CN117007703A - Diagnostic marker for urinary calculus, diagnostic kit and application thereof - Google Patents
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Abstract
Description
技术领域Technical field
本发明涉及医学生物检测技术领域,具体地说,是关于一组泌尿系结石的诊断标志物及其诊断试剂盒和应用。The present invention relates to the technical field of medical biological detection, and specifically relates to a group of diagnostic markers for urinary tract stones and their diagnostic kits and applications.
背景技术Background technique
尿路结石又称尿石症,是最常见的泌尿外科疾病之一,我国是世界泌尿结石发生的高发区之一,我国每年的新发病例数为(150~200)/10万人,其中25%患者需要住院治疗,南方地区发病率高达5%~10%,在国内南部,发病率为10%,10年内复发率更是高达80%,而据最新数据统计,17个中国成年人中就有一个患有肾结石。由于大多数患者都是在出现症状之后进行治疗才发现结石,无法在早期作出评价,同时目前也缺乏准确有效的检测方式,因此早期能检测泌尿系统结石对患者具有重要意义。Urinary tract stones, also known as urolithiasis, are one of the most common urological diseases. my country is one of the areas with high incidence of urinary stones in the world. The number of new cases in my country every year is (150-200)/100,000 people, among which 25% of patients require hospitalization. The incidence rate in southern China is as high as 5% to 10%. In the southern part of the country, the incidence rate is 10%. The recurrence rate within 10 years is as high as 80%. According to the latest statistics, 17 Chinese adults One had kidney stones. Since most patients only discover stones after treatment after the onset of symptoms, early evaluation cannot be made, and there is currently a lack of accurate and effective detection methods. Therefore, early detection of urinary system stones is of great significance to patients.
中文专利CN113030327A,公开日2021.06.25,公开了一种基于高效液相色谱-串联质谱检测受试者生物样本中标志物组合含量的试剂盒,属于泌尿结石标志物检测领域。其中,所述试剂盒包括所述标志物组合的分离检测试剂,所述标志物组合包括柠檬酸和异柠檬酸,进一步地,所述标志物组合还包括草酸和胱氨酸。利用该发明,可能实现尿液中柠檬酸含量的精准测定,可以进一步用于诊断受试者是否患有泌尿结石,或者用于预测受试者是否具有患泌尿结石风险,或者用于评估泌尿结石患者接受结石治疗的效果,或者用于预测泌尿结石患者治疗痊愈后是否具有复发风险,具有重大的临床意义和巨大的经济效益。中文文献(闫晓煜,黄志红.泌尿系统结石相关标志物的研究进展[J].国际检验医学杂志,2018,39(7):4.)中论述了T-H蛋白、骨桥蛋白、草酸、枸橼酸以及易感基因等不同标志物与结石的相关性,提示尿中标志物的检测对使用抑制物防治尿石症有一定的临床意义,且能够为剂量的调节提供参考。Chinese patent CN113030327A, published on June 25, 2021, discloses a kit for detecting the combined content of markers in biological samples of subjects based on high-performance liquid chromatography-tandem mass spectrometry, which belongs to the field of urinary stone marker detection. Wherein, the kit includes a separation detection reagent for the marker combination, the marker combination includes citric acid and isocitrate, and further, the marker combination also includes oxalic acid and cystine. Using this invention, it is possible to accurately measure the citric acid content in urine, which can be further used to diagnose whether a subject has urinary stones, or to predict whether a subject is at risk of suffering from urinary stones, or to evaluate urinary stones. The effect of patients receiving stone treatment, or being used to predict whether patients with urinary stones have a risk of recurrence after treatment, has great clinical significance and huge economic benefits. Chinese literature (Yan Xiaoyu, Huang Zhihong. Research progress on markers related to urinary tract stones [J]. International Journal of Laboratory Medicine, 2018, 39(7):4.) discusses T-H protein, osteopontin, oxalic acid, and citric acid As well as the correlation between different markers such as susceptibility genes and stones, it is suggested that the detection of markers in urine has certain clinical significance for the use of inhibitors to prevent and treat urolithiasis, and can provide a reference for dose adjustment.
由于前述检测方法(CN113030327A)是对泌尿系结石病人尿液中的标志物的检测,而目前如本发明的一组泌尿系结石病人血浆中的诊断标志物及其诊断试剂盒和应用还未见报道。Since the aforementioned detection method (CN113030327A) is for detecting markers in the urine of patients with urinary tract stones, a group of diagnostic markers in the plasma of urinary tract stone patients and their diagnostic kits and applications such as the present invention have not yet been seen. Report.
发明内容Contents of the invention
本发明目的是,针对现有技术中的不足,提供一组泌尿系结石的诊断标志物及其诊断试剂盒和应用。The purpose of the present invention is to provide a set of diagnostic markers for urinary tract stones and their diagnostic kits and applications in view of the deficiencies in the prior art.
一方面,提供了一组用于检测泌尿系结石的诊断标志物,所述的诊断标志物为血浆中的代谢物。In one aspect, a set of diagnostic markers for detecting urinary tract stones is provided, and the diagnostic markers are metabolites in plasma.
作为一个优选例,所述的代谢物包括:3-(2-羟苯基)丙酸、N-乙酰-L-谷氨酰胺、β-丙氨酰-L-精氨酸、赤藓糖醇、5-甲硫腺苷、反式-3-羟基肉桂酸乙酯、异鼠李素、2(3h)-苯并噻唑酮、邻苯二甲酸二丁酯和富马酸,反丁烯二酸。As a preferred example, the metabolites include: 3-(2-hydroxyphenyl)propionic acid, N-acetyl-L-glutamine, β-alanyl-L-arginine, and erythritol , 5-methylthioadenosine, trans-ethyl 3-hydroxycinnamate, isorhamnetin, 2(3h)-benzothiazolones, dibutyl phthalate and fumaric acid, fumarate acid.
