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Dissecting the Genetic Etiology of Lupus at ETS1 Locus

Lu, Xiaoming
http://orcid.org/0000-0001-6689-7154
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1505209355822185

Abstract Details

2017, PhD, University of Cincinnati, Medicine: Immunology.
Systemic lupus erythematosus (SLE) is a complex autoimmune disease with strong evidence for genetics factor involvement. Genome-wide association studies have identified 84 risk loci associated with SLE. However, the specific genotype-dependent (allelic) molecular mechanisms connecting these lupus-genetic risk loci to immunological dysregulation are mostly still unidentified. ~ 90% of these loci contain variants that are non-coding, and are thus likely to act by impacting subtle, comparatively hard to predict mechanisms controlling gene expression. Here, we developed a strategic approach to prioritize non-coding variants, and screen them for their function. This approach involves computational prioritization using functional genomic databases followed by experimental analysis of differential binding of transcription factors (TFs) to risk and non-risk alleles. For both electrophoretic mobility shift assay (EMSA) and DNA affinity precipitation assay (DAPA) analysis of genetic variants, a synthetic DNA oligonucleotide (oligo) is used to identify factors in the nuclear lysate of disease or phenotype-relevant cells. This strategic approach was then used for investigating SLE association at ETS1 locus. Genetic variants at chromosomal region 11q23.3, near the gene ETS1, have been associated with systemic lupus erythematosus (SLE), or lupus, in independent cohorts of Asian ancestry. Several recent studies have implicated Ets1 as a critical driver of immune cell function and differentiation, and mice deficient in Ets1 develop an SLE-like autoimmunity. We performed a fine-mapping study of 14,551 subjects from multi-ancestral cohorts by starting with genotyped variants and imputing to all common variants spanning ETS1. By constructing genetic models via frequentist and Bayesian association methods, we identified 16 variants that are statistically likely to be causal. We functionally assessed each of these variants based on their likelihood of affecting transcription factor binding, miRNA binding, or chromatin state. Of the four variants that we have experimentally examined, only rs6590330 differentially binds lysate from B cells in EMSA. Using DAPA-mass spectrometry, we found more binding of the transcription factor signal transducer and activator of transcription 1 (STAT1) to DNA near the risk allele of rs6590330 than near the non-risk allele. Immunoblot analysis and chromatin immunoprecipitation of pSTAT1 in B cells heterozygous for rs6590330 confirmed that the risk allele increased binding to the active form of STAT1. Analysis with expression quantitative trait loci (eQTL) indicated that the risk allele of rs6590330 is associated with decreased ETS1 expression in Han Chinese, but not other ancestral cohorts. We propose a model in which the risk allele of rs6590330 is associated with decreased ETS1 expression and increases SLE risk by enhancing the binding of pSTAT1. However, whether this differential gene expression caused by rs6590330 is biologically relevant or not has not been answered. We then 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, which can mimic this differential gene expression caused by genetic variants. The investigation of this small differential gene expression may make important progress in the field of human genetics and especially the complex genetic disease etiology of SLE.
John Harley, M.D. Ph.D. (Committee Chair)
Lili Ding (Committee Member)
Kasper Hoebe, Ph.D. (Committee Member)
Leah Kottyan, Ph.D (Committee Member)
Harinder Singh (Committee Member)
Matthew Weirauch, Ph.D. (Committee Member)
172 p.
Genetics
SLE; ETS1; Fine Mapping; DAPA; STAT1; SNP

Recommended Citations

Citations

  • Lu, X. (2017). Dissecting the Genetic Etiology of Lupus at ETS1 Locus [Doctoral dissertation, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1505209355822185

    APA Style (7th edition)

  • Lu, Xiaoming. Dissecting the Genetic Etiology of Lupus at ETS1 Locus. 2017. University of Cincinnati, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1505209355822185.

    MLA Style (8th edition)

  • Lu, Xiaoming. "Dissecting the Genetic Etiology of Lupus at ETS1 Locus." Doctoral dissertation, University of Cincinnati, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1505209355822185

    Chicago Manual of Style (17th edition)

ucin1505209355822185
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This open access ETD is published by University of Cincinnati and OhioLINK.