三種典型復(fù)雜生物體系代謝組學(xué)的NMR研究
發(fā)布時(shí)間：2018-07-28 13:12
【摘要】：代謝組學(xué)是一門(mén)通過(guò)分析復(fù)雜生物體系中小分子化合物的整體變化來(lái)探索生命過(guò)程本質(zhì)的學(xué)科。NMR因其具有樣品處理簡(jiǎn)單、譜編輯手段豐富、檢測(cè)無(wú)偏向性、重復(fù)性好等優(yōu)點(diǎn),一直都是代謝組學(xué)研究最常用的一種檢測(cè)技術(shù)。代謝組學(xué)研究的復(fù)雜生物體系包括生物體液、組織和器官等,這些體系含有大量各種各樣的代謝物,而所有的生物代謝物又都含有質(zhì)子。因此,基于1H NMR技術(shù)的代謝組學(xué)分析方法是研究復(fù)雜生物體系強(qiáng)有力的工具。基于NMR的代謝組學(xué)研究中,我們得到的原始數(shù)據(jù)通常是一組NMR圖譜。使用化學(xué)計(jì)量學(xué)模型深度分析這些NMR圖譜數(shù)據(jù)之前,我們首先需要對(duì)NMR圖譜進(jìn)行數(shù)據(jù)降維,以方便后續(xù)的統(tǒng)計(jì)分析。目前,最常用的NMR圖譜降維方法是分段積分法,該方法將原始圖譜分為若干個(gè)寬度為2 Hz左右的小區(qū)間,然后對(duì)每個(gè)區(qū)間積分得到積分譜。分段積分法的優(yōu)點(diǎn)是高效、易于自動(dòng)化,特別適合大規(guī)模樣品研究；缺點(diǎn)是得到的數(shù)據(jù)變量多、圖譜分辨率降低,為后期特征變量的歸屬埋下隱患。當(dāng)樣品數(shù)較少時(shí),我們還可以采用分峰擬合法對(duì)NMR圖譜進(jìn)行降維。分峰擬合法利用各種代謝物的標(biāo)準(zhǔn)圖譜對(duì)實(shí)驗(yàn)譜進(jìn)行擬合得到代謝物的濃度數(shù)據(jù),該方法的優(yōu)點(diǎn)是得到的數(shù)據(jù)變量少,利于后續(xù)統(tǒng)計(jì)分析;缺點(diǎn)是對(duì)代謝物的圖譜數(shù)據(jù)庫(kù)依賴性強(qiáng)、不易實(shí)現(xiàn)自動(dòng)化,因此僅適合樣品數(shù)較少的初期研究。本論文第二章選取C57BL/6J大鼠建立轉(zhuǎn)移黑色素瘤動(dòng)物模型,并獲取大鼠的脾臟和胃部組織為研究對(duì)象。在這一章中,我們首先選取大鼠的脾臟組織數(shù)據(jù),分析和對(duì)比了分段積分和分峰擬合兩種NMR圖譜降維方法對(duì)主成分分析(Principal Component Analysis, PCA)模型和正交偏最小二乘分析(Orthogonal Proj ection to Latent Structures, OPLS)模型的影響。然后,我們分析了轉(zhuǎn)移黑色素瘤在大鼠脾臟和胃部組織引起的代謝表型變化。研究結(jié)果表明,實(shí)驗(yàn)組和對(duì)照組樣品具有明顯的區(qū)分,轉(zhuǎn)移黑色素瘤可能嚴(yán)重干擾了組織細(xì)胞中的多個(gè)代謝通路。本論文第三章采用與第二章相同的研究策略,選取C57BL/6J大鼠建立動(dòng)物模型,分析了吸煙對(duì)正常體重和肥胖大鼠肺部組織代謝表型的影響。OPLS模型分析表明,不論大鼠是否肥胖,吸煙都會(huì)顯著降低組織中腺苷衍生物ATP、ADP和AMP的含量,并且,肌苷和尿苷的含量會(huì)明顯的升高。同時(shí),我們還發(fā)現(xiàn),僅吸煙并不會(huì)明顯改變大鼠肺部組織中GPC/PC的比值,而肥胖這個(gè)單因素則足以顯著提高GPC/PC比值,并且吸煙會(huì)增強(qiáng)這一變化趨勢(shì)。本論文第二章和第三章研究的是不同組別樣品間的差異,而忽略了組內(nèi)樣品的個(gè)體差異。組內(nèi)樣品的個(gè)體差異同樣很重要,它可以反映不同個(gè)體對(duì)同一外部刺激的不同響應(yīng)程度。因此,本論文第四章對(duì)樣品的個(gè)體差異做了一些初步探討。本章,我們選取布洛芬(IBP)為模型藥物,研究了IBP與血漿相互作用的個(gè)體差異。本章內(nèi)容是對(duì)本課題組先前一項(xiàng)研究工作內(nèi)容的補(bǔ)充和延伸。在本章中,我們重新定義了相互作用指數(shù)(interaction index, Idist)和多樣性指數(shù)(diversity index, Idiv)來(lái)表征血漿組分的個(gè)體差異及其對(duì)IBP-血漿相互作用的影響。重新定義的Idist能更多地提取NMR圖譜中的信息,重新定義的Idiv具有唯一性和確定性,并且,Idist與Idiv之間表現(xiàn)出極為顯著的線性相關(guān)性(p2.2e-16)。同時(shí),我們分析了Idist與NMR圖譜、Idist與臨床數(shù)據(jù)以及臨床數(shù)據(jù)與NMR圖譜之間的關(guān)聯(lián)。研究發(fā)現(xiàn),IBP與血漿相互作用的個(gè)體化差異主要體現(xiàn)在血漿中小分子代謝物與脂蛋白結(jié)合強(qiáng)弱以及IBP與脂蛋白結(jié)合強(qiáng)弱的個(gè)體化差異。同時(shí)我們還發(fā)現(xiàn),血漿中游離乳酸含量越高,或者總甘油三酯、白蛋白或膽堿濃度越低,對(duì)IBP越敏感；并且,體重較輕或者肥胖指數(shù)BMI較小者對(duì)IBP較敏感。本課題招募的這批志愿者中,年齡越大的人其血漿中葡萄糖、糖蛋白的濃度越大,纈氨酸、絡(luò)氨酸、肌酐和脂蛋白顆粒中含膽堿磷脂的濃度越低。我們還可以通過(guò)OPLS模型的相關(guān)系數(shù)編碼的負(fù)載圖挖掘出NMR譜中與目標(biāo)代謝物處于相同或者相近代謝通路的其他代謝物。
