Characterization and Molecular Profiling of PSEN1 Familial Alzheimer’s Disease iPSC-Derived Neural Progenitors

Presenilin 1 (PSEN1) encodes the catalytic subunit of γ-secretase, and PSEN1 mutations are the most common cause of early onset familial Alzheimer’s disease (FAD). In order to elucidate pathways downstream of PSEN1, we characterized neural progenitor cells (NPCs) derived from FAD mutant PSEN1 subjects. Thus, we generated induced pluripotent stem cells (iPSCs) from affected and unaffected individuals from two families carrying PSEN1 mutations. PSEN1 mutant fibroblasts, and NPCs produced greater ratios of Aβ42 to Aβ40 relative to their control counterparts, with the elevated ratio even more apparent in PSEN1 NPCs than in fibroblasts. Molecular profiling identified 14 genes differentially-regulated in PSEN1 NPCs relative to control NPCs. Five of these targets showed differential expression in late onset AD/Intermediate AD pathology brains. Therefore, in our PSEN1 iPSC model, we have reconstituted an essential feature in the molecular pathogenesis of FAD, increased generation of Aβ42/40, and have characterized novel expression changes.

Introduction

Although the majority of Alzheimer’s disease (AD) cases are late onset and likely result from a mixture of genetic predisposition and environmental factors, there are autosomal dominant genetic forms of the disease that affect patients at much earlier ages (FAD). Known familial early-onset genes include mutations in amyloid precursor protein (APP), presenilin-1 (PSEN/PS1), and presenilin-2 (PSEN2/PS2)[1]. PSEN1 mutations are responsible for the most common form of inherited AD and are 100% penetrant [1]–[3]. The most prevalent theory for the underlying cause of AD is the “amyloid hypothesis”, in which toxic oligomerogenic forms of Aβ, a cleavage product of APP, accumulate and cause neuronal dysfunction and cell death [4]. PS1/PS2 are key components of the γ-secretase complex that mediates one of the two APP cleavage events, and mutations in PS1 increase the relative ratios of the more oligomerogenic Aβ species (i.e. Aβ42) to less oligomerogenic species (Aβ40).

Most investigation of the molecular phenotypes caused by the PSEN1 mutations has focused on this microheterogeneous cleavage at the carboxy terminus of Aβ. This qualitative change is believed to be associated with hypomorphism in processivity [5] and has implications for misprocessing of multiple substrates other than APP [6]. Further, the magnitude of the mutant PSEN1-associated perturbations of Aβ42:Aβ40 varies widely, and, in some mutations (e.g., PSEN1 L271V in the Tas-1 family;[7]) alterations in the Aβ42:Aβ40 ratio have been either minimal or difficult to demonstrate. This raises the possibility that PS1 could have physiological or pathological effects independent of its effects on APP processing. This is an important issue to investigate thoroughly since PSEN1 mutations are present in virtually all of the cell- and mouse-based models used to develop hypotheses and treatments for common, sporadic AD. However, in common, sporadic AD, no PSEN1 mutation is present. Indeed, PSEN1-mutation-related AD is conceived as a disease of Aβ anabolism while at least some forms of common, sporadic AD (i.e., that linked to APOE4;[8]) are conceived as a disease of Aβ catabolism. Other genes linked to common, sporadic AD (e.g., CR1) appear to act via the immune response and may modulate cerebral amyloidosis in unexpected ways [9].

Recently several groups have generated human iPSC or transdifferentiation models of AD, with studies primarily focused on FAD neurons [10]–[13]. None of these studies addressed whether there are any differences between AD and control NPCs prior to neuronal differentiation. NPCs are a potentially relevant system to study aspects of disease on neuronal differentiation. Some FAD mouse models demonstrate deficits in neurogenesis as the animals age, and NPCs taken from AD brains of recently deceased patients have decreased neurogenic potential in comparison to those from similarly aged healthy controls [14], [15]. Newly born adult neurons in mouse models of AD have also been reported to have significantly decreased viability relative to control mice [16]. In addition, the brains of early-onset Alzheimer’s patients might have developmental alterations that could affect the progression of the disease. This possibility has been recently speculated in response to a report that young adults from the Colombian FAD kindred (PS1 E280A) have changes in grey matter and synaptic function potentially prior to formation of Aβ plaques [17](http://dx.doi.org/10.1016/S1474-4422(12)​70256-9). NPCs are also a more homogenous population that might reduce the experimental variability of mature neurons produced by current neuronal differentiation protocols, and thus could be a better system to identify novel molecules potentially important for early events in AD. We used gene expression profiling (GEP) of this population to identify novel candidate genes and confirmed hits in brains from common, sporadic AD with advanced or intermediate pathology by qPCR and by comparison to published transcriptomes of laser captured microdissected (LCM) cortical neurons from brains with AD pathology.

Results

Generation of iPSC Lines

In order to create PSEN1 mutant and wild-type control iPSC lines, established fibroblast lines were obtained from the cell bank repository at the Coriell Institute (Camden, NJ). Non-EBV transformed fibroblast lines were selected from the “Canadian” (FAD1, A246E PS1 mutation) and the “Italian” (FAD4, M146L PS1 mutation) EOFAD kindreds. Heterozygosity in the PSEN1 locus was confirmed in AD patients for fibroblasts (data not shown) and subsequently derived iPSCs via sequencing. Fibroblast lines were reprogrammed using four high-titer retroviral constructs prepared by the Harvard Gene Therapy Core Facility that encoded human Oct4, KLF4, SOX2 and c-Myc, respectively [18]. iPSC colonies were initially selected by morphology, passaged several times to remove transformed cells, and expanded before characterization.

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Citation: Sproul AA, Jacob S, Pre D, Kim SH, Nestor MW, et al. (2014) Characterization and Molecular Profiling of PSEN1 Familial Alzheimer’s Disease iPSC-Derived Neural Progenitors. PLoS ONE 9(1): e84547. doi:10.1371/journal.pone.0084547

Editor: David R. Borchelt, University of Florida, United States of America

Received: August 10, 2013; Accepted: November 15, 2013; Published: January 8, 2014

Copyright: © 2014 Sproul et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: This work is generously supported by grants to Scott Noggle by Charles Evans Foundation, Alzheimer′s Drug Discovery Foundation, and NY Community Trust. Scott Noggle and Sam Gandy are jointly supported by National Institutes of Health (NIH) grants R21AG042965 and 1U01AG046170-01, and the Cure Alzheimer’s Fund. Ottavio Arancio is supported by NIH grant NS049442. Alex Dranovsky is supported by NIH grant R01MH091844. Soong Ho Kim is supported by the BrightFocus Foundation. The authors express their sincerest gratitude to the patients and staff of the Taub Institute for Research on Alzheimer’s Disease & the Aging Brain at Columbia University (P50AG08702, RO1AG037212, P01AG07232). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

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