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| Status |
Public on Mar 06, 2024 |
| Title |
Excitatory Neurons Derived from Human-Induced Pluripotent Stem Cells Show Transcriptomic Differences in Alzheimer’s Patients from Controls |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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) and used lentiviral delivery to differentiate them into excitatory glutamatergic neurons, on which we performed RNA sequencing. We compared transcriptomes of cells derived from 7 Alzheimer’s disease (AD) and 6 control patients. 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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| Overall design |
cells from 7 Alzheimers patients and 6 controls were used to create hiPSCs and then differentiated to excitatory neurons. RNA was extracted and subjected to RNA sequencing, after which the transcriptomes of patient and control derived cells were compared. Details in our publication Cells 2023, 12(15), 1990; https://doi.org/10.3390/cells12151990
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| Contributor(s) |
Sagar R, Azoidis I, Zivko C, Xydia A, Oh ES, Rosenberg PB, Lyketsos CG, Mahairaki V, Avramopoulos D |
| Citation(s) |
37566069, 38566045 |
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| Submission date |
Mar 05, 2024 |
| Last update date |
Apr 17, 2024 |
| Contact name |
Dimitrios Avramopoulos |
| E-mail(s) |
adimitr1@jhmi.edu
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| Organization name |
Johns Hopkins University
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| Department |
Genetic Medicine
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| Street address |
733 North Broadway
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA1083885 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE260873_countsNormalized_fromDeseq2.csv.gz |
1.7 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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