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Comprehensive exploration of the effects of miRNA SNPs on monocyte gene expression
Nicolas Greliche1, Tanja Zeller, Philipp S Wild
1INSERM UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France.
Abstract:
We aimed to assess whether pri-miRNA SNPs (miSNPs) could influence monocyte gene expression, either through marginal association or by interacting with polymorphisms located in 3'UTR regions (3utrSNPs). We then conducted a genome-wide search for marginal miSNPs effects and pairwise miSNPs × 3utrSNPs interactions in a sample of 1,467 individuals for which genome-wide monocyte expression and genotype data were available. Statistical associations that survived multiple testing correction were tested for replication in an independent sample of 758 individuals with both monocyte gene expression and genotype data. In both studies, the hsa-mir-1279 rs1463335 was found to modulate in cis the expression of LYZ and in trans the expression of CNTN6, CTRC, COPZ2, KRT9, LRRFIP1, NOD1, PCDHA6, ST5 and TRAF3IP2 genes, supporting the role of hsa-mir-1279 as a regulator of several genes in monocytes. In addition, we identified two robust miSNPs × 3utrSNPs interactions, one involving HLA-DPB1 rs1042448 and hsa-mir-219-1 rs107822, the second the H1F0 rs1894644 and hsa-mir-659 rs5750504, modulating the expression of the associated genes.As some of the aforementioned genes have previously been reported to reside at disease-associated loci, our findings provide novel arguments supporting the hypothesis that the genetic variability of miRNAs could also contribute to the susceptibility to human diseases.
Insights
Genetic variations in primary microRNA (pri-miRNA) single nucleotide polymorphisms (SNPs) influence monocyte gene expression. These microRNA SNPs (miSNPs) can act alone or interact with 3' untranslated region (3utr) SNPs, impacting disease susceptibility.
Area of Science:
- Genetics
- Molecular Biology
- Immunology
Background:
- Single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, termed miSNPs, are increasingly recognized for their regulatory roles.
- Understanding how miSNPs affect gene expression in immune cells like monocytes is crucial for deciphering disease mechanisms.
Purpose of the Study:
- To investigate whether pri-miRNA SNPs (miSNPs) influence monocyte gene expression.
- To explore both marginal effects of miSNPs and their interactions with polymorphisms in 3' untranslated regions (3utrSNPs).
Main Methods:
- Genome-wide association study (GWAS) for marginal miSNP effects and miSNP × 3utrSNP interactions in monocytes.
- Utilized gene expression and genotype data from 1,467 individuals.
- Replication analysis in an independent cohort of 758 individuals.
Main Results:
- Identified hsa-mir-1279 rs1463335 as a modulator of LYZ (in cis) and several other genes (in trans) in monocytes.
- Discovered two significant miSNP × 3utrSNP interactions involving HLA-DPB1 rs1042448/hsa-mir-219-1 rs107822 and H1F0 rs1894644/hsa-mir-659 rs5750504.
- The identified genes are implicated in disease-associated loci.
Conclusions:
- Genetic variability in miRNAs significantly impacts monocyte gene expression.
- miRNA genetic variations, including interactions with 3utrSNPs, may contribute to human disease susceptibility.
- Findings highlight the functional relevance of miSNPs in immune cell regulation.
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