Relationships of APOE Genotypes With Small RNA and Protein Cargo of Brain Tissue Extracellular Vesicles From Patients With Late-Stage AD

Yiyao Huang; Tom A P Driedonks; Lesley Cheng; Harinda Rajapaksha; Andrey Turchinovich; David A Routenberg; Rajini Nagaraj; Javier Redding-Ochoa; Tanina Arab; Bonita H Powell; Olga Pletnikova; Juan C Troncoso; Lei Zheng; Andrew F Hill; Vasiliki Mahairaki; Kenneth W Witwer

doi:10.1212/NXG.0000000000200026

Relationships of APOE Genotypes With Small RNA and Protein Cargo of Brain Tissue Extracellular Vesicles From Patients With Late-Stage AD

Neurol Genet. 2022 Oct 26;8(6):e200026. doi: 10.1212/NXG.0000000000200026. eCollection 2022 Dec.

Authors

Yiyao Huang¹, Tom A P Driedonks¹, Lesley Cheng¹, Harinda Rajapaksha¹, Andrey Turchinovich¹, David A Routenberg¹, Rajini Nagaraj¹, Javier Redding-Ochoa¹, Tanina Arab¹, Bonita H Powell¹, Olga Pletnikova¹, Juan C Troncoso¹, Lei Zheng¹, Andrew F Hill¹, Vasiliki Mahairaki¹, Kenneth W Witwer¹

Affiliation

¹ Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD.

Abstract

Background and objectives: Variants of the apolipoprotein E (APOE) gene are the greatest known risk factors for sporadic Alzheimer disease (AD). Three major APOE isoform alleles, ε2, ε3, and ε4, encode and produce proteins that differ by only 1-2 amino acids but have different binding partner interactions. Whereas APOE ε2 is protective against AD relative to ε3, ε4 is associated with an increased risk for AD development. However, the role of APOE in gene regulation in AD pathogenesis has remained largely undetermined. Extracellular vesicles (EVs) are lipid bilayer-delimited particles released by cells to dispose of unwanted materials and mediate intercellular communication, and they are implicated in AD pathophysiology. Brain-derived EVs (bdEVs) could act locally in the tissue and reflect cellular changes. To reveal whether APOE genotype affects EV components in AD brains, bdEVs were separated from patients with AD with different APOE genotypes for parallel small RNA and protein profile.

Methods: bdEVs from late-stage AD brains (BRAAK stages 5-6) from patients with APOE genotypes ε2/3 (n = 5), ε3/3 (n = 5), ε3/4 (n = 6), and ε4/4 (n = 6) were separated using our published protocol into a 10,000g pelleted extracellular fraction (10K) and a further purified EV fraction. Counting, sizing, and multiomic characterization by small RNA sequencing and proteomic analysis were performed for 10K, EVs, and source tissue.

Results: Comparing APOE genotypes, no significant differences in bdEV total particle concentration or morphology were observed. Overall small RNA and protein profiles of 10K, EVs, and source tissue also did not differ substantially between different APOE genotypes. However, several differences in individual RNAs (including miRNAs and tRNAs) and proteins in 10K and EVs were observed when comparing the highest and lowest risk groups (ε4/4 and ε2/3). Bioinformatic analysis and previous publications indicate a potential regulatory role of these molecules in AD.

Discussion: For patients with late-stage AD in this study, only a few moderate differences were observed for small RNA and protein profiles between APOE genotypes. Among these, several newly identified 10K and EV-associated molecules may play roles in AD progression. Possibly, larger genotype-related differences exist and are more apparent in or before earlier disease stages.

Abstract

Grants and funding