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Circulating nucleic acids, particularly those associated with extracellular vesicles (EVs), represent a promising class of molecular biomarkers in liquid biopsy for ‘non-invasive’ disease diagnostics, for better prognosis, and for therapeutic monitoring. However, the translation of this new circulating biomarker source into clinical practice is mostly hindered by methodological variability and a lack of standardization across the analytical workflow. This article highlights the implementation of international academic guidelines, such as Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) and Minimal Information for Studies of Extracellular Vesicles (MISEV), in the entire analytical procedure in promoting the integrity, reproducibility, and validity of EV-associated nucleic acid markers in molecular diagnostics. By standardizing the liquid biopsy workflow from tissue sampling up to data analysis and statistics, these established guidelines lay the necessary scientific basis for a robust, reproducible, reliable, and valid RNA and DNA biomarker discovery in EVs. The ultimate goal is the successful implementation of the developed biomarker signature into the clinical diagnostic routine, but this requires further rounds of rigorous validation. The regularly updated guidelines should not be seen as optional recommendations, but more like an essential pillars of scientific rigor and standardization in order to achieve better and biological meaningful biomarker results in liquid biopsy.

Extracellular vesicles (EVs) have recently come into the spotlight as potential cancer biomarkers. Isolation of pure EVs is complex, so wider use requires reliable and time-efficient isolation methods. In the present study, galectin-based magnetic glycan recognition particles, EXOBead[R] were investigated for their practicality as a novel EV isolation technique, exemplified here for squamous cell carcinoma of the head and neck. Analysis of the isolation method showed a high concentration of pure EVs with detection of specific EV markers such as CD9, CD63, CD81 and TSG101. No apolipoprotein A1 was shown in the isolates, indicating low contamination of this isolation technique compared with size exclusion chromatography. In addition, common leukocyte antigen (CD45), three HNSCC [epithelial cell adhesion molecule (EpCAM), pan-cytokeratin and programmed death-ligand 1 (PD-L1)] and PanEV markers (premixed CD9, CD63 and CD81 antibodies) were measured by bead-based flow cytometry (BFC). BFC revealed that CD4[5.sup.Neg] PanE[V.sup.+], EpCA[M.sup.+] PanE[V.sup.+] and PD-L[1.sup.+] PanE[V.sup.+] were significantly higher in tumor patients compared with healthy control plasma. CD4[5.sup.Neg] PanE[V.sup.+] and CD4[5.sup.+] PanE[V.sup.+] carrying two or three HNSCC biomarkers were also significantly higher in tumor patients compared with healthy controls (BFC). Comparison of the functional immunosuppression effect of eluted tumor patient plasma EVs from EXOBead[R] and commercial polyethylene glycol isolation showed a significant tumor-dependent increase in concentration of EVs. A peripheral blood mononuclear cell activation assay also showed that the T-cell functionality of tumor patient plasma EVs isolated with EXOBead[R] was preserved in vitro. In conclusion, isolation using galectin-based magnetic glycan recognition particles is a novel method for isolating plasma EVs with low lipoprotein contamination. Bead-based flow cytometry provided an easy way to understand EV subpopulations. EXOBead[R] therefore showed great potential as a new isolation tool with high throughput capacity that could potentially be used in a clinical setting. Key words: extracellular vesicles, exosomes, novel isolation technique, biomarker, head and neck squamous cell carcinoma, tumor-derived extracellular vesicles, galectin-based glycan recognition particles, beads-based flow cytometry

Extracellular vesicles (EVs) such as exosomes are key regulators of intercellular communication that can be found in almost all bio fluids. Although studies in the last decade have made great headway in discerning the role of EVs in many physiological and pathophysiological processes, the bioavailability and impact of dietary EVs and their cargo still remain to be elucidated. Due to its widespread consumption and high content of EV-associated microRNAs and proteins, a major focus in this field has been set on EVs in bovine milk and colostrum. Despite promising in vitro studies in recent years that show high resiliency of milk EVs to degradation and uptake of milk EV cargo in a variety of intestinal and blood cell types, in vivo experiments continue to be inconclusive and sometimes outright contradictive. To resolve this discrepancy, we assessed the potential postprandial transfer of colostral EVs to the circulation of newborn calves by analysing colostrum-specific protein and miRNAs, including specific isoforms (isomiRs) in cells, EV isolations and unfractionated samples from blood and colostrum. Our findings reveal distinct populations of EVs in colostrum and blood from cows that can be clearly separated by density, particle concentration and protein content (BTN1A1, MFGE8). Postprandial blood samples of calves show a time-dependent increase in EVs that share morphological and protein characteristics of colostral EVs. Analysis of miRNA expression profiles by Next-Generation Sequencing gave a different picture however. Although significant postprandial expression changes could only be detected for calf EV samples, expression profiles show very limited overlap with highly expressed miRNAs in colostral EVs or colostrum in general. Taken together our results indicate a selective uptake of membrane-associated protein cargo but not luminal miRNAs from colostral EVs into the circulation of neonatal calves.

