C. T. Stankey, C. Bourges, L. M. Haag, T. Turner-Stokes, A. P. Piedade et al.
Increasing rates of autoimmune and inflammatory disease present a burgeoning threat to human health. This is compounded by the limited efficacy of available treatments and high failure rates during drug development, highlighting an urgent need to better understand disease mechanisms. Here we show how functional genomics could address this challenge. By investigating an intergenic haplotype on chr21q22—which has been independently linked to inflammatory bowel disease, ankylosing spondylitis, primary sclerosing cholangitis and Takayasu’s arteritis—we identify that the causal gene, ETS2, is a central regulator of human inflammatory macrophages and delineate the shared disease mechanism that amplifies ETS2 expression. Genes regulated by ETS2 were prominently expressed in diseased tissues and more enriched for inflammatory bowel disease GWAS hits than most previously described pathways. Overexpressing ETS2 in resting macrophages reproduced the inflammatory state observed in chr21q22-associated diseases, with upregulation of multiple drug targets, including TNF and IL-23. Using a database of cellular signatures, we identified drugs that might modulate this pathway and validated the potent anti-inflammatory activity of one class of small molecules in vitro and ex vivo. Together, this illustrates the power of functional genomics, applied directly in primary human cells, to identify immune-mediated disease mechanisms and potential therapeutic opportunities.
C. T. Stankey, C. Bourges, L. M. Haag, T. Turner-Stokes, A. P. Piedade, C. Palmer-Jones, I. Papa, M. Silva dos Santos, Q. Zhang, A. J. Cameron, A. Legrini, T. Zhang, C. S. Wood, F. N. New, L. O. Randzavola, L. Speidel, A. C. Brown, A. Hall, F. Saffioti, E. C. Parkes, W. Edwards, H. Direskeneli, P. C. Grayson, L. Jiang, P. A. Merkel, G. Saruhan-Direskeneli, A. H. Sawalha, E. Tombetti, A. Quaglia, D. Thorburn, J. C. Knight, A. P. Rochford, C. D. Murray, P. Divakar, M. Green, E. Nye, J. I. MacRae, N. B. Jamieson, P. Skoglund, M. Z. Cader, C. Wallace, D. C. Thomas, J. C. Lee. A disease-associated gene desert directs macrophage inflammation through ETS2. 2024-06-05. https://doi.org/10.1038/s41586-024-07501-1
An episomal MPRA library tested 114-nucleotide genomic sequences tiling the chr21q22 candidate-SNP region at 50-bp intervals, together with allele-specific constructs for candidate variants and control constructs. TPP macrophages from eight healthy donors were transfected; RNA was collected 24 hours later and compared with four input-DNA library replicates.
The MPRA vector library was transfected into TPP macrophages from six healthy donors, followed by minimal-sonication PU.1 immunoprecipitation and barcode sequencing. The processed table contains the source six-donor allele-specific PU.1-binding readout for three SNPs in the chr21q22 enhancer.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 6 files (ZIP)GSE229472_barcode_counts.txt.gzGSE229472_family.soft.gzGSE229472_normalised_collapsed_constructs.txt.gzSource_Data_Extended_Data_Fig_3.xlsxSource_Data_Extended_Data_Fig_4.xlsxSource_Data_Fig_1.xlsx