Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
[Preprint]. 2024 Dec 4:rs.3.rs-5338140.
doi: 10.21203/rs.3.rs-5338140/v1.

Ancestral Genomic Functional Differences in Oligodendroglia: Implications for Alzheimer's Disease

Aura M Ramirez  1 , Luciana Bertholim-Nasciben  1 , Sofia Moura  1 , Lauren E Coombs  1 , Farid Rajabli  1 , Brooke A DeRosa  1 , Patrice G Whitehead  1 , Larry D Adams  1 , Takiyah D Starks  2 , Pedro Mena  1 , Maryenela Illannes-Manrique  3 , Sergio J Tejada  1 , Goldie S Byrd  2 , Allison Caban-Holt  2 , Michael Cuccaro  1 , Katalina McInerney  1 , Mario Cornejo-Olivas  4 , Briseida Feliciano-Astacio  5 , Liyong Wang  1 , Maria C Robayo  1 , Wanying Xu  6 , Fulai Jin  6 , Margaret A Pericak-Vance  1 , Anthony J Griswold  1 , Derek M Dykxhoorn  1 , Juan I Young  1 , Jeffery M Vance  1
Affiliations

Ancestral Genomic Functional Differences in Oligodendroglia: Implications for Alzheimer's Disease

Aura M Ramirez et al. Res Sq. .

Update in

  • Ancestral genomic functional differences in oligodendroglia: implications for Alzheimer's disease.
    Ramirez AM, Nasciben LB, Moura S, Coombs L, Rajabli F, DeRosa BA, Whitehead PL, Adams LD, Starks TD, Mena PR, Illanes-Manrique M, Tejada S, Byrd GS, Caban-Holt A, Cuccaro ML, McInerney K, Cornejo-Olivas MR, Feliciano-Astacio BE, Wang L, Robayo MC, Xu W, Jin F, Pericak-Vance MA, Griswold AJ, Young JI, Dykxhoorn DM, Vance JM. Ramirez AM, et al. Alzheimers Dement. 2025 Sep;21(9):e70593. doi: 10.1002/alz.70593. Alzheimers Dement. 2025. PMID: 40937943 Free PMC article.

Abstract

Background: This study aims to elucidate ancestry-specific changes to the genomic regulatory architecture in induced pluripotent stem cell (iPSC)-derived oligodendroglia, focusing on their implications for Alzheimer's disease (AD). This work addresses the lack of diversity in previous iPSC studies by including ancestries that contribute to African American (European/African) and Hispanic/Latino populations (Amerindian/African/European).

Methods: We generated 12 iPSC lines-four African, four Amerindian, and four European- from both AD patients and non-cognitively impaired individuals, with varying APOE genotypes (APOE3/3 and APOE4/4). These lines were differentiated into neural spheroids containing oligodendrocyte lineage cells. Single-nuclei RNA sequencing and ATAC sequencing were employed to analyze transcriptional and chromatin accessibility profiles, respectively. Differential gene expression, chromatin accessibility, and Hi-C analyses were conducted, followed by pathway analysis to interpret the results.

Results: We identified ancestry-specific differences in gene expression and chromatin accessibility. Notably, numerous AD GWAS-associated genes were differentially expressed across ancestries. The largest number of differentially expressed genes (DEGs) were found in European vs. Amerindian and African vs. Amerindian iPSC-derived oligodendrocyte progenitor cells (OPCs). Pathway analysis of APOE4/4 carriers vs APOE3/3 carriers exhibited upregulation of a large number of disease and metabolic pathways in APOE4/4 individuals of all ancestries. Of particular interest was that APOE4/4 carriers had significantly upregulated cholesterol biosynthesis genes relative to APOE3/3 individuals across all ancestries, strongest in iOPCs. Comparison of iOPC and iOL transcriptome data with corresponding human frontal cortex data demonstrated a high correlation (R2 > 0.85).

