单细胞 RNA 测序揭示了与心肌梗死相关的内皮细胞的枢纽基因。
Single-cell RNA sequencing reveals hub genes of myocardial infarction-associated endothelial cells.
机构信息
Department of Cardiovascular Medicine, Zhejiang Greentown Cardiovascular Hospital, No.409 Gudun Road, Hangzhou, 310000, Zhejiang, China.
Department of Geriatrics, The Second Affiliated Hospital of Zhejiang Chinese Medical University, No. 318 Chaowang Road, Hangzhou, 310005, Zhejiang, China.
出版信息
BMC Cardiovasc Disord. 2024 Jan 24;24(1):70. doi: 10.1186/s12872-024-03727-z.
BACKGROUND
Myocardial infarction (MI) is a cardiovascular disease that seriously threatens human health. Dysangiogenesis of endothelial cells (ECs) primarily inhibits recovery from MI, but the specific mechanism remains to be further elucidated.
METHODS
In this study, the single-cell RNA-sequencing data from both MI and Sham mice were analyzed by the Seurat Package (3.2.2). The number of ECs in MI and Sham groups were compared by PCA and tSNE algorithm. FindMarkers function of Seurat was used to analyze the DEGs between the MI and Sham groups. Then, the ECs was further clustered into 8 sub-clusters for trajectory analysis. The BEAM was used to analyze the branch point 3 and cluster the results. In addition, the DEGs in the microarray data set of MI and Sham mice were cross-linked, and the cross-linked genes were used to construct PPI networks. The key genes with the highest degree were identified and analyzed for functional enrichment. Finally, this study cultured human umbilical vein endothelial cells (HUVECs), established hypoxia models, and interfered with hub gene expression in cells. The impact of hub genes on the migration and tube formation of hypoxic-induced HUVECs were verified by Wound healing assays and tubule formation experiments.
RESULTS
The number and proportion of ECs in the MI group were significantly lower than those in the Sham group. Meantime, 225 DEGs were found in ECs between the MI and Sham groups. Through trajectory analysis, EC4 was found to play an important role in MI. Then, by using BEAM to analyze the branch point 3, and clustering the results, a total of 495 genes were found to be highly expressed in cell Fate2 (mainly EC4). In addition, a total of 194 DEGs were identified in Micro array dataset containing both MI and Sham mice. The hub genes (Timp1 and Fn1) with the highest degree were identified. Inhibiting Timp1 and Fn1 expression promoted the migration and tube formation of HUVECs.
CONCLUSIONS
Our data highlighted the non-linear dynamics of ECs in MI, and provided a foothold for analyzing cardiac homeostasis and pro-angiogenesis in MI.
背景
心肌梗死（MI）是一种严重威胁人类健康的心血管疾病。内皮细胞（ECs）的血管生成障碍主要抑制了 MI 的恢复，但具体机制仍有待进一步阐明。
方法
本研究通过 Seurat 包（3.2.2）分析 MI 和 Sham 小鼠的单细胞 RNA 测序数据。通过 PCA 和 tSNE 算法比较 MI 和 Sham 组中 ECs 的数量。使用 Seurat 的 FindMarkers 函数分析 MI 和 Sham 组之间的 DEGs。然后，将 ECs 进一步聚类为 8 个亚群进行轨迹分析。使用 BEAM 分析分支点 3 并对结果进行聚类。此外，对 MI 和 Sham 小鼠微阵列数据集的 DEGs 进行交联，并将交联基因用于构建 PPI 网络。鉴定并分析具有最高度数的关键基因，进行功能富集分析。最后，本研究培养人脐静脉内皮细胞（HUVECs），建立缺氧模型，并在细胞中干扰枢纽基因的表达。通过划痕愈合实验和管形成实验验证了枢纽基因对缺氧诱导的 HUVECs 迁移和管形成的影响。
结果
MI 组 ECs 的数量和比例明显低于 Sham 组。同时，在 MI 和 Sham 组的 ECs 之间发现了 225 个 DEGs。通过轨迹分析，发现 EC4 在 MI 中起重要作用。然后，通过使用 BEAM 分析分支点 3，并对结果进行聚类，发现总共 495 个基因在细胞 Fate2 中高表达（主要为 EC4）。此外，在包含 MI 和 Sham 小鼠的 Microarray 数据集中共鉴定出 194 个 DEGs。鉴定出具有最高度数的枢纽基因（Timp1 和 Fn1）。抑制 Timp1 和 Fn1 的表达促进了 HUVECs 的迁移和管形成。
结论
我们的数据突出了 MI 中 ECs 的非线性动力学，为分析 MI 中心脏稳态和促血管生成提供了立足点。
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