scholarly journals Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts: A Next-Generation Sequencing and Bioinformatics Study

2019 ◽  
Vol 8 (3) ◽  
pp. 308 ◽  
Author(s):  
Chau-Chyun Sheu ◽  
Wei-An Chang ◽  
Ming-Ju Tsai ◽  
Ssu-Hui Liao ◽  
Inn-Wen Chong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Next Generation Sequencing ◽  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Protein Interactions ◽  
Next Generation ◽  
Protein Protein Interactions ◽  
Bioinformatics Study ◽  
Generation Sequencing

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal interstitial lung disease. Therapeutic options for IPF remain limited. Nintedanib, a tyrosine kinase inhibitor approved for IPF treatment, is known to inhibit fibroblasts proliferation, migration and transformation to myofibroblasts. However, how nintedanib changes gene regulations in IPF has never been systematically investigated. We conducted a next-generation sequencing and bioinformatics study to evaluate the changes of mRNA and miRNA profiles in IPF fibroblasts treated with 2 µM and 4 µM nintedanib, compared to those without treatment. We identified 157 upregulated and 151 downregulated genes and used STRING and DAVID databases for analysis of protein–protein interactions, biological pathways, and molecular functions. We found strong protein–protein interactions within these dysregulated genes, mostly involved in the pathways of cell cycle and mitotic cell cycle. We also discovered 13 potential miRNA–mRNA interactions associated with nintedanib treatment. After validation using miRDB, TargetScan, and RT-qPCR, we identified 4 downregulated genes (DDX11, E2F1, NPTX1, and PLXNA4) which might be repressed by the upregulated hsa-miR-486-3p. According to the proposed functions of DDX11, E2F1, and PLXNA4 reported in previous studies, these gene expression changes together might contribute to decreased proliferation of fibroblasts and decreased angiogenesis in the microenvironment of IPF. Our findings need further studies to confirm.

scholarly journals The Potential Effects of Curcumin on Pulmonary Fibroblasts of Idiopathic Pulmonary Fibrosis (IPF)—Approaching with Next-Generation Sequencing and Bioinformatics

Molecules ◽  
2020 ◽  
Vol 25 (22) ◽  
pp. 5458
Author(s):  
Wei-An Chang ◽  
Chia-Min Chen ◽  
Chau-Chyun Sheu ◽  
Ssu-Hui Liao ◽  
Ya-Ling Hsu ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Next Generation Sequencing ◽  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Cell Cycle Progression ◽  
Next Generation ◽  
Protein Coding ◽  
Cycle Arrest ◽  
Depth Study ◽  
Generation Sequencing

Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial lung disease. Currently, therapeutic options are limited for this fatal disease. Curcumin, with its pleiotropic effects, has been studied for its potential therapeutic utilities in various diseases, including pulmonary fibrosis. However, the detailed mechanisms have not been studied comprehensively. We conducted a next-generation sequencing and bioinformatics study to investigate changes in the profiles of mRNA and microRNA after curcumin treatment in IPF fibroblasts. We identified 23 downregulated and 8 upregulated protein-coding genes in curcumin-treated IPF fibroblasts. Using STRING and IPA, we identified that suppression of cell cycle progression was the main cellular function associated with these differentially expressed genes. We also identified 13 downregulated and 57 upregulated microRNAs in curcumin-treated IPF fibroblasts. Further analysis identified a potential microRNA-mediated gene expression alteration in curcumin-treated IPF fibroblasts, namely, downregulated hsa-miR-6724-5p and upregulated KLF10. Therefore, curcumin might decrease the level of hsa-miR-6724-5p, leading to increased KLF10 expression, resulting in cell cycle arrest in curcumin-treated IPF fibroblasts. In conclusion, our findings might support the potential role of curcumin in the treatment of IPF, but further in-depth study is warranted to confirm our findings.

scholarly journals Next-Generation Sequencing for Binary Protein–Protein Interactions

