A miRNA181a/NFAT5 axis links impaired T cell tolerance induction with autoimmune type 1 diabetes.

Molecular checkpoints that trigger the onset of islet autoimmunity or progression to human type 1 diabetes (T1D) are incompletely understood. Using T cells from children at an early stage of islet autoimmunity without clinical T1D, we find that a microRNA181a (miRNA181a)-mediated increase in signal strength of stimulation and costimulation links nuclear factor of activated T cells 5 (NFAT5) with impaired tolerance induction and autoimmune activation. We show that enhancing miRNA181a activity increases NFAT5 expression while inhibiting FOXP3+ regulatory T cell (Treg) induction in vitro. Accordingly, Treg induction is improved using T cells from NFAT5 knockout (NFAT5ko) animals, whereas altering miRNA181a activity does not affect Treg induction in NFAT5ko T cells. Moreover, high costimulatory signals result in phosphoinositide 3-kinase (PI3K)-mediated NFAT5, which interferes with FoxP3+ Treg induction. Blocking miRNA181a or NFAT5 increases Treg induction in murine and humanized models and reduces murine islet autoimmunity in vivo. These findings suggest targeting miRNA181a and/or NFAT5 signaling for the development of innovative personalized medicines to limit islet autoimmunity.

Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes.

Strawberry fruits (Fragaria vesca) are valued for their sweet fruity flavor, juicy texture, and characteristic red color caused by anthocyanin pigments. To gain a deeper insight into the regulation of anthocyanin biosynthesis, we performed comparative metabolite profiling and transcriptome analyses of one red-fruited and two natural white-fruited strawberry varieties in two tissues and three ripening stages. Developing fruit of the three genotypes showed a distinctive pattern of polyphenol accumulation already in green receptacle and achenes. Global analysis of the transcriptomes revealed that the ripening process in the white-fruited varieties is already affected at an early developmental stage. Key polyphenol genes showed considerably lower transcript levels in the receptacle and achenes of both white genotypes, compared to the red genotype. The expression of the anthocyanidin glucosyltransferase gene and a glutathione S-transferase, putatively involved in the vacuolar transport of the anthocyanins, seemed to be critical for anthocyanin formation. A bHLH transcription factor is among the differentially expressed genes as well. Furthermore, genes associated with flavor formation and fruit softening appear to be coordinately regulated and seem to interact with the polyphenol biosynthesis pathway. This study provides new information about polyphenol biosynthesis regulators in strawberry, and reveals genes unknown to affect anthocyanin formation.

Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow.

Small RNA-Seq has emerged as a powerful tool in transcriptomics, gene expression profiling and biomarker discovery. Sequencing cell-free nucleic acids, particularly microRNA (miRNA), from liquid biopsies additionally provides exciting possibilities for molecular diagnostics, and might help establish disease-specific biomarker signatures. The complexity of the small RNA-Seq workflow, however, bears challenges and biases that researchers need to be aware of in order to generate high-quality data. Rigorous standardization and extensive validation are required to guarantee reliability, reproducibility and comparability of research findings. Hypotheses based on flawed experimental conditions can be inconsistent and even misleading. Comparable to the well-established MIQE guidelines for qPCR experiments, this work aims at establishing guidelines for experimental design and pre-analytical sample processing, standardization of library preparation and sequencing reactions, as well as facilitating data analysis. We highlight bottlenecks in small RNA-Seq experiments, point out the importance of stringent quality control and validation, and provide a primer for differential expression analysis and biomarker discovery. Following our recommendations will encourage better sequencing practice, increase experimental transparency and lead to more reproducible small RNA-Seq results. This will ultimately enhance the validity of biomarker signatures, and allow reliable and robust clinical predictions.

Comparison of the miRNome and piRNome of bovine blood and plasma by small RNA sequencing.

OBJECTIVES: The small RNAs of bovine plasma and whole blood were analysed using next-generation sequencing to quantify, profile and compare the microRNAs (miRNA) and piRNA signatures in both bio fluids. RESULTS: Evaluating read-count data resulted in a proportion of 5.0 ± 2.9 % of miRNAs in plasma while 38.2 ± 3.4 % were identified in whole blood. Regarding piRNAs, the percentages in both matrices were nearly the same: 1.4 ± 0.8 % of piRNAs in plasma and 1.9 ± 0.8 % in whole blood. Investigation of the ten most abundant miRNAs and piRNAs in both bio fluids revealed that two miRNAs and seven piRNAs were identical. Comparing the read-count values of these matching pairs highlighted that miRNA and piRNA levels in blood exceeded the abundance of their corresponding miRNAs and piRNAs in plasma, except liver-specific miR-122 and three piRNAs. CONCLUSIONS: The data strengthened evidence that the circulating small RNA signature in plasma is not only influenced by hematocytes and certain small RNAs could originate from other sources than cellular blood components.

