Circulating microRNA trafficking and regulation: computational principles and practice.

Rapid advances in genomics discovery tools and a growing realization of microRNA's implication in intercellular communication have led to a proliferation of studies of circulating microRNA sorting and regulation across cells and different species. Although sometimes, reaching controversial scientific discoveries and conclusions, these studies have yielded new insights in the functional roles of circulating microRNA and a plethora of analytical methods and tools. Here, we consider this body of work in light of key computational principles underpinning discovery of circulating microRNAs in terms of their sorting and targeting, with the goal of providing practical guidance for applications that is focused on the design and analysis of circulating microRNAs and their context-dependent regulation. We survey a broad range of informatics methods and tools that are available to the researcher, discuss their key features, applications and various unsolved problems and close this review with prospects and broader implication of this field.

Regio- and Enantioselective Synthesis of Dihydropyrido[1,2-a]indoles via Catalytic Asymmetric Annulative Allylic Alkylation.

A palladium-catalyzed asymmetric annulative allylic alkylation reaction of 2-[(1H-indol-2-yl)methyl]malonates with (E)-but-2-ene-1,4-diyl dicarbonates is described, leading to the regio- and enantioselective synthesis of dihydropyrido[1,2-a]indoles with a chiral cyclic allyl stereocenter adjacent to the ring-junction nitrogen atom in moderate to good yields. The salient features of this protocol include mild conditions, a broad substrate scope, and good compatibility with substituents as well as high regio- and stereoselectivities, providing a catalytic asymmetric entry for fabricating chiral pyridoindole scaffolds.

The associations of serum valine with mild cognitive impairment and Alzheimer's disease.

BACKGROUND: The introduction of metabolomics makes it possible to study the characteristic changes of peripheral metabolism in Alzheimer's disease (AD). Recent studies have found that the levels of valine are related to mild cognitive impairment (MCI) and AD. AIMS: This study aimed to further clarify the characteristics of valine levels in MCI and AD. METHODS: A total of 786 participants from the Alzheimer's Disease Neuroimaging Initiative-1 (ADNI-1) cohort were selected to evaluate the relationships between serum valine and cerebrospinal fluid (CSF) biomarkers, brain structure (magnetic resonance imaging, MRI), cerebral glucose metabolism (18F-fluorodeoxyglucose-positron emission tomography, FDG-PET), and cognitive declines, through different cognitive subgroups. RESULTS: Serum valine was decreased in patients with AD compared with cognitive normal (CN) and stable MCI (sMCI), and in progressive MCI (pMCI) compared with CN. Serum valine was negatively correlated with CSF total tau (t-tau) and phosphorylated tau (p-tau) in pMCI. Serum valine significantly predicted conversion from MCI to AD. In addition, serum valine was related to the rate of change of cerebral glucose metabolism during the follow-up period in pMCI. CONCLUSIONS: Serum valine may be a peripheral biomarker of pMCI and AD, and its level predicts the progression of MCI to AD. Our study may help to reveal the metabolic changes during AD disease trajectory and its relationship to clinical phenotype.

Synthesis, Characterization of Low Molecular Weight Chitosan Selenium Nanoparticles and Its Effect on DSS-Induced Ulcerative Colitis in Mice.

Selenium nanoparticles have attracted extensive attention due to their good bioavailability and activity. In the present study, a new form of selenium nanoparticle (Low molecular weight chitosan selenium nanoparticles (LCS-SeNPs)) were synthesized in a system of sodium selenite and acetic acid. The size, element state, morphology and elementary composition of LCS-SeNPs were characterized by using various spectroscopic and microscopic measurements. The protection of LCS-SeNPs against dextran sulfate sodium (DSS)-induced intestinal barrier dysfunction and the inherent mechanisms of this process were investigated. The results showed that LCS-SeNPs, with an average diameter of 198 nm, zero-valent and orange-red relatively uniform spherical particles were prepared. LCS-SeNPs were mainly composed of C, N, O and Se elements, of which Se accounted for 39.03% of the four elements C, N, O and Se. LCS-SeNPs reduced colon injury and inflammation symptoms and improved intestinal barrier dysfunction. LCS-SeNPs significantly reduced serum and colonic inflammatory cytokines TNF-α and IL-6 levels. Moreover, LCS-SeNPs remarkably increased antioxidant enzyme GSH-Px levels in serum and colonic tissue. Further studies on inflammatory pathways showed that LCS-SeNPs alleviated DSS-induced colitis through the NF-κB signaling pathway, and relieved inflammatory associated oxidative stress through the Nrf2 signaling pathway. Our findings suggested that LCS-SeNPs are a promising selenium species with potential applications in the treatment of oxidative stress related inflammatory intestinal diseases.

