Reversing Mechanoinductive DSP Expression by CRISPR/dCas9-mediated Epigenome Editing

• Published in: American journal of respiratory and critical care medicine 2018-09, Vol.198 (5), p.599-609
• Main Authors: Qu, Jing, Zhu, Lanyan, Zhou, Zijing, Chen, Ping, Liu, Shuyan, Locy, Morgan L, Thannickal, Victor J, Zhou, Yong
• Format: Article
• Language: English
• Subjects: Animals; Cancer; Cardiomyopathy; Clustered Regularly Interspaced Short Palindromic Repeats; CRISPR; Deoxyribonucleic acid; Desmoplakins - genetics; Disease Models, Animal; DNA; DNA methylation; DNA Methylation - genetics; DNA Methyltransferase 3A; Epigenetics; Epigenomics - methods; Fibroblasts; Gene Editing - methods; Gene expression; Genome-Wide Association Study - methods; Genomes; Humans; Idiopathic Pulmonary Fibrosis - genetics; Mice; Mice, Inbred C57BL; Mutation; Pathogenesis; Proteins; Pulmonary fibrosis; Rats; Statistical analysis; Transcription factors
• ISSN: 1073-449X; 1535-4970
• DOI: 10.1164/rccm.201711-2242oc

DSP (desmoplakin), the most abundant component of desmosomes, which maintain the mechanical integrity of epithelium, is a genome-wide association study-identified genetic risk locus in human idiopathic pulmonary fibrosis (IPF). Subjects with IPF express a significantly higher level of DSP than control subjects. Determine potential mechanisms by which DSP is regulated in lung fibrosis. Matrigel-coated soft and stiff polyacrylamide gels were made to simulate the stiffness of normal and fibrotic lungs. Quantitative chromatin immunoprecipitation and electrophoretic mobility shift assay were used to evaluate transcription factor binding to the DSP promoter. Targeted DNA methylation was achieved by CRISPR (clustered regularly interspaced short palindromic repeats)/dCas9 (deactivated CRISPR-associated protein-9 nuclease)-mediated Dnmt3A (DNA methyltransferase 3A) expression under the guidance of sequence-specific single guide RNAs. Stiff matrix promotes DSP gene expression in both human and rodent lung epithelial cells as compared with soft matrix. A conserved region in the proximal DSP promoter is hypermethylated under soft matrix conditions and becomes hypomethylated/demethylated under stiff matrix conditions. Demethylation of this conserved DSP promoter region is associated with transactivation of transcription factor EGR1 (early growth response protein 1), resulting in EGR1-dependent DSP overexpression. Targeted DNA methylation by CRISPR/dCas9/Dnmt3A-mediated epigenome editing blocks EGR1 binding to the DSP promoter and inhibits stiff matrix-induced DSP overexpression. DSP is a matrix stiffness-regulated mechanosensitive gene. CRISPR/dCas9-Dnmt3A-mediated epigenome editing reverses DSP overexpression by reestablishment of the epigenetic control of DSP under the mechanically homeostatic environment. It provides a useful tool for investigations of the functional role of DSP in the pathogenesis of lung fibrosis.