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The endosomal-lysosomal pathway is dysregulated by APOE4 expression in vivo

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Abstract

Possession of the ε4 allele of apolipoprotein E (APOE) is the major genetic risk factor for late-onset Alzheimer’s disease (AD). Although numerous hypotheses have been proposed, the precise cause of this increased AD risk is not yet known. In order to gain a more comprehensive understanding of APOE4's role in AD, we performed RNA-sequencing on an AD-vulnerable vs. an AD-resistant brain region from aged APOE targeted replacement mice. This transcriptomics analysis revealed a significant enrichment of genes involved in endosomal-lysosomal processing, suggesting an APOE4-specific endosomal-lysosomal pathway dysregulation in the brains of APOE4 mice. Further analysis revealed clear differences in the morphology of endosomal-lysosomal compartments, including an age-dependent increase in the number and size of early endosomes in APOE4 mice. These findings directly link the APOE4 genotype to endosomal-lysosomal dysregulation in an in vivo, AD pathology-free setting, which may play a causative role in the increased incidence of AD among APOE4 carriers.

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Crossref · 10.3389/fnins.2017.00702

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Figures

Figure 1 Transcriptomics analysis was performed on RNA extracted from the EC and PVC of aged APOE3/4 vs. APOE3/3 mice. RNA-sequencing was performed to analyze the effects of differential APOE isoform expression on RNA levels in the PVC and EC of aged APOE mice APOE3/4 (19 APOE3/4 males vs. 10 APOE3/3 males). (A) A heat map visualizing the Euclidean distance between samples, with darker red colors indicating increased similarity. (B) Volcano plots visualizing the fold change and adjusted p-values of each gene that was differentially expressed in the PVC and EC of APOE3/4 vs. APOE3/3 mice.
Figure 1 Transcriptomics analysis was performed on RNA extracted from the EC and PVC of aged APOE3/4 vs. APOE3/3 mice. RNA-sequencing was performed to analyze the effects of differential APOE isoform expression on RNA levels in the PVC and EC of aged APOE mice APOE3/4 (19 APOE3/4 males vs. 10 APOE3/3 males). (A) A heat map visualizing the Euclidean distance between samples, with darker red colors indicating increased similarity. (B) Volcano plots visualizing the fold change and adjusted p-values of each gene that was differentially expressed in the PVC and EC of APOE3/4 vs. APOE3/3 mice.CC BY · PubMed Central
Figure 2 Pathway analysis reveals numerous pathways affected by differential APOE isoform expression. A pathway analysis was performed on the differentially expressed EC genes using Cytoscape's ClueGo application. Shown here are the significantly enriched KEGG pathways observed in the EC of APOE3/4 vs. APOE3/3 mice, with the 9 differentially expressed V-type ATPase genes circled. (Further details can be found in Table 1).
Figure 2 Pathway analysis reveals numerous pathways affected by differential APOE isoform expression. A pathway analysis was performed on the differentially expressed EC genes using Cytoscape's ClueGo application. Shown here are the significantly enriched KEGG pathways observed in the EC of APOE3/4 vs. APOE3/3 mice, with the 9 differentially expressed V-type ATPase genes circled. (Further details can be found in Table 1).CC BY · PubMed Central
Figure 3 Genes related to endosomal–lysosomal system function are upregulated in the EC of APOE3/4 mice. Our RNA-Seq analysis of EC genes from aged APOE3/4 vs. APOE3/3 mice revealed an enrichment of upregulated genes related to endosomal–lysosomal system function. (A) Differentially regulated V-type ATPases in the EC of APOE3/4 vs. APOE3/3 mice. (B) Differentially regulated Rab GTPases in the EC of APOE3/4 vs. APOE3/3 mice. (**p < 0.01; ***p < 0.001; ****p < 0.0001).
Figure 3 Genes related to endosomal–lysosomal system function are upregulated in the EC of APOE3/4 mice. Our RNA-Seq analysis of EC genes from aged APOE3/4 vs. APOE3/3 mice revealed an enrichment of upregulated genes related to endosomal–lysosomal system function. (A) Differentially regulated V-type ATPases in the EC of APOE3/4 vs. APOE3/3 mice. (B) Differentially regulated Rab GTPases in the EC of APOE3/4 vs. APOE3/3 mice. (**p < 0.01; ***p < 0.001; ****p < 0.0001).CC BY · PubMed Central
Figure 4 The number and area fraction of Rab5a- and CatD-immunoreactive compartments are increased in the EC of aged APOE4/4 vs. APOE3/3 mice. Rab5a-immunoreactive early endosomes and CatD-immunoreactive lysosomes were quantified in the entorhinal cortex of 18 month-old APOE3/3 and APOE4/4 mice. (A) Representative images showing Rab5a and CatD immunolabeling (red), co-stained with Nissl (green). Black and white images were generated in ImageJ and used for quantification. (B–D) Quantification of average Rab5a- and CatD-positive compartment number (B), size (C), and area fraction (D) in APOE4/4 vs. APOE3/3 mice. (*p < 0.05; ***p < 0.001).
Figure 4 The number and area fraction of Rab5a- and CatD-immunoreactive compartments are increased in the EC of aged APOE4/4 vs. APOE3/3 mice. Rab5a-immunoreactive early endosomes and CatD-immunoreactive lysosomes were quantified in the entorhinal cortex of 18 month-old APOE3/3 and APOE4/4 mice. (A) Representative images showing Rab5a and CatD immunolabeling (red), co-stained with Nissl (green). Black and white images were generated in ImageJ and used for quantification. (B–D) Quantification of average Rab5a- and CatD-positive compartment number (B), size (C), and area fraction (D) in APOE4/4 vs. APOE3/3 mice. (*p < 0.05; ***p < 0.001).CC BY · PubMed Central
Figure 5 The number, size and area fraction of Rab5a-immunoreactive early endosomes are increased in the cingulate cortex of APOE4/4 vs. APOE3/3 mice with age. Rab5a-immunoreactive early endosomes were quantified in the cingulate cortex of 6, 12, 18, and 25 month-old APOE3/3 and APOE4/4 mice. (A) Representative images showing Rab5a immunolabeling (red). Black and white images were generated in ImageJ and used for quantification. (B–D) Quantification of average Rab5a-positive early endosome number (B), size (C), and area fraction (D) in APOE4/4 vs. APOE3/3 mice. (***p < 0.001; findings are normalized to the mean APOE3/3 value at each age in order to compare between age groups).
Figure 5 The number, size and area fraction of Rab5a-immunoreactive early endosomes are increased in the cingulate cortex of APOE4/4 vs. APOE3/3 mice with age. Rab5a-immunoreactive early endosomes were quantified in the cingulate cortex of 6, 12, 18, and 25 month-old APOE3/3 and APOE4/4 mice. (A) Representative images showing Rab5a immunolabeling (red). Black and white images were generated in ImageJ and used for quantification. (B–D) Quantification of average Rab5a-positive early endosome number (B), size (C), and area fraction (D) in APOE4/4 vs. APOE3/3 mice. (***p < 0.001; findings are normalized to the mean APOE3/3 value at each age in order to compare between age groups).CC BY · PubMed Central

