APOER2 splicing repertoire in Alzheimer’s disease: Insights from long-read RNA sequencing
Christina M. Gallo, Sabrina A. Kistler, Anna Natrakul, Adam T. Labadorf, Uwe Beffert, Angela Ho
Abstract
Disrupted alternative splicing plays a determinative role in neurological diseases, either as a direct cause or as a driver in disease susceptibility. Transcriptomic profiling of aged human postmortem brain samples has uncovered hundreds of aberrant mRNA splicing events in Alzheimer’s disease (AD) brains, associating dysregulated RNA splicing with disease. We previously identified a complex array of alternative splicing combinations across apolipoprotein E receptor 2 (APOER2), a transmembrane receptor that interacts with both the neuroprotective ligand Reelin and the AD-associated risk factor, APOE. Many of the human APOER2 isoforms, predominantly featuring cassette splicing events within functionally important domains, are critical for the receptor’s function and ligand interaction.
Introduction
Over 90% of human genes undergo alternative splicing to encode proteins with different functions [1]. It is estimated that 10–15% of disease-causing mutations are located at splice sites [2,3]. This number increases when considering mutations that impact splicing regulatory elements such as splicing silencers and enhancers. Notably, the brain exhibits a higher expression of alternatively spliced genes compared to other tissues, particularly within neurons [4,5]. Hence, disruptive splicing plays a significant role in neurological diseases, either as a direct causative factor, or as a contributor to disease susceptibility [6].
Materials and method
Ethics statement
Animal studies were approved by the Institutional Animal Care and Use Committee (IACUC), protocol number, PROTO201800553 and recombinant DNA studies were approved by the Institutional Biosafety Committee, protocol number, 24–1555.
Human tissue obtained from NIH Neurobiobank was institutional approved by Boston University. Written informed consent was provided to the NIH Neurobiobank.
Results
APOER2 transcript mapping in the human AD parietal cortex
To map the APOER2 isoform landscape in human postmortem AD brains, we isolated total RNA from the parietal cortex of three individuals with Braak stage IV pathology, and three non-AD age-matched controls (Fig 1A). All individuals were female and had an APOE ɛ3/ɛ3 genotype. RNA was subjected to an APOER2 specific cDNA synthesis, and RT-PCR was used to amplify the entire APOER2 coding region (Fig 1B).
Discussion
Our study reveals that a multitude of full-length APOER2 isoforms exist in the human brain, specifically in the hippocampus and parietal cortex, as determined by single molecule, long-read RNA sequencing. In our analysis, we identified over 200 unique APOER2 isoforms in these regions from individuals with AD and age-matched controls (Figs 1 and 2). In the parietal cortex, 183 isoforms were common to both the control and AD groups, with 20 isoforms exclusive to the control group and 6 unique to the AD group.
Acknowledgments
We would like to thank Anna-Maria Marinescu for her technical help.
Citation: Gallo CM, Kistler SA, Natrakul A, Labadorf AT, Beffert U, Ho A (2024) APOER2 splicing repertoire in Alzheimer’s disease: Insights from long-read RNA sequencing. PLoS Genet 20(7): e1011348. https://doi.org/10.1371/journal.pgen.1011348
Editor: Derek Michael Dykxhoorn, University of Miami Miller School of Medicine, UNITED STATES OF AMERICA
Received: January 26, 2024; Accepted: June 21, 2024; Published: July 22, 2024
Copyright: © 2024 Gallo 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: Raw sequencing datasets are available in Sequence Read Archive (SRA) NCBI, public repository under BioProject SRA ID: PRJNA1114762. BioSample and SRA accession numbers with respective URLs are listed in S7 Table.
Funding: This work was supported by the National Institutes of Health R01AG059762 to UB, a F31AG069498 predoctoral award to CMG, a T32GM008541 (NIGMS) support to CMG; and the Harold and Margaret Southerland Alzheimer’s Research Fund to AH and UB. The funding supported authors that includes salary support (AH, CMG, SAK, UB), and research expenses. 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.
