Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis

BackgroundHuman peripheral blood is a promising material for biomedical research. However, various kinds of biological and technological factors result in a large degree of variation in blood gene expression profiles. Methodology/Principal FindingsHuman peripheral blood samples were drawn from healthy volunteers and analysed using the Human Genome U133Plus2 Microarray. We applied a novel approach using the Principle Component Analysis and Eigen-R2 methods to dissect the overall variation of blood gene expression profiles with respect to the interested biological and technological factors. The results indicated that the predominating sources of the variation could be traced to the individual heterogeneity of the relative proportions of different blood cell types (leukocyte subsets and erythrocytes). The physiological factors like age, gender and BMI were demonstrated to be associated with 5.3% to 9.2% of the total variation in the blood gene expression profiles. We investigated the gene expression profiles of samples from the same donors but with different levels of RNA quality. Although the proportion of variation associated to the RNA Integrity Number was mild (2.1%), the significant impact of RNA quality on the expression of individual genes was observed. ConclusionsBy characterizing the major sources of variation in blood gene expression profiles, such variability can be minimized by modifications to study designs. Increasing sample size, balancing confounding factors between study groups, using rigorous selection criteria for sample quality, and well controlled experimental processes will significantly improve the accuracy and reproducibility of blood transcriptome study.研究背景：人类外周血是极具应用价值的生物医学研究样本材料。然而，多种生物学与技术层面的因素会导致血液基因表达谱存在较大程度的变异。 研究方法与主要结果：本研究从健康志愿者体内采集外周血样本，采用人类基因组U133Plus2微阵列（Human Genome U133Plus2 Microarray）进行基因表达谱分析。我们创新性地结合主成分分析（Principal Component Analysis）与Eigen-R2方法，针对研究关注的生物学与技术因素，解析血液基因表达谱的整体变异来源。结果显示，变异的主要来源可归因于不同血液细胞类型（白细胞亚群与红细胞）相对比例的个体异质性。研究证实，年龄、性别与体质量指数（BMI）等生理因素与血液基因表达谱总变异的5.3%至9.2%相关联。我们还对同一供体但RNA质量水平存在差异的样本开展了基因表达谱分析：尽管与RNA完整性数（RNA Integrity Number）相关的变异占比仅为2.1%，但仍观察到RNA质量对单个基因的表达具有显著影响。 研究结论：通过系统表征血液基因表达谱的主要变异来源，可通过优化研究设计来最小化此类变异。具体措施包括扩大样本量、平衡研究组间的混杂因素、采用严格的样本质量筛选标准，以及严格控制实验流程，上述策略将显著提升血液转录组研究的准确性与可重复性。