Uptake of dietary milk miRNAs by adult humans: a validation study

Breast milk is replete with nutritional content as well as nucleic acids including microRNAs (miRNAs). In a recent report, adult humans who drank bovine milk appeared to have increased circulating levels of miRNAs miR-29b-3p and miR-200c-3p. Since these miRNAs are homologous between human and cow, these results could be explained by xeno-miRNA influx, endogenous miRNA regulation, or both. More data were needed to validate the results and explore for additional milk-related alterations in circulating miRNAs. Samples from the published study were obtained, and 223 small RNA features were profiled with a custom OpenArray, followed by individual quantitative PCR assays for selected miRNAs. Additionally, small RNA sequencing (RNA-seq) data obtained from plasma samples of the same project were analyzed to find human and uniquely bovine miRNAs. OpenArray revealed no significantly altered miRNA signals after milk ingestion, and this was confirmed by qPCR. Plasma sequencing data contained no miR-29b or miR-200c reads and no intake-consistent mapping of uniquely bovine miRNAs. In conclusion, the results do not support transfer of dietary xenomiRs into the circulation of adult humans.

[1]  M. Halushka,et al.  Dataset: Uptake of dietary milk miRNAs by adult humans: a validation study , 2016 .

[2]  M. Halushka,et al.  A benchmark for microRNA quantification algorithms using the OpenArray platform , 2016, BMC Bioinformatics.

[3]  Jens Allmer,et al.  One Step Forward, Two Steps Back; Xeno-MicroRNAs Reported in Breast Milk Are Artifacts , 2016, PloS one.

[4]  K. Witwer.  Contamination or artifacts may explain reports of plant miRNAs in humans. , 2015, The Journal of nutritional biochemistry.

[5]  Akhilesh Pandey,et al.  miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy , 2015, PloS one.

[6]  J. Zempleni,et al.  Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation , 2015, PloS one.

[7]  J. Zempleni,et al.  The Intestinal Transport of Bovine Milk Exosomes Is Mediated by Endocytosis in Human Colon Carcinoma Caco-2 Cells and Rat Small Intestinal IEC-6 Cells. , 2015, The Journal of nutrition.

[8]  M. Stoffel,et al.  Uptake and Function Studies of Maternal Milk-derived MicroRNAs* , 2015, The Journal of Biological Chemistry.

[9]  Anton J. Enright,et al.  Chimira: analysis of small RNA sequencing data and microRNA modifications , 2015, Bioinform..

[10]  N. Kosaka,et al.  Bovine milk exosomes contain microRNA and mRNA and are taken up by human macrophages. , 2015, Journal of dairy science.

[11]  X. Chen,et al.  Effective detection and quantification of dietetically absorbed plant microRNAs in human plasma. , 2015, The Journal of nutritional biochemistry.

[12]  L. Hofseth,et al.  A novel chemopreventive strategy based on therapeutic microRNAs produced in plants , 2015, Cell Research.

[13]  J. Zempleni,et al.  Loss of miRNAs during processing and storage of cow's (Bos taurus) milk. , 2015, Journal of agricultural and food chemistry.

[14]  S. Le Guillou,et al.  No effect of an elevated miR-30b level in mouse milk on its level in pup tissues , 2015, RNA biology.

[15]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[16]  K. Witwer.  Diet-responsive mammalian miRNAs are likely endogenous. , 2014, The Journal of nutrition.

[17]  J. Zempleni,et al.  MicroRNAs are absorbed in biologically meaningful amounts from nutritionally relevant doses of cow milk and affect gene expression in peripheral blood mononuclear cells, HEK-293 kidney cell cultures, and mouse livers. , 2014, The Journal of nutrition.

[18]  Toby C. Cornish,et al.  Lessons from miR-143/145: the importance of cell-type localization of miRNAs , 2014, Nucleic acids research.

[19]  Hugo Naya,et al.  Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS , 2014, RNA.

[20]  K. Hirschi,et al.  Transfer and functional consequences of dietary microRNAs in vertebrates: Concepts in search of corroboration , 2014, BioEssays : news and reviews in molecular, cellular and developmental biology.

[21]  J. Garssen,et al.  Recovery of extracellular vesicles from human breast milk is influenced by sample collection and vesicle isolation procedures , 2014, Journal of extracellular vesicles.

[22]  Ana Kozomara,et al.  miRBase: annotating high confidence microRNAs using deep sequencing data , 2013, Nucleic Acids Res..

[23]  A. Jackson,et al.  Safety assessment of food and feed from biotechnology-derived crops employing RNA-mediated gene regulation to achieve desired traits: a scientific review. , 2013, Regulatory toxicology and pharmacology : RTP.

[24]  K. Witwer,et al.  Comparison of Methods for miRNA Extraction from Plasma and Quantitative Recovery of RNA from Cerebrospinal Fluid , 2013, Front. Genet..

[25]  J. Nielsen,et al.  MicroRNA-29a is up-regulated in beta-cells by glucose and decreases glucose-stimulated insulin secretion. , 2012, Biochemical and biophysical research communications.

[26]  K. Witwer.  XenomiRs and miRNA homeostasis in health and disease , 2012, RNA biology.

[27]  X. Chen,et al.  Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA , 2011, Cell Research.

[28]  A. Pandey,et al.  miR-29a levels are elevated in the db/db mice liver and its overexpression leads to attenuation of insulin action on PEPCK gene expression in HepG2 cells , 2011, Molecular and Cellular Endocrinology.

[29]  X. Chen,et al.  Identification and characterization of microRNAs in raw milk during different periods of lactation, commercial fluid, and powdered milk products , 2010, Cell Research.

[30]  L. O’Driscoll,et al.  Identification of microRNAs with a role in glucose stimulated insulin secretion by expression profiling of MIN6 cells. , 2010, Biochemical and biophysical research communications.

[31]  N. Kosaka,et al.  microRNA as a new immune-regulatory agent in breast milk , 2010, Silence.

[32]  Hervé Seitz,et al.  Redefining MicroRNA Targets , 2009, Current Biology.

[33]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[34]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[35]  Roger E Bumgarner,et al.  MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis , 2008, Genome Biology.

[36]  Thomas Tuschl,et al.  The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members , 2008, Development.

[37]  Aibin He,et al.  Overexpression of micro ribonucleic acid 29, highly up-regulated in diabetic rats, leads to insulin resistance in 3T3-L1 adipocytes. , 2007, Molecular endocrinology.

[38]  K. Livak,et al.  Real-time quantification of microRNAs by stem–loop RT–PCR , 2005, Nucleic acids research.

[39]  T. Tuschl,et al.  Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. , 2004, Molecular cell.

[40]  W. Filipowicz.  Faculty Opinions recommendation of A microRNA in a multiple-turnover RNAi enzyme complex. , 2002 .

[41]  Michael Mcfaul,et al.  One Step Forward, Two Steps Back , 2000 .

[42]  Tanya Barrett,et al.  The Gene Expression Omnibus Database , 2016, Statistical Genomics.

[43]  S. Chan,et al.  Diet-Derived MicroRNAs: Separating the Dream from Reality , 2014 .

[44]  Kang Li,et al.  Circulating microRNA-1 as a potential novel biomarker for acute myocardial infarction. , 2010, Biochemical and biophysical research communications.

[45]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..