Functional Variant Discovery Identifies SPRY2 as a Genetic Mechanism Linking Wood Smoke with Asthma

Climate change is impacting human health through a historic rise in wildfire smoke across the United States and the world. Whereas the deleterious effects of wildfire smoke and associated air pollution on asthma outcomes are well-established epidemiologically, genetic risks and molecular mechanisms of how wildfire smoke affects asthma are unknown. This knowledge gap hinders the identification of high-risk individuals and the creation of targeted therapies or recommendations to protect these individuals. Here, we employ a genetic approach to identify common variant (minor allele frequency > 0.05) exposure-conditional genetic risk variants that localize with genomic responses to wood smoke particles (WSP), a model of wildfire smoke exposure, and associate with asthma in the Genetic Epidemiology Research on Aging (GERA) cohort. Our novel approach used nascent transcriptional signatures derived from WSP-exposed Beas-2B airway epithelial cells to reduce the genome sequence for discovery and allow a permutation-based statistical approach to identify 52 candidate SNPs. We applied biologic and bioinformatic filters to prioritize variants for direct testing of allele-dependent transcriptional regulatory function in plasmid reporters. The rs3861144 variant identified by this approach controls WSP responses of airway epithelial cells to SPRY2, which we showed is involved in mechanical injury repair in cell culture. Our results demonstrate that wildfire particulates contribute to asthma risk at the molecular level, and we have identified mechanistic targets and genetic variant candidates to apply for clinical risk prediction and development of targeted therapies for high-risk individuals. Overall design: ATAC-seq profiling of live airway epithelial cells obtained from 3 healthy non-smoking adult donors. Cells were dissociated from cytology brushes and processed for ATAC-seq directly without treatment or manipulation. RNA-seq analysis of Beas-2B airway epithelial cells transfected with scrambled control (siCTRL) or SPRY2-targeting siRNA (siSPRY2) and exposed to wood smoke particles (WSP, 1 mg/ml) for 2 and 4 hours.