主动脉瘤单细胞转录组的系统性分析与探索

doi:10.3969/j.issn.1674-8115.2025.06.008

摘要/Abstract

摘要：

目的·利用单细胞RNA测序（single-cell RNA sequencing，scRNA-seq）技术探究主动脉瘤（aortic aneurysm，AA）的单细胞图景。方法·通过系统性检索高通量基因表达数据库（Gene Expression Omnibus，GEO），收集所有符合纳入标准的数据集。使用R语言和Seurat软件包分析AA组织与正常对照组织的细胞构成占比变化；使用CellChat软件包通过细胞受体-配体对的基因表达水平评估细胞间相互作用；使用AUCell软件包依据SenMayo Senescence基因集进行细胞衰老程度评分并进行对比；通过将单细胞转录数据模拟为普通转录组数据，对周细胞进行差异基因筛选及基因通路富集分析。结果·共纳入9组数据集，经质量控制及合并后获得104 570个细胞的RNA计数数据，其中对照组48 311个、AA组56 259个。细胞被划分为19个簇，被注释为14种细胞类型。与对照组相比，AA组的周细胞比例显著降低（P<0.001），而单核/巨噬细胞和树突状细胞的数量占比显著上升（P=0.020，P=0.045）。此外，AA组细胞相互作用多于对照组，但血管平滑肌细胞参与的相互作用减少，周细胞与自身相互作用的强度亦有所降低。对照组特有的细胞相互作用有5种，AA组特有的细胞相互作用有13种，其中相对信息流量最大的相互作用是SPP1。除脂肪细胞外，AA组其余细胞种类的衰老评分均显著升高（均P<0.001），衰老阳性细胞数量明显增加（P<0.001），其中成纤维细胞占比最大。周细胞差异表达基因分析结果显示，AA组相比对照组有185个基因表达上调、151个表达下调，上调幅度最大的基因为Spp1。趋化因子活动通路及CXC趋化因子受体结合通路等促炎作用通路显著富集。结论·AA组织中的细胞构成发生显著变化，细胞间相互作用增强，细胞衰老程度上升，Spp1是关键基因。

关键词: 主动脉瘤, 单细胞测序, 细胞通信, 细胞衰老

Abstract:

Objective ·To explore the single-cell landscape of aortic aneurysm (AA) utilizing single-cell RNA sequencing (scRNA-seq) technology. Methods ·A systematic search of the Gene Expression Omnibus (GEO) was conducted to collect all datasets meeting the inclusion criteria. Changes in the percentage of cellular composition of AA tissues versus normal control tissues were analyzed using R language and the Seurat package. Cell-cell interactions were assessed by gene expression levels of cellular receptor-ligand pairs using the CellChat package. Cellular senescence was scored and compared based on the SenMayo Senescence gene set using the AUCell package.Single-cell transcriptional data were simulated as traditional transcriptome data for differential gene screening and gene pathway enrichment analysis of pericytes. Results ·A total of nine datasets meeting the criteria were included. After quality control and merging, RNA count data for 104 570 cells were obtained, comprising 48 311 in the control group and 56 259 in the AA group. Cells were categorized into 19 clusters and annotated into 14 cell types. Compared with the control group, the proportion of pericytes in the AA group significantly decreased (P<0.001), while the proportions of monocytes/macrophages and dendritic cells increased (P=0.020, P=0.045). The number of intercellular interactions in the AA group was markedly higher than that in the control group; however, yet the interactions involving smooth muscle cells decreased, and the interaction intensity among pericytes diminished. There were 5 unique intercellular interactions in the control group and 13 unique interactions in the AA group, with the interaction involving SPP1 showing the highest relative information flow. Except for adipocytes, all cell types in the AA group exhibited significantly higher senescence scores (P<0.001), with an overall increase in the number of senescent cells (P<0.001), predominantly fibroblasts. Differential expression analysis of pericytes showed 185 upregulated genes and 151 downregulated genes in the AA group, with Spp1 exhibiting the highest upregulation. Pro-inflammatory pathways related to chemokine activity and CXC chemokine receptor binding were significantly enriched. Conclusion ·The cellular composition in AA tissues undergoes significant alterations, characterized by an increase in intercellular interactions and elevated levels of cellular senescence, with Spp1 identified as a key gene.