更优选地,上述的代谢物在泌尿系结石的患者中上调的为3-(2-羟苯基)丙酸、N-乙酰-L-谷氨酰胺、β-丙氨酰-L-精氨酸、赤藓糖醇和5-甲硫腺苷;上述的代谢物在泌尿系结石的患者中下调的为反式-3-羟基肉桂酸乙酯、异鼠李素、2(3h)-苯并噻唑酮、邻苯二甲酸二丁酯和富马酸和反丁烯二酸。More preferably, the above-mentioned metabolites that are up-regulated in patients with urinary tract stones are 3-(2-hydroxyphenyl)propionic acid, N-acetyl-L-glutamine, and β-alanyl-L-arginine. acid, erythritol and 5-methylthioadenosine; the above-mentioned metabolites down-regulated in patients with urinary stones are trans-3-hydroxycinnamate ethyl ester, isorhamnetin, 2(3h)-benzo Thiazolones, dibutyl phthalate and fumaric and fumaric acids.
第二方面,提供了一种用于泌尿系结石的诊断试剂盒,所述的试剂盒的唯一有效成分为:检测上述任一所述的诊断标志物表达量的试剂。In a second aspect, a diagnostic kit for urinary tract stones is provided. The only active ingredient of the kit is a reagent for detecting the expression of any one of the above diagnostic markers.
作为一个优选例,所述的检测样本为血浆。As a preferred example, the test sample is plasma.
第三方面,提供了一种泌尿系结石的诊断试剂,所述试剂用于检测上述任一所述的诊断标志物的表达量。In a third aspect, a diagnostic reagent for urinary tract stones is provided, the reagent being used to detect the expression of any one of the above diagnostic markers.
第四方面,提供了上述试剂在制备泌尿系结石诊断试剂盒中的应用以及上述的诊断标志物在制备泌尿系结石诊断试剂或试剂盒中的应用。The fourth aspect provides the application of the above-mentioned reagents in preparing a diagnostic kit for urinary stones and the application of the above-mentioned diagnostic markers in preparing diagnostic reagents or kits for urinary stones.
本发明优点在于:The advantages of the present invention are:
利用非靶向代谢组学鉴定出泌尿系结石病人与健康对照患者中10种最显著改变的代谢物,且每个代谢物的ROC曲线下面积均大于0.9,试验诊断准确性高。目前还没有利用血浆代谢物作为泌尿系结石病人的诊断标志物,具有良好的应用前景。Untargeted metabolomics was used to identify the 10 most significantly altered metabolites in patients with urinary tract stones and healthy control patients, and the area under the ROC curve of each metabolite was greater than 0.9, indicating high diagnostic accuracy. At present, plasma metabolites have not been used as diagnostic markers for patients with urinary tract stones, and they have good application prospects.
附图说明:Picture description:
附图1为基峰色谱图,A:正离子模式;B:负离子模式。Figure 1 is the base peak chromatogram, A: positive ion mode; B: negative ion mode.
附图2为QC样本质控的PCA分析图,A:正离子模式;B:负离子模式。Figure 2 is the PCA analysis chart of QC sample quality control, A: positive ion mode; B: negative ion mode.
附图3-5为多元统计分析结果图,分别通过主成分分析(PCA)、偏最小二乘判别分析(PLS-DA)、正交-偏最小二乘判别分析(OPLS-DA)方法获得,其中A:正离子模式;B:负离子模式。Figures 3-5 are diagrams of multivariate statistical analysis results, obtained through principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and orthogonal-partial least squares discriminant analysis (OPLS-DA) methods. Among them, A: positive ion mode; B: negative ion mode.
附图6为表示两组样本的差异代谢物分布情况的火山图,A:正离子模式;B:负离子模式。Figure 6 is a volcano plot showing the differential metabolite distribution of the two groups of samples, A: positive ion mode; B: negative ion mode.
附图7为差异代谢物质荷比与P值散点图,A:正离子模式;B:负离子模式。Figure 7 is a scatter plot of differential metabolite charge ratios and P values, A: positive ion mode; B: negative ion mode.
附图8为差异代谢物总数量统计图。Figure 8 is a statistical chart of the total number of differential metabolites.
附图9为两组样本的差异代谢物分布情况的火山图-MS/MS。Figure 9 is a volcano plot-MS/MS of the differential metabolite distribution of the two groups of samples.
附图10为代谢物的质荷比与P值绘制散点图-MS/MS。Figure 10 is a scatter plot-MS/MS of the mass-to-charge ratio and P value of metabolites.
附图11为最显著的10个差异代谢物的箱式图,A-E为最显著的上调差异代谢物箱式图,代谢物分别为:3-(2-Hydroxyphenyl)propanoic acid【3-(2-羟苯基)丙酸】、N-Formyl-L-glutamic acid【N-乙酰-L-谷氨酰胺】、Beta-Alanyl-L-arginine【β-丙氨酰-L-精氨酸】、Erythritol【赤藓糖醇】、5’-Methylthioadenosine【5-甲硫腺苷】;F-J为最显著的下调差异代谢物箱式图,代谢物分别为Trans-3-Hydroxycinnamate【反式-3-羟基肉桂酸乙酯】、Isorhamnetin【异鼠李素】、2(3H)-Benzothiazolethione【2(3h)-苯并噻唑酮】、Dibutyl phthalate【邻苯二甲酸二丁酯】、Fumaric acid【富马酸,反丁烯二酸】,****P<0.0001。Figure 11 is a box plot of the 10 most significant differential metabolites. A-E are the box plots of the most significantly up-regulated differential metabolites. The metabolites are: 3-(2-Hydroxyphenyl)propanoic acid [3-(2- Hydroxyphenyl) propionic acid], N-Formyl-L-glutamic acid [N-acetyl-L-glutamine], Beta-Alanyl-L-arginine [β-alanyl-L-arginine], Erythritol [Erythritol], 5'-Methylthioadenosine [5-methylthioadenosine]; F-J are the box plots of the most significantly down-regulated metabolites, and the metabolites are Trans-3-Hydroxycinnamate [trans-3-hydroxycinnamate] Ethyl acid ester], Isorhamnetin [Isorhamnetin], 2(3H)-Benzothiazolethione [2(3h)-benzothiazolones], Dibutyl phthalate [dibutyl phthalate], Fumaric acid [fumaric acid, fumaric acid], ****P<0.0001.