2015 ◽  
Vol 6 ◽  
Author(s):  
Bernhard Suter ◽  
Xinmin Zhang ◽  
C. Gustavo Pesce ◽  
Andrew R. Mendelsohn ◽  
Savithramma P. Dinesh-Kumar ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Protein Interactions ◽  
Next Generation ◽  
Protein Protein Interactions ◽  
Generation Sequencing

scholarly journals Paired genetic analysis by next‐generation sequencing of lung cancer and associated idiopathic pulmonary fibrosis

2020 ◽  
Vol 111 (7) ◽  
pp. 2482-2487
Author(s):  
Kohei Otsubo ◽  
Eiji Iwama ◽  
Kayo Ijichi ◽  
Naoki Kubo ◽  
Yasuto Yoneshima ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Genetic Analysis ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals The Effects of Epigallocatechin Gallate (EGCG) on Pulmonary Fibroblasts of Idiopathic Pulmonary Fibrosis (IPF)—A Next-Generation Sequencing and Bioinformatic Approach

2019 ◽  
Vol 20 (8) ◽  
pp. 1958 ◽  
Author(s):  
Ming-Ju Tsai ◽  
Wei-An Chang ◽  
Ssu-Hui Liao ◽  
Kuo-Feng Chang ◽  
Chau-Chyun Sheu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Next Generation Sequencing ◽  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Epigallocatechin Gallate ◽  
Differentially Expressed ◽  
Pulmonary Fibroblasts ◽  
Generation Sequencing

Idiopathic pulmonary fibrosis (IPF) is a disabling and lethal chronic progressive pulmonary disease. Epigallocatechin gallate (EGCG) is a polyphenol, which is the major biological component of green tea. The anti-oxidative, anti-inflammatory, and anti-fibrotic effects of EGCG have been shown in some studies, whereas its effects in altering gene expression in pulmonary fibroblasts have not been systematically investigated. This study aimed to explore the effect of EGCG on gene expression profiles in fibroblasts of IPF. The pulmonary fibroblasts from an IPF patient were treated with either EGCG or water, and the expression profiles of mRNAs and microRNAs were determined by next-generation sequencing (NGS) and analyzed with the bioinformatics approach. A total of 61 differentially expressed genes and 56 differentially expressed microRNAs were found in EGCG-treated IPF fibroblasts. Gene ontology analyses revealed that the differentially expressed genes were mainly involved in the biosynthetic and metabolic processes of cholesterol. In addition, five potential altered microRNA–mRNA interactions were found, including hsa-miR-939-5p–PLXNA4, hsa-miR-3918–CTIF, hsa-miR-4768-5p–PDE5A, hsa-miR-1273g-3p–VPS53, and hsa-miR-1972–PCSK9. In summary, differentially expressed genes and microRNAs in response to EGCG treatment in IPF fibroblasts were identified in the current study. Our findings provide a scientific basis to evaluate the potential benefits of EGCG in IPF treatment, and warrant future studies to understand the role of molecular pathways underlying cholesterol homeostasis in the pathogenesis of IPF.

scholarly journals Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows

PLoS ONE ◽  
2011 ◽  
Vol 6 (7) ◽  
pp. e22953 ◽  
Author(s):  
Stefan Siebert ◽  
Mark D. Robinson ◽  
Sophia C. Tintori ◽  
Freya Goetz ◽  
Rebecca R. Helm ◽  
...  
Keyword(s):  
Gene Expression ◽  
Next Generation Sequencing ◽  
Differential Gene Expression ◽  
Next Generation ◽  
Differential Gene ◽  
Generation Sequencing

scholarly journals DNA Methylation Landscape of 16 Canine Somatic Tissues by Methylation-Sensitive Restriction Enzyme-Based Next Generation Sequencing