Key words: aortic aneurysm (AA), single-cell RNA sequencing (scRNA-seq), cell communication, cell senescence

中图分类号:

R543.1

张星语, 李若谷. 主动脉瘤单细胞转录组的系统性分析与探索[J]. 上海交通大学学报（医学版）, 2025, 45(6): 735-744.

ZHANG Xingyu, LI Ruogu. Systematic analysis and exploration of single-cell transcriptomes in aortic aneurysm[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2025, 45(6): 735-744.

图/表 8

图1 AA scRNA-seq数据集筛选及整合Note： A. Dataset screening flowchart. B. Cell numbers in each group. C/D. UMAP diagram of distribution of cells before (C) and after (D) Harmony integration.

Fig 1 Screening and integration of AA scRNA-seq datasets

表1 各数据集的造模方法、取材时间及测序平台

Tab1 Induction method， harvest time point and sequencing platform of each dataset

Method for AA model establishment	Harvest time point/d	Sequencing platform	GSE number
ApoE knockout + angiotensin Ⅱ infusion	28	Illumina HiSeq 4000	GSE141732
ApoE knockout + angiotensin Ⅱ infusion	7	Illumina NovaSeq 6000	GSE233625
ApoE knockout + angiotensin Ⅱ infusion	28	Illumina NovaSeq 6000	GSE221789
ApoE knockout + angiotensin Ⅱ infusion	7	Illumina NovaSeq 6000	GSE213735
ApoE knockout + angiotensin Ⅱ infusion	28	Illumina HiSeq 4000	GSE141726
ApoE knockout + angiotensin Ⅱ infusion	28	Illumina HiSeq 4000	GSE186865
Paravascular CaCl₂ injection	4	Illumina NovaSeq 6000	GSE164678
Paravascular elastase injection	14	Illumina HiSeq 4000	GSE152583

图2 scRNA-seq数据降维聚类及细胞注释结果Note： A. UMAP plot of clustering distribution of cell subpopulations. B.UMAP plot of the distribution of cell subpopulations after annotation.

Fig 2 Dimension reduction clustering and cell annotation results of scRNA-seq data

图3 各细胞群的特征基因气泡图

Fig 3 Bubble plot of marker genes of each cluster

图4 细胞数量占比的组间比较Note： ①P<0.001, ②P=0.020, ③P=0.045.

Fig 4 Intergroup comparison of cell percentages

图5 细胞间相互作用的组间比较Note： A. Number and strength of inferred interactions in both groups. B. Differential number of interactions between the groups. Red arrows indicate a increased number of interactions in the AA group, and blue arrows indicate a decrease. C. Differential interaction strength between the groups. Red arrows indicate increased interaction strength in the AA group, and blue arrows indicate decreased strength. D. Overall information flow of each signaling pathway in both groups. E. Signaling changes of pericytes in the AA group compared to the control group.

Fig 5 Intergroup comparison of cell-cell interactions

图6 SenMayo senescence细胞衰老评分Note： A. Senescence-positive threshold determination based on the SenMayo senescence score. B. Comparison of SenMayo senescence scores for each cell type between the two groups. C. Number of senescence-positive cells of each cell type in both groups. ①P<0.001.

Fig 6 SenMayo senescence score of cells

图7 周细胞的差异表达基因筛选与富集分析Note： A. Volcano plot of gene expression changes in the AA group compared to the control group. B. GSEA plot of the top enriched pathways.

Fig 7 Screening and enrichment analysis of differentially expressed genes in pericytes

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