|
| Status |
Public on Jul 31, 2019 |
| Title |
MicroRNA and mRNA profiling in the idiopathic inflammatory myopathies |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Objectives: The idiopathic inflammatory myopathies (IIMs) are heterogeneous autoimmune conditions of skeletal muscle inflammation and weakness. MicroRNAs (miRNAs) are short, non-coding RNA which regulate gene expression of target mRNAs. The aim of this study was to profile miRNA and mRNA in IIM and identify miRNA-mRNA relationships which may be relevant to disease.
Materials and methods: mRNA and miRNA in whole blood samples from 7 polymyositis (PM), 7 dermatomyositis (DM), 5 inclusion body myositis (IBM) and 5 non-myositis controls was profiled using next generation RNA sequencing. Gene ontology and pathway analyses were performed using GOseq and Ingenuity Pathway Analysis. Dysregulation of miRNAs and opposite dysregulation of predicted target mRNAs in IIM subgroups was validated using RTqPCR and investigated by transfecting human skeletal muscle cells with miRNA mimic.
Results Analysis of differentially expressed genes showed that interferon signalling and anti-viral response pathways were upregulated in PM and DM compared to controls. An anti-Jo1 autoantibody positive subset of PM and DM (n=5) had more significant upregulation and predicted activation of interferon signalling and highlighted T-helper (Th1 and Th2) cell pathways. In miRNA profiling miR-96-5p was significantly upregulated in PM, DM and the anti-Jo1positive subset. RTqPCR replicated miR-96-5p upregulation and predicted mRNA target (ADK, CD28 and SLC4A10) downregulation. Transfection of a human skeletal muscle cell line with miR-96-5p mimic resulted in significant downregulation of ADK.
Conclusion: MiRNA and mRNA profiling identified dysregulation of interferon signalling, anti-viral response and T-helper cell pathways, and indicates a possible role for miR-96-5p regulation of ADK in pathogenesis of IIM.
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| |
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| Overall design |
Whole blood microRNA and mRNA profiles of idiopathic inflammatory myopathy patients compared to controls generated by RNA sequencing, using Illumina HiSeq 4000
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| |
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| Contributor(s) |
Parkes JE, Lamb JA, Chinoy H, Day PJ |
| Citation(s) |
32529172 |
| |
| Submission date |
Jan 31, 2019 |
| Last update date |
Jun 16, 2020 |
| Contact name |
Joanna Parkes |
| E-mail(s) |
jparkes@binghamton.edu
|
| Organization name |
Binghamton University
|
| Department |
School of Pharmacy and Pharmaceutical Sciences
|
| Street address |
Pharmacy Building
|
| City |
Johnson City |
| State/province |
NY |
| ZIP/Postal code |
13790 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
|
| Samples (48)
|
|
| Relations |
| BioProject |
PRJNA518143 |
| SRA |
SRP183096 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE125977_mRNA_all_jo1_vs_controls_DESeq2.xls.gz |
5.0 Mb |
(ftp)(http) |
XLS |
| GSE125977_mRNA_and_miRNA_metadata.xls.gz |
33.9 Kb |
(ftp)(http) |
XLS |
| GSE125977_mRNA_star_DM_vis_CONTROL_Wald_DESeq2.xls.gz |
5.8 Mb |
(ftp)(http) |
XLS |
| GSE125977_mRNA_star_IBM_vis_CONTROL_Wald_DESeq2.xls.gz |
5.3 Mb |
(ftp)(http) |
XLS |
| GSE125977_mRNA_star_PM_vis_CONTROL_Wald_DESeq2.xls.gz |
5.9 Mb |
(ftp)(http) |
XLS |
| GSE125977_microRNA_all_jo1_vs_controls_DESeq2.xls.gz |
100.2 Kb |
(ftp)(http) |
XLS |
| GSE125977_microRNA_star_DM_vis_CONTROL_Wald_DESeq2.xls.gz |
117.1 Kb |
(ftp)(http) |
XLS |
| GSE125977_microRNA_star_IBM_vis_CONTROL_Wald_DESeq2.xls.gz |
110.0 Kb |
(ftp)(http) |
XLS |
| GSE125977_microRNA_star_PM_vis_CONTROL_Wald_DESeq2.xls.gz |
121.8 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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