附图12为最显著差异代谢物的ROC曲线图,A-E为最显著的上调差异代谢物的ROC曲线图,A:3-(2-Hydroxyphenyl)propanoic acid【3-(2-羟苯基)丙酸】,ROC曲线下面积为0.959;B:N-Formyl-L-glutamic acid【N-乙酰-L-谷氨酰胺】,ROC曲线下面积为0.998;C:Beta-Alanyl-L-arginine【β-丙氨酰-L-精氨酸】,ROC曲线下面积为0.928、D:Erythritol【赤藓糖醇】,ROC曲线下面积为0.994;E:5’-Methylthioadenosine【5-甲硫腺苷】,ROC曲线下面积为0.939;F-J为最显著的下调差异代谢物的ROC曲线图,F:Trans-3-Hydroxycinnamate【反式-3-羟基肉桂酸乙酯】,ROC曲线下面积为1;G:Isorhamnetin【异鼠李素】,ROC曲线下面积为0.996;H:2(3H)-Benzothiazolethione【2(3h)-苯并噻唑酮】,ROC曲线下面积为0.956;I:Dibutyl phthalate【邻苯二甲酸二丁酯】,ROC曲线下面积为0.997;J:Fumaric acid【富马酸,反丁烯二酸】,ROC曲线下面积为0.930。Figure 12 is the ROC curve of the most significant differential metabolite, A-E is the ROC curve of the most significantly up-regulated differential metabolite, A: 3-(2-Hydroxyphenyl)propanoic acid [3-(2-hydroxyphenyl)propanoic acid] Acid], the area under the ROC curve is 0.959; B: N-Formyl-L-glutamic acid [N-acetyl-L-glutamine], the area under the ROC curve is 0.998; C: Beta-Alanyl-L-arginine [β -Alanyl-L-arginine], the area under the ROC curve is 0.928, D: Erythritol [erythritol], the area under the ROC curve is 0.994; E: 5'-Methylthioadenosine [5-methylthioadenosine] , the area under the ROC curve is 0.939; F-J are the ROC curves of the most significantly down-regulated differential metabolites, F: Trans-3-Hydroxycinnamate [trans-3-hydroxycinnamate ethyl ester], the area under the ROC curve is 1; G : Isorhamnetin [Isorhamnetin], the area under the ROC curve is 0.996; H: 2(3H)-Benzothiazolethione [2(3h)-benzothiazolethione], the area under the ROC curve is 0.956; I: Dibutyl phthalate [phthalate] Dibutyl dicarboxylate], the area under the ROC curve is 0.997; J: Fumaric acid [fumaric acid, fumaric acid], the area under the ROC curve is 0.930.
具体实施方式Detailed ways
下面结合具体实施方式,进一步阐述本发明。应理解,这些实施例仅用于说明本发明而不用于限制本发明的范围。此外应理解,在阅读了本发明记载的内容之后,本领域技术人员可以对本发明作各种改动或修改,这些等价形式同样落于本申请所附权利要求书所限定的范围。The present invention will be further described below in conjunction with specific embodiments. It should be understood that these examples are only used to illustrate the invention and are not intended to limit the scope of the invention. In addition, it should be understood that after reading the content described in the present invention, those skilled in the art can make various changes or modifications to the present invention, and these equivalent forms also fall within the scope defined by the appended claims of this application.
实施例1Example 1
1实验方法1Experimental method
1.1代谢物提取1.1 Metabolite extraction
将血浆样本在4℃条件下解冻,解冻后样本涡旋1min,混合均匀;精确移取适量样本放入2ml离心管中;加入400uL甲醇溶液(-20℃保存),涡旋1min;12000rpm 4℃离心10min,取全部上清液,转移至新的2mL离心管中,浓缩干燥;准确加入150uL80%甲醇水配制的2-氯-L-笨丙氨酸(4ppm)溶液(4℃保存)复溶样品,取上清液过0.22um膜过滤,过滤液加入到检测瓶中,用于液相色谱-质谱联用(LC-MS)检测。Thaw the plasma sample at 4°C. After thawing, the sample is vortexed for 1 minute and mixed evenly; accurately transfer an appropriate amount of sample into a 2ml centrifuge tube; add 400uL methanol solution (stored at -20°C), vortex for 1 minute; 12000rpm 4°C Centrifuge for 10 minutes, take all the supernatant, transfer to a new 2mL centrifuge tube, concentrate and dry; accurately add 150uL of 2-chloro-L-alanine (4ppm) solution prepared with 80% methanol and water (stored at 4°C) to reconstitute. Sample, take the supernatant and filter it through a 0.22um membrane, and add the filtrate into the detection bottle for liquid chromatography-mass spectrometry (LC-MS) detection.
1.2上机检测1.2 On-machine detection
1)色谱条件1) Chromatographic conditions
Thermo Vanquish(Thermo Fisher Scientific,USA)超高效液相系统,使用ACQUITYUPLC HSS T3(2.1×150mm,1.8um)(Waters,Milford,MA,USA)色谱柱,0.25mL/min的流速,40℃的柱量,进样量2uL。Thermo Vanquish (Thermo Fisher Scientific, USA) ultra-high performance liquid phase system, using ACQUITYUPLC HSS T3 (2.1×150mm, 1.8um) (Waters, Milford, MA, USA) chromatographic column, flow rate of 0.25mL/min, column at 40°C The injection volume is 2uL.
正离子模式,流动相为0.1%甲酸乙腈(B2)和0.1%甲酸水(A2),梯度洗脱程序为:0~1min,2%B2;1~9min,2%~50%B2;9~12min,50%~98%B2;12~13.5min,98%B2;13.5~14min,98%~2%B2;14~20min,2%B2。In positive ion mode, the mobile phase is 0.1% formic acid acetonitrile (B2) and 0.1% formic acid water (A2). The gradient elution program is: 0 to 1 min, 2% B2; 1 to 9 min, 2% to 50% B2; 9 to 12min, 50% ~ 98% B2; 12 ~ 13.5min, 98% B2; 13.5 ~ 14min, 98% ~ 2% B2; 14 ~ 20min, 2% B2.
负离子模式,流动相为乙腈(B3)和5mM甲酸铵水(A3),梯度洗脱程序为:0~1min,2%B3;1~9min,2%~50%B3;9~12min,50%~98%B3;12~13.5min,98%B3;13.5~14min,98%~2%B3,14~17min,2%B3。Negative ion mode, the mobile phase is acetonitrile (B3) and 5mM ammonium formate water (A3), and the gradient elution program is: 0 to 1 min, 2% B3; 1 to 9 min, 2% to 50% B3; 9 to 12 min, 50% ~98% B3; 12~13.5min, 98%B3; 13.5~14min, 98%~2%B3, 14~17min, 2%B3.
