Investigation of the transability of dietary small non-coding RNAs to animals

Our daily diet not only provides essential nutrients needed for survival and growth but also supplies bioactive ingredients to promote health and prevent disease. Recent studies have shown that exogenous microRNAs (miRNAs), xenomiRs, may enter the consumer’s body through dietary intake and regulate gene expression. This fascinating phenomenon suggests that xenomiRs can act as a new class of bioactive substances associated with mammalian systems. In contrast, several studies have failed to detect xenomiRs in consumers and reported that the observed diet-derived miRNAs in the previous studies can be related to the false positive effects of experiments. This discrepancy can be attributed to the potential artifacts related to the process of experiments, small sample size, and inefficient bioinformatics pipeline. Since this hypothesis is not generally accepted yet, more studies are required. Here, a stringent and reliable bioinformatics pipeline was used to analyze 133 miRNA sequencing data from seven different studies to investigate this phenomenon. Generally, our results do not support the transfer of diet-derived miRNAs into the animal/human tissues in every situation. Briefly, xenomiRs were absent from most samples, and also, their expressions were very low in the samples where they were present, which is unlikely to be sufficient to regulate cell transcripts. Furthermore, this study showed that the possibility of miRNAs being absorbed through animals’ diets and thus influencing gene expression during specific periods of biological development is not inconceivable. In this context, our results were in agreement with the theory of the transfer of small RNAs under certain conditions and periods as xenomiRs were found in colostrum which may modulate infants’ immune systems via post-transcriptional regulation. These findings provide evidence for the selective absorption of diet-derived small RNAs, which need to be investigated in future studies to shed light on the mechanisms underlying the transference of diet-derived miRNAs.

MicroRNAs, Cancer and Diet: Facts and New Exciting Perspectives

BACKGROUND

MicroRNAs (miRNAs) are small non-coding RNAs able to regulate gene expression at multiple levels. They are detected in tissues, blood, and other body fluids with high stability and have a recognized role in maintaining of tissue homeostasis. Aberrant expression profile of miRNAs has been observed in several diseases, primarily cancer. As a consequence, the analysis of miRNA signature has recognized diagnostic and prognostic role in human diseases, and the development of miRNA-based therapies is currently under investigation. Recently, emerging but controversial data have revealed the possibility that diet-derived miRNAs might be transferred from food in living organisms to regulate gene expression. Thus, exogenous dietderived miRNAs might substantially contribute to the pool of circulating miRNAs to preserve tissue homeostasis and health status in recipient's organisms, opening new perspectives for diet in heath and disease.

OBJECTIVE

This brief review aims at summarizing data concerning the recognized role of miRNAs as biomarkers, drugs and therapeutic targets in cancer and the detection and the activity of diet-derived miRNAs in both physiological and pathological conditions.

CONCLUSION

MiRNAs have emerged as crucial molecules in anticancer therapies and diet-derived miRNAs might contribute to the pool of circulating miRNAs to preserve, maintain or restore health.

Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma

Background: A 2017 study reported that “Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi”. Analysis of two human blood plasma sequencing datasets was said to provide evidence for uptake of plant miRNAs into human plasma. The results were also purportedly inconsistent with contamination.

Methods: Sequences from public datasets and miRNA databases were compared with results downloaded from the website of the reporting journal.

Results: Only one putative plant miRNA (“peu-MIR2910) mapped consistently above background, and this sequence is found with 100% identity in a human rRNA. Several other rarer but consistently mapped putative plant miRNAs also have 100% or near 100% matches to human transcripts or genomic sequences, and some do not appear to map to plant genomes at all.

Conclusions: Reanalysis of public data suggests that dietary plant xenomiR uptake is not supported, but instead confirms previous findings that detection of rare plant miRNAs in mammalian sequencing datasets is artifactual. Some putative plant miRNAs, including MIR2910 and MIR2911, may represent human sequence contamination or other artifacts in plant studies, emphasizing the need for rigorous controls and data filtering strategies when assessing possible xenomiRNAs.

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.

Real-time quantitative PCR and droplet digital PCR for plant miRNAs in mammalian blood provide little evidence for general uptake of dietary miRNAs: limited evidence for general uptake of dietary plant xenomiRs

Evidence that exogenous dietary miRNAs enter the bloodstream and tissues of ingesting animals has been accompanied by an indication that at least one plant miRNA, miR168, participates in “cross-kingdom” regulation of a mammalian transcript. If confirmed, these findings would support investigation of miRNA-based dietary interventions in disease. Here, blood was obtained pre- and post-prandially (1, 4, 12 h) from pigtailed macaques that received a miRNA-rich plant-based substance. Plant and endogenous miRNAs were measured by RT-qPCR. Although low-level amplification was observed for some plant miRNA assays, amplification was variable and possibly non-specific, as suggested by droplet digital PCR. A consistent response to dietary intake was not observed. While our results do not support general and consistent uptake of dietary plant miRNAs, additional studies are needed to establish whether or not plant or animal xenomiRs are transferred across the gut in sufficient quantity to regulate endogenous genes.