Stankey et al., Nature, 2024, 630, 447–456.
Genetic locus on chromosome 21q22 regulates macrophage inflammation and is associated with multiple autoimmune diseases.
Increasing rates of autoimmune and inflammatory diseases represent a growing threat to human health, compounded by limited treatment efficacy. This study investigated the functional role of a disease-associated genetic locus on chromosome 21q22, previously linked to inflammatory bowel disease, ankylosing spondylitis, primary sclerosing cholangitis and Takayasu’s arteritis, to identify a shared disease mechanism.
Study Design
Researchers employed a multi-faceted approach, combining genetic and functional genomic analyses. Genome-wide association study (GWAS) data were used for co-localization analyses. Promoter-capture Hi-C and expression quantitative trait loci (eQTL) data were used to identify potential target genes. CRISPR-Cas9 genome editing was applied to primary human monocytes to create knockout models of the identified gene. Massively parallel reporter assays (MPRA) were used to identify causal variants affecting enhancer activity. RNA sequencing (RNA-seq) was employed to determine gene expression changes resultant from gene disruption and finally, flow cytometry and Western blotting were used to corroborate findings and examine protein levels.
Patient Population
The study utilized primary human monocytes differentiated into macrophages from multiple healthy donors and patients with ankylosing spondylitis. Specific characteristics of the patient cohort (age, sex, disease duration/severity) were not a primary focus of the research. The study design prioritised isolating cellular mechanisms rather than characterising clinical cohorts.
Key Findings
The study identified ETS2 as a central regulator of human inflammatory macrophages underlying the association between the chr21q22 locus and multiple autoimmune diseases. The risk haplotype at the chr21q22 locus was found to correlate with increased ETS2 expression. Genetic fine-mapping and functional analyses using MPRA pinpointed a causal variant (rs2836882) within a macrophage-specific enhancer region. This variant promoted binding of the transcription factor PU.1, increasing enhancer activity and, consequently, ETS2 expression. CRISPR-Cas9-mediated ETS2 disruption in primary human macrophages resulted in reduced production of pro-inflammatory cytokines (IL-6, IL-8, IL-1β) and impaired phagocytosis and reactive oxygen species (ROS) production. RNA sequencing revealed widespread transcriptional changes following ETS2 disruption, with down-regulation of numerous inflammatory genes. Over 80% of genes downregulated following ETS2 disruption were similarly downregulated following deletion of the chr21q22 enhancer, highlighting a direct link between the genetic locus and ETS2-mediated inflammation. Finally, drug screening identified small molecules with potential to modulate the ETS2-driven inflammatory pathway.
Discussion
This research provides a mechanistic link between a complex genetic locus and an immune-mediated disease pathway. The identification of ETS2 as a central regulator of macrophage inflammation offers potential new therapeutic targets. The study offers proof-of-concept data suggesting that modulating ETS2 expression or its downstream targets may alleviate inflammatory responses. The finding of candidate small molecule inhibitors offers an avenue for further preclinical and potentially clinical development. Safety and tolerability profiles of said inhibitors weren’t directly assessed in this study. The study’s focus on primary human macrophages strengthens the translational relevance of the findings, distinguishing it from studies based on animal models or immortalised cell lines.
Authors’ Conclusions
The authors conclude that the chr21q22 locus directs macrophage inflammation through ETS2 and represents a shared disease mechanism contributing to the pathogenesis of multiple autoimmune diseases. The study highlights the power of functional genomics, applied directly in primary human cells, to identify immune-mediated disease mechanisms and potential therapeutic opportunities.
Reference
Stankey CT, Bourges C, Haag LM, et al. A disease-associated gene desert directs macrophage inflammation through ETS2. Nature. 2024;630(8019):447–456. doi:10.1038/s41586-024-07501-1.