PT - JOURNAL ARTICLE AU - Andrew B. Caldwell AU - Qing Liu AU - Gary P. Schroth AU - Douglas R. Galasko AU - Shauna H. Yuan AU - Steven L. Wagner AU - Shankar Subramaniam TI - Dedifferentiation and neuronal repression define Familial Alzheimer’s Disease AID - 10.1101/531202 DP - 2019 Jan 01 TA - bioRxiv PG - 531202 4099 - http://biorxiv.org/content/early/2019/11/18/531202.short 4100 - http://biorxiv.org/content/early/2019/11/18/531202.full AB - Early-Onset Familial Alzheimer’s Disease (EOFAD) is a dominantly inherited neurodegenerative disorder elicited by over 300 mutations in the PSEN1, PSEN2, and APP genes1. Hallmark pathological changes and symptoms observed, namely the accumulation of misfolded Amyloid-β (Aβ) in plaques and Tau aggregates in neurofibrillary tangles associated with memory loss and cognitive decline, are understood to be temporally accelerated manifestations of the more common sporadic Late-Onset Alzheimer’s Disease. The complete penetrance of EOFAD-causing mutations has allowed for experimental models which have proven integral to the overall understanding of AD2. However, the failure of pathology-targeting therapeutic development suggests that the formation of plaques and tangles may be symptomatic and not describe the etiology of the disease3,4. In this work, we used an integrative, multi-omics approach and systems-level analysis in hiPSC-derived neurons to generate a mechanistic disease model for EOFAD. Using patient-specific cells from donors harboring mutations in PSEN1 differentiated into neurons, we characterized the disease-related gene expression and chromatin accessibility changes by RNA-Seq, ATAC-Seq, and histone methylation ChIP-Seq. Here, we show that the defining disease-causing mechanism of EOFAD is dedifferentiation, causing neurons to traverse the lineage-defining chromatin landscape along an alternative axis to a mixed-lineage cell state with gene signature profiles indicative of less-defined ectoderm as well as non-ectoderm lineages via REST-mediated repression of neuronal lineage specification gene programs and the activation of non-specific germ layer precursor gene programs concomitant with modifications in chromatin accessibility. Further, a reanalysis of existing transcriptomic data from PSEN1 patient brain samples demonstrates that the mechanisms identified in our experimental system recapitulate EOFAD in the human brain. Our results comprise a disease model which describes the mechanisms culminating in dedifferentiation that contribute to neurodegeneration.