Tunable Electrocatalytic Annulations of o-Arylalkynylanilines: Green and Switchable Syntheses of Skeletally Diverse Indoles.

Tunable electrocatalytic annulation reactions of o-arylalkynylanilines have been established, leading to green and divergent syntheses of skeletally diverse indoles by adjusting the electrolytes and the solvents. The presence of ammonium halides as the electrolytes enabled the halogenation of o-arylalkynylanilines to give C3-halogenated indoles whereas naphtho[1',2':4,5]furo[3,2-b]indoles could be obtained by changing the electrolyte from ammonium halides to KI. Interestingly, by combining acetone as the solvent and both NH4I and NH4Cl as the electrolytes, the reaction worked through an intramolecular annulation and [5 + 1] cyclization cascade to form naphtho[1',2':5,6][1,3]oxazino[3,4-a]indoles.

Cyclic Oxime Esters as Deconstructive Bifunctional Reagents for Cyanoalkyl Esterification of 1,6-Enynes.

A concise copper catalysis strategy for the addition-cyclization of cyclic oxime esters across 1,6-enynes with high stereoselectivity to generate 1-indanones bearing an all-carbon quaternary center is reported. In this process, single-electron reduction of cyclic oxime esters enables deconstructive carbon-carbon cleavage to provide a key cyanopropyl radical poised for the addition-cyclization. This reaction is redox-neutral, exhibits good functional group compatibility, and features 100% atomic utilization. This process driven by copper catalyst makes readily available cyclic oxime esters as bifunctional reagents to demonstrate convergent synthesis.

Diagnosis of a giant left atrial appendage aneurysm by contrast-enhanced echocardiography: Case report and literature review.

Left atrial appendage aneurysm (LAAA) is a rare pathologic entity that can be congenital or, more frequently, acquired. Its complications include arrhythmias and thromboembolic events, palpitations, hiccups, chest pain, dyspnea, and myocardial infarction. LAAA can be isolated or associated with other congenital anomalies such as atrial septal defect, ventricular septal defect, anomalous renal artery, Noonan syndrome, and Hurler-Scheie syndrome. We report a rare case of giant LAA with intra-aneurysmal thrombus diagnosed by contrast-enhanced echocardiography.

Milk exosomes and miRNA cross the placenta and promote embryo survival in mice.

Exosomes facilitate cell-to-cell communication by transferring regulatory molecules such as miRNA from donor to recipient cells, for example, miR-21-5p and miR-30d promote placentation. Exosomes and their miRNA cargos are not exclusively obtained from endogenous synthesis but may also be absorbed from dietary sources, such as milk. This study assessed the effects of milk exosomes and miRNA cargos on embryo development and fertility in C57BL/6 mice. Fluorophore-labeled milk exosomes, miR-21-5p and miR-30d accumulated in murine placenta and embryos following oral gavage. Seventeen mRNAs, miR-21-5p and miR-30d were differentially expressed in placentas of pregnant mice fed a milk exosome and RNA-depleted (ERD) diet or a milk exosome and RNA-sufficient (ERS) diet. Eight of these mRNAs encode proteins implicated in the synthesis of extracellular matrix components, cell adhesion and migration. Changes in mRNA expression were associated with corresponding changes in protein expression, for example, collagen type I. The size of litters born to dams fed ERD was 25-50% smaller than those born to ERS controls. This study implicates dietary exosomes and miRNA in placenta development and embryo survival.

Palladium/N,N'-Disulfonyl Bisimidazoline-Catalyzed Enantioselective Addition of Arylboronic Acids to Cyclic N-Sulfonyl Ketimines.

