山柰酚治疗乳腺癌机制的网络药理学与生物信息学分析及机制相关预后模型构建
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湖南师范大学附属第一医院/湖南省人民医院 乳甲外科,湖南 长沙 410005

作者简介:

肖美灵,湖南师范大学附属第一医院/湖南省人民医院硕士研究生,主要从事乳腺及甲状腺疾病方面的研究。

基金项目:

湖南省自然科学基金资助项目(2022JJ30335)。


Network pharmacology and bioinformatics analysis of the mechanism of kaempferol in the treatment of breast cancer and construction of a mechanism-related prognostic model
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Department of Breast and Thyroid Surgery, the First Affiliated Hospital of Hunan Normal University/Hunan Provincial People's Hospital, Changsha410005, China

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    摘要:

    背景与目的 山柰酚是一种天然黄酮类化合物,可以调节各种与癌症相关的过程和活动,如细胞周期、氧化应激、细胞凋亡、增殖、转移和血管生成,且其抗乳腺癌的潜力已得到了一些研究的验证,但其作用机制尚不清楚。因此,本研究探讨山柰酚治疗乳腺癌的潜在作用靶点和通路,并建立预后模型。方法 基于网络药理学和生物信息学方法,利用HERB、GeneCards、STRING、Pubchem、RSCD PDB、TCGA等数据库获取山柰酚治疗乳腺癌的交集靶点进行蛋白互作、GO分析及KEGG通路富集分析,并进行分子对接进行验证。用LASSO-Cox回归分析获取预后相关基因并建立风险评分模型,分别对单基因进行预后分析,并分析风险评分和免疫浸润的相关性。结果 网络药理学分析获得55个交集靶点,蛋白互作分析结果获得5个潜在关键基因(Akt1、Bcl2、CASP3、ESR1、AR)。GO分析结果发现山柰酚治疗乳腺癌涉及1 604个生物学过程条目、20个细胞组成条目,121个分子功能条目。KEGG通路富集主要包括化学致癌-活性氧信号通路、糖尿病并发症中的AGE-RAGE信号通路、TNF信号通路、IL-17信号通路等。分子对接结果表明,山柰酚与关键靶点具有强大的亲和力,与ESR1结合效果最好(-9.1 kcal/mol)。通过LASSO-Cox回归分析获得了10个预后基因(Bcl2、CYP1B1、DPP4、GSTM1、GSTM2、MMP1、NCOA2、NOS2、NR1I3、PTGS2),并以此建立风险评分模型。该模型预测乳腺癌患者预后的AUC>0.5。单基因预后分析提示,Bcl2(HR=0.61,95% CI=0.43~0.86,P=0.005)、CYP1B1(HR=0.68,95% CI=0.49~0.94,P=0.022)、GSTM1(HR=0.68,95% CI=0.47~0.98,P=0.037)、GSTM2(HR=0.64,95% CI=0.46~0.90,P=0.010)、PTGS2(HR=0.62,95% CI=0.44~0.86,P=0.005)高表达组的总生存(OS)期均高于各自的低表达组;MMP1(HR=1.72,95% CI=1.22~2.41,P=0.002)、NCOA2(HR=1.71,95% CI=1.12~2.60,P=0.013)、NOS2(HR=1.67,95% CI=1.20~2.32,P=0.002)、NR1I3(HR=1.69,95% CI=1.21~2.37,P=0.002)高表达组的OS均低于各自的低表达组。预后模型评分与T细胞、CD8+ T细胞、髓样树突细胞、NK细胞、B细胞的浸润呈负相关,与单核/巨噬细胞的浸润呈正相关(均P<0.05)。结论 山柰酚可通过多靶点、多通路发挥治疗乳腺癌作用。基于其作用相关靶点筛选出来的预后基因及建立的预后模型可为乳腺癌的临床治疗提供指导;预后模型与免疫的相关性可为下一步实验研究提供了方向。

    Abstract:

    Background and Aims Kaempferol is a natural flavonoid compound that can regulate various processes and activities associated with cancer, such as the cell cycle, oxidative stress, apoptosis, proliferation, metastasis, and angiogenesis. Its potential for treating breast cancer has been validated in some studies, but its mechanism of action remains unclear. Therefore, this study was conducted to explore the potential targets and pathways of kaempferol in the treatment of breast cancer and establish a prognostic model.Methods Using network pharmacology and bioinformatics approaches, the intersection targets of kaempferol for the treatment of breast cancer were obtained from databases such as HERB, GeneCards, STRING, PubChem, RCSB PDB, and TCGA. Protein interaction, GO analysis, and KEGG pathway enrichment analysis were performed, followed by molecular docking for validation. Prognostic-related genes were identified through LASSO-Cox regression analysis to establish a risk score model. The prognostic analysis for each gene, and the correlation between risk score and immune infiltration were analyzed.Results Network pharmacology analysis identified 55 intersection targets. Protein interaction analysis revealed five potential key genes (Akt1, Bcl2, CASP3, ESR1, AR). GO analysis showed that kaempferol treatment of breast cancer involved 1 604 biological process entries, 20 cellular component entries, and 121 molecular function entries. KEGG pathway enrichment mainly included pathways related to chemical carcinogenesis, reactive oxygen species signaling, AGE-RAGE signaling in diabetic complications, TNF signaling, and IL-17 signaling. Molecular docking results indicated that kaempferol had a strong affinity for key targets, with the best binding effect observed with ESR1 (-9.1 kcal/mol). Ten prognostic genes (Bcl2, CYP1B1, DPP4, GSTM1, GSTM2, MMP1, NCOA2, NOS2, NR1I3, PTGS2) were obtained through LASSO-Cox regression analysis, and a risk score model was established. The AUC of this model for predicting breast cancer patient prognosis was greater than 0.5. Single-gene survival analysis indicated that higher expression of Bcl2 (HR=0.61, 95% CI=0.43-0.86, P=0.005), CYP1B1 (HR=0.68, 95% CI=0.49-0.94, P=0.022), GSTM1 (HR=0.68, 95% CI=0.47-0.98, P=0.037), GSTM2 (HR=0.64, 95% CI=0.46-0.90, P=0.010), and PTGS2 (HR=0.62, 95% CI=0.44-0.86, P=0.005) correlated with a higher overall survival (OS), while higher expression of MMP1 (HR=1.72, 95% CI=1.22-2.41, P=0.002), NCOA2 (HR=1.71, 95% CI=1.12-2.60, P=0.013), NOS2 (HR=1.67, 95% CI=1.20-2.32, P=0.002), and NR1I3 (HR=1.69, 95% CI=1.21-2.37, P=0.002) was associated with worse OS. The risk score was negatively correlated with the infiltration of T cells, CD8+ T cells, myeloid dendritic cells, NK cells, and B cells, and positively correlated with monocyte/macrophage infiltration (all P<0.05).Conclusion Kaempferol exerts therapeutic effects on breast cancer through multiple targets and pathways. The prognostic genes identified based on its related targets, along with the established prognostic model, can guide clinical treatment of breast cancer. The correlation between the prognostic model and immune infiltration provides direction for future experimental studies.

