Transcriptome analysis of mesenchymal stem cells pretreated with ginsenoside Rb1 and mining of key genes for treating acute kidney injury

doi:10.3877/cma.j.issn.2095-3216.2025.01.005

Abstract

Abstract:

Objective

This study employed transcriptomic sequencing and bioinformatics analyses to identify differentially expressed genes （DEGs） in mesenchymal stem cells （MSCs） treated with ginsenoside Rb1， in order to uncover key genes with potential therapeutic effects on acute kidney injury（AKI）， thereby providing novel insights for AKI treatment.

Methods

In this study， R4.4.2 software was employed to analyze the GSE207667 dataset for identifying DEGs in MSCs after ginsenoside Rb1 treatment.AKI-related key genes were then selected via Gene Ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） enrichment analyses.The selected key genes were further examined through functional annotations， literature review， and database analysis.

Results

From the MSCs treated with ginsenoside Rb1， 2969 DEGs were identified， comprising 1567 upregulated genes and 1402 downregulated genes（|log₂FC|＞0.585）.GO enrichment analysis revealed that these DEGs were primarily about biological and molecular functions， including the positive regulation of cell population proliferation and apoptotic cell clearance.KEGG analysis further indicated significant enrichment of DEGs in pathways of cytokine-cytokine receptor interaction， IL-17 signaling， ferroptosis， cell senescence， and efferocytosis （P＜0.05）.Based on functional annotations， this study identified 43 potential key genes related to AKI intervention， and discussed focusing on genes of BMP2， MMP13， ATG5， PTN， and NGF.These genes were implicated in critical biological processes as cell proliferation， apoptosis， inflammation， and tissue repair， and may be closely linked to the mechanism in which MSCs pretreated by ginsenoside Rb1 modulated AKI.

Conclusion

Ginsenoside Rb1 may exert therapeutic effects on AKI by modulating biological processes of cell proliferation and apoptosis in MSCs.The five key genes identified in this study （BMP2， MMP13， ATG5， PTN， and NGF） may offer potential targets for the application of ginsenoside Rb1-treated MSCs in AKI therapy.

Key words: Acute kidney injury, RNA sequencing, Network pharmacology, Mesenchymal stem cells, Ginsenoside Rb1

Keying Zhang, Yuwei Ji, Zhangning Fu, Yifan Zhang, Xiaochen Wang, Yan Yang, Xiangmei Chen, Guangyan Cai, Quan Hong. Transcriptome analysis of mesenchymal stem cells pretreated with ginsenoside Rb1 and mining of key genes for treating acute kidney injury[J]. Chinese Journal of Kidney Disease Investigation(Electronic Edition), 2025, 14(01): 26-33.

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References 58

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富集分析	分组	信号通路	分子缩写	中文全称	Log₂FC	P值	表达变化
KEGG	-	细胞因子-细胞因子受体相互作用	TSLP	胸腺基质淋巴生成物	1. 07	0. 0413	上调
			NGF	神经生长因子	0. 60	0. 0453	上调
			BMP2	骨形态发生蛋白2	0. 61	0. 0006	上调
		IL-17 信号通路	MMP13	基质金属蛋白酶　13	0. 59	0. 0019	上调
			SRSF1	丝氨酸/ 精氨酸富集剪接因子	0. 61	0. 0025	上调
		铁死亡	ACSL4	酰基辅酶a 合成酶长链家族成员4	0. 73	0. 0011	上调
			ACSL3	酰基辅酶a 合成酶长链家族成员3	0. 63	0. 0035	上调
			ATG5	自噬相关蛋白5	0. 68	0. 0004	上调
		细胞衰老	PPP1CB	蛋白磷酸酶1 催化亚基	0. 63	0. 0189	上调
			CCNE2	细胞周期蛋白E2	0. 61	0. 0006	上调
			PPID	肽基脯氨酰异构酶　D	0. 69	0. 0015	上调
		胞葬作用	CASP1	半胱天冬酶1	0. 82	0. 0405	上调
			GULP1	含吞噬适配器的GULP　PTB 结构域1	0. 84	0. 0269	上调
GO	生物过程	凋亡过程的正向调节	DDX3	DEAD-box 解旋酶3	0. 61	0. 0034	上调
			PTN	多效生长因子	0. 62	0. 0247	上调
			STK3	丝氨酸/ 苏氨酸激酶	0. 60	0. 0031	上调
			CCAR1	细胞分裂周期与凋亡调控因子1	0. 61	0. 0006	上调
			BMP2	骨形态发生蛋白2	0. 82	0. 0405	上调
			CASP1	半胱天冬酶1	0. 60	0. 0029	上调
			PMAIP1	PMA 诱导蛋白1	0. 69	0. 0015	上调
			PPID	肽基脯氨酰异构酶D	1. 07	0. 0413	上调
		细胞群增殖的正向调节	TSLP	胸腺基质淋巴生成素	0. 61	0. 0034	上调
			PTN	多效生长因子	0. 60	0. 0453	上调
			NGF	神经生长因子	0. 60	0. 0031	上调
			CCAR1	细胞分裂周期与凋亡调控因子1	0. 69	0. 0013	上调
			KITLG	KIT 配体	0. 61	0. 0006	上调
			BMP2	骨形态发生蛋白2	0. 68	0. 0219	上调
			CNOT7	CCR4-NOT 转录复合体亚基7	0. 52	0. 0008	上调
			RPS15A	核糖体蛋白S15A	0. 94	0. 0125	上调
			EPCAM	上皮细胞粘附分子	0. 61	0. 0034	上调

