Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma
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
Affiliations
Kyung Duk Koh
Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
Luke R. Bonser
Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
Walter L. Eckalbar
Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
Ofer Yizhar-Barnea
Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
Jiangshan Shen
Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
Xiaoning Zeng
Department of Pulmonary & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
Kirsten L. Hargett
Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
Dingyuan I. Sun
Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
Lorna T. Zlock
Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
Walter E. Finkbeiner
Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
Nadav Ahituv
Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Corresponding author
David J. Erle
Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; Corresponding author
Summary: Epithelial responses to the cytokine interleukin-13 (IL-13) cause airway obstruction in asthma. Here we utilized multiple genomic techniques to identify IL-13-responsive regulatory elements in bronchial epithelial cells and used these data to develop a CRISPR interference (CRISPRi)-based therapeutic approach to downregulate airway obstruction-inducing genes in a cell type- and IL-13-specific manner. Using single-cell RNA sequencing (scRNA-seq) and acetylated lysine 27 on histone 3 (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) in primary human bronchial epithelial cells, we identified IL-13-responsive genes and regulatory elements. These sequences were functionally validated and optimized via massively parallel reporter assays (MPRAs) for IL-13-inducible activity. The top secretory cell-selective sequence from the MPRA, a novel, distal enhancer of the sterile alpha motif pointed domain containing E-26 transformation-specific transcription factor (SPDEF) gene, was utilized to drive CRISPRi and knock down SPDEF or mucin 5AC (MUC5AC), both involved in pathologic mucus production in asthma. Our work provides a catalog of cell type-specific genes and regulatory elements involved in IL-13 bronchial epithelial response and showcases their use for therapeutic purposes.