2)质谱条件2) Mass spectrometry conditions
Thermo Orbitrap Exploris 120质谱检测器(Thermo Fisher Scientific,USA),电喷雾离子源(ESI),正负离子模式分别采集数据。正离子喷雾电压为3.50kV,负离子喷雾电压为-2.50kV,鞘气30arb,辅助气10arb。毛细管温度325℃,以分辨率60000进行一级全扫描,一级离子扫描范围m/z 100~1000,并采用HCD进行二级裂解,碰撞能量为30%,二级分辨率为15000,采集信号前4离子进行碎裂,同时采用动态排除去除无必要的MS/MS信息。Thermo Orbitrap Exploris 120 mass spectrometer detector (Thermo Fisher Scientific, USA), electrospray ion source (ESI), and positive and negative ion modes were used to collect data respectively. The positive ion spray voltage is 3.50kV, the negative ion spray voltage is -2.50kV, the sheath gas is 30arb, and the auxiliary gas is 10arb. The capillary temperature is 325°C, a first-level full scan is performed with a resolution of 60,000, the first-level ion scanning range is m/z 100~1000, and HCD is used for second-level cleavage, the collision energy is 30%, the second-level resolution is 15,000, and the signal is collected The first 4 ions are fragmented, and dynamic exclusion is used to remove unnecessary MS/MS information.
2数据处理与分析2Data processing and analysis
2.1样本数据预处理2.1 Sample data preprocessing
通过Proteowizard软件包(v3.0.8789)中MSConvert工具将原始质谱下机文件转换为mzXML文件格式。采用RXCMS软件包进行峰检测、峰过滤、峰对齐处理,得到物质定量列表,参数设置为ppm<30ppm。基于QC样本的LOESS信号校正方法实现数据矫正,消除系统误差。数据质控中过滤掉QC样本中RSD>30%的物质。The original mass spectrum offline files were converted into mzXML file format through the MSConvert tool in the Proteowizard software package (v3.0.8789). The RXCMS software package was used for peak detection, peak filtering, and peak alignment processing to obtain a quantitative list of substances. The parameters were set to ppm <30 ppm. The LOESS signal correction method based on QC samples realizes data correction and eliminates systematic errors. In data quality control, substances with RSD>30% in QC samples are filtered out.
采用R软件包Ropls分别对样本数据进行主成分分析(PCA)、偏最小二乘判别分析(PLS-DA)、正交偏最小二乘判别分析(OPLS-DA)降维分析。对数据进行缩放处理,并分别绘制得分图、载荷图、Splot图,展示各样本间代谢物组成的差异。用置换检验方法对模型进行过拟合检验。R2X和R2Y分别表示所建模型对X和Y矩阵的解释率,Q2标示模型的预测能力,它们的值越接近1表明模型的拟合度越好,训练集的样本越能够被准确划分到其原始归属中。根据统计检验计算P value值、OPLS-DA降维方法计算变量投影重要度(VIP)、fold change(FC)计算组间差异倍数,衡量各代谢物组分含量对样本分类判别的影响强度和解释能力,辅助标志代谢物的筛选。当P value值<0.05和VIP>1时,认为代谢物分子具有统计学意义。The R software package Ropls was used to perform principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and orthogonal partial least squares discriminant analysis (OPLS-DA) dimensionality reduction analysis on the sample data. The data were scaled and plotted with score plots, load plots, and Splot plots to show the differences in metabolite composition between samples. Use the permutation test method to test the model for overfitting. R2X and R2Y represent the explanation rate of the X and Y matrices of the built model respectively, and Q2 marks the predictive ability of the model. The closer their values are to 1, the better the fit of the model, and the more accurately the samples of the training set can be divided into other categories. Under original ownership. Calculate the P value based on statistical tests, calculate the variable importance of projection (VIP) using the OPLS-DA dimensionality reduction method, and calculate the difference fold between groups using fold change (FC) to measure the intensity and interpretation of the impact of each metabolite component content on sample classification discrimination. Ability to assist in the screening of marker metabolites. Metabolite molecules were considered statistically significant when the P value was <0.05 and VIP>1.
2.2通路分析2.2 Pathway analysis
采用MetaboAnalyst软件包对筛选差异代谢分子进行功能通路富集和拓扑学分析。富集得到的通路采用KEGG Mapper可视化工具进行差异代谢物与通路图的浏览。The MetaboAnalyst software package was used to conduct functional pathway enrichment and topology analysis of the screened differential metabolic molecules. The enriched pathways were browsed using the KEGG Mapper visualization tool for differential metabolite and pathway maps.
2.3数据检查2.3 Data check
1)基峰色谱图1) Base peak chromatogram
经色谱分离流出的组分不断进入质谱,质谱连续扫描进行数据采集。每一次扫描得到一张质谱图,选择每张质谱图中强度最大的离子连续扫描,以离子强度为纵坐标、时间为横坐标,得到的图谱,即为基峰色谱图(见图1)。The components flowing out after chromatographic separation continue to enter the mass spectrometer, and the mass spectrometer continuously scans for data collection. A mass spectrum is obtained for each scan, and the ion with the highest intensity in each mass spectrum is selected for continuous scanning. With the ion intensity as the ordinate and time as the abscissa, the obtained spectrum is the base peak chromatogram (see Figure 1).
2)质量控制(QC)2) Quality Control (QC)
在基于质谱技术的代谢组学研究中,为了获得可靠且高质量的代谢组学数据,需要进行质量控制(Quality Control,QC)。本实验在LC-MS检测时利用QC样本进行质控。理论上,QC样本都是相同的,但是在样本提取、检测分析过程中会有系统误差,导致QC样本间会有差异,差异越小说明方法稳定性越高数据质量越好,体现在PCA分析图上就是QC样本密级分布,说明数据可靠(见图2)。In metabolomics research based on mass spectrometry technology, in order to obtain reliable and high-quality metabolomics data, quality control (QC) is required. This experiment uses QC samples for quality control during LC-MS detection. Theoretically, QC samples are all the same, but there will be systematic errors in the sample extraction, detection and analysis process, resulting in differences between QC samples. The smaller the difference, the higher the stability of the method and the better the data quality, which is reflected in PCA analysis. The picture shows the density distribution of QC samples, indicating that the data is reliable (see Figure 2).
