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Published on: April 12, 2015
An innovative approach to predict immune-associated genes mutually targeted by cow and human milk microRNAs
Kaj Chokeshaiusaha1, Thanida Sananmuang1, Denis Puthier2
1Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand.
Aim:
Milk is rich in miRNAs - the endogenous small non-coding RNA responsible for gene post-transcriptional silencing. Milk miRNAs were previously evidenced to affect consumer's immune response. While most studies relied on a few well-characterized milk miRNAs to relate their immunoregulatory roles on target genes among mammals, this study introduced a procedure to predict the target genes based on overall milk miRNA expression profiles - the miRNome data of cow and human.
Materials And Methods:
Cow and human milk miRNome expression datasets of cow and human milk lipids at 2, 4, and 6 months of lactation periods were preprocessed and predicted for their target genes using TargetScanHuman. Enrichment analysis was performed using target genes to extract the immune-associated gene ontology (GO) terms shared between the two species. The genes within these terms with more than 50 different miRNAs of each species targeting were selected and reviewed for their immunological functions.
Results:
A total of 146 and 129 miRNAs were identified in cow and human milk with several miRNAs reproduced from other previous reports. Enrichment analysis revealed nine immune-related GO terms shared between cow and human (adjusted p≤0.01). There were 14 genes related to these terms with more than 50 miRNA genes of each species targeting them. These genes were evidenced for their major roles in lymphocyte stimulation and differentiation.
Conclusion:
A novel procedure to determine mutual immune-associated genes targeted by milk miRNAs was demonstrated using cow and human milk miRNome data. As far as we know, this was the 1st time that milk miRNA target genes had been identified based on such cross-species approach. Hopefully, the introduced strategy should hereby facilitate a variety of cross-species miRNA studies in the future.
Insights
This study introduces a novel cross-species method to identify immune-related genes targeted by milk microRNAs (miRNAs) using cow and human milk miRNome data, revealing key genes involved in lymphocyte function.
Area of Science:
- * Molecular Biology
- * Immunology
- * Bioinformatics
Background:
- * Milk contains microRNAs (miRNAs), small non-coding RNAs that regulate gene expression post-transcriptionally.
- * Milk miRNAs are known to influence the consumer's immune response.
- * Previous research focused on a limited number of well-characterized milk miRNAs and their target genes.
Purpose of the Study:
- * To develop a novel procedure for predicting target genes based on comprehensive milk miRNA expression profiles (miRNome data).
- * To identify shared immune-associated genes targeted by milk miRNAs across species (cow and human).
- * To investigate the immunological functions of these cross-species identified target genes.
Main Methods:
- * Cow and human milk miRNome datasets from different lactation stages were analyzed.
- * Target genes were predicted using TargetScanHuman.
- * Enrichment analysis identified shared immune-associated Gene Ontology (GO) terms between species, followed by selection and review of specific target genes.
Main Results:
- * Identified 146 miRNAs in cow milk and 129 miRNAs in human milk.
- * Discovered nine immune-related GO terms common to both cow and human milk (adjusted p≤0.01).
- * Selected 14 genes within these terms targeted by over 50 miRNAs from each species, demonstrating roles in lymphocyte stimulation and differentiation.
Conclusions:
- * A novel cross-species procedure for identifying mutual immune-associated genes targeted by milk miRNAs was successfully demonstrated.
- * This study represents the first identification of milk miRNA target genes using a cross-species approach.
- * The developed strategy is expected to advance future cross-species miRNA research.
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