Grass pollen allergens are known to be one of the major triggers of hay fever with an increasing number of humans affected by pollen associated health impacts. Climate change characterized by increasing air temperature and more frequent drought periods might affect plant development and pollen characteristics. In this study a one-year (2017) field experiment was conducted in Bavaria, Germany, simulating drought by excluding rain and elevated air temperature by installing a heating system to investigate their effects primarily on the allergenic potential of eight selected cultivars of the two grass species timothy and perennial ryegrass. It could be shown for timothy that especially under drought and heat conditions the allergen content is significantly lower accompanied by a decrease in pollen weight and protein content. In perennial ryegrass the response to drought and heat conditions in terms of allergen content, pollen weight, and protein content was more dependent on the respective cultivar probably due to varying requirements for their growth conditions and tolerance to drought and heat. Results support recommendations which cultivars should be grown preferentially. The optimal choice of grass species and respective cultivars under changing climate conditions should be a major key aspect for the public health sector in the future.

Drugs that target histone deacetylase (HDAC) entered the pharmacopoeia in the 2000s. However, some enigmatic phenotypes suggest off-target engagement. Here, we developed a quantitative chemical proteomics assay using immobilized HDAC inhibitors and mass spectrometry that we deployed to establish the target landscape of 53 drugs. The assay covers 9 of the 11 human zinc-dependent HDACs, questions the reported selectivity of some widely-used molecules (notably for HDAC6) and delineates how the composition of HDAC complexes influences drug potency. Unexpectedly, metallo-β-lactamase domain-containing protein 2 (MBLAC2) featured as a frequent off-target of hydroxamate drugs. This poorly characterized palmitoyl-CoA hydrolase is inhibited by 24 HDAC inhibitors at low nanomolar potency. MBLAC2 enzymatic inhibition and knockdown led to the accumulation of extracellular vesicles. Given the importance of extracellular vesicle biology in neurological diseases and cancer, this HDAC-independent drug effect may qualify MBLAC2 as a target for drug discovery.Lechner et al. used an affinity-based chemical proteomics approach to investigate the target landscape of HDAC inhibitors, and identified an extracellular vesicle regulator MBLAC2 as a universal off-target of 24 hydroxamate inhibitors.

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.

Grass pollen is the main cause of hay fever and allergic asthma in warm temperate climates during summer. The aim of this study was to determine the content of group 5 major allergens in pollen grains of agriculturally important grass species/cultivars. For each cultivar flowering dates and pollen production of cut anthers were observed in the field and in a climate chamber, respectively. An ELISA was used to quantify the group 5 allergens (Phl p5) in pollen extracts which were gained from the grass species Kentucky bluegrass, perennial rye grass, timothy, cocksfoot, annual / Italian rye grass, hybrid rye grass and festulolium. The group 5 allergen content of species varied between 0.01 ng (Kentucky bluegrass) and 0.06 ng (timothy) per pollen grain. On cultivar level the pollen allergenic content differed up to 74-times within the selected grass species. Results from this study might be helpful for the reduction of allergen exposure coming from agriculture grass production e.g. by an adapted grass selection or by the cultivation of grasses with low allergenic content in plant breeding.

Adipocyte-derived extracellular vesicles (AdEVs) are membranous nanoparticles that convey communication from adipose tissue to other organs. Here, to delineate their role as messengers with glucoregulatory nature, we paired fluorescence AdEV-tracing and SILAC-labeling with (phospho)proteomics, and revealed that AdEVs transfer functional insulinotropic protein cargo into pancreatic β-cells. Upon transfer, AdEV proteins were subjects for phosphorylation, augmented insulinotropic GPCR/cAMP/PKA signaling by increasing total protein abundances and phosphosite dynamics, and ultimately enhanced 1st-phase glucose-stimulated insulin secretion (GSIS) in murine islets. Notably, insulinotropic effects were restricted to AdEVs isolated from obese and insulin resistant, but not lean mice, which was consistent with differential protein loads and AdEV luminal morphologies. Likewise, in vivo pre-treatment with AdEVs from obese but not lean mice amplified insulin secretion and glucose tolerance in mice. This data suggests that secreted AdEVs can inform pancreatic β-cells about insulin resistance in adipose tissue in order to amplify GSIS in times of increased insulin demand. Extracellular vesicles (EVs) convey inter-organ communication in health and disease. Here, the authors report that adipocyte-derived EVs isolated from insulin-resistant obese but not lean male mice stimulate insulin secretion via the targeted transfer of insulinotropic proteins from adipose tissue to β-cells.

There is growing interest in digital PCR (dPCR) because technological progress makes it a practical and increasingly affordable technology. dPCR allows the precise quantification of nucleic acids, facilitating the measurement of small percentage differences and quantification of rare variants. dPCR may also be more reproducible and less susceptible to inhibition than quantitative real-time PCR (qPCR). Consequently, dPCR has the potential to have a substantial impact on research as well as diagnostic applications. However, as with qPCR, the ability to perform robust meaningful experiments requires careful design and adequate controls. To assist independent evaluation of experimental data, comprehensive disclosure of all relevant experimental details is required. To facilitate this process we present the Minimum Information for Publication of Quantitative Digital PCR Experiments guidelines. This report addresses known requirements for dPCR that have already been identified during this early stage of its development and commercial implementation. Adoption of these guidelines by the scientific community will help to standardize experimental protocols, maximize efficient utilization of resources, and enhance the impact of this promising new technology.

Background: Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader’s ability to evaluate critically the quality of the results presented or to repeat the experiments. Content: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement. Summary: Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.