A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association study

A chronic inflammatory state to a large extent explains sickle cell disease (SCD) pathophysiology. Nonetheless, the principal dysregulated factors affecting this major pathway and their mechanisms of action still have to be fully identified and elucidated. Integrating gene expression and genome-wide association study (GWAS) data analysis represents a novel approach to refining the identification of key mediators and functions in complex diseases. Here, we performed gene expression meta-analysis of five independent publicly available microarray datasets related to homozygous SS patients with SCD to identify a consensus SCD transcriptomic profile. The meta-analysis conducted using the MetaDE R package based on combining p values (maxP approach) identified 335 differentially expressed genes (DEGs; 224 upregulated and 111 downregulated). Functional gene set enrichment revealed the importance of several metabolic pathways, of innate immune responses, erythrocyte development, and hemostasis pathways. Advanced analyses of GWAS data generated within the framework of this study by means of the atSNP R package and SIFT tool identified 60 regulatory single-nucleotide polymorphisms (rSNPs) occurring in the promoter of 20 DEGs and a deleterious SNP, affecting CAMKK2 protein function. This novel database of candidate genes, transcription factors, and rSNPs associated with SCD provides new markers that may help to identify new therapeutic targets.慢性炎症状态在很大程度上阐释了镰状细胞病（Sickle Cell Disease, SCD）的病理生理学机制。然而，影响这一核心通路的主要失调因子及其作用机制仍有待全面鉴定与阐明。整合基因表达与全基因组关联研究（Genome-Wide Association Study, GWAS）数据分析，是优化复杂疾病关键介导因子及功能鉴定的全新策略。本研究针对5个独立公开的、与镰状细胞病纯合SS型患者相关的微阵列数据集开展基因表达荟萃分析，以确定该病的一致性转录组特征。本研究采用基于P值合并（maxP法）的MetaDE R包开展荟萃分析，共鉴定出335个差异表达基因（Differentially Expressed Genes, DEGs；其中224个上调、111个下调）。功能基因集富集分析显示，多条代谢通路、天然免疫应答、红细胞发育及凝血通路在该病中发挥关键作用。本研究框架内生成的GWAS数据经atSNP R包与SIFT工具开展高级分析后，共鉴定出60个位于20个DEGs启动子区的调控性单核苷酸多态性（Regulatory Single-Nucleotide Polymorphisms, rSNPs），以及1个影响CAMKK2蛋白功能的有害单核苷酸多态性。本研究构建的镰状细胞病相关候选基因、转录因子及rSNPs新型数据库，可为新型治疗靶点的筛选提供潜在标志物。