Systems Analysis of Transcriptomic and Proteomic Profiles Identifies Novel Regulation of Fibrotic Programs by miRNAs in Pulmonary Fibrosis Fibroblasts
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Culture
2.2. RNA-seq and miRNA-seq Analysis
2.3. Real-Time Reverse Transcription-Polymerase Chain Reaction
2.4. Gene Ontology and Signature Analysis
2.5. miRNA Mimic Transfection and Nanostring Gene Expression Analysis
2.6. Extracellular matrix Proteomic Profiling
3. Results
3.1. Transcriptional Profiling Identified Similar Dysregulated Gene Expression Programs in Idiopathic Pulmonary Fibrosis and Systemic Sclerosis Lung Fibroblasts
3.2. Idiopathic Pulmonary Fibrosis and Systemic Sclerosis Lung Fibroblast Disease Signatures are Associated with Pro-Fibrotic Pathways and Extracellular Matrix
3.3. Global microRNA Profiling Identified Similar Fibrotic microRNA Signatures in Idiopathic Pulmonary Fibrosis and Systemic Sclerosis Lung Fibroblasts
3.4. Differentially Expressed microRNAs in Idiopathic Pulmonary Fibrosis and Systemic Sclerosis Fibroblasts Regulate Expression of Fibrosis-Associated Genes
3.5. Proteomic Profiling Characterized a Distinct Fibrotic Matrisome Deposited by Idiopathic Pulmonary Fibrosis and Systemic Sclerosis Lung Fibroblasts
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Mullenbrock, S.; Liu, F.; Szak, S.; Hronowski, X.; Gao, B.; Juhasz, P.; Sun, C.; Liu, M.; McLaughlin, H.; Xiao, Q.; et al. Systems Analysis of Transcriptomic and Proteomic Profiles Identifies Novel Regulation of Fibrotic Programs by miRNAs in Pulmonary Fibrosis Fibroblasts. Genes 2018, 9, 588. https://doi.org/10.3390/genes9120588
Mullenbrock S, Liu F, Szak S, Hronowski X, Gao B, Juhasz P, Sun C, Liu M, McLaughlin H, Xiao Q, et al. Systems Analysis of Transcriptomic and Proteomic Profiles Identifies Novel Regulation of Fibrotic Programs by miRNAs in Pulmonary Fibrosis Fibroblasts. Genes. 2018; 9(12):588. https://doi.org/10.3390/genes9120588
Chicago/Turabian StyleMullenbrock, Steven, Fei Liu, Suzanne Szak, Xiaoping Hronowski, Benbo Gao, Peter Juhasz, Chao Sun, Mei Liu, Helen McLaughlin, Qiurong Xiao, and et al. 2018. "Systems Analysis of Transcriptomic and Proteomic Profiles Identifies Novel Regulation of Fibrotic Programs by miRNAs in Pulmonary Fibrosis Fibroblasts" Genes 9, no. 12: 588. https://doi.org/10.3390/genes9120588