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Transcriptome network analysis identifies protective role of the LXR/SREBP-1c axis in murine pulmonary fibrosis
Shigeyuki Shichino, Satoshi Ueha, Shinichi Hashimoto, Mikiya Otsuji, Jun Abe, Tatsuya Tsukui, Shungo Deshimaru, Takuya Nakajima, Mizuha Kosugi-Kanaya, Francis H.W. Shand, Yutaka Inagaki, Hitoshi Shimano, Kouji Matsushima
Shigeyuki Shichino, Satoshi Ueha, Shinichi Hashimoto, Mikiya Otsuji, Jun Abe, Tatsuya Tsukui, Shungo Deshimaru, Takuya Nakajima, Mizuha Kosugi-Kanaya, Francis H.W. Shand, Yutaka Inagaki, Hitoshi Shimano, Kouji Matsushima
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Research Article Inflammation Pulmonology

Transcriptome network analysis identifies protective role of the LXR/SREBP-1c axis in murine pulmonary fibrosis

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Abstract

Pulmonary fibrosis (PF) is an intractable disorder with a poor prognosis. Although lung fibroblasts play a central role in PF, the key regulatory molecules involved in this process remain unknown. To address this issue, we performed a time-course transcriptome analysis on lung fibroblasts of bleomycin- and silica-treated murine lungs. We found gene modules whose expression kinetics were associated with the progression of PF and human idiopathic PF (IPF). Upstream analysis of a transcriptome network helped in identifying 55 hub transcription factors that were highly connected with PF-associated gene modules. Of these hubs, the expression of Srebf1 decreased in line with progression of PF and human IPF, suggesting its suppressive role in fibroblast activation. Consistently, adoptive transfer and genetic modification studies revealed that the hub transcription factor SREBP-1c suppressed PF-associated gene expression changes in lung fibroblasts and PF pathology in vivo. Moreover, therapeutic pharmacological activation of LXR, an SREBP-1c activator, suppressed the Srebf1-dependent activation of fibroblasts and progression of PF. Thus, SREBP-1c acts as a protective hub of lung fibroblast activation in PF. Collectively, the findings of the current study may prove to be valuable in the development of effective therapeutic strategies for PF.

Authors

Shigeyuki Shichino, Satoshi Ueha, Shinichi Hashimoto, Mikiya Otsuji, Jun Abe, Tatsuya Tsukui, Shungo Deshimaru, Takuya Nakajima, Mizuha Kosugi-Kanaya, Francis H.W. Shand, Yutaka Inagaki, Hitoshi Shimano, Kouji Matsushima

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Figure 5

SREBP-1c broadly suppresses fibrosis-caused gene expression changes in activated lung fibroblasts.

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SREBP-1c broadly suppresses fibrosis-caused gene expression changes in a...
(A) Experimental scheme of transcriptome analysis of intratracheally transferred genetically modified lung fibroblasts. In total, 2,009 genes were identified as differentially expressed genes as a result of ectopic expression of trSrebf1c. (B) Network of significantly enriched functional terms of the 2,009 genes. Biological events associated with the 2,009 genes were explored and term network was clustered using Cytoscape 3.3.0 with ClueGO and Allegrolayout plugins. Each node and its size represent functional term and enrichment significance, respectively. Red nodes represent functional terms for which genes from upregulated 1,296 genes comprised over 60% of all genes. Blue nodes represent functional terms for which genes from downregulated 713 genes comprised over 60% of all genes. Statistical significance was calculated for each term by using the 2-sided hypergeometric test with the Benjamini-Hochberg correction. (C and D) Details of lipid-related genes (C) and extracellular matrix–related (ECM-related) (D) genes identified by gene ontology network analysis. Each column represents group, whereas each row represents an individual gene. (E and F) qPCR analysis of expression changes of lipid-related (E) and ECM–related (F) genes. Graphs show the mean ± SEM of n = 4 (control) and n = 5 (trSrebf1c). A representative result of 2 independent experiments is shown. *P < 0.05, ***P < 0.001 (2-tailed unpaired Student’s t test). Effect size (d) is shown on the bottom of the graph. Col-GFP, Col1a2-GFP reporter; trSrebf1c active form of Srebf1c; ΔhLNGFR, truncated form of human low-affinity nerve growth factor receptor; SAGE, serial analysis of gene expression.

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