In Silico Detection and Characterization of microRNAs and Their Target Genes in microRNA Microarray Datasets from Patients with Systemic Sclerosis-Interstitial Lung Disease

DNA and Cell Biology
Yanqi HeYu Chen

Abstract

Interstitial lung disease (ILD) is the main reason of death in patients with systemic sclerosis (SSc). The potential microRNA (miRNA)-messenger RNA (mRNA) interaction networks of SSc-ILD from a systematic biological perspective are unclear. To characterize differentially expressed miRNAs (DE-miRNAs) and differentially expressed genes (DEGs) likely related to SSc-ILD, we downloaded the miRNA microarray dataset (GSE81923) and mRNA datasets (GSE76808 and GSE81292) from the Gene Expression Omnibus database. Comprehensive bioinformatic analyses were conducted to predict target genes for DE-miRNAs and generate an miRNA-hub gene network with SSc-ILD. In total, 26 DE-miRNAs were detected in SSc-ILD, among which 2 were upregulated and 24 were downregulated. Additionally, 178 common DEGs (55 upregulated and 123 downregulated) were identified. miRNAs were primarily enriched in pathways involving inflammation and regulation of fibroblasts. The hub genes identified were MMP7, IER2, HBEGF, CCL4, NFKBIA, JUNB, LIF, SERPINE1, FOSL1, and NAMPT. We discovered the miRNA-mediated regulatory network in SSc-ILD using an integrated bioinformatic analysis. The findings provide novel insight and expand our comprehension of the molecular mechanisms part...Continue Reading

References

Oct 27, 2004·PLoS Biology·Bino JohnDebora S Marks
Apr 6, 2006·Clinical & Developmental Immunology·Bianca MarasiniMaria Luisa Biondi
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Aug 31, 2006·Methods in Enzymology·Mark Reimers, Vincent J Carey
Dec 13, 2006·La Presse médicale·Amélie ServettazLuc Mouthon
Jul 24, 2008·PloS One·Ausra MilanoMichael L Whitfield
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Feb 12, 2010·Annals of the New York Academy of Sciences·Jan Davidson-MoncadaWayne Tam
Apr 17, 2010·American Journal of Respiratory and Critical Care Medicine·Kusum V PanditNaftali Kaminski
Nov 4, 2010·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Nov 11, 2010·Methods in Molecular Biology·Michael KohlBettina Warscheid
May 7, 2011·Arthritis and Rheumatism·Michael D RothUNKNOWN Scleroderma Lung Study Research Group
Dec 14, 2011·Laboratory Investigation; a Journal of Technical Methods and Pathology·Jordan R OliverJim Hu
Mar 22, 2012·Cell and Tissue Research·Outi LeppärantaKatri Koli
Jun 1, 2012·Nucleic Acids Research·Ioannis S VlachosArtemis G Hatzigeorgiou
Aug 23, 2012·PloS One·Subbiah RajasekaranSekhar P Reddy
Dec 21, 2012·Human Pathology·Elisa Lappi-BlancoRiitta L Kaarteenaho
Aug 3, 2013·Nature Reviews. Immunology·Dirk Baumjohann, K Mark Ansel
Jun 24, 2014·The International Journal of Biochemistry & Cell Biology·Barbara BerschneiderMelanie Königshoff
Nov 8, 2014·Nucleic Acids Research·Nathan Wong, Xiaowei Wang
Dec 19, 2014·BMC Systems Biology·Chia-Hao ChinChung-Yen Lin
Jan 22, 2015·Current Rheumatology Reports·Swati Bhattacharyya, John Varga
Apr 4, 2015·Genes & Development·Fotini M KouriAlexander H Stegh
Jan 20, 2016·The Journal of Dermatology·Takamitsu Makino, Masatoshi Jinnin
Jul 6, 2016·Arthritis Research & Therapy·Romy B ChristmannRobert Lafyatis
Sep 18, 2016·International Journal of Dermatology·Saeideh Jafarinejad-FarsangiAhmad Reza Jamshidi
Jan 1, 2017·Clinical Immunology : the Official Journal of the Clinical Immunology Society·Nicholas A YoungWael N Jarjour
May 19, 2017·European Respiratory Review : an Official Journal of the European Respiratory Society·Gianluca BagnatoSebastiano Gangemi
Apr 19, 2018·Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology·Xinliu ZengYajie Li
Oct 12, 2018·Nature Reviews. Rheumatology·Chiara AngiolilliTimothy R D J Radstake

❮ Previous
Next ❯

Citations

Jun 12, 2020·Therapeutic Advances in Musculoskeletal Disease·Bianca Saveria FiorettoMarco Matucci-Cerinic

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE81293
GSE76808
GSE81292
GPL18991
GPL571
GPL16384

Methods Mentioned

BETA
biopsy

Software Mentioned

DIANA miRPath
Bioconductor
STRING
Cytoscape
cytoHubba
R
mirSVR
Search Tool for the Retrieval of ( STRING
ggplot2
miRanda

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.