2.4多元统计分析2.4 Multivariate statistical analysis
由于代谢组数据具有多维且某些变量间高度相关的特点,运用传统的单变量分析无法快速、充分、准确地挖掘数据内潜在的信息。因此在分析代谢组数据需要运用化学计量学原理和多元统计的方法,对采集的多维数据进行降维和归类分析,从中挖掘提炼出最有用的信息。Because metabolome data is multidimensional and some variables are highly correlated, traditional univariate analysis cannot quickly, fully, and accurately mine potential information in the data. Therefore, when analyzing metabolome data, it is necessary to use chemometric principles and multivariate statistical methods to perform dimensionality reduction and classification analysis on the collected multidimensional data, so as to mine and extract the most useful information.
通常,在对代谢组学数据进行多元统计分析之前,需要将数据进行适当的权重转换,即标准化处理。本分析在进行此样本分型前对数据采用自适换算处理,以获得更加可靠且更加直观的结果。Usually, before performing multivariate statistical analysis on metabolomic data, the data need to be transformed by appropriate weights, that is, normalized. This analysis uses adaptive conversion processing on the data before typing this sample to obtain more reliable and intuitive results.
本分析中使用的多元统计分析(R语言Ropls包)方法有:主成分分析(PrincipalComponent Analysis,PCA);偏最小二乘判别分析(Partial Least Squares-DiscriminantAnalysis,PLS-DA);正交-偏最小二乘判别分析(Orthognal Partial Least SquaresDiscriminant Analysis,OPLS-DA)。The multivariate statistical analysis (R language Ropls package) methods used in this analysis include: Principal Component Analysis (PCA); Partial Least Squares-Discriminant Analysis (PLS-DA); Orthogonal-Partial Minimum Squares discriminant analysis (Orthognal Partial Least SquaresDiscriminant Analysis, OPLS-DA).
1)主成分分析1) Principal component analysis
主成分分析(Principal Component Analysis,PCA)将代谢物变量按一定的权重通过线性组合后产生新的特征变量,通过主要新变量(主成分)对各组数据进行归类,去除重复性差的样本(离群样本)和异常样本。Principal Component Analysis (PCA) generates new characteristic variables by linearly combining metabolite variables according to certain weights, classifying each set of data through the main new variables (principal components), and removing samples with poor repeatability ( outlier samples) and abnormal samples.
因无外加人为因素,得到的PCA模型反映了代谢组数据的原始状态,有利于掌握数据的整体情况并对数据从整体上进行把握,尤其是有利于发现和剔除异常样本,并提高模型的准确性。经过PCA计算出的数字模型是否可靠需要进行严格的验证,不可靠的数学模型不仅不能很好地描述代谢组学数据特点,还可能严重影响正确结果的获得甚至误导分析结果。Since there are no external human factors, the resulting PCA model reflects the original state of the metabolome data, which is helpful for grasping the overall situation of the data and grasping the data as a whole, especially for discovering and eliminating abnormal samples, and improving the accuracy of the model. sex. Whether the numerical model calculated by PCA is reliable needs to be rigorously verified. Unreliable mathematical models not only cannot describe the characteristics of metabolomics data well, but may also seriously affect the acquisition of correct results and even mislead the analysis results.
模型的交叉验证主要参考R2X等参数,R2X是模型的可解释度。通常情况下,R2高于0.5较好。各个样本在各个主成分的得分就是其在计算的数学模型中的空间坐标,直观地反映了各个样本在数学模型空间中的分布情况。从PCA得分图可观察样本的聚集、离散程度。样本分布点越靠近,说明这些样本中所含有的变量/分子的组成和浓度越接近;反之,样本点越远离,其差异越大,见图3。The cross-validation of the model mainly refers to parameters such as R2X, which is the interpretability of the model. Usually, R2 higher than 0.5 is better. The score of each principal component of each sample is its spatial coordinate in the calculated mathematical model, which intuitively reflects the distribution of each sample in the mathematical model space. The degree of aggregation and dispersion of samples can be observed from the PCA score plot. The closer the sample distribution points are, the closer the composition and concentration of the variables/molecules contained in these samples are; conversely, the farther the sample points are, the greater the difference, see Figure 3.
2)偏最小二乘判别分析PLS-DA2) Partial least squares discriminant analysis PLS-DA
无监督分析方法(如PCA)不能忽略组内误差、消除与研究目的无关的随机误差,过分关注于细节、忽略了整体和规律,最终不利于发现组间差异和差异化合物。在这种情况下,就需要利用样本的先验知识将数据分析,进一步聚焦到我们要研究的方面,采用有监督模式识别方法,如偏最小二乘法-判别分析(PLS-DA)。Unsupervised analysis methods (such as PCA) cannot ignore intra-group errors and eliminate random errors irrelevant to the research purpose. They focus too much on details and ignore the overall pattern and patterns, which is ultimately not conducive to discovering differences and differential compounds between groups. In this case, we need to use the prior knowledge of the sample to further focus the data analysis on the aspects we want to study, and use supervised pattern recognition methods, such as partial least squares-discriminant analysis (PLS-DA).
与PCA只有一个数据集不同,PLS-DA在分析时必须对样本进行指定并分组,这样模型会自动加上另外一个隐含的数据集Y,该数据集变量数等于组别数。PLS-DA是目前代谢组学数据分析中最常使用的一种分类方法,它在降维的同时结合了回归模型,并利用一定的判别阈值对回归结果进行判别分析。Unlike PCA, which has only one data set, PLS-DA must specify and group samples during analysis, so that the model will automatically add another implicit data set Y, whose number of variables is equal to the number of groups. PLS-DA is currently the most commonly used classification method in metabolomics data analysis. It combines a regression model while reducing dimensionality, and uses a certain discriminant threshold to perform discriminant analysis on the regression results.
