Involvement of lncRNA MIR205HG in idiopathic pulmonary fibrosis and IL-33 regulation via Alu elements
Tsuyoshi Takashima, Chao Zeng, Eitaro Murakami, Naoko Fujiwara, Masaharu Kohara, Hideki Nagata, Zhaozu Feng, Ayako Sugai, Yasue Harada, Rika Ichijo, Daisuke Okuzaki, Satoshi Nojima, Takahiro Matsui, Yasushi Shintani, Gota Kawai, Michiaki Hamada, Tetsuro Hirose, Kazuhiko Nakatani, Eiichi Morii
Tsuyoshi Takashima, Chao Zeng, Eitaro Murakami, Naoko Fujiwara, Masaharu Kohara, Hideki Nagata, Zhaozu Feng, Ayako Sugai, Yasue Harada, Rika Ichijo, Daisuke Okuzaki, Satoshi Nojima, Takahiro Matsui, Yasushi Shintani, Gota Kawai, Michiaki Hamada, Tetsuro Hirose, Kazuhiko Nakatani, Eiichi Morii
View: Text | PDF
Research Article Inflammation Pulmonology

Involvement of lncRNA MIR205HG in idiopathic pulmonary fibrosis and IL-33 regulation via Alu elements

Abstract

Idiopathic pulmonary fibrosis (IPF) causes remodeling of the distal lung. Pulmonary remodeling is histologically characterized by fibrosis, as well as appearance of basal cells; however, the involvement of basal cells in IPF remains unclear. Here, we focus on the long noncoding RNA MIR205HG, which is highly expressed in basal cells, using RNA sequencing. Through RNA sequencing of genetic manipulations using primary cells and organoids, we discovered that MIR205HG regulates IL-33 expression. Mechanistically, the AluJb element of MIR205HG plays a key role in IL-33 expression. Additionally, we identified a small molecule that targets the AluJb element, leading to decreased IL-33 expression. IL-33 is known to induce type 2 innate lymphoid cells (ILC2s), and we observed that MIR205HG expression was positively correlated with the number of ILC2s in patients with IPF. Collectively, these findings provide insights into the mechanisms by which basal cells contribute to IPF and suggest potential therapeutic targets.

Authors

Tsuyoshi Takashima, Chao Zeng, Eitaro Murakami, Naoko Fujiwara, Masaharu Kohara, Hideki Nagata, Zhaozu Feng, Ayako Sugai, Yasue Harada, Rika Ichijo, Daisuke Okuzaki, Satoshi Nojima, Takahiro Matsui, Yasushi Shintani, Gota Kawai, Michiaki Hamada, Tetsuro Hirose, Kazuhiko Nakatani, Eiichi Morii

×

Figure 7

Downregulation of MIR205HG decreases IL33 mRNA and IL-33 protein expression in basal cells.

Options: View larger image (or click on image) Download as PowerPoint
Downregulation of MIR205HG decreases IL33 mRNA and IL-33 protein express...
(A) Experimental procedure for the identification of genes positively regulated by MIR205HG in NHBE cells using the CRISPR interference/dCas9-KRAB (CRISPR/dCas9) system. (B) qRT-PCR showing MIR205HG expression in NV and MIR205HG-KD NHBE cells. NC, negative control. (C) Cell growth assay in NV and MIR205HG-KD NHBE cells. (D) Venn diagram showing downregulated genes in MIR205HG-KD NHBE cells (bulk RNA-Seq, left) and basal cell enriched genes in Figure 1D (scRNA-Seq, right). The cutoff values were log2FC > 1 (bulk RNA-Seq and scRNA-Seq). Two common mRNAs are listed below. (E) Heatmap showing common mRNAs that are downregulated genes in MIR205HG-KD NHBE cells and basal cell enriched genes shown in D. Fragments per kilobase of exon per million mapped fragment (FPKM) > 0.5 mRNAs were visualized. (F) qRT-PCR showing IL33 mRNA expression in NV and MIR205HG-KD NHBE cells. (G) Western blot showing IL-33 protein expression in NV and MIR205HG-KD NHBE cells. (H) Schematic of experimental design for identification of MIR205HG-regulated genes in IPF patient–derived airway organoids using the CRISPR/dCas9 system. (I) qRT-PCR showing MIR205HG expression in NV and MIR205HG-KD IPF patient–derived airway organoids. (J) qRT-PCR showing IL33 mRNA expression in NV and MIR205HG-KD of IPF patient–derived airway organoids. (K) Volcano plot of DEGs in MIR205HG– basal cell and MIR205HG+ basal cell in public scRNA-Seq data (GSE136831). The cutoff values were log2FC > 1, FDR < 0.05. (L) Representative images of MIR205HG ISH and IL-33 IHC staining in patients with IPF. Scale bar: 10 μm. (B, C, F, I, and J) Data represent mean ± SD. *P < 0.05, **P < 0.01, ***P < 0.001; P values were determined by 1-way ANOVA with Holm-Šídák post hoc test.