2021 ◽  
Author(s):  
Jumpei Yamazaki ◽  
Yuki Matsumoto ◽  
Jaroslav Jelinek ◽  
Teita Ishizaki ◽  
Shingo Maeda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Next Generation Sequencing ◽  
Restriction Enzyme ◽  
Companion Animals ◽  
Next Generation ◽  
Cpg Sites ◽  
Somatic Tissues ◽  
Methylation Sensitive Restriction Enzyme ◽  
Generation Sequencing

Abstract Background: DNA methylation plays important functions in gene expression regulation that is involved in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in companion animals like dog. Results: Using methylation-sensitive restriction enzyme-based next generation sequencing (Canine DREAM), we obtained canine DNA methylation maps from 16 somatic tissues. In total, we evaluated 130,861 CpG sites. The majority of CpG sites were either highly methylated (>70%, 52.5%-64.6% of all CpG sites analyzed) or unmethylated (<30%, 22.5%-28.0% of all CpG sites analyzed) which are methylation patterns similar to other species. The overall methylation status of CpG sites across the 32 methylomes were remarkably similar. However, the tissue types were clearly defined by principle component analysis and hierarchical clustering analysis with DNA methylome. We found 6416 CpG sites located closely at promoter region of genes and inverse correlation between DNA methylation and gene expression of these genes. Conclusions: Our study provides basic dataset for DNA methylation profiles in dogs.

243 GENE EXPRESSION PROFILING BY NEXT-GENERATION SEQUENCING OF cDNA SAMPLES FROM INNER CELL MASS AND TROPHECTODERM OF A SINGLE-DAY 12 PORCINE EMBRYO

2010 ◽  
Vol 22 (1) ◽  
pp. 279
Author(s):  
S. C. Isom ◽  
R. S. Prather
Keyword(s):  
Gene Expression ◽  
Next Generation Sequencing ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Cdna Fragments ◽  
Generation Sequencing

Traditional microarray approaches to gene expression profiling often require RNA or cDNA amplification when working with extremely small or valuable tissue samples.This process is generally viewed as being undesirable because there is potential for bias to be introduced during amplification. Very recently, the so-called next-generation sequencing technologies were adapted for use in global gene expression profiling. Herein we report our efforts to apply these sequencing technologies to assess relative transcript abundances in pre-implantation-stage porcine embryos, without additional nucleic acid amplification before sequencing. As a proof-of-principle experiment, we have isolated total RNA from the embryonic disc (inner cell mass; ICM) and a small piece of trophectoderm (TE) from a Day 12 in vivo-produced embryo, which were estimated to be composed of 500 to 1000 cells each. The RNA was reverse transcribed using oligo-dT priming followed by second-strand cDNA synthesis. The double-stranded cDNA was then randomly sheared by sonication, and 10 ng of double-stranded cDNA fragments was used for sample preparation before sequencing. Prepared cDNA fragments (at 7 picomolar concentrations) were submitted for sequencing using the Illumina/Solexa platform as recommended. The millions of short (36 bp) reads generated by Illumina sequencing for each sample were then aligned to the swine UniGene database from NCBI, allowing for zero or one mismatches. Relative transcript abundances between cell types were profiled by considering the read counts for a given UniGene member as a percentage of the total number of reads generated for each cell type. It was demonstrated that approximately 11 000 and 9000 UniGene members were represented by a normalized average of 5 or more short reads per lane (0.001% of the total) in the ICM and TE samples, respectively. As expected, pluripotency factors, chromatin remodeling components, and cell-cell communication molecules were overrepresented in the ICM sample as compared with the TE sample. Conversely, epithelial determinants, ion transporters, and components of the steroid biosynthesis pathways were more abundant in the TE sample than in the ICM sample. Relative abundances of representative transcripts in these samples were verified by quantitative RT-PCR. In conclusion, we demonstrate the utility of next-generation sequencing technologies for gene expression profiling using even minute tissue samples and show that such analyses are possible even in species without a sequenced genome.

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