Construction of a lncRNA–miRNA–mRNA Network to Determine the Key Regulators of the Th1/Th2 Imbalance in Multiple Sclerosis

Abstract

Aim: The exact epigenetic mechanisms that determine the balance of T helper (Th)1 and Th2 cells and autoimmune responses in multiple sclerosis (MS) remain unclear. We aim to clarify these. Methods: A combination of bioinformatics analysis and molecular evaluations was utilized to identify master hub genes. Results: A competitive endogenous RNA network containing six long noncoding RNAs (lncRNAs), 21 miRNAs and 86 mRNAs was provided through enrichment analysis and a protein–protein interaction network. NEAT1 and MALAT1 were found as differentially expressed lncRNAs using Gene Expression Omnibus (GSE21942). Quantitative real-time PCR results demonstrate dysregulation in the RUNX3 (a regulator of Th1/Th2 balance), GATA3 and TBX21, as well as miR-544a and miR-210-3p (which directly targetRUNX3). ELISA also confirmed an imbalance in IFN-γ (Th1)/IL-4 (Th2) in MS patients. Conclusion: Our findings introduce novel biomarkers leading to Th1/Th2 imbalance in MS.

Lay abstract

Studies have shown that irregular control of noncoding RNAs (ncRNAs) in immune responses can lead to multiple sclerosis. T helper (Th)1 and Th2 cells balance plays an important role in regulating inflammation in this disease. In this study, to investigate the molecular factors that may disrupt this balance, we investigated the role of ncRNAs. Our results suggest that miR-210-3p and miR-544a irregularities can disrupt the Th1/Th2 balances through targeting the RUNX3 gene, which consequently leads to IFNγ/IL4 imbalance. It is also clarified that NEAT1 and MALAT1 long noncoding RNAs also have a role in this imbalance exerting their effect through miR-210-3p and miR-544a. This molecular pathway may provide significant information on multiple sclerosis disease development.

Graphical abstract

Keywords::

• ceRNA network
• miR-210-3p
• miR-544a
• multiple sclerosis
• real-time PCR
• RUNX3
• Th1/Th2 imbalance

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2021-0296

Author contributions

H Azari: conceptualization, methodology, investigation and writing original draft; E Karimi: investigation and writing original draft; A Tahmasebi: software and formal analysis; A Nikpoor: formal analysis and methodology; AA Negahi: resources; M Shekari: supervision; N Sanadgol: review and editing and P Mousavi: supervision, data curation, review and editing.

Acknowledgments

The authors would like to thank the patients and staff of Special Diseases Center Abu Rayhan, Shahid Mohammadi Hospital in Bandar Abbas, Iran.

Financial & competing interests disclosure

This work has been supported by grant 980044 from the office of the Vice-Chancellor for Research, the Hormozgan University of Medical Sciences, Bandar Abbas, Iran. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval from the Local Medical Ethics Committee (IR.HUMS.REC.1398.030). In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This work has been supported by grant 980044 from the office of the Vice-Chancellor for Research, the Hormozgan University of Medical Sciences, Bandar Abbas, Iran. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.