Conclusions: This research emphasizes the importance of including diverse ancestries in AD research to uncover critical gene expression differences between populations and ancestries that may influence disease susceptibility and therapeutic interventions. The upregulation of cholesterol biosynthesis genes in APOE4/4 carriers of all three ancestries supports the concept that APOE4 may produce disease effects early in life, which could have therapeutic implications as we move forward towards specific therapy for APOE4 carriers. These findings and the high correlation between brain and iPSC-derived OPC and OL transcriptomes support the relevance of this approach as a model for disease study.

PubMed Disclaimer

Conflict of interest statement

Competing interests The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. Characterization of iPSC-derived neural spheroids with different ancestral backgrounds.
A. Representative image of immunocytochemistry analysis of iPSC derived neural 3D cultures. B.Visualization of single nuclei clusters from 47,898 nuclei integrated across 12 samples of iPS-derived neural 3D cultures including 4 samples from each ancestry (AF, AI, EU).Clustering of single nuclei from the integrated datasets representing the identified cellular clusters based on scRNA-seq data and grouped by cell type. C. Visualization of different cell marker expression in the different cell clusters shown in B. Cells are Expression depicted from purple (low) to yellow (high).
Figure 2
Figure 2. Ancestry-Related Transcriptomic Changes in Oligodendroglia.
Volcano plots illustrating differential gene expression analyses for oligodendroglia clusters, specifically Oligodendrocyte Progenitor Cells (OPC) and mature Oligodendrocytes, across diverse ancestry backgrounds. Each plot represents a pairwise comparison of ancestry groups, highlighting the number of differentially expressed genes (DEGs). A. European vs. Amerindian comparison in the OPC cluster. B. European vs. Amerindian comparison in the Oligodendrocyte. C. African vs. Amerindian comparison in the OPC cluster. D. African vs. Amerindian comparison in the Oligodendrocyte cluster. E. European vs. African comparison in the OPC cluster. F. European vs. African comparison in the Oligodendrocyte cluster.
Figure 3
Figure 3. Ancestry-Dependent Expression of Alzheimer’s Disease GWAS Hits and Related Genes in iOPC and iOligodendrocyte Clusters.
Boxplots showing gene expression differences between A.oligodendrocyte precursor cells (OPC) and B. oligodendrocytes (OL) in relation to Alzheimer’s disease (AD) and ancestry-dependent changes.
Figure 4
Figure 4. Transcriptional Changes in Oligodendroglia Based on APOE Genotype.
Differential gene expression occurring in oligodendroglia based on APOE genotype, comparing the APOE3/3lines to the APOE4/4 lines, irrespective of their ancestry. A. Volcano plot showing DEGs between APOE3/3 and APOE4/4 samples in the iOPC cluster. Genes that have been reported as AD GWAS hits are labeled. B. Dot plot illustrating the pseudo-bulk expression of the differentially expressed AD GWAS hits in the iOPC cluster. C. Volcano plot showing DEGs between APOE3/3and APOE4/4 samples in the iOL cluster. Genes that have been reported as AD GWAS hits are labeled. D. Dot plot illustrating the pseudo-bulk expression of the differentially expressed AD GWAS hits in the iOL cluster.
Figure 5
Figure 5
Pathway analysis of DEGs found in oligodendroglia when compared by APOE genotype and AD status A.Pathways enriched in OPCs from APOE4/4 carriers compared to APOE3/3 carriers. B. Pathways enriched in iOLs from APOE4/4 carriers compared to APOE3/3carriers iOPC. C. Pathways enriched in iOPCs from AD compared to NCI. D. Pathways enriched in iOLs from AD compared to NCI.
Figure 6
Figure 6. Differential expression of genes implicated in cholesterol biosynthesis and myelination between iPSC derived OPCs with different APOE genotypes.
