Female cortical cellular mosaicism underlies shared MeCP2 and PCB impacted gene pathways - PubMed (original) (raw)

Female cortical cellular mosaicism underlies shared MeCP2 and PCB impacted gene pathways

Osman Sharifi et al. bioRxiv. 2025.

Abstract

Etiologies of neurodevelopmental disorders involve genes and environment however their interactions are understudied. Rett Syndrome (RTT) is an X-linked, dominant neurodevelopmental disorder caused by mutations in MECP2, encoding the epigenetic regulator methyl CpG binding protein. Epigenetic features of MECP2 expression due to X-linked cellular mosaicism and the variability in severity and timing of progression in RTT suggest interaction with environmental neurotoxicants such as lipophilic polychlorinated biphenyls (PCBs). To understand shared mechanisms, we exposed WT and Mecp2e1 -/+ female mice to a human-relevant PCB mixture and dose, then performed single-nucleus 5' RNA-seq from cortex. We identified significant overlap in dysregulated genes and 71 shared pathways between the effects of PCB exposure and MeCP2 mutation, and co-mitigation of their transcriptional impacts. PCBs influenced the non-cell-autonomous transcriptional effects of MeCP2 mutations in wild-type-expressing neurons within the mosaic mutant female cortex in both mouse and human, suggesting that the interactions predominantly involve homeostatic gene networks.

Keywords: Rett syndrome; X chromosome inactivation; autism spectrum disorders; epigenetics; neurodevelopmental disorders; persistent organic pollutants; polychlorinated biphenyls; systems biology.

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Conflict of interest statement

Declarations of interest: Osman Sharifi, Dag H. Yasui, and Janine M. LaSalle are co-founders of 2C Bioscience Inc. The remaining authors declare no competing interests.

Figures

Figure 1 :

Figure 1 :. Single nuclear transcriptome study design to investigate effects of Mecp2 mutation and PCB exposure.

A. Schematic showing cortical samples from PCB or vehicle treatment groups of two genotypes (Mecp2e1+/+ WT or _Mecp2e1_−/+ HET) for snRNA-seq 5’. B. UMAP unsupervised clustering of cell types identified in cortex from all samples. C. Dot plot of the top marker genes for each cell type identified. D. UMAP plot of cell cluster by treatment group.

Figure 2:

Figure 2:. Interaction between Mecp2 genotype and PCB exposure in frequency and cell type distribution of differentially expressed genes (DEG).

A. Bar graph showing the significant number of DEGs for each experiment. B, C. Heatmaps showing the top DEGs by log-fold change (adjusted p-value ≤ 0.05) per cell type for comparing Vehicle vs PCB and comparing WT vs Mecp2e1−/+ HET cortices respectively.

Figure 3:

Figure 3:. KEGG pathway analysis shows convergent biological pathways between Mecp2 genotype and PCB exposure.

A. Bar graphs showing the number of significant dysregulated KEGG pathways per cell type. B. Upset plot showing the number of significant pathways overlapping across the 4 experimental pairwise comparisons. C. Dot plot showing the top overlapping pathways per cell type.

Figure 4:

Figure 4:. Mosaic cellular parsing reveals PCB effects on non-cell-autonomous transcriptional dysregulation in RTT mouse model.

A, B, C, D. UMAP plots showing WT_ Mecp2 and MUT_ Mecp2 expression in WT and Mecp2e1 mutant heterozygous cortices. E. DEG experiments comparing WT (green) or mutant (purple) single cells across sample type in Glutamatergic and GABAergic cells15 experimental comparisons (y-axis) for DEGs (bar graphs; red, up; blue, down for right group) revealed opposite PCB effects on Glutamatergic vs GABAergic neurons in bulk HET (#1) and opposite effects of mutant-expression within HET vs WT cortical GABAergic neurons (#14–15). No mutant-expressing cells were detected in WT cortex, as expected. Cells were down-sampled to the lowest number of cells per pair, n=3 mice/group

Figure 5:

Figure 5:. hdWGCNA analysis reveals correlated transcriptional networks impacted by Mecp2e1 mutation and PCBs.

A. Weighted gene network showing 7 modules and their corresponding hub genes. B. Dot plot showing the top 5 KEGG pathways for each module. C. Dot plot showing the overlap of cell type markers and gene modules.

Figure 6:

Figure 6:. Comparative analysis of mouse and human Rett cortex PCB-associated DEGs in GABAergic, Glutamatergic, and Non-Neuronal Cells.

A. UMAP plot of PCB and non-PCB exposed cell clustering. B. UMAP plot of unsupervised cell type clustering. C. UMAP plot of cell types grouped in two three broad cell types. D. Volcano plots of human and mouse DEGs in the three broad cell types. Significant DEGs are in Blue and Magenta. E, F. Dot plots of top 10 human and mouse KEGG terms respectively.

Figure 7:

Figure 7:. Overlap of mouse and human Rett cortex PCB-associated DEGs and KEGG terms in GABAergic, Glutamatergic, and Non-Neuronal Cells.

A, B. Upset plots of significant (adjusted p-value ≤ 0.05) DEGs and KEGG terms across human and mouse broad cell types respectively.

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