富集分析	分组	信号通路	分子缩写	中文全称	Log₂FC	P值	表达变化
KEGG	-	细胞因子-细胞因子受体相互作用	TSLP	胸腺基质淋巴生成物	1. 07	0. 0413	上调
			NGF	神经生长因子	0. 60	0. 0453	上调
			BMP2	骨形态发生蛋白2	0. 61	0. 0006	上调
		IL-17 信号通路	MMP13	基质金属蛋白酶　13	0. 59	0. 0019	上调
			SRSF1	丝氨酸/ 精氨酸富集剪接因子	0. 61	0. 0025	上调
		铁死亡	ACSL4	酰基辅酶a 合成酶长链家族成员4	0. 73	0. 0011	上调
			ACSL3	酰基辅酶a 合成酶长链家族成员3	0. 63	0. 0035	上调
			ATG5	自噬相关蛋白5	0. 68	0. 0004	上调
		细胞衰老	PPP1CB	蛋白磷酸酶1 催化亚基	0. 63	0. 0189	上调
			CCNE2	细胞周期蛋白E2	0. 61	0. 0006	上调
			PPID	肽基脯氨酰异构酶　D	0. 69	0. 0015	上调
		胞葬作用	CASP1	半胱天冬酶1	0. 82	0. 0405	上调
			GULP1	含吞噬适配器的GULP　PTB 结构域1	0. 84	0. 0269	上调
GO	生物过程	凋亡过程的正向调节	DDX3	DEAD-box 解旋酶3	0. 61	0. 0034	上调
			PTN	多效生长因子	0. 62	0. 0247	上调
			STK3	丝氨酸/ 苏氨酸激酶	0. 60	0. 0031	上调
			CCAR1	细胞分裂周期与凋亡调控因子1	0. 61	0. 0006	上调
			BMP2	骨形态发生蛋白2	0. 82	0. 0405	上调
			CASP1	半胱天冬酶1	0. 60	0. 0029	上调
			PMAIP1	PMA 诱导蛋白1	0. 69	0. 0015	上调
			PPID	肽基脯氨酰异构酶D	1. 07	0. 0413	上调
		细胞群增殖的正向调节	TSLP	胸腺基质淋巴生成素	0. 61	0. 0034	上调
			PTN	多效生长因子	0. 60	0. 0453	上调
			NGF	神经生长因子	0. 60	0. 0031	上调
			CCAR1	细胞分裂周期与凋亡调控因子1	0. 69	0. 0013	上调
			KITLG	KIT 配体	0. 61	0. 0006	上调
			BMP2	骨形态发生蛋白2	0. 68	0. 0219	上调
			CNOT7	CCR4-NOT 转录复合体亚基7	0. 52	0. 0008	上调
			RPS15A	核糖体蛋白S15A	0. 94	0. 0125	上调
			EPCAM	上皮细胞粘附分子	0. 61	0. 0034	上调

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