Background/Purpose: Genome-wide association studies and large-scale sequencing studies identify many non-coding genetic variants that increase disease risk. At least 60% of these loci have been associated with genotype-dependent expression of nearby genes. It remains to be determined that 50-100% expression differences are biologically relevant in specific immune cell types. We focus on the expression quantitative trait loci (eQTL) at the ETS1 lupus-risk locus.Patients with lupus have 50% less peripheral blood mononuclear cell mRNA expression of ETS1 than people without SLE, and people with the risk haplotype at the ETS1 locus have 50% less mRNA expression than people with the non-risk haplotype. Since ETS1 is a transcription factor, differential ETS1 expression could have easily measurable consequences on transcription factor binding and downstream gene expression. There are nearly 800 genes that are known to be dysregulated in subjects with SLE.

Methods: We developed a system combining the Clustered regularly interspaced short palindromic repeats (CRISPR) Homology-directed Repair technique with Tet-inducible Controlled Gene Expression technique to precisely control gene expression. This system allows us to mimic the differential gene expressions caused by genetic variants.

Results: Our analyses of these genes using publically available ChIP-seq data sets from B cell line GM12878 and epithelial cell line K562 indicates that 191 and 151 of these genes, respectively, have ETS1 binding sites proximal to the transcription start site (enrichment of 3-4 fold compared to randomly chosen gene sets, p<10^-46). We hypothesize that these changes in ETS1 levels are important in 1) ETS1 binding throughout the genome, 2) expression of ETS1 downstream target genes (such as BLIMP1), and 3) immunological dysfunction and hyperactivity of B cells. We test these hypotheses by analyzing the binding of ETS1 (ChIP-seq) and the changes to the transcriptome of cells with 2-fold differences in ETS1expression (RNA-seq). Our CRISPR system successfully mimics the differential gene expressions.

Conclusion: The investigation of the ETS1 eQTL will allows us to make important progress in the field of human genetics and especially complex genetic disease etiology.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/precisely-controlled-differential-gene-expression-system-to-investigate-the-effect-of-eqtl/