[Abstract]:Metabonomics is a subject to explore the essence of life process by analyzing the overall changes of small and medium molecular compounds in complex biological systems..NMR has the advantages of simple sample processing, rich spectrum editing, unbiased detection and good reproducibility. It has always been a most commonly used detection technique in metabolomics research. The complex biological systems include biological fluids, tissues and organs, which contain a large variety of metabolites, and all biological metabolites contain protons. Therefore, the metabonomics analysis method based on 1H NMR technology is a powerful tool for the study of complex biological systems. In the study of NMR based metabolomics, we have to The original data is usually a set of NMR atlas. Before using the chemometrics model to analyze these NMR data, we first need to reduce the data of the NMR atlas to facilitate the subsequent statistical analysis. At present, the most commonly used NMR map reduction method is a piecewise integral method, which divides the original map into a number of 2 widths. The advantages of the piecewise integral method are high efficiency, easy to automate, and are especially suitable for large-scale sample research. The disadvantage is that the obtained data are more variable, the resolution of the atlas is lower, and the later feature variables are buried. When the number of samples is less, we can also use the peaks. The NMR map is reduced by the fitting method. The peak fitting method uses the standard atlas of various metabolites to fit the experimental spectrum to get the concentration data of the metabolite. The advantage of this method is that the obtained data are less variable and benefit to the subsequent statistical analysis; the disadvantage is that the data base of the metabolite's Atlas data base is strong and not easy to automate, so it is only suitable. In the second chapter of this paper, C57BL/6J rats were selected to establish the animal model of metastatic melanoma and to obtain the spleen and stomach tissues of the rats as the research object. In this chapter, we first selected the spleen tissue data of rats, and analyzed and compared the subsection integral and the peak fitting of the two methods to reduce the dimension of the NMR map. Effects of Principal Component Analysis (PCA) model and orthogonal partial least square analysis (Orthogonal Proj ection to Latent Structures, OPLS). Then, we analyzed the metabolic phenotypic changes caused by metastatic melanoma in the spleen and stomach tissues of rats. The results showed that the experimental group and the control group were samples. The third chapter of this paper uses the same research strategy as the second chapter to establish the animal model of C57BL/6J rats, and