MicroRNA is responsible for the fine-tuning of fundamental cellular activities and human disease development. The altered availability of microRNAs, target mRNAs, and other types of endogenous RNAs competing for microRNA interactions reflects the dynamic and conditional property of microRNA-mediated gene regulation that remains under-investigated. Here we propose a new integrative method to study this dynamic process by considering both competing and cooperative mechanisms and identifying functional modules where different microRNAs co-regulate the same functional process. Specifically, a new pipeline was built based on a meta-Lasso regression model and the proof-of-concept study was performed using a large-scale genomic dataset from ~4,200 patients with 9 cancer types. In the analysis, 10,726 microRNA-mRNA interactions were identified to be associated with a specific stage and/or type of cancer, which demonstrated the dynamic and conditional miRNA regulation during cancer progression. On the other hands, we detected 4,134 regulatory modules that exhibit high fidelity of microRNA function through selective microRNA-mRNA binding and modulation. For example, miR-18a-3p, −320a, −193b-3p, and −92b-3p co-regulate the glycolysis/gluconeogenesis and focal adhesion in cancers of kidney, liver, lung, and uterus. Furthermore, several new insights into dynamic microRNA regulation in cancers have been discovered in this study.

Objectives Exosomes are natural nanoparticles that can be found in most body fluids including milk. Bovine milk exosomes (BME) are bioavailable and transfer cargos such as RNAs, lipids and proteins across species boundaries. Previous competitor studies implicated galactose-modifications in exosome surface proteins in exosome transport. The objectiveof our study was to assess the importance of glycan modifications in BME surface glycoproteins for BME uptake and distribution in human intestinal cells (FHs cells) and mice. Methods BME were isolated from milk by differential centrifugation (Fig. 1). Putative glycan binding sites on the surfaces of BME were identified by LC/MS-MS and bioinformatics protocols and confirmed by eastern blotting. Surface glycans were altered using proteases, glycosidases and blocking of glycans with lectins for subsequent transport and distribution studies (Table 1). The uptake of BME by FHs cells was assessed using membrane and RNA cargo-labeled BME. The distribution of BME in mice was assessed using BME transfected with fluorophore (IRDye)-labeled synthetic miR-320a in C57BL/6 mice and MGAT-1 tamoxifen inducible conditional knockout (CKO) mice ages 5–8 weeks. One-way ANOVA and Bonferroni's multiple comparison were used for statistical analyses; P < 0.05 was considered significant. Results We identified 49 (N), 13 (O) and 13 (C) putative glycan binding sites on the BME surface, and confirmed the presence of mannose, galactose, N-acetylgalactose, fucose and neuraminate (Fig. 2). Galactose and N-acetylgalactosamine residues on the surface of BME were of particular importance for their uptake by FHs cells, whereas N-acetylglucosamine on the surface of FHs cells was more important than other glycans for BME uptake (Fig. 3). Enzymatic and genetic removal of glycans in BME and MGAT-1 CKO, respectively, caused a loss of BME accumulation in murine livers and pancreas (Fig. 4). Conclusions Distinct glycan features are essential for the uptake of BME in mice. The study laid a foundation to assess the importance of glycan modifications in infant formulas and the homing of drug-loaded exosomes to sites of disease. Funding Sources NIFA, NIH, Bill & Melinda Gates Foundation, PureTech Health, and USDA Hatch & Multistate. J.Z. is a consultant for PureTech. Supporting Tables, Images and/or Graphs

Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes. In this article, we present microRNA Discovery (miRDis), a new small RNA sequencing data analysis pipeline for both endogenous and exogenous miRNA detection. Specifically, we developed and deployed a Web service that supports the annotation and expression profiling data of known host miRNAs and the detection of novel miRNAs, other noncoding RNAs, and the exogenous miRNAs from dietary species. As a proof-of-concept, we analyzed a set of human plasma sequencing data from a milk-feeding study where 225 human miRNAs were detected in the plasma samples and 44 show elevated expression after milk intake. By examining the bovine-specific sequences, data indicate that three bovine miRNAs (bta-miR-378, -181* and -150) are present in human plasma possibly because of the dietary uptake. Further evaluation based on different sets of public data demonstrates that miRDis outperforms other state-of-the-art tools in both detection and quantification of miRNA from either animal or plant sources. The miRDis Web server is available at: http://sbbi.unl.edu/miRDis/index.php.

Personal diet management is key to fighting the obesity epidemic. Recent advances in smartphones and wearable sensor technologies have empowered automated food monitoring through food image processing and eating episode detection, with the goal to conquer drawbacks of traditional food journaling that is labour intensive, inaccurate, and low adherent. In this paper, we present a new interactive mobile system that enables automated food recognition and assessment based on user food images and provides dietary intervention while tracking users’ dietary and physical activities. In addition to using techniques in computer vision and machine learning, one unique feature of this system is the realization of real-time energy balance monitoring through metabolic network simulation. As a proof of concept, we have demonstrated the use of this system through an Android application.

Objectives Exosomes are endogenous nanoparticles that participate in cell-to-cell communication through the transfer of cargos such RNAs, lipids and proteins from donor cells to recipient cells. Previously, we showed that mammals absorb exosomes from milk. Ultrasonication causes a transient disruption of the exosome membranes, leading to loss of microRNAs. When mice were fed diets based on the AIN-93G formulation, modified to contain a physiological amount of milk exosomes (exosome and RNA-sufficient diet, ERS) or sonicated exosomes (exosome and RNA-depleted diet, ERD), we observed a loss of circulating and tissue microRNAs and phenotypes such as aberrant purine metabolism. The objective of this study was to conduct a comprehensive analysis ofthe effects of sonication on exosomes cargos and bioavailability, thereby generating insights into mechanisms through which ERD elicits phenotypes. Methods Exosomes were isolated from ultrasonicated (USE) and non-sonicated (NSE) bovine milk by ultracentrifugation and authenticated following guidelines of the International Society for Extracellular Vesicles. MicroRNAs were analyzed by small RNA-sequencing. Lipids and proteins were analyzed by LC/MS-MS. Intestinal transport was assessed using FM 4-64-labeled exosomes in primary human small intestine cells (FHs cells). Bioavailability of exosomes transfected with IRDye-labeled miR-320a was assessed using oral gavage in C57BL/6 mice.The unpaired t-test was used for statistical analysis P < 0.05 was considered statistically significant. Results Ultrasonication affected the vesicle count and exosome morphology. Western blot analysis detected marker proteins only in NSE. The content of microRNAs was about 93% lower in USE than NSE. Significant difference was noted for lipid and protein identities between NSE and USE. Reduced uptake of USE by intestinal cells and loss of cargo accumulation in murine livers and pancreas for USE compared to NSE (Fig. 1-5). Conclusions Ultrasonication causesa loss of microRNAs in milk exosomes. The unique patterns of proteins and lipids likely is due to an exchangeof membranes between exosomes and other vesicles during ultrasonication, which might explain the lower bioavailability of USE compared to NSE. We currently test the exchange of lipids during ultrasonication. Funding Sources NIFA, NIH, Gates Foundation, PureTech, Inc. and USDA Hatch and Multistate. J.Z. is a consultant for PureTech. Supporting Tables, Images and/or Graphs