The Effects of Globin on Microarray-based Gene Expression Analysis of Mouse Blood

Peripheral whole blood-based gene expression profiling has become one of the most common strategies exploited in the development of clinically relevant biomarkers. However, the ability to identify biologically meaningful conclusions from gene expression patterns in whole blood is highly problematic. First, it is difficult to know whether or not expression patterns in whole blood capture those in primary tissues. Second, if explicit steps are not taken to accommodate the extremely elevated expression levels of globin in blood then large-scale multi-probe microarray-based studies can be severely compromised. Many studies consider the use of mouse blood as a model for human blood in addition to considering blood gene expression levels as a general surrogate for gene expression levels in other tissues. We explored the effects of globin reduction on peripheral mouse blood in the detection of genes known to be expressed in human tissues. Globin reduction resulted in 1.) a significant increase in the number of probes detected (5840 ± 944 vs 12411 ± 1904); 2.) increased expression for 4128 probe sets compared to non-globin reduced blood (p < .001, ≥ two-fold); 3.) improved detection of genes associated with many biological pathways and diseases; and 4.) an increased ability to detect genes expressed in 27 human tissues (p < 10-4). This study suggests that although microarray-based mouse blood gene expression studies that do not consider the effects of globin are severely compromised, globin-reduced mouse whole blood gene expression studies can be used to capture the expression profiles of genes known to contribute to various human diseases. Whole and GLOBINclear-treated paired blood samples from 18 mice representing 3 mice from 6 different isogenic mice strains.

基于外周全血的基因表达谱分析（gene expression profiling）已成为开发临床相关生物标志物（biomarker）的最常用策略之一。然而，从全血基因表达模式中提取具有生物学意义的结论仍面临诸多挑战：其一，难以确定全血中的基因表达模式是否能够反映原发组织的基因表达特征；其二，若未采取针对性措施抵消血液中珠蛋白（globin）极高表达水平的干扰，基于多探针基因微阵列（microarray）的大规模研究结果将受到严重影响。诸多研究在将血液基因表达水平作为其他组织基因表达水平的通用替代指标的同时，还将小鼠血液作为人类血液的研究模型。本研究针对珠蛋白消减对小鼠外周血中已知在人类组织中表达的基因检测的影响展开了探究。结果显示，珠蛋白消减可带来如下显著改变：1） 检出探针数量大幅提升（从5840±944提升至12411±1904）；2） 相较于未进行珠蛋白消减的血液样本，4128个探针组的基因表达水平显著上调（p<0.001，差异倍数≥2）；3） 对诸多生物学通路及疾病相关基因的检测效能得到改善；4） 对27种人类组织中表达基因的检测能力显著增强（p<10⁻⁴）。本研究表明，尽管未考虑珠蛋白影响的基于基因微阵列的小鼠血液基因表达研究结果会受到严重干扰，但经过珠蛋白消减处理的小鼠全血基因表达研究，可用于获取已知与多种人类疾病相关的基因表达谱。本研究的样本来自6个同基因小鼠品系（每个品系3只，共18只小鼠），包含其全血样本与经GLOBINclear处理后的配对血液样本。