Genome-wide integrative analysis identified SNP-miRNA-mRNA interaction networks in peripheral blood mononuclear cells

Abstract

Aim: To detect SNP-miRNA-mRNA interaction networks and to elucidate miRNA-mediated regulation effects on mRNA expression. Materials & methods: In human peripheral blood mononuclear cells of 43 females, SNP-miRNA-mRNA interaction networks were established through an integrative analysis. Then causal inference test was followed to detect miRNA-mediated effects on mRNA expressions. Results: About 167 trios corresponding to 56 SNPs, 20 miRNAs and 47 target-mRNAs have the SNP-miRNA-mRNA interactions, but only 22 trios have miRNA-mediated effects between SNP and mRNA. For the three miRNAs (hsa-miR-222–3p, hsa-miR-181b-5p and hsa-miR-106b-5p), each mediates at least four correlations between SNP and mRNA. The mRNAs in interaction play an important role in energy metabolism, cellular and tissue homeostasis. Conclusion: This study represents the first effort of constructing an integrative interaction network of SNP-miRNA-mRNA and miRNA-mediated regulatory effects that provide helpful clues for future investigations of peripheral blood mononuclear cell-related physiological process and immunological diseases.

Keywords::

• CIT
• eQTLs
• interaction networks
• miRNAs

Financial & competing interests disclosure

The study was supported by National Natural Science Foundation of China (81473046, 81373010, 81401343, 81541068, 31401079, 31271336, and 31071097), the Natural Science Foundation of Jiangsu Province (BK20130300, BK20150346), the project funded by China Postdoctoral Science Foundation (2014M551649), the Natural Science Research Project of Jiangsu Provincial Higher Education (16KJA330001), the Startup Fund from Soochow University (Q413900112, Q413900712) and a project of the Priority Academic Program Development of Jiangsu Higher Education Institutions. 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.

Supplementary data

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Additional information

Funding

The study was supported by National Natural Science Foundation of China (81473046, 81373010, 81401343, 81541068, 31401079, 31271336, and 31071097), the Natural Science Foundation of Jiangsu Province (BK20130300, BK20150346), the project funded by China Postdoctoral Science Foundation (2014M551649), the Natural Science Research Project of Jiangsu Provincial Higher Education (16KJA330001), the Startup Fund from Soochow University (Q413900112, Q413900712) and a project of the Priority Academic Program Development of Jiangsu Higher Education Institutions. 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.