The combination of Pd(TFA)2 and an N,N'-disulfonyl bisimidazoline ligand shows high catalytic activity and excellent asymmetric induction in the addition of arylboronic acids to cyclic N-sulfonyl ketimines including benzo[d]isothiazole-1,1-dioxides, benzo[e][1,2,3]oxathiazine-2,2-dioxides, and 1,2,5-thiadiazole-1,1-dioxides, by which three types of chiral quaternary carbon-containing sultams with substantial substitution diversity were synthesized with high yields and excellent enantioselectivities (up to >99% ee). The current catalysis demonstrated a remarkable tolerance to oxygen and thus provided an operationally simple approach for constructing enantioenriched cyclic quaternary stereocenters.

Ligand-Free Pd-Catalyzed Synthesis of 3-Allylbenzofurans by Merging Decarboxylative Allylation and Nucleophilic Cyclization.

A new single Pd-catalyzed decarboxylative allylation-nucleophilic cyclization relay is reported by using α-alkynyl arylols and vinylethylene carbonates (or vinyl carbamates), and a wide range of 3-allyl benzofurans with generally good yields were stereoselectively synthesized under mild conditions, among which the complete stereoselectivity of some cases was also observed. Notably, the present catalysts can tolerate air conditions without any ligand, additive, or base, opening new avenues to build up oxa-heterocycle frameworks through catalytic difunctionalization of internal alkynes.

Generation of 1,3-Dimethylene-Substituted Isobenzofurans via Pd(II)-Catalyzed Selective Oxo-cyclization/SO2 Insertion Cascade of ß-Alkynyl Ketones.

A new palladium(II)-catalyzed cyclization-radical addition cascade enables the direct construction of 1,3-dimethylene-substituted isobenzofuran derivatives containing a vinyl aryl sulfone unit in good yields by treating with ß-alkynyl ketones, aryl diazonium salts, and DABCO·(SO2)2. The oxidant-free multicomponent reaction features good substrate scope and functional group tolerance, which proceeds through a sequence of Heck coupling, oxo-cyclization, and SO2 insertion.

Synthesis of Diastereoenriched 1-Indanones via Double-Base Cooperatively Promoted 1,4-Oxo-Migration/Cyclization of ß-Alkynyl Ketones.

A double-base copromoted 1,4-oxo-migration/cyclization cascade of ß-alkynyl ketones was reported, enabling to form a range of functionalized 1-indanones with moderate to good yields and high diastereoselectivity in the presence of t-BuOK as a Brønsted base and N,N'-dimethylethanediamine (DMEDA) as a Lewis base. Some of these 1-indanones were successfully transformed into 2-haloethyl benzoates with one all-carbon quaternary stereocenter by 1,2-dichloroethane (DCE) or 1,2-dibromoethane (DBE) as both a reactant and a reaction media. This method also features high atomic utilization (100%), high diastereoselectivity, and mild reaction conditions.

Completely Stereoselective Synthesis of Sulfonated 1,3-Dihydroisobenzofurans via Radical Multicomponent Reactions.

Two types of new oxidant-free radical multicomponent reactions of ß-alkynyl ketones, aryldiazonium salts, and DABCO·(SO2)2 (DABSO) were established, leading to the tunable generation of two class of sulfonated 1,3-dihydroisobenzofurans with moderate to good yields and complete stereoselectivity under the mild conditions. The radical-induced scission/recombination of the C(sp3)-C(sp3) bond enabled direct 1,8-halosulfonylation of ß-alkynyl ketones, giving 1,3-dimethylene-substituted (1Z,3Z)-1,3-dihydroisobenzofurans with substituent diversity by p-nitrobenzyl bromide (PNBB) or p-nitrobenzyl chloride (PNBC) as the halo source. Fine-tuning substituents to strong electron-withdrawing ones, such as nitro, cyano, and trifluoromethyl, linked to aryldiazonium tetrafluoroborates allowed a different annulation/1,5-azosulfonylation process to access sulfonated (Z)-1,3-dihydroisobenzofurans with one quaternary carbon-amino functionality.

Storage of Extracellular Vesicles in Human Milk, and MicroRNA Profiles in Human Milk Exosomes and Infant Formulas.

