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

Cell Genomics (Jan 2023)

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

Journal volume & issue: Vol. 3, no. 1
p. 100229

Abstract

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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.

Published in Cell Genomics

ISSN: 2666-979X (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Biology (General): Genetics; Medicine: Internal medicine
Website: https://www.cell.com/cell-genomics/home

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