Food derived microRNAs

MicroRNAs and the Mediterranean diet: a nutri-omics perspective for lung cancer

Lung cancer is the deadliest cancer type worldwide with ~ 1.8 million deaths per-year. Smoking accounts for ~ 85% of all cases, with a described joint effect with unhealthy diet in lung cancer risk increase. Public health policies to prevent carcinogens exposure, promote smoking cessation and advocacy for healthy nutrition, are therefore highly recommended. Here we have examined the benefits of the Mediterranean Diet (MedDiet) in protecting against some non-communicable diseases including lung cancer, highlighting the epidemiological and biomolecular aspects of MedDiet anti-inflammatory effect and its interaction with smoking habits closely linked to risk of lung cancer. Considering the high incidence and mortality rates of lung cancer, we discussed also about the global impact that a Planeterranean extension of the benefits of MedDiet could have on controlling lung cancer risk. We also debated the impact of personalized nutrition on lung cancer prevention, considering individual heterogeneity in response to diet plans as well as recent advancements on nutri-omics in lung cancer research, with a specific focus on the role of microRNAs (miRNAs) as a promising nutritional molecular hub for lung cancer prevention. We strongly believe that a deep understanding of the molecular link between food components and genetic/epigenetics factors can expand effective intervention strategies.

Trials and Tribulations of MicroRNA Therapeutics

The discovery of the link between microRNAs (miRNAs) and a myriad of human diseases, particularly various cancer types, has generated significant interest in exploring their potential as a novel class of drugs. This has led to substantial investments in interdisciplinary research fields such as biology, chemistry, and medical science for the development of miRNA-based therapies. Furthermore, the recent global success of SARS-CoV-2 mRNA vaccines against the COVID-19 pandemic has further revitalized interest in RNA-based immunotherapies, including miRNA-based approaches to cancer treatment. Consequently, RNA therapeutics have emerged as highly adaptable and modular options for cancer therapy. Moreover, advancements in RNA chemistry and delivery methods have been pivotal in shaping the landscape of RNA-based immunotherapy, including miRNA-based approaches. Consequently, the biotechnology and pharmaceutical industry has witnessed a resurgence of interest in incorporating RNA-based immunotherapies and miRNA therapeutics into their development programs. Despite substantial progress in preclinical research, the field of miRNA-based therapeutics remains in its early stages, with only a few progressing to clinical development, none reaching phase III clinical trials or being approved by the US Food and Drug Administration (FDA), and several facing termination due to toxicity issues. These setbacks highlight existing challenges that must be addressed for the broad clinical application of miRNA-based therapeutics. Key challenges include establishing miRNA sensitivity, specificity, and selectivity towards their intended targets, mitigating immunogenic reactions and off-target effects, developing enhanced methods for targeted delivery, and determining optimal dosing for therapeutic efficacy while minimizing side effects. Additionally, the limited understanding of the precise functions of miRNAs limits their clinical utilization. Moreover, for miRNAs to be viable for cancer treatment, they must be technically and economically feasible for the widespread adoption of RNA therapies. As a result, a thorough risk evaluation of miRNA therapeutics is crucial to minimize off-target effects, prevent overdosing, and address various other issues. Nevertheless, the therapeutic potential of miRNAs for various diseases is evident, and future investigations are essential to determine their applicability in clinical settings.

Garlic-derived exosome-like nanovesicles alleviate dextran sulphate sodium-induced mouse colitis via the TLR4/MyD88/NF-κB pathway and gut microbiota modulation

Plant-derived exosome-like nanovesicles play an important role in transferring their biological cargos to recipient cells. The effect of garlic-derived exosome-like nanovesicles (GENs) against inflammatory bowel disease (IBD) remains unknown. This study aimed to investigate the effect of GENs on dextran sulphate sodium (DSS)-induced colitis in mice. A comprehensive analysis of bioactive components in GENs was performed. Data showed that GENs contained 26 lipids, 61 proteins and 127 known microRNAs (miRNAs). Han-miR3630-5p in GENs could bind to the 3' untranslated region of toll-like receptor 4 (TLR4), which led to the inhibition of TLR4 expression. Besides, GENs significantly up-regulated the expression of barrier-related proteins and inhibited the overproduction of pro-inflammatory cytokines in LPS-induced Caco-2 cells. As a result, pretreatment with GENs at 100 mg kg-1 efficiently ameliorated the inflammatory bowel behavior, intestinal histological pathological damage, and tight junction protein dysfunction induced by DSS in the colon tissue. Intake of GENs significantly down-regulated the expressions of TLR4, myeloid differentiation primary response gene 88 (MyD88), and nuclear factor kappa-B (NF-κB), which suppressed the downstream cascades and led to less secretion of pro-inflammatory cytokines induced by DSS. Furthermore, pretreatment with GENs altered the gut microbiota profile of colitis mice by recovering the relative abundance of Lachnospiraceae and reducing the relative abundance of Helicobacter. Totally, GENs had potential to protect the colon against DSS-induced damage through inhibiting the TLR4/MyD88/NF-κB signaling pathway and regulating gut microbiota. This study clarified the role of miRNAs of GENs in anti-colitis and proved that GENs had a potential application for IBD prevention.

