Christophe Bourges, Abigail F Groff, Oliver S Burren, Chiara Gerhardinger, Kaia Mattioli et al.
Deriving mechanisms of immune-mediated disease from GWAS data remains a formidable challenge, with attempts to identify causal variants being frequently hampered by strong linkage disequilibrium. To determine whether causal variants could be identified from their functional effects, we adapted a massively parallel reporter assay for use in primary CD4 T cells, the cell type whose regulatory DNA is most enriched for immune-mediated disease SNPs. This enabled the effects of candidate SNPs to be examined in a relevant cellular context and generated testable hypotheses into disease mechanisms. To illustrate the power of this approach, we investigated a locus that has been linked to six immune-mediated diseases but cannot be fine-mapped. By studying the lead expression-modulating SNP, we uncovered an NF-κB-driven regulatory circuit which constrains T-cell activation through the dynamic formation of a super-enhancer that upregulates TNFAIP3 (A20), a key NF-κB inhibitor. In activated T cells, this feedback circuit is disrupted—and super-enhancer formation prevented—by the risk variant at the lead SNP, leading to unrestrained T-cell activation via a molecular mechanism that appears to broadly predispose to human autoimmunity.
Christophe Bourges, Abigail F Groff, Oliver S Burren, Chiara Gerhardinger, Kaia Mattioli, Anna Hutchinson, Theodore Hu, Tanmay Anand, Madeline W Epping, Chris Wallace, Kenneth GC Smith, John L Rinn, James C Lee. Resolving mechanisms of immune-mediated disease in primary CD4 T cells. 2020-04-01. https://doi.org/10.15252/emmm.202012112
The complete RSV-promoter plasmid library, containing both SNP allele constructs and 114-bp enhancer tiles, was transfected into Jurkat E6.1 cells in resting and stimulated states. This table reports construct-level median RNA/DNA activity derived from the GEO-supplied quantile-normalized collapsed counts for the four Jurkat RNA replicates per state.
The RSV-promoter episomal barcode MPRA tested three overlapping 114-bp reference/alternate constructs per candidate SNP, together with synthetic and genomic controls, in resting primary CD4 T cells from 12 healthy donors. This table contains the authors' QuASAR-MPRA fixed-effect meta-analysis results from Dataset EV2, joined to the corresponding library sequences and coordinates.
The same RSV-promoter plasmid MPRA library included 114-bp enhancer oligonucleotides tiled at approximately 50-bp intervals across 14 autoimmune disease-associated loci and positive/negative control regions. This table reports primary-CD4-T-cell median quantile-normalized RNA/DNA activity in resting and stimulated states for every enhancer construct retained in the GEO processed file, with locus-level driver annotations from Appendix Table S1.
The RSV-promoter episomal barcode MPRA tested three overlapping 114-bp reference/alternate constructs per candidate SNP, together with synthetic and genomic controls, in stimulated primary CD4 T cells from 12 healthy donors. This table contains the authors' QuASAR-MPRA fixed-effect meta-analysis results from Dataset EV3, joined to the corresponding library sequences and coordinates.
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