RF02 Using functional genomic techniques to help us understand the TYK2 pathway in psoriasis

Abstract

Abstract Genetic screens have identified around 126 genetic signals associated with psoriasis through genome-wide association studies (GWAS) and rare variant analyses (Tsoi LC, Stuart PE, Tian C et al. Large scale meta-analysis characterizes genetic architecture for common psoriasis associated variants. Nat Commun 2017; 8:15382). The aim of this study was to use genome-editing techniques to investigate and validate the effect of a psoriasis-associated genetic signal on the expression of TYK2. GWAS have linked TYK2 to psoriasis susceptibility through the association of a protein-changing, exonic variant where TYK2 impairment confers protection against the development of psoriasis and other autoimmune diseases. The vast majority of disease risk-associated variants are found outside gene-coding regions. Functional experimental techniques may help characterize the effect of these variants on gene expression. The development of genome editing technology, clustered regularly interspaced short-palindromic repeat-Cas9 (CRISPR-Cas9), has made it possible to edit cell genomes. We used CRISPR-Cas9 to validate functionally the psoriasis-associated single nucleotide polymorphism (SNP) rs892085 on TYK2 expression in immortal T-cell lines. In-house data from our centre revealed the presence of long-range physical interactions between rs892085 and TYK2. We are the first to investigate functionally this signal and characterize this physical connection. We used CRISPR-Cas9 systems to both activate and inhibit the region around rs892085 and then measured the consequence of this through informative functional readouts using quantitative reverse transcription polymerase chain reaction. This revealed consistent alteration of TYK2 expression upon inhibition and activation of rs892085. This supports previous observations, where this regulatory region harbouring GWAS-implicated variation operates through direct long-distance contact. Previously, the closest or most biologically relevant gene was often assigned to a GWAS variant. We have shown that this is unreliable, with DNA regions looping over large distances to control genes. This work provides the first functional validation of the psoriasis-associated SNP rs892085. TYK2 is a recognized drug target with one therapy, deucravacitinib, approved by the US Food and Drug Administration. Drugs entering the clinical development stage that have used human genetic data to select drug targets may be more likely to succeed. This work demonstrates the potential complexity of how risk alleles may work to dysregulate TYK2 signalling in disease, with both gene function and expression increasing the risk of disease. Ultimately, genetic risk scores, incorporating functional evidence from studies like this, may be generated to predict how patients with different genetically perturbed biology pathways may respond to therapy.