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Metadata

Authors
Nuriel, T., Peng, K. Y., Ashok, A., Dillman, A. A., Figueroa, H. Y., Apuzzo, J., Ambat, J., Levy, E., Cookson, M. R., Mathews, P. M., & Duff, K. E.
Affiliations
  • Columbia University Irving Medical Center (US)
  • NYU Langone Health (US)
  • National Institutes of Health (US)
  • Nathan Kline Institute for Psychiatric Research (US)
Corresponding author
  • Mathews, Paul M.
  • Duff, Karen E.
Venue
Frontiers in Neuroscience
Published
2017-12-12
Volume
11
Pages
702-702
ISSN
1662-453X (ISSN-L)
OpenAlex
W2775642640
Cited by
140
References
59
Citations by year
2026: 10 · 2025: 17 · 2024: 16 · 2023: 15 · 2022: 19 · 2021: 21 · 2020: 23 · 2019: 17 · 2018: 2
FWCI
8.50
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Frontiers in Neuroscience (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Institute on Aging (AG048408, AG047797, AG017617)
  • National Institute of Neurological Disorders and Stroke (NS071836)
  • BrightFocus Foundation (A2014200F)
  • Cure Alzheimer's Fund
Topics
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Alzheimer's disease research and treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Autophagy in Disease and Therapy
Keywords
APOE ε4, apolipoprotein E, endolysosomal pathway, Alzheimer's disease, late-onset Alzheimer's disease, early endosomes, lysosomal dysfunction, genetic risk factors, transcriptomics

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