analyzes the effect of smoking on the metabolic phenotype of lung tissue in normal weight and obese rats by.OPLS model analysis. No matter whether rats were obese, smoking significantly reduced the levels of adenosine derivatives ATP, ADP and AMP, and the content of inosine and uridine increased significantly. We also found that smoking alone did not significantly change the ratio of GPC/PC in the lung tissue of rats, and obesity was sufficient to significantly increase the GPC/PC ratio, and The second and third chapters of this paper are to study the differences between different groups of samples and ignore the individual differences in the samples in the group. The individual differences in the samples in the group are also important, which can reflect the different responses of different individuals to the same external stimuli. Therefore, the fourth chapter of this paper is on the sample. In this chapter, we selected Bloven (IBP) as a model drug and studied the individual differences in the interaction between IBP and plasma. The content of this chapter is a supplement and extension of the previous research work of this group. In this chapter, we redefined the interaction index (Idist) and The diversity index (diversity index, Idiv) was used to characterize the individual differences in plasma components and their effects on IBP- plasma interactions. The redefined Idist could extract more information from the NMR map, the redefined Idiv has uniqueness and certainty, and there is a very significant linear correlation between Idist and Idiv (p2.2e-16). At the same time, we analyzed the association between Idist and NMR atlas, Idist and clinical data as well as clinical data and NMR atlas. The study found that the individual differences in the interaction between IBP and plasma were mainly reflected in the individual differences in the combination of small and medium molecular metabolites with lipoproteins and the strong and weak combination of IBP and lipoprotein. Now, the higher the content of free lactic acid in the plasma, or the total triglyceride, the lower the concentration of albumin or choline, the more sensitive to IBP; and the lighter weight or the less obese index BMI is more sensitive to IBP. The older the volunteers recruited in this project, the greater the concentration of glucose and glycoprotein in the plasma, valine, complexon, and muscle. The lower the concentration of choline phosphatidylcholine in the anhydride and lipoprotein particles, we can also excavate other metabolites in the NMR spectrum that are in the same or similar metabolic pathways through the load map encoded by the correlation coefficient of the OPLS model.