PLS与PCA不同之处在于PLS即分解自变量X矩阵,也分解因变量Y矩,并在分解时利用其协方差信息,从而使降维效果较PCA能够更高效的提取组间变异信息。The difference between PLS and PCA is that PLS decomposes the independent variable
模型的交叉验证主要参考R2X、R2Y、Q2等参数,R2X是模型X变量(自变量)的可解释度,R2Y为模型Y变量(因变量)的可解释率,Q2是模型的可预测度(理论上,R2X、Q2数值越接近1说明模型越好,越低说明模型的拟合准确性越差,通常情况下,R2、Q2高于0.5较好,且两者差值不应过大,R2和Q2最大值为1)。当R2值较小时,往往意味着测试集中重复性较差(背景噪音高时);Q2值较小时,表示测试集中具有较高的背景噪音,或者模型具有较多的异常样本。The cross-validation of the model mainly refers to parameters such as R2X, R2Y, and Q2. R2X is the interpretability of the model X variable (independent variable), R2Y is the interpretability rate of the model Y variable (dependent variable), and Q2 is the predictability of the model ( Theoretically, the closer the R2X and Q2 values are to 1, the better the model, and the lower the value, the worse the fitting accuracy of the model. Under normal circumstances, it is better for R2X and Q2 to be higher than 0.5, and the difference between the two should not be too large. The maximum value of R2 and Q2 is 1). When the R2 value is small, it often means that the repeatability in the test set is poor (when the background noise is high); when the Q2 value is small, it means that the test set has high background noise, or the model has more abnormal samples.
结果见图4,图4A为正离子模式:KS(结石患者),HC(健康对照),R2X=0.384,R2Y=0.987,Q2=0.973,两个组别能够区分开;图4B为负离子模式KS(结石患者)HC(健康对照),R2X=0.181,R2Y=0.983,Q2=0.966可以看到两个组别能够区分开。The results are shown in Figure 4. Figure 4A shows the positive ion mode: KS (stone patients), HC (healthy control), R2X=0.384, R2Y=0.987, Q2=0.973. The two groups can be distinguished; Figure 4B shows the negative ion mode KS (Stone patients) HC (healthy control), R2X=0.181, R2Y=0.983, Q2=0.966. It can be seen that the two groups can be distinguished.
3)正交-偏最小二乘判别分析OPLS-DA3) Orthogonal-Partial Least Squares Discriminant Analysis OPLS-DA
代谢组学数据分析中另一种常用的方法是正交-偏最小二乘判别分析(OPLS-DA),为PLS-DA的扩展。相比PLS-DA,该方法可以在不降低模型预测能力的前提下,有效减少模型的复杂性和增强模型的解释能力,从而最大程度查看组间差异。Another commonly used method in metabolomics data analysis is orthogonal partial least squares discriminant analysis (OPLS-DA), which is an extension of PLS-DA. Compared with PLS-DA, this method can effectively reduce the complexity of the model and enhance the explanatory power of the model without reducing the predictive power of the model, thereby maximizing the visibility of differences between groups.
OPLS-DA使用正交信号校正技术,将X矩阵信息分解成与Y相关和不相关的两类信息,然后过滤掉与分类无关的信息,相关的信息主要集中在第一个预测成分。与PLS-DA模型相同,OPLS-DA同样可以用R2X、R2Y、Q2、CV ANOVA和OPLS-DA得分图来评价模型的分类效果。通常,根据VIP值来说明变量(特征峰)能解释X数据集和关联Y数据集的重要性。所有VIP值的平方之和与模型中的变量总数相等,因此,其平均值为1,当某个变量的VIP>1时,说明该变量是重要的,通常将此作为潜在生物标记物的筛选条件之一。OPLS-DA uses orthogonal signal correction technology to decompose the X matrix information into two types of information related to Y and irrelevant to Y, and then filters out the information irrelevant to the classification. The relevant information is mainly concentrated in the first prediction component. Like the PLS-DA model, OPLS-DA can also use R2X, R2Y, Q2, CV ANOVA and OPLS-DA score plots to evaluate the classification effect of the model. Usually, the significance of variables (feature peaks) in explaining the X data set and the associated Y data set is stated in terms of VIP values. The sum of the squares of all VIP values is equal to the total number of variables in the model. Therefore, its average value is 1. When the VIP of a variable is >1, it means that the variable is important and is usually used as a screening for potential biomarkers. One of the conditions.
结果见图5,图5A为正离子模式,R2X=0.384,R2Y=0.987,Q2=0.965,图5B为负离子模式,R2X=0.181,R2Y=0.983,Q2=0.965,均能看出两个组别明显区分。The results are shown in Figure 5. Figure 5A shows the positive ion mode, R2X=0.384, R2Y=0.987, Q2=0.965. Figure 5B shows the negative ion mode, R2X=0.181, R2Y=0.983, Q2=0.965. Both groups can be seen. Clearly differentiated.
4)差异代谢物筛选4) Differential metabolite screening
从样本一级物质列表中寻找差异代谢物,以统计检验中预设的P value和VIP阈值进行筛选。(P<0.05、VIP>1)Find differential metabolites from the sample primary substance list and filter with the preset P value and VIP threshold in the statistical test. (P<0.05, VIP>1)
利用火山图可直观的表现两组样本的差异代谢物的分布情况。通常横坐标用log2(FC)表示,差异越大的代谢物分布在两端,纵坐标用-log10(Pvalue)表示,为统计检验的显著性P值的负对数,图中FC、P value以及VIP的过滤参数为分析预设阈值。The volcano plot can be used to intuitively display the distribution of differential metabolites between the two groups of samples. Usually the abscissa is represented by log2(FC), with metabolites with greater differences distributed at both ends. The ordinate is represented by -log10(Pvalue), which is the negative logarithm of the significant P value of the statistical test. In the figure, FC and P value And the VIP filtering parameters are preset thresholds for analysis.
结果见图6,图中每一个点表示一种代谢物,横坐标表示某代谢物在两样本中定量差异倍数的Log2的对数值;纵坐标表示P值的-log10的对数值。横坐标绝对值越大,说明某代谢物在两样本间的表达量倍数差异越大;纵坐标值越大,表明差异表达越显著,筛选得到的差异表达代谢物越可靠。The results are shown in Figure 6. Each point in the figure represents a metabolite. The abscissa represents the logarithm of Log2 of the quantitative difference fold of a certain metabolite in the two samples; the ordinate represents the logarithm of -log10 of the P value. The larger the absolute value of the abscissa, the greater the difference in the expression fold of a certain metabolite between the two samples; the larger the value of the ordinate, the more significant the differential expression, and the more reliable the differentially expressed metabolites obtained by screening.
