in 295 publications, including Quadrato et al., 2017, which used this antibody on human brain organoids. The Nanog antibody (Cell Signaling, 4903) is reactive to human tissue, and has been cited in 159 publications, including Zhao et al., 2017, from our lab, which used this antibody for iPSC characterization. The TRA-1-60 antibody (Abcam, ab16288) is reactive to human tissue, and has been cited in 74 publications, including Zhao et al., 2017, from our lab, which used this antibody for iPSC characterization. The SSEA4 antibody (Abcam, ab16287) is reactive to human tissue, has been cited in 114 publications, including Zhao et al., 2017, from our lab, which used this antibody for iPSC characterization. The Sox17 antibody (Abcam, ab84990) is reactive to human tissue, and has been cited in 11 publications. The Brachyury antibody (R&D, AF2085) is reactive to human tissue, and has been cited in 68 publications. The Nestin antibody (Abcam, ab18102) is reactive to human tissue, has been cited in 9 publications. The Sox2 antibody (Abcam, ab97959) is reactive to human tissue, has been cited in 358 publications, Ballabio C et al. 2020, which used this antibody for cerebral organoid. The TUJ1 antibody (Abcam, ab78078) is reactive to human tissue, has been cited in 110 publications. The TUJ1 antibody (Sigma, T2200) is reactive to human tissue, has been cited in 291 publications. The SATB2 antibody (Abcam, ab34735) is reactive to human tissue, has been cited in 43 publications. The GFAP antibody (Millipore, MAB360) is reactive to human tissue, has been cited in 384 publications for both immunostaining and western blots. The AT8 antibody (Thermo Fisher Scientific, MN1020) is reactive to human tissue, has been cited in 600 publications for both immunostaining and western blots. The G3BP antibody (BD, 611126) is reactive to human tissue, has been cited in 2 publications. The Caspase-3 antibody (Cell Signaling Technology, 9662) is reactive to human tissue, has been cited in 2240 publications.