【學(xué)位授予單位】：中國(guó)科學(xué)院研究生院(武漢物理與數(shù)學(xué)研究所)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2016
【分類號(hào)】：Q591
，
本文編號(hào)：2150257
[Abstract]:Metabonomics is a subject to explore the essence of life process by analyzing the overall changes of small and medium molecular compounds in complex biological systems..NMR has the advantages of simple sample processing, rich spectrum editing, unbiased detection and good reproducibility. It has always been a most commonly used detection technique in metabolomics research. The complex biological systems include biological fluids, tissues and organs, which contain a large variety of metabolites, and all biological metabolites contain protons. Therefore, the metabonomics analysis method based on 1H NMR technology is a powerful tool for the study of complex biological systems. In the study of NMR based metabolomics, we have to The original data is usually a set of NMR atlas. Before using the chemometrics model to analyze these NMR data, we first need to reduce the data of the NMR atlas to facilitate the subsequent statistical analysis. At present, the most commonly used NMR map reduction method is a piecewise integral method, which divides the original map into a number of 2 widths. The advantages of the piecewise integral method are high efficiency, easy to automate, and are especially suitable for large-scale sample research. The disadvantage is that the obtained data are more variable, the resolution of the atlas is lower, and the later feature variables are buried. When the number of samples is less, we can also use the peaks. The NMR map is reduced by the fitting method. The peak fitting method uses the standard atlas of various metabolites to fit the experimental spectrum to get the concentration data of the metabolite. The advantage of this method is that the obtained data are less variable and benefit to the subsequent statistical analysis; the disadvantage is that the data base of the metabolite's Atlas data base is strong and not easy to automate, so it is only suitable. In the second chapter of this paper, C57BL/6J rats were selected to establish the animal model of metastatic melanoma and to obtain the spleen and stomach tissues of the rats as the research object. In this chapter, we first selected the spleen tissue data of rats, and analyzed and compared the subsection integral and the peak fitting of the two methods to reduce the dimension of the NMR map. Effects of Principal Component Analysis (PCA) model and orthogonal partial least square analysis (Orthogonal Proj ection to Latent Structures, OPLS). Then, we analyzed the metabolic phenotypic changes caused by metastatic melanoma in the spleen and stomach tissues of rats. The results showed that the experimental group and the control group were samples. The third chapter of this paper uses the same research strategy as the second chapter to establish the animal model of C57BL/6J rats, and analyzes the effect of smoking on the metabolic phenotype of lung tissue in normal weight and obese rats by.OPLS model analysis. No matter whether rats were obese, smoking significantly reduced the levels of adenosine derivatives ATP, ADP and AMP, and the content of inosine and uridine increased significantly. We also found that smoking alone did not significantly change the ratio of GPC/PC in the lung tissue of rats, and obesity was sufficient to significantly increase the GPC/PC ratio, and The second and third chapters of this paper are to study the differences between different groups of samples and ignore the individual differences in the samples in the group. The individual differences in the samples in the group are also important, which can reflect the different responses of different individuals to the same external stimuli. Therefore, the fourth chapter of this paper is on the sample. In this chapter, we selected Bloven (IBP) as a model drug and studied the individual differences in the interaction between IBP and plasma. The content of this chapter is a supplement and extension of the previous research work of this group. In this chapter, we redefined the interaction index (Idist) and The diversity index (diversity index, Idiv) was used to characterize the individual differences in plasma components and their effects on IBP- plasma interactions. The redefined Idist could extract more information from the NMR map, the redefined Idiv has uniqueness and certainty, and there is a very significant linear correlation between Idist and Idiv (p2.2e-16). At the same time, we analyzed the association between Idist and NMR atlas, Idist and clinical data as well as clinical data and NMR atlas. The study found that the individual differences in the interaction between IBP and plasma were mainly reflected in the individual differences in the combination of small and medium molecular metabolites with lipoproteins and the strong and weak combination of IBP and lipoprotein. Now, the higher the content of free lactic acid in the plasma, or the total triglyceride, the lower the concentration of albumin or choline, the more sensitive to IBP; and the lighter weight or the less obese index BMI is more sensitive to IBP. The older the volunteers recruited in this project, the greater the concentration of glucose and glycoprotein in the plasma, valine, complexon, and muscle. The lower the concentration of choline phosphatidylcholine in the anhydride and lipoprotein particles, we can also excavate other metabolites in the NMR spectrum that are in the same or similar metabolic pathways through the load map encoded by the correlation coefficient of the OPLS model.
【學(xué)位授予單位】：中國(guó)科學(xué)院研究生院(武漢物理與數(shù)學(xué)研究所)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2016
【分類號(hào)】：Q591
，
本文編號(hào)：2150257
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