其中图6A为正离子模式,图中默认显示P value最小的前5个代谢物名称,其中上调的代谢物为:219.0431,175.0533;下调的代谢物为:259.1101、202.0893、162.0546。颜色最浅的代表检测到但未满足过滤参数筛选的代谢物。图6B为负离子模式,下调的代谢物为:207.1023、251.1407、164.0355、243.0656、340.1538。Figure 6A shows the positive ion mode. The top five metabolite names with the smallest P value are displayed by default. The up-regulated metabolites are: 219.0431, 175.0533; the down-regulated metabolites are: 259.1101, 202.0893, 162.0546. The lightest colors represent metabolites that were detected but did not meet the filtering parameters. Figure 6B shows the negative ion mode, and the down-regulated metabolites are: 207.1023, 251.1407, 164.0355, 243.0656, 340.1538.
差异代谢物质荷比与P值散点图见图7,根据代谢物的质荷比与P值绘制散点图,可以较为清楚地看出物质在样本中差异物质的分布情况。其中图7A为正离子模式,前5个最显著的上调差异物质为:219.0431、175.0533、153.0544、309.2259、367.2686;前5个最显著的下调差异物质为:259.1101、202.0893、162.0546、180.0649、339.2315。图7B为负离子模式,前5个最显著的上调差异物质分别为:460.0339、165.0556、166.0591、245.1026、257.0932;前5个最显著的下调差异物质分别为:207.1023、251.1407、164.0355、243.0656、340.1538。The scatter plot of charge ratio and P value of differential metabolites is shown in Figure 7. Drawing a scatter plot based on the mass to charge ratio and P value of metabolites can clearly see the distribution of differential substances in the sample. Figure 7A shows the positive ion mode. The top five most significant up-regulated differential substances are: 219.0431, 175.0533, 153.0544, 309.2259, 367.2686; the top five most significant down-regulated differential substances are: 259.1101, 202.0893, 162.0546, 180.0649, 339.23 15. Figure 7B shows the negative ion mode. The top five most significant up-regulated differential substances are: 460.0339, 165.0556, 166.0591, 245.1026, 257.0932; the top five most significant down-regulated differential substances are: 207.1023, 251.1407, 164.0355, 243.0656, 340.1 538.
差异代谢物鉴定-MS/MS:代谢物鉴定首先根据精确分子量进行确认,后续根据MS/MS碎片模式对Human Metabolome Database(HMDB),massbank,LipidMaps,mzcloud确认注释获得代谢物。Differential metabolite identification-MS/MS: Metabolite identification is first confirmed based on the precise molecular weight, and then the metabolites are obtained by confirming the annotations of Human Metabolome Database (HMDB), massbank, LipidMaps, and mzcloud based on the MS/MS fragmentation pattern.
从样本一级物质列表中寻找差异代谢物,以统计检验中预设的P value和VIP阈值进行筛选,筛选后的差异代谢物总数量统计图见图8,其中上调的有122个,下调的有96个。Find differential metabolites from the first-level substance list of the sample, and filter with the preset P value and VIP threshold in the statistical test. The statistical chart of the total number of differential metabolites after screening is shown in Figure 8, of which 122 were up-regulated and 122 were down-regulated. There are 96.
火山图-MS/MS见图9:可直观的表现两组样本的差异代谢物的分布情况,通常横坐标用log2(FC)表示,差异越大的代谢物分布在两端,纵坐标用-log10(P value)表示,为统计检验的显著性P值的负对数,P值最小的前5个代谢物名称为:3-(2-Hydroxyphenyl)propanoic acid【3-(2-羟苯基)丙酸】、N-Formyl-L-glutamic acid【N-乙酰-L-谷氨酰胺】、Erythritol【赤藓糖醇】、Trans-3-Hydroxycinnamate【反式-3-羟基肉桂酸乙酯】、Isorhamnetin【异鼠李素】。Volcano plot-MS/MS is shown in Figure 9: it can intuitively show the distribution of differential metabolites between the two groups of samples. Usually the abscissa is represented by log2(FC). Metabolites with greater differences are distributed at both ends, and the ordinate is - Log10 (P value) represents the negative logarithm of the significant P value of the statistical test. The names of the top five metabolites with the smallest P value are: 3-(2-Hydroxyphenyl)propanoic acid [3-(2-hydroxyphenyl) ) propionic acid], N-Formyl-L-glutamic acid [N-acetyl-L-glutamine], Erythritol [erythritol], Trans-3-Hydroxycinnamate [trans-ethyl 3-hydroxycinnamate] , Isorhamnetin [Isorhamnetin].
差异代谢物质荷比与P值散点图-MS/MS见图10,可以较为清楚地看出物质在样本中差异物质的分布情况。The scatter plot of charge ratio and P value of differential metabolites - MS/MS is shown in Figure 10, which can clearly see the distribution of differential substances in the sample.
其中前5个最显著的上调差异代谢物分别为:3-(2-Hydroxyphenyl)propanoicacid【3-(2-羟苯基)丙酸】、N-Formyl-L-glutamic acid【N-乙酰-L-谷氨酰胺】、Beta-Alanyl-L-arginine【β-丙氨酰-L-精氨酸】、Erythritol【赤藓糖醇】、5’-Methylthioadenosine【5-甲硫腺苷】;Among them, the top five most significantly up-regulated differential metabolites are: 3-(2-Hydroxyphenyl)propanoic acid [3-(2-hydroxyphenyl)propionic acid], N-Formyl-L-glutamic acid [N-acetyl-L -Glutamine], Beta-Alanyl-L-arginine [β-alanyl-L-arginine], Erythritol [erythritol], 5'-Methylthioadenosine [5-methylthioadenosine];
前5个最显著的下调差异代谢物分别为:Trans-3-Hydroxycinnamate【反式-3-羟基肉桂酸乙酯】、Isorhamnetin【异鼠李素】、2(3H)-Benzothiazolethione【2(3h)-苯并噻唑酮、Dibutyl phthalate【邻苯二甲酸二丁酯】、Fumaric acid【富马酸,反丁烯二酸】。The top five most significantly down-regulated differential metabolites are: Trans-3-Hydroxycinnamate [trans-3-hydroxycinnamate ethyl ester], Isorhamnetin [isorhamnetin], 2(3H)-Benzothiazolethione [2(3h) - Benzothiazolone, Dibutyl phthalate [dibutyl phthalate], Fumaric acid [fumaric acid, fumaric acid].
