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Functional Characterization of a Single Nucleotide Polymorphism Associated With Alzheimer’s Disease in a Hipsc-based Neuron Model

Lindsay R. Stolzenburg, Sahar Esmaeeli, Ameya S. Kulkarni, Erin Murphy, Taekyung Kwon, Christina Preiss, Lamiaa Bahnassawy, Joshua D. Stender, Justine D. Manos, Peter Reinhardt, Fedik Rahimov, Jeffrey F. Waring, Cyril Y. Ramathal

Abstract

Neurodegenerative diseases encompass a group of debilitating conditions resulting from progressive nerve cell death. Of these, Alzheimer’s disease (AD) occurs most frequently, but is currently incurable and has limited treatment success. Late onset AD, the most common form, is highly heritable but is caused by a combination of non-genetic risk factors and many low-effect genetic variants whose disease-causing mechanisms remain unclear. By mining the FinnGen study database of phenome-wide association studies, we identified a rare variant, rs148726219, enriched in the Finnish population that is associated with AD risk and dementia, and appears to have arisen on a common haplotype with older AD-associated variants such as rs429358. The rs148726219 variant lies in an overlapping intron of the FosB proto-oncogene (FOSB) and ERCC excision repair 1 (ERCC1) genes.

Introduction

Alzheimer’s Disease (AD) is an age-related neurodegenerative condition that affects more than 35 million people worldwide, with cases projected to increase as life expectancy continues to rise [1]. AD is characterized by progressive memory loss and cognitive decline and is pathologically marked by amyloid beta plaques and tau-based neurofibrillary tangles [2]. Genetically, AD etiology exists as two distinct forms: 1) early-onset familial AD (FAD), caused by rare mutations in high-impact genes usually inherited in an autosomal dominant fashion, and 2) late-onset AD (LOAD), the more common form. Heritability estimates for LOAD are between 58–79% [3], suggesting significant genetic contribution to disease development and/or progression.

Materials and method

The BIONi010-C-13 line (donor biosample SAMEA103988285) with doxycycline (DOX)-inducible neurogenin 2 (NGN2) transgene was obtained and is available from the European Bank for Induced pluripotent Stem Cells (EBiSC, www.ebisc.org) [14]. The line is derived from a dermal fibroblast sample donated by an 18 year-old healthy male of African-American descent. The EBiSC Bank acknowledges SAMEA103988285 as the source of human induced pluripotent stem cell line BIONi010-C-13 which was generated with support from EFPIA companies and the European Union (IMI-JU).

Results

The FinnGen study database contains genetic information and disease phenotype data from individuals of Finnish descent, a population displaying a founder effect and therefore possessing greater potential to pinpoint disease-associated variants compared to more heterogeneous populations. Finland has one of the highest rates of Alzheimer’s disease mortality worldwide [13]. To identify novel AD-associated variants that are specifically enriched in Finns and that may contribute to this high AD prevalence,

Discussion

Although the number of GWAS-identified variants associated with Alzheimer’s disease have skyrocketed, very little is known about the mechanisms by which most of these may impact disease. Using Finnish population-based PheWAS, our study nominated an AD-associated SNP tightly linked to a causal APOE variant but with potential for an additive effect on LOAD risk in the Finnish population. To functionally characterize rs148726219, we engineered heterozygous and homozygous alleles into hiPSCs, and investigated molecular consequences of this SNP throughout multiple hiPSC-to-neuron differentiation stages. Collectively, we observed that rs148726219-harboring lines develop into early-stage cortical neurons equally as well as WT lines, but their transcriptomes diverge from the WT line almost exclusively in mature iNs. Our data strongly suggest that expression of nearby genes are affected and important signaling pathways relevant to AD pathogenesis are dysregulated in the presence of the risk allele in a mature neuronal context, corroborative of its role as a risk allele for LOAD in the Finnish population.

Acknowledgments

We want to acknowledge the participants and investigators of the FinnGen study. Thank you to AbbVie employees Areej Ammar for performing whole genome sequencing, Bridget Riley-Gillis for conditional GWAS and Victor Coll for manuscript figure organization. Special thanks to Allison Ebert (Medical College of Wisconsin, no funding to disclose) for consulting on valuable scientific discussions.

Citation: Stolzenburg LR, Esmaeeli S, Kulkarni AS, Murphy E, Kwon T, Preiss C, et al. (2023) Functional characterization of a single nucleotide polymorphism associated with Alzheimer’s disease in a hiPSC-based neuron model. PLoS ONE 18(9): e0291029. https://doi.org/10.1371/journal.pone.0291029

Editor: Amy McCart Reed, The University of Queensland Faculty of Medicine, AUSTRALIA

Received: May 3, 2023; Accepted: August 20, 2023; Published: September 26, 2023

Copyright: © 2023 Stolzenburg 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.

Data Availability: All relevant data are within the paper and its Supporting information files. Additionally, all RNA sequencing files are available from the GEO database (accession https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239367.

Funding: The author(s) received no specific funding for this work.

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

 

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0291029#ack

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