Exogenous miRNAs from Moringa oleifera Lam. recover a dysregulated lipid metabolism

A balanced diet is critical for human health, and edible plants play an important role in providing essential micronutrients as well as specific microRNAs (miRNAs) that can regulate human gene expression. Here we present the effects of Moringa oleifera (MO) miRNAs (mol-miRs) on lipid metabolism. Through in silico studies we identified the potential genes involved in lipid metabolism targeted by mol-miRs. To this end, we tested the efficacy of an aqueous extract of MO seeds (MOES), as suggested in traditional African ethnomedicine, or its purified miRNAs. The biological properties of MO preparations were investigated using a human derived hepatoma cell line (HepG2) as a model. MOES treatment decreased intracellular lipid accumulation and induced apoptosis in HepG2. In the same cell line, transfection with mol-miRs showed similar effects to MOES. Moreover, the effect of the mol-miR pool was investigated in a pre-obese mouse model, in which treatment with mol-miRs was able to prevent dysregulation of lipid metabolism.

Nutrition, Epigenetics, and Major Depressive Disorder: Understanding the Connection

Major depressive disorder (MDD) is a complex, multifactorial disorder of rising prevalence and incidence worldwide. Nearly, 280 million of people suffer from this leading cause of disability in the world. Moreover, patients with this condition are frequently co-affected by essential nutrient deficiency. The typical scene with stress and hustle in developed countries tends to be accompanied by eating disorders implying overnutrition from high-carbohydrates and high-fat diets with low micronutrients intake. In fact, currently, coronavirus disease 2019 (COVID-19) pandemic has drawn more attention to this underdiagnosed condition, besides the importance of the nutritional status in shaping immunomodulation, in which minerals, vitamins, or omega 3 polyunsaturated fatty acids (ω-3 PUFA) play an important role. The awareness of nutritional assessment is greater and greater in the patients with depression since antidepressant treatments have such a significant probability of failing. As diet is considered a crucial environmental factor, underlying epigenetic mechanisms that experience an adaptation or consequence on their signaling and expression mechanisms are reviewed. In this study, we included metabolic changes derived from an impairment in cellular processes due to lacking some essential nutrients in diet and therefore in the organism. Finally, aspects related to nutritional interventions and recommendations are also addressed.

Personalized Nutrition Approach in Pregnancy and Early Life to Tackle Childhood and Adult Non-Communicable Diseases

The development of childhood and adult non-communicable diseases (NCD) is associated with environmental factors, starting from intrauterine life. A new theory finds the roots of epigenetic programming in parental gametogenesis, continuing during embryo development, fetal life, and finally in post-natal life. Maternal health status and poor nutrition are widely recognized as implications in the onset of childhood and adult diseases. Early nutrition, particularly breastfeeding, also plays a primary role in affecting the health status of an individual later in life. A poor maternal diet during pregnancy and lack of breastfeeding can cause a nutrient deficiency that affects the gut microbiota, and acts as a cofactor for many pathways, impacting the epigenetic controls and transcription of genes involved in the metabolism, angiogenesis, and other pathways, leading to NCDs in adult life. Both maternal and fetal genetic backgrounds also affect nutrient adsorption and functioning at the cellular level. This review discusses the most recent evidence on maternal nutrition and breastfeeding in the development of NCD, the potentiality of the omics technologies in uncovering the molecular mechanisms underlying it, with the future prospective of applying a personalized nutrition approach to prevent and treat NCD from the beginning of fetal life.

Uptake of MicroRNAs from Exosome-Like Nanovesicles of Edible Plant Juice by Rat Enterocytes

MicroRNAs (miRNAs) are small RNAs present in extracellular vesicles (EVs) that, when transferred to a target cell, affect its biological functions. Plant miRNAs regulate the expression of certain mammalian genes. Here, we characterized EVs in fruit and vegetable juice, and their miRNA cargo, and investigated whether such miRNA-containing EVs could be taken up by mammalian enterocytes in vitro. Using filtration and ultra-centrifugation methods, EVs were purified from commercially available and manually squeezed plant juice. EV morphological features and subcellular localization were analyzed using the NanoSight tracking system and electron microscopy. Plant EV miRNA levels were evaluated using quantitative reverse transcription PCR. For the in vitro EV uptake experiments, rat intestinal epithelial cells (IEC6) were used. Plant EVs shared morphological features with mammalian EVs and contained miR156a-5p, miR166a-3p, and miR168a-5p. EVs were present in the cell sap-filled central vacuoles and were taken up by IEC6 cells. Edible plant cells produce EVs that contain various miRNAs and release them into the central vacuole. The exogenous plant EVs are taken up by mammalian enterocytes in vitro. These findings suggest the possibility that exogenous plant miRNAs carried by EVs can be absorbed via the gastrointestinal tract.

Environmental risk assessment of the DvSSJ1 dsRNA and the IPD072Aa protein to non-target organisms

Event DP-Ø23211-2 (hereafter referred to as DP23211) maize expresses the DvSSJ1 double-stranded RNA (DvSSJ1 dsRNA) and the IPD072Aa protein, encoded by the ipd072Aa gene. DvSSJ1 dsRNA and the IPD072Aa protein each provide control of corn rootworms (Diabrotica spp.) when expressed in plants. As part of the environmental risk assessment (ERA), the potential hazard to non-target organisms (NTOs