Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

Abstract

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 highcoverage 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 countassociated 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.genome sequencing | GWAS | basophils | hematopoiesis | CEBPA

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“…WGS covers the entire genome and can detect rare variants (with MAF<1 %), as well as other types of functionally important variations (copy number variations, insertions/deletions). 57, 58 Importantly, WGS gives single base resolution of the entire genome which is ~100–300-fold finer resolution than that provided by GWAS chips. Also, WGS is not biased by, or restricted to, the SNPs that have been placed on commercially available SNP chips (assumes commonly used chip-based methods).…”

“…Also, WGS is not biased by, or restricted to, the SNPs that have been placed on commercially available SNP chips (assumes commonly used chip-based methods). 57, 58 It provides the best possible resource for linkage disequilibrium (LD) mapping due to the maximal marker density and lack of ascertainment bias.…”

Concise Review: Epigenetic Regulation of Hematopoiesis: Biological Insights and Therapeutic Applications

“…CRISPR‐Cas9‐mediated mutagenesis of this region in HSPCs led to CEBPA downregulation and impairment of basophil production and maturation (Fig. ) . Interestingly, disease‐causing variants affecting the binding sites of the erythroid master regulator GATA1 were identified in regulatory elements of the ALAS2 , UROS , PKLR , and HBD genes.…”

“…Starting from this observation, Sankaran et al unraveled the role of cyclin D3 in the regulation of erythrocyte number and size through gene disruption studies . Other studies dissected the regulatory elements harboring genetic variants associated with particular phenotypes . A recent GWAS identified a SNP, associated with low basophil counts, 39 kb downstream of the gene encoding CCAAT/enhancer binding protein alpha (CEBPA), a master regulator implicated in basophil specification .…”

“…Other studies dissected the regulatory elements harboring genetic variants associated with particular phenotypes . A recent GWAS identified a SNP, associated with low basophil counts, 39 kb downstream of the gene encoding CCAAT/enhancer binding protein alpha (CEBPA), a master regulator implicated in basophil specification . This SNP overlaps with an enhancer targeted by the myeloid master regulators GATA2 and RUNX1 and identified specifically in CMPs, which give rise to several lineages including basophils.…”