The objectives of this study were to lay the methodological groundwork for field studies of microRNA analysis in exosomes from small sample volumes of human milk, and assess exosome and microRNA content in infant formulas. When human milk was stored at 4°C for 4 weeks, the count of exosome-sized vesicles decreased progressively to 49% ±â€Š13% of that in fresh milk. Exosomes were purified from 1 mL of fresh human milk and their microRNA content was assessed by microRNA-sequencing analysis and compared with that in infant formulas. We identified 221 microRNAs in exosomes from 3 samples of fresh human milk; 84 microRNAs were present in all 3 samples. MicroRNAs were not detectable in infant formulas and their exosome-sized vesicles, which appeared to be casein micelles. We conclude that large-scale studies of microRNAs in human milk exosomes are feasible, and exosomes and microRNAs are not detectable in formulas.

A systematic approach to RNA-associated motif discovery.

BACKGROUND: Sequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The downstream analysis of RNA binding sites has encouraged the investigation of novel sequence motifs, which resulted in exceptional new challenges for identifying motifs from very short sequences (e.g., small non-coding RNAs or truncated messenger RNAs), where conventional methods tend to be ineffective. To address these challenges, we propose a novel motif-finding method and validate it on a wide range of RNA applications. RESULTS: We first perform motif analysis on microRNAs and longer RNA fragments from various cellular and exosomal sources, and then validate our prediction through literature search and experimental test. For example, a 4 bp-long motif, GUUG, was detected to be responsible for microRNA loading in exosomes involved in human colon cancer (SW620). Additional performance comparisons in various case studies have shown that this new approach outperforms several existing state-of-the-art methods in detecting motifs with exceptional high coverage and explicitness. CONCLUSIONS: In this work, we have demonstrated the promising performance of a new motif discovery approach that is particularly effective in current RNA applications. Important discoveries resulting from this work include the identification of possible RNA-loading motifs in a variety of exosomes, as well as novel insights in sequence features of RNA cargos, i.e., short non-coding RNAs and messenger RNAs may share similar loading mechanism into exosomes. This method has been implemented and deployed as a new webserver named MDS2 which is accessible at http://sbbi-panda.unl.edu/MDS2/ , along with a standalone package available for download at https://github.com/sbbi/MDS2 .

Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model.

BACKGROUND: MicroRNA regulation is fundamentally responsible for fine-tuning the whole gene network in human and has been implicated in most physiological and pathological conditions. Studying regulatory impact of microRNA on various cellular and disease processes has resulted in numerous computational tools that investigate microRNA-mRNA interactions through the prediction of static binding site highly dependent on sequence pairing. However, what hindered the practical use of such target prediction is the interplay between competing and cooperative microRNA binding that complicates the whole regulatory process exceptionally. RESULTS: We developed a new method for improved microRNA target prediction based on Dirichlet Process Gaussian Mixture Model (DPGMM) using a large collection of molecular features associated with microRNA, mRNA, and the interaction sites. Multiple validations based on microRNA-mRNA interactions reported in recent large-scale sequencing analyses and a screening test on the entire human transcriptome show that our model outperformed several state-of-the-art tools in terms of promising predictive power on binding sites specific to transcript isoforms with reduced false positive prediction. Last, we illustrated the use of predicted targets in constructing conditional microRNA-mediated gene regulation networks in human cancer. CONCLUSION: The probability-based binding site prediction provides not only a useful tool for differentiating microRNA targets according to the estimated binding potential but also a capability highly important for exploring dynamic regulation where binding competition is involved.

Concentrations of Purine Metabolites Are Elevated in Fluids from Adults and Infants and in Livers from Mice Fed Diets Depleted of Bovine Milk Exosomes and their RNA Cargos.

