Yao Yao, Yang Jia, Qin Qian, Tang Chao, Li Zhidan, Chen Li, Li Kailong, Ren Chunyan, Chen Lu, Rao Shuquan
Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Medicine, West China Second Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, China.
School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
Commun Biol. 2020 Dec 18;3(1):790. doi: 10.1038/s42003-020-01527-7.
Genome-wide association studies (GWAS) have identified multiple genomic loci linked to blood cell traits, however understanding the biological relevance of these genetic loci has proven to be challenging. Here, we performed a transcriptome-wide association study (TWAS) integrating gene expression and splice junction usage in neutrophils (N = 196) with a neutrophil count GWAS (N = 173,480 individuals). We identified a total of 174 TWAS-significant genes enriched in target genes of master transcription factors governing neutrophil specification. Knockout of a TWAS candidate at chromosome 5q13.2, TAF9, in CD34 hematopoietic and progenitor cells (HSPCs) using CRISPR/Cas9 technology showed a significant effect on neutrophil production in vitro. In addition, we identified 89 unique genes significant only for splice junction usage, thus emphasizing the importance of alternative splicing beyond gene expression underlying granulopoiesis. Our results highlight the advantages of TWAS, followed by gene editing, to determine the functions of GWAS loci implicated in hematopoiesis.
全基因组关联研究（GWAS）已经确定了多个与血细胞性状相关的基因组位点，然而，要理解这些基因位点的生物学相关性已被证明具有挑战性。在这里，我们进行了一项转录组全关联研究（TWAS），将嗜中性粒细胞（N = 196）中的基因表达和剪接连接使用情况与嗜中性粒细胞计数GWAS（N = 173,480个体）相结合。我们总共鉴定出174个TWAS显著基因，这些基因在控制嗜中性粒细胞特化的主要转录因子的靶基因中富集。使用CRISPR/Cas9技术在CD34造血和祖细胞（HSPCs）中敲除位于5q13.2染色体上的一个TWAS候选基因TAF9，在体外对嗜中性粒细胞的产生有显著影响。此外，我们鉴定出89个仅对剪接连接使用情况有显著意义的独特基因，从而强调了可变剪接在粒细胞生成的基因表达基础之外的重要性。我们的结果突出了TWAS随后进行基因编辑在确定参与造血作用的GWAS位点功能方面的优势。
