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Single-nucleus RNA sequencing reveals cell type-specific transcriptome alterations of Down syndrome hippocampus using the Dp16 mouse model

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Abstract

Background

Down syndrome (DS), the most frequently occurring human chromosomal disorder, is caused by trisomy 21. The exact molecular effects of trisomy on certain cell populations in the brain remain poorly understood.

Objective

The purpose of this study was to investigate the effects of trisomy on the transcriptomes of various types of neurons and nonneuronal cells in the hippocampus.

Methods

A total of 8993 nuclei from the WT and 6445 nuclei from the Dp16 hippocampus were analyzed by single-nucleus RNA sequencing (snRNA-seq). Cell clustering was achieved by the Seurat program.

Results

Hippocampal cells were grouped into multiple neuronal and nonneuronal populations. Only a limited number of trisomic genes were upregulated (q < 0.001) over 1.25-fold in a specific type of hippocampal cell. Specifically, deregulation of genes associated with synaptic signaling and organization was observed in multiple cell populations, including excitatory neurons, oligodendrocytes, and microglia. This observation suggests the potential importance of synapse deficits in DS. Interestingly, GO annotation of the upregulated genes suggested potential activation of the immune system by hippocampal excitatory neurons. Fewer trisomic genes were altered in nonneuronal cells than in neurons. Notably, microglial transcriptome analysis revealed significantly (q < 0.001) increased expression of C1qb and C1qc, which suggested potential involvement of complement-mediated synapse loss mediated by microglia in DS.

Conclusion

The trisomy-related hippocampal deficits should be driven by a small amount, not all, of the trisomic genes in a specific type of cell. Our work may help to narrow down both the molecular and cellular targets for future gene therapies in DS.

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Data availability

The raw sequence data reported in this study have been deposited in the National Genomics Data Center of China (https://ngdc.cncb.ac.cn/gsa) under the accession number CRA008321.

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Acknowledgements

This work was partly supported by the Fundamental Research Funds for the Central Universities (226-2022-00035), National Natural Science Foundation of China (81600986), and the start-up funding of The Children’s Hospital, Zhejiang University School of Medicine to XJ.

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Authors and Affiliations

  1. The Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, 310051, Zhejiang, China

    Zuolin Zhou, Chunchun Zhi, Die Chen & Xiaoling Jiang

  2. Laboratory Animal Research Center, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China

    Zhaowei Cai

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  1. Zuolin Zhou
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  2. Chunchun Zhi
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  3. Die Chen
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  4. Zhaowei Cai
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Correspondence to Xiaoling Jiang.

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13258_2023_1433_MOESM1_ESM.tif

Supplementary file1 (TIF 12531 KB) Supplementary Figure S1. Violin plots of gene number and transcript number detected per nucleus in the WT and Dp16 hippocampi

Supplementary file1 (XLSX 10 KB) Supplementary Table S1. snRNA-seq data summary

Supplementary file3 (XLSX 13 KB) Supplementary Table S2. The number of cells in each cell type

13258_2023_1433_MOESM4_ESM.xlsx

Supplementary file4 (XLSX 557 KB) Supplementary Table S3. The differentially expressed genes between Dp16 and WT across different cell types with log2|fold change|> 0.25

Supplementary file5 (XLSX 11 KB) Supplementary Table S4. Primers used for quantitative RT‒PCR

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Zhou, Z., Zhi, C., Chen, D. et al. Single-nucleus RNA sequencing reveals cell type-specific transcriptome alterations of Down syndrome hippocampus using the Dp16 mouse model. Genes Genom 45, 1305–1315 (2023). https://doi.org/10.1007/s13258-023-01433-2

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