Guo Michael H, Nandakumar Satish K, Ulirsch Jacob C, Zekavat Seyedeh M, Buenrostro Jason D, Natarajan Pradeep, Salem Rany M, Chiarle Roberto, Mitt Mario, Kals Mart, Pärn Kalle, Fischer Krista, Milani Lili, Mägi Reedik, Palta Priit, Gabriel Stacey B, Metspalu Andres, Lander Eric S, Kathiresan Sekar, Hirschhorn Joel N, Esko Tõnu, Sankaran Vijay G
Broad Institute of MIT and Harvard, Cambridge, MA 02142.
Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115.
Proc Natl Acad Sci U S A. 2017 Jan 17;114(3):E327-E336. doi: 10.1073/pnas.1619052114. Epub 2016 Dec 28.
Genetic variants affecting hematopoiesis can influence commonly measured blood cell traits. To identify factors that affect hematopoiesis, we performed association studies for blood cell traits in the population-based Estonian Biobank using high-coverage whole-genome sequencing (WGS) in 2,284 samples and SNP genotyping in an additional 14,904 samples. Using up to 7,134 samples with available phenotype data, our analyses identified 17 associations across 14 blood cell traits. Integration of WGS-based fine-mapping and complementary epigenomic datasets provided evidence for causal mechanisms at several loci, including at a previously undiscovered basophil count-associated locus near the master hematopoietic transcription factor CEBPA The fine-mapped variant at this basophil count association near CEBPA overlapped an enhancer active in common myeloid progenitors and influenced its activity. In situ perturbation of this enhancer by CRISPR/Cas9 mutagenesis in hematopoietic stem and progenitor cells demonstrated that it is necessary for and specifically regulates CEBPA expression during basophil differentiation. We additionally identified basophil count-associated variation at another more pleiotropic myeloid enhancer near GATA2, highlighting regulatory mechanisms for ordered expression of master hematopoietic regulators during lineage specification. Our study illustrates how population-based genetic studies can provide key insights into poorly understood cell differentiation processes of considerable physiologic relevance.
影响造血作用的基因变异可影响常见的血细胞特征。为了确定影响造血作用的因素，我们在基于人群的爱沙尼亚生物银行中，对血细胞特征进行了关联研究，对2284个样本进行了高覆盖全基因组测序（WGS），并对另外14904个样本进行了单核苷酸多态性（SNP）基因分型。利用多达7134个有可用表型数据的样本，我们的分析在14种血细胞特征中确定了17个关联。基于WGS的精细定位和互补表观基因组数据集的整合为几个位点的因果机制提供了证据，包括在主要造血转录因子CEBPA附近一个先前未发现的嗜碱性粒细胞计数相关位点。CEBPA附近这个嗜碱性粒细胞计数关联的精细定位变异与常见髓系祖细胞中活跃的一个增强子重叠，并影响其活性。在造血干细胞和祖细胞中通过CRISPR/Cas9诱变对该增强子进行原位扰动表明，它在嗜碱性粒细胞分化过程中对CEBPA表达是必需的且具有特异性调节作用。我们还在GATA2附近另一个多效性更强的髓系增强子处鉴定出与嗜碱性粒细胞计数相关的变异，突出了谱系特化过程中主要造血调节因子有序表达的调控机制。我们的研究说明了基于人群的基因研究如何能够为理解不足但具有相当生理相关性的细胞分化过程提供关键见解。
