Stable Patterns of Gene Expression Regulating Carbohydrate Metabolism Determined by Geographic Ancestry. Homo sapiens

Individuals of African descent in the United States suffer disproportionately from diseases with a metabolic etiology (obesity, metabolic syndrome, and diabetes), and from the pathological consequences of these disorders (hypertension and cardiovascular disease). Using a combination of genetic/genomic and bioinformatics approaches, we identified a large number of genes that were both differentially expressed between American subjects self-identified to be of either African or European ancestry and that also contained single nucleotide polymorphisms that distinguish distantly related ancestral populations. Several of these genes control the metabolism of simple carbohydrates and are direct targets for the SREBP1, a metabolic transcription factor also differentially expressed between our study populations. These data support the concept of stable patterns of gene transcription unique to a geographic ancestral lineage. The coordinated transcriptional adaptation of carbohydrate metabolism to dietary environmental pressures suggests a genetic and transcriptional mechanism for the disproportionate levels of obesity, diabetes, and cardiovascular disease observed in Americans with African ancestry. Keywords: Ancestry-dependent gene expression, functional genomics, personalized medicine, multi-factoral disease, nutrition, diabetes Overall design: We utilized a “sample x reference” experimental design strategy in which RNA extracted from human peripheral blood mononuclear cells was hybridized to the microarray slide in the presence of labeled Universal Human Reference RNA (UHRR, Stratagene, LaJolla, CA). A total of 161 subjects were used in this analysis. Briefly, five hundred nanograms of total RNA were used for gene expression profiling following reverse transcription and T-7 polymerase-mediated amplification/labeling with Cyanine-5 CTP. Labeled subject cRNA was co-hybridized to Agilent G4112A Whole Human Genome 44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Slides were hybridized, washed, and scanned on an Axon 4000b microarray scanner. The data were processed using GenePix Pro 6 software

美国非裔人群相较于其他族群，不成比例地更高发代谢病因相关疾病（肥胖、代谢综合征与糖尿病），以及此类疾病引发的病理并发症（高血压与心血管疾病）。本研究结合遗传/基因组学与生物信息学手段，鉴定出大量同时满足以下两个条件的基因：一是在自我报告为非洲或欧洲血统的美国受试者中呈现差异表达，二是携带可区分远缘祖先群体的单核苷酸多态性（single nucleotide polymorphism, SNP）。其中多个基因调控简单碳水化合物的代谢，且为代谢转录因子SREBP1的直接靶标；该转录因子在本研究的受试人群中同样存在差异表达。上述数据支持「地理祖先谱系具有独特的稳定基因转录模式」这一概念。碳水化合物代谢对饮食环境压力的协同转录适应机制，可为非裔美国人群中观测到的肥胖、糖尿病及心血管疾病高发态势提供遗传与转录层面的合理解释。

关键词：血统依赖性基因表达（Ancestry-dependent gene expression）、功能基因组学（functional genomics）、个性化医疗（personalized medicine）、多因素疾病（multi-factoral disease）、营养学（nutrition）、糖尿病（diabetes）

整体实验设计：本研究采用「样本-参考」实验设计策略，将从人外周血单个核细胞中提取的RNA，与标记有荧光的通用人类参考RNA（Universal Human Reference RNA, UHRR，斯特拉塔基因公司，加利福尼亚州拉霍亚市）共同杂交至微阵列玻片。本分析共纳入161名受试者。简言之，取500纳克总RNA进行基因表达谱分析，具体流程为：先完成逆转录，再通过T7聚合酶介导的扩增与花青5-CTP（Cyanine-5 CTP）标记。将标记完成的受试者cRNA与等摩尔量的花青3-CTP（Cyanine-3 CTP）标记的UHRR共同杂交至安捷伦G4112A型全人类基因组44K寡核苷酸微阵列芯片。玻片完成杂交、洗涤后，使用Axon 4000b型微阵列扫描仪进行扫描。数据处理采用GenePix Pro 6软件完成。