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Excitatory Neurons Derived from Human-Induced Pluripotent Stem Cells Show Transcriptomic Differences in Alzheimer’s Patients from Controls

Sagar, Ram, Azoidis, Ioannis, Zivko, Cristina, Xydia, Ariadni, Oh, Esther S., Rosenberg, Paul B., Lyketsos, Constantine G., Mahairaki, Vasiliki, Avramopoulos, Dimitrios·2023·Cells
DOI 10.3390/cells12151990PMC PMC10417412

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Abstract

The recent advances in creating pluripotent stem cells from somatic cells and differentiating them into a variety of cell types is allowing us to study them without the caveats associated with disease-related changes. We generated induced Pluripotent Stem Cells (iPSCs) from eight Alzheimer’s disease (AD) patients and six controls and used lentiviral delivery to differentiate them into excitatory glutamatergic neurons. We then performed RNA sequencing on these neurons and compared the Alzheimer’s and control transcriptomes. We found that 621 genes show differences in expression levels at adjusted p < 0.05 between the case and control derived neurons. These genes show significant overlap and directional concordance with genes reported from a single-cell transcriptome study of AD patients; they include five genes implicated in AD from genome-wide association studies and they appear to be part of a larger functional network as indicated by an excess of interactions between them observed in the protein–protein interaction database STRING. Exploratory analysis with Uniform Manifold Approximation and Projection (UMAP) suggests distinct clusters of patients, based on gene expression, who may be clinically different. Our research outcomes will enable the precise identification of distinct biological subtypes among individuals with Alzheimer’s disease, facilitating the implementation of tailored precision medicine strategies.

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Figure 1 Characterization of iPSCs: (a) Brightfield microscope shows the iPSC morphology (Scale bars: 400 μm). (b) Fluorescent immunostaining by using pluripotency markers (TRA-1-60, OCT4, Nanog) (Scale bars: 100 μm). (c) Flow-cytometry shows the purity of the iPSCs by pluripotency marker (TRA-1-60+ cells).
Figure 1 Characterization of iPSCs: (a) Brightfield microscope shows the iPSC morphology (Scale bars: 400 μm). (b) Fluorescent immunostaining by using pluripotency markers (TRA-1-60, OCT4, Nanog) (Scale bars: 100 μm). (c) Flow-cytometry shows the purity of the iPSCs by pluripotency marker (TRA-1-60+ cells).CC BY · PubMed Central
Figure 2 Expression of marker genes in human brain. Heatmap of the expression of the genes in Table 2 in human excitatory neurons from the single-cell expression database available from the Allen Brain Atlas. For details on subtypes and single cells, see the Allen Brain Atlas database.
Figure 2 Expression of marker genes in human brain. Heatmap of the expression of the genes in Table 2 in human excitatory neurons from the single-cell expression database available from the Allen Brain Atlas. For details on subtypes and single cells, see the Allen Brain Atlas database.CC BY · PubMed Central
Figure 3 Principal component analysis (PCA) using all genes on AD and control samples.
Figure 3 Principal component analysis (PCA) using all genes on AD and control samples.CC BY · PubMed Central
Figure 4 Identification of AD patients’ clusters by UMAP.
Figure 4 Identification of AD patients’ clusters by UMAP.CC BY · PubMed Central

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Metadata

Authors
Sagar, R., Azoidis, I., Zivko, C., Xydia, A., Oh, E. S., Rosenberg, P. B., Lyketsos, C. G., Mahairaki, V., & Avramopoulos, D.
Affiliations
  • Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
  • The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
ORCID
Venue
Cells
Publisher
MDPI AG
Published
2023-08-02
Volume
12
Issue
15
Pages
1990
ISSN
2073-4409
DOI
10.3390/cells12151990
PMC
PMC10417412
Cited by
8
References
5
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • R21 AG067016 NIH
  • Johns Hopkins Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease
  • Richman Family Foundation
  • Rick Sharp Alzheimer’s Foundation
  • Sharp Family Foundation
  • R01AG052510

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