Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma

• DOI: 10.1016/j.xgen.2022.100229
• Publication Date: 2022-12-07T15:38:32Z
• Authors: Kyung Duk Koh; Luke R. Bonser; Walter L. Eckalbar; Ofer Yizhar-Barnea; Jiangshan Shen; Xiaoning Zeng; Kirsten L. Hargett; Dingyuan I. Sun; Lorna T. Zlock; Walter E. Finkbeiner; Nadav Ahituv; David J. Erle
• Keywords: Characterization

Epithelial responses to the cytokine interleukin-13 (IL-13) cause airway obstruction in asthma. Here we utilized multiple genomic techniques identify IL-13-responsive regulatory elements bronchial epithelial cells and used these data develop a CRISPR interference (CRISPRi)-based therapeutic approach downregulate obstruction-inducing genes cell type- IL-13-specific manner. Using single-cell RNA sequencing (scRNA-seq) acetylated lysine 27 on histone 3 (H3K27ac) chromatin immunoprecipitation (ChIP-seq) primary human cells, identified elements. These sequences were functionally validated optimized via massively parallel reporter assays (MPRAs) for IL-13-inducible activity. The top secretory cell-selective sequence from MPRA, novel, distal enhancer of sterile alpha motif pointed domain containing E-26 transformation-specific transcription factor (SPDEF) gene, was drive CRISPRi knock down SPDEF or mucin 5AC (MUC5AC), both involved pathologic mucus production Our work provides catalog type-specific IL-13 response showcases their use purposes.