Background: Humans and mice absorb bovine milk exosomes and their RNA cargos. Objectives: The objectives of this study were to determine whether milk exosome- and RNA-depleted (ERD) and exosome- and RNA-sufficient (ERS) diets alter the concentrations of purine metabolites in mouse livers, and to determine whether diets depleted of bovine milk alter the plasma concentration and urine excretion of purine metabolites in adults and infants, respectively. Methods: C57BL/6 mice were fed ERD (providing 2% of the microRNA cargos compared with ERS) and ERS diets starting at age 3 wk; livers were collected at age 7 wk. Plasma and 24-h urine samples were collected from healthy adults who consumed (DCs) or avoided (DAs) dairy products. Spot urine samples were collected from healthy infants fed human milk (HM), milk formula (MF), or soy formula (SF) at age 3 mo. Purine metabolites were analyzed in liver, plasma, and urine; mRNAs and microRNAs were analyzed in the livers of female mice. Results: We found that 9 hepatic purine metabolites in ERD-fed mice were 1.76 ± 0.43 times the concentrations in ERS-fed mice (P < 0.05). Plasma concentrations and urine excretion of purine metabolites in DAs was ≤1.62 ± 0.45 times the concentrations in DCs (P < 0.05). The excretion of 13 purine metabolites in urine from SF infants was ≤175 ± 39 times the excretion in HM and MF infants (P < 0.05). mRNA expression of 5'-nucleotidase, cytosolic IIIB, and adenosine deaminase in mice fed ERD was 0.64 ± 0.52 and 0.60 ± 0.28 times the expression in mice fed ERS, respectively. Conclusion: Diets depleted of bovine-milk exosomes and RNA cargos caused increases in hepatic purine metabolites in mice, and in plasma and urine from human adults and infants, compared with exosome-sufficient controls. These findings are important, because purines play a role in intermediary metabolism and cell signaling.

Analyzing the interactions of mRNAs, miRNAs, lncRNAs and circRNAs to predict competing endogenous RNA networks in glioblastoma.

Cross-talk between competitive endogenous RNAs (ceRNAs) may play a critical role in revealing potential mechanisms of tumor development and physiology. Glioblastoma is the most common type of malignant primary brain tumor, and the mechanisms of tumor genesis and development in glioblastoma are unclear. Here, to investigate the role of non-coding RNAs and the ceRNA network in glioblastoma, we performed paired-end RNA sequencing and microarray analyses to obtain the expression profiles of mRNAs, lncRNAs, circRNAs and miRNAs. We identified that the expression of 501 lncRNAs, 1999 mRNAs, 2038 circRNAs and 143 miRNAs were often altered between glioblastoma and matched normal brain tissue. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed on these differentially expressed mRNAs and miRNA-mediated target genes of lncRNAs and circRNAs. Furthermore, we used a multi-step computational framework and several bioinformatics methods to construct a ceRNA network combining mRNAs, miRNAs, lncRNAs and circRNA, based on co-expression analysis between the differentially expressed RNAs. We identified that plenty of lncRNAs, CircRNAs and their downstream target genes in the ceRNA network are related to glutamatergic synapse, suggesting that glutamate metabolism is involved in glioma biological functions. Our results will accelerate the understanding of tumorigenesis, cancer progression and even therapeutic targeting in glioblastoma.

Pd(II)-Catalyzed Carbonyl-Directing Activation of Alkenes: Selective Fluorosulfonylation and Aminosulfonylation of 1,7-Enynes.

A new Pd(II)-catalyzed carbonyl-directing activation of alkenes has been established, enabling radical-induced selective fluorosulfonylation and aminosulfonylation of carbonyl-tethered 1,7-enynes with sulfinic acids and N-fluorobenzenesulfonimide (NFSI) under mild and redox neutral conditions to access densely functionalized ( E)-3,4-dihydronaphthalen-1(2 H)-ones with generally good yields and high stereoselectivity. The selectivity of these bifunctionalizations relies on the electronic nature of substituents on both aryl rings of 1,7-enynes.

Substrate-Controlled Generation of 3-Sulfonylated 1-Indenones and 3-Arylated ( Z)-Indenes via Cu-Catalyzed Radical Cyclization Cascades of o-Alkynylbenzonitriles.

Substrate-controlled generation of 3-sulfonylated 1-indenones and 3-arylated ( Z)-indenes through radical cyclization cascades of o-alkynylbenzonitriles with sulfonyl hydrazides was established by combining copper(II) with tert-butyl hydroperoxide (TBHP) as a catalytic oxidative system. With the installation of the aryl group (R1) into the alkynyl unit, sulfonyl radicals triggered addition-cyclization cascades to access 3-sulfonylated 1-indenones with good yields by using a Cu/TBHP system, whereas a series of new functionalized 3-arylated ( Z)-indenes were obtained in good yields when o-alkynylbenzonitriles bearing the alkyl group in the alkynyl unit were subjected with arylsulfonyl hydrazides with an electron-rich nature under the above conditions.