Optimization of extraction of circulating RNAs from plasma--enabling small RNA sequencing.

There are several protocols and kits for the extraction of circulating RNAs from plasma with a following quantification of specific genes via RT-qPCR. Due to the marginal amount of cell-free RNA in plasma samples, the total RNA yield is insufficient to perform Next-Generation Sequencing (NGS), the state-of-the-art technology in massive parallel sequencing that enables a comprehensive characterization of the whole transcriptome. Screening the transcriptome for biomarker signatures accelerates progress in biomarker profiling for molecular diagnostics, early disease detection or food safety. Therefore, the aim was to optimize a method that enables the extraction of sufficient amounts of total RNA from bovine plasma to generate good-quality small RNA Sequencing (small RNA-Seq) data. An increased volume of plasma (9 ml) was processed using the Qiagen miRNeasy Serum/Plasma Kit in combination with the QIAvac24 Plus system, a vacuum manifold that enables handling of high volumes during RNA isolation. 35 ng of total RNA were passed on to cDNA library preparation followed by small RNA high-throughput sequencing analysis on the Illumina HiSeq2000 platform. Raw sequencing reads were processed by a data analysis pipeline using different free software solutions. Seq-data was trimmed, quality checked, gradually selected for miRNAs/piRNAs and aligned to small RNA reference annotation indexes. Mapping to human reference indexes resulted in 4.8±2.8% of mature miRNAs and 1.4±0.8% of piRNAs and of 5.0±2.9% of mature miRNAs for bos taurus.

Identification of a potential gene expression biomarker signature in bovine liver to detect the abuse of growth promoters.

The misuse of anabolic agents in animal husbandry is a ubiquitous problem. The ban of growth promoters in food producing animals in the European Union is well controlled, but there are still application regimes, such as new designed drugs or hormone cocktails, that are difficult to detect. Therefore, the idea of identifying molecular biomarkers that are based on the physiological effect of treatment has come into focus. In a previous study we identified mRNA biomarker candidates in liver samples that enable the separation of untreated animals from animals treated with a combination of androgens plus estrogens. In the present study those candidates were validated in calves treated with a combination of progesterone plus estradiol or clenbuterol, respectively. Therefore, the candidate genes were quantified in liver samples of those calves via RT-qPCR. Using dynamic principal component analysis (PCA), a signature of 11 genes could be selected. This set of genes enabled the separation of treated and control animals independent of the applied drug. Additional quantification of these genes in a set of control samples from another animal trial resulted in a PCA that also showed a separation of those samples from treated animals. This study showed that gene expression biomarkers have a high potential to enable the detection of physiological changes caused by the application of growth-promoting substances independent of the given drug, but further studies are necessary to broaden the spectrum of anabolic substance groups for which those biomarker candidates can be used.

Effects of rapeseed and soybean oil dietary supplementation on bovine fat metabolism, fatty acid composition and cholesterol levels in milk.

The main goal of this experiment was to study the effect of milk fat depression, induced by supplementing diet with plant oils, on the bovine fat metabolism, with special interest in cholesterol levels. For this purpose 39 cows were divided in three groups and fed different rations: a control group (C) without any oil supplementation and two groups with soybean oil (SO) or rapeseed oil (RO) added to the partial mixed ration (PMR). A decrease in milk fat percentage was observed in both oil feedings with a higher decrease of -1·14 % with SO than RO with -0·98 % compared with the physiological (-0·15 %) decline in the C group. There was no significant change in protein and lactose yield. The daily milk cholesterol yield was lower in both oil rations than in control ration, while the blood cholesterol level showed an opposite variation. The milk fatty acid pattern showed a highly significant decrease of over 10 % in the amount of saturated fatty acids (SFA) in both oil feedings and a highly significant increase in mono (MUFA) and poly (PUFA) unsaturated fatty acids, conjugated linoleic acids (CLA) included. The results of this experiment suggest that the feeding of oil supplements has a high impact on milk fat composition and its significance for human health, by decreasing fats with a potentially negative effect (SFA and cholesterol) while simultaneously increasing others with positive (MUFA, PUFA, CLA).