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

doi:10.1016/j.xgen.2022.100229

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

Cell Genom. 2022 Dec 7;3(1):100229. doi: 10.1016/j.xgen.2022.100229. eCollection 2023 Jan 11.

Authors

Kyung Duk Koh^{1

2}, Luke R Bonser^{1

2}, Walter L Eckalbar^{1

3}, Ofer Yizhar-Barnea^{2

4}, Jiangshan Shen^{1

2}, Xiaoning Zeng⁵, Kirsten L Hargett², Dingyuan I Sun⁶, Lorna T Zlock⁶, Walter E Finkbeiner⁶, Nadav Ahituv^{2

4}, David J Erle^{1

2

3}

Affiliations

¹ Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
² Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.
³ CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA.
⁴ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
⁵ Department of Pulmonary & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
⁶ Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA.

Abstract

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.

Keywords: CRISPRi; HBEC; IL-13; SPDEF; asthma; cell-specific; enhancer.

Abstract

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