Dot plot illustrates the pseudo-bulk expression of the differentially expressed genes (p_val_adj<0.05 and Fold change >1 or <−1)
Figure 7
Figure 7. Pathway analysis for DEGs Across Ancestries.
DEGs found for each pairwise ancestry comparison in both oligodendroglia clusters were used for pathway analysis. A. Pathways enriched between AF and AI iOPCs. B. Pathways enriched between AF and AI iOLs. C. Pathways enriched between EU and AI iOPCs. D. Pathways enriched between EU and AI iOLs. E. Pathways enriched between EU and AI OPCs
Figure 8
Figure 8. Visualization of single nuclei clusters from 76409 nuclei integrated across 12 samples of iPS-derived neural 3D cultures including 4 samples from each ancestry (AF, AI, EU)
A. Clustering of single nuclei from the integrated datasets representing the identified cellular clusters based on ATAC-seq data. B. Visualization of oligodendroglia markers expression in the different cell clusters shown in A. Accessibility depicted from purple (low) to yellow (high).
Figure 9
Figure 9. Ancestry-Related Chromatin Accessibility Changes in Oligodendroglia.
Volcano plots illustrating differential chromatin accessibility across different ancestral backgrounds in oligodendroglia clusters, specifically iOPC and mature iOligodendrocytes. Each plot represents a pairwise comparison of ancestry groups, highlighting the genes with differentially accessible chromatin. A. African vs. Amerindian comparison in the iOPC cluster B. European vs. Amerindian comparison in the iOL. (C) African vs. European comparison in the iOPC cluster D. African vs. Amerindian comparison in the iOL cluster. E.European vs. Amerindian comparison in the OPC cluster. F. European vs. African comparison in the Oligodendrocyte cluster.
Figure 10
Figure 10. Comparison of Differentially Accessible Genes and Differentially Expressed Genes.
Venn Diagram Analysis showing the overlap between differentially accessible genes, differentially expressed genes, and AD GWAS hits for the different pairwise comparisons made based on global ancestry for the OPC (A, B and C) and the OL (D, E and F) clusters.
Figure 11
Figure 11. Chromatin accessibility and Hi-C loops overview for a subregion of FGF12 in oligodendroglia of different ancestries.
Highlighted in yellow is a DAP between ancestries with a profile that correlates with FGF12 expression.
Figure 12
Figure 12. Comparative analysis of differentially expressed genes (DEGs) and genes with differentially accessible peaks (DAPs) in oligodendroglia based on APOE genotype.
A-B. Comparison of APOE3/3 OPCs to APOE4/4 OPCs. C-D Comparison of APOE3/3Oligodendrocytes to APOE4/4 Oligodendrocytes.
Figure 13
Figure 13. Comparative analysis of differentially expressed genes (DEGs) and genes with differentially accessible peaks (DAPs) in oligodendroglia based on Alzheimer’s disease status.
A-B. Comparison of OPCs from affected donors to non-cognitively impaired donors OPCs. C-D Comparison of Oligodendrocytes from affected donors to Oligodendrocytes from unaffected controls.
See this image and copyright information in PMC

References

    1. Bellenguez C., et al. , New insights into the genetic etiology of Alzheimer’s disease and related dementias. Nat Genet, 2022. 54(4): p. 412–436. - PMC - PubMed
    1. Kunkle B.W., et al. , Genome-wide linkage analyses of non-Hispanic white families identify novel loci for familial late-onset Alzheimer’s disease. Alzheimers Dement, 2016. 12(1): p. 2–10. - PMC - PubMed
    1. Kunkle B.W., et al. , Novel Alzheimer Disease Risk Loci and Pathways in African American Individuals Using the African Genome Resources Panel: A Meta-analysis. JAMA Neurol, 2021. 78(1): p. 102–113. - PMC - PubMed
    1. Lake J., et al. , Multi-ancestry meta-analysis and ne-mapping in Alzheimer’s disease. Mol Psychiatry, 2023. 28(7): p. 3121–3132. - PMC - PubMed
    1. de Rojas I., et al. , Common variants in Alzheimer’s disease and risk stratification by polygenic risk scores. Nat Commun, 2021. 12(1): p. 3417. - PMC - PubMed

Publication types

LinkOut - more resources