Integrative Functional Genomics Identifies Systemic Lupus Erythematosus Causal Genetic Variant in the IRF5 Risk Locus

Abstract

Objective IRF5 plays a crucial role in the development of lupus. Genome‐wide association studies have identified several systemic lupus erythematosus (SLE) risk single‐nucleotide polymorphisms (SNPs) enriched in the IRF5 locus. However, no comprehensive genome editing–based functional analysis exists to establish a direct link between these variants and altered IRF5 expression, particularly for enhancer variants. This study was undertaken to dissect the regulatory function and mechanisms of SLE IRF5 enhancer risk variants and to explore the utilization of clustered regularly interspaced short palindromic repeat interference (CRISPRi) to regulate the expression of disease risk gene to intervene in the disease. Methods Epigenomic profiles and expression quantitative trait locus analysis were applied to prioritize putative functional variants in the IRF5 locus. CRISPR‐mediated deletion, activation, and interference were performed to investigate the genetic function of rs4728142. Allele‐specific chromatin immunoprecipitation–quantitative polymerase chain reaction and allele‐specific formaldehyde‐assisted isolation of regulatory element–quantitative polymerase chain reaction were used to decipher the mechanism of alleles differentially regulating IRF5 expression. The CRISPRi approach was used to evaluate the intervention effect in monocytes from SLE patients. Results SLE risk SNP rs4728142 was located in an enhancer region, indicating a disease‐related regulatory function, and risk allele rs4728142‐A was closely associated with increased IRF5 expression. We demonstrated that an rs4728142‐containing region could act as an enhancer to regulate the expression of IRF5. Moreover, rs4728142 affected the binding affinity of zinc finger and BTB domain–containing protein 3 (ZBTB3), a transcription factor involved in regulation. Furthermore, in monocytes from SLE patients, CRISPR‐based interference with the regulation of this enhancer attenuated the production of disease‐associated cytokines. Conclusion These results demonstrate that the rs4728142‐A allele increases the SLE risk by affecting ZBTB3 binding, chromatin status, and regulating IRF5 expression, establishing a biologic link between genetic variation and lupus pathogenesis.

Functional Genome Analysis for Immune Cells Provides Clues for Stratification of Systemic Lupus Erythematosus

“…In ImmuNexUT, on the other hand, rs3757387 in the enhancer region of IRF5 exhibited the strongest eQTL effect in neutrophils, plasmacytoid dendritic cells, CD4 + T cells, and CD8 + T cells ( ). Hou et al reanalyzed the SLE GWAS results, focusing on enhancers near IRF5, and found that rs4728142 located within an enhancer in linkage disequilibrium with rs3757387 was associated most strongly with SLE [ 42 ]. They reported that the SLE-risk genotype of rs4728142 enhanced transcription factor ZBTB3, and deletion of the rs4728142 region in monocytes reduced the expression of IRF5, IL6, and IFNB.…”

Three‐Dimensional Chromosomal Landscape Revealing miR‐146a Dysfunctional Enhancer in Lupus and Establishing a CRISPR‐Mediated Approach to Inhibit the Interferon Pathway

“…Targeting disease‐associated enhancers is a novel potential strategy for disease therapy 6,38 . Here, we found that targeting the SLE‐associated 32.5‐kb enhancer with the CRISPRa system effectively down‐regulated the activity of the IFN pathway and the production of inflammatory cytokines, suggesting a promising target for therapy in the future.…”

Type I IFN in Glomerular Disease: Scarring beyond the STING

“…The most compelling evidence suggesting the direct involvement of the IFN-I pathway in the development and progression of GD comes from patients diagnosed with multiple sclerosis, hepatitis C, and some types of cancer, all developing glomerular lesions after receiving recombinant IFN therapy [ 16 , 17 , 18 , 19 ]. Moreover, patients with inborn errors causing enhanced IFN-I production such as Aicardi–Goutières syndrome [ 20 ], STING-associated vasculopathy with onset in infancy (SAVI) [ 21 , 22 ], and systemic lupus erythematosus (SLE) [ 23 ] also present with glomerular lesions.…”