5)最显著差异物质的箱式图展示5) Box plot display of the most significantly different substances
结果见图11,其中图11A-E展示了前5个最显著的上调差异代谢物的箱式图,分别为A:3-(2-Hydroxyphenyl)propanoic acid【3-(2-羟苯基)丙酸】、B:N-Formyl-L-glutamicacid【N-乙酰-L-谷氨酰胺】、C:Beta-Alanyl-L-arginine【β-丙氨酰-L-精氨酸】、D:Erythritol【赤藓糖醇】、E:5’-Methylthioadenosine【5-甲硫腺苷】,****P<0.0001。The results are shown in Figure 11, where Figure 11A-E shows the box plot of the top five most significantly up-regulated differential metabolites, respectively A: 3-(2-Hydroxyphenyl)propanoic acid [3-(2-hydroxyphenyl) Propionic acid], B: N-Formyl-L-glutamicacid [N-acetyl-L-glutamine], C: Beta-Alanyl-L-arginine [β-alanyl-L-arginine], D: Erythritol [erythritol], E: 5'-Methylthioadenosine [5-methylthioadenosine], ****P<0.0001.
图11F-J展示了前5个最显著的下调差异代谢物的箱式图,分别为F:Trans-3-Hydroxycinnamate【反式-3-羟基肉桂酸乙酯】、G:Isorhamnetin【异鼠李素】、H:2(3H)-Benzothiazolethione【2(3h)-苯并噻唑酮】、I:Dibutyl phthalate【邻苯二甲酸二丁酯】、J:Fumaric acid【富马酸,反丁烯二酸】,****P<0.0001。Figure 11F-J shows the box plot of the top five most significantly down-regulated differential metabolites, respectively F: Trans-3-Hydroxycinnamate [trans-3-hydroxycinnamate ethyl ester], G: Isorhamnetin [Isorhamnetin] [Principle], H: 2(3H)-Benzothiazolethione [2(3h)-benzothiazoleone], I: Dibutyl phthalate [dibutyl phthalate], J: Fumaric acid [fumaric acid, fumaric acid] acid], ****P<0.0001.
2.5灵敏度和特异性的验证2.5 Verification of sensitivity and specificity
利用检测到显著差异代谢物进行ROC曲线的绘制,结果见图12,图12A-E为前5个最显著的上调差异代谢物ROC曲线图,分别为A:3-(2-Hydroxyphenyl)propanoic acid【3-(2-羟苯基)丙酸】,ROC曲线下面积为0.959,诊断价值较高;B:N-Formyl-L-glutamic acid【N-乙酰-L-谷氨酰胺】,ROC曲线下面积为0.998,诊断价值较高;C:Beta-Alanyl-L-arginine【β-丙氨酰-L-精氨酸】,ROC曲线下面积为0.928,诊断价值较高;D:Erythritol【赤藓糖醇】,ROC曲线下面积为0.994,诊断价值较高;E:5’-Methylthioadenosine【5-甲硫腺苷】,ROC曲线下面积为0.939,诊断价值较高。The detected significantly different metabolites were used to draw the ROC curve. The results are shown in Figure 12. Figure 12A-E are the ROC curves of the top 5 most significantly up-regulated differential metabolites, respectively A: 3-(2-Hydroxyphenyl)propanoic acid [3-(2-Hydroxyphenyl)propionic acid], the area under the ROC curve is 0.959, with high diagnostic value; B: N-Formyl-L-glutamic acid [N-acetyl-L-glutamine], ROC curve The area under the ROC curve is 0.998, and the diagnostic value is high; C: Beta-Alanyl-L-arginine [β-alanyl-L-arginine], the area under the ROC curve is 0.928, and the diagnostic value is high; D: Erythritol [red Physitol], the area under the ROC curve is 0.994, and the diagnostic value is high; E: 5'-Methylthioadenosine [5-methylthioadenosine], the area under the ROC curve is 0.939, and the diagnostic value is high.
图12F-J为前5个最显著的下调差异代谢物的ROC曲线图,分别为F:Trans-3-Hydroxycinnamate【反式-3-羟基肉桂酸乙酯】,ROC曲线下面积为1,诊断价值高;G:Isorhamnetin【异鼠李素】ROC曲线下面积为0.996,诊断价值高;H:2(3H)-Benzothiazolethione【2(3h)-苯并噻唑酮】,ROC曲线下面积为0.956,诊断价值高;I:Dibutyl phthalate【邻苯二甲酸二丁酯】,ROC曲线下面积为0.997,诊断价值高;J:Fumaricacid【富马酸,反丁烯二酸】,ROC曲线下面积为0.930,诊断价值高。Figure 12F-J are the ROC curves of the top five most significantly down-regulated differential metabolites, respectively F: Trans-3-Hydroxycinnamate [trans-3-hydroxycinnamate ethyl ester], the area under the ROC curve is 1, diagnosis High value; G: Isorhamnetin [Isorhamnetin], the area under the ROC curve is 0.996, high diagnostic value; H: 2(3H)-Benzothiazolethione [2(3h)-benzothiazolethione], the area under the ROC curve is 0.956, High diagnostic value; I: Dibutyl phthalate [dibutyl phthalate], the area under the ROC curve is 0.997, high diagnostic value; J: Fumaricacid [fumaric acid, fumaric acid], the area under the ROC curve is 0.930 , high diagnostic value.
综上,利用非靶向代谢组学鉴定出泌尿系结石病人与健康对照患者中10中最显著改变的代谢物,且每个代谢物的ROC曲线下面积均大于0.9,试验诊断准确性高,可用于临床诊断泌尿结石。In summary, non-targeted metabolomics was used to identify the 10 most significantly changed metabolites in patients with urinary tract stones and healthy control patients, and the area under the ROC curve of each metabolite was greater than 0.9. The diagnostic accuracy of the test is high. Can be used for clinical diagnosis of urinary stones.
以上所述仅是本发明的优选实施方式,应当指出,对于本技术领域的普通技术人员,在不脱离本发明方法的前提下,还可以做出若干改进和补充,这些改进和补充也应视为本发明的保护范围。The above are only the preferred embodiments of the present invention. It should be pointed out that those of ordinary skill in the art can also make several improvements and supplements without departing from the method of the present invention. These improvements and supplements should also be regarded as It is the protection scope of the present invention.
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