    表 1 TCGA数据库962例乳腺癌患者的临床与生存信息[n(%)]Table 1 Clinical and survival information of 962 breast cancer patients from the TCGA database [n (%)]
    表 2 核心靶点及其度值Table 2 Core targets and their degree values
    表 3 山柰酚与核心靶点的分子对接结果Table 3 Molecular docking results of kaempferol with core targets
    图1 山柰酚与乳腺癌交集靶点韦恩图Fig.1 Venn chart of the overlapping of kaempferol and breast cancer
    图2 山柰酚-靶点相互作用网络图Fig.2 Kaempferol-target interaction network
    图3 山柰酚治疗乳腺癌靶点PPI网络Fig.3 PPI network of kaempferol targets in the treatment of breast cancer
    图4 GO分析 A:BP气泡图;B:CC气泡图;C:MF气泡图Fig.4 GO analysis A: BP bubble chart; B: CC bubble chart; C: MF bubble chart
    图5 KEGG分析Fig.5 KEGG analysis
    图6 山柰酚与核心靶点的分子对接Fig.6 Molecular docking of kaempferol to core targets
    图7 LASSO-Cox预后回归筛选风险变量 A:LASSO-Cox回归结果;B:交叉验证图Fig.7 LASSO-Cox prognostic regression to select risk variables A: LASSO-Cox regression results; B: Cross-validation graph
    图8 乳腺癌患者高危组与低危组生存曲线Fig.8 Survival curves of breast cancer patients in high-risk and low-risk groups
    图9 ROC曲线验证预后回归模型的准确性Fig.9 ROC curve to validate the accuracy of the prognostic regression model
    图10 风险曲线、风险和生存散点图Fig.10 Risk curve, risk, and survival scatter plot
    图11 预后基因的表达热图Fig.11 Heatmap of the expression of prognostic genes
    图12 单基因表达与乳腺癌预后关系Fig.12 Relationship between single gene expression and breast cancer prognosis
    图13 风险评分与免疫细胞浸润相关性的散点图Fig.13 Scatter plot of the correlation between risk score and immune cell infiltration
    图1 山柰酚与乳腺癌交集靶点韦恩图Fig.1 Venn chart of the overlapping of kaempferol and breast cancer
    图2 山柰酚-靶点相互作用网络图Fig.2 Kaempferol-target interaction network
    图3 山柰酚治疗乳腺癌靶点PPI网络Fig.3 PPI network of kaempferol targets in the treatment of breast cancer
    图4 GO分析 A:BP气泡图;B:CC气泡图;C:MF气泡图Fig.4 GO analysis A: BP bubble chart; B: CC bubble chart; C: MF bubble chart
    图5 KEGG分析Fig.5 KEGG analysis
    图6 山柰酚与核心靶点的分子对接Fig.6 Molecular docking of kaempferol to core targets
    图7 LASSO-Cox预后回归筛选风险变量 A:LASSO-Cox回归结果;B:交叉验证图Fig.7 LASSO-Cox prognostic regression to select risk variables A: LASSO-Cox regression results; B: Cross-validation graph
    图8 乳腺癌患者高危组与低危组生存曲线Fig.8 Survival curves of breast cancer patients in high-risk and low-risk groups
    图9 ROC曲线验证预后回归模型的准确性Fig.9 ROC curve to validate the accuracy of the prognostic regression model
    图10 风险曲线、风险和生存散点图Fig.10 Risk curve, risk, and survival scatter plot
    图11 预后基因的表达热图Fig.11 Heatmap of the expression of prognostic genes
    图12 单基因表达与乳腺癌预后关系Fig.12 Relationship between single gene expression and breast cancer prognosis
    图13 风险评分与免疫细胞浸润相关性的散点图Fig.13 Scatter plot of the correlation between risk score and immune cell infiltration
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肖美灵,易嘉宁,阳孝琛,喻洁,黄婷,曾杰.山柰酚治疗乳腺癌机制的网络药理学与生物信息学分析及机制相关预后模型构建[J].中国普通外科杂志,2024,33(11):1854-1865.
DOI:10.7659/j. issn.1005-6947.2024.11.012

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  • 收稿日期:2024-08-06
  • 最后修改日期:2024-11-22
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  • 在线发布日期: 2024-12-18