SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression

Abstract

Since most variants that impact polygenic disease phenotypes localize to non-coding genomic regions, understanding the consequences of regulatory element variants will advance understanding of human disease mechanisms. Here, we report that the systemic lupus erythematosus (SLE) risk variant rs2431697 as likely causal for SLE through disruption of a regulatory element, modulating miR-146a expression. Using epigenomic analysis, genome-editing and 3D chromatin structure analysis, we show that rs2431697 tags a cell-type dependent distal enhancer specific for miR-146a that physically interacts with the miR-146a promoter. NF-kB binds the disease protective allele in a sequence-specific manner, increasing expression of this immunoregulatory microRNA. Finally, CRISPR activation-based modulation of this enhancer in the PBMCs of SLE patients attenuates type I interferon pathway activation by increasing miR-146a expression. Our work provides a strategy to define non-coding RNA functional regulatory elements using disease-associated variants and provides mechanistic links between autoimmune disease risk genetic variation and disease etiology.

Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine

“…This SNP lies within a celltype specific enhancer that forms a cognate enhancer-promoter loop with the promoter of miR-146a, a miRNA with significantly downregulated expression in patients with Systemic lupus erythematosus. Presence of the high-risk T allele lowers the binding affinity of NF-κB binding site, which then leads to the decreased expression levels of miR-146a (this result was also verified by FAIRE-seq and ATAC-seq) [300].…”

“…Mutated versions of Cas9 with nickase activity combined to the use of two distinct sgRNAs for a single target, which effectively reduces off-target effects are the preferred strategy for precise SNP editing [295,296]. CRISPR-activation (CRISPR-a) [297,298] or CRISPR-inhibition (CRISPR-i) [299], both of which rely on catalytically inactive forms of Cas9 that are coupled to transcriptional activators or inhibitors to endogenously modulate transcriptional activity, can precede SNP editing in order to precisely link the surrounding sequence of the variant with gene expression of specific targets [300,301]. Examples include a CRISPR-a based methodology that has been applied in the study of mutations in regulatory elements of KRAS in colorectal cancer [302].…”

Quantitative Proteomic Analysis of Plasma Exosomes to Identify the Candidate Biomarker of Imatinib Resistance in Chronic Myeloid Leukemia Patients

“…Digested samples were subjected to LC-MS/MS detection using a minor modifications of previously described method by Hou et al (18). The tryptic peptide mixture was resuspended in solvent A (0.1% formic acid) and directly inject into a home-made reversed-phase analytical column (15 cm length, 75 mm i.d.).…”

CRISPRa screen on a genetic risk locus shared by multiple autoimmune diseases identifies a dysfunctional enhancer that affects IRF8 expression through cooperative lncRNA and DNA methylation machinery

“…Enhancers have been considered effective therapeutic targets for disease intervention because targeting enhancers might aid in precise treatment, due to the celltype specific nature of enhancers 15,[54][55][56] . For instance, editing the erythroid-specific enhancer of BCL11A by CRISPR-Cas9 restores γ-globin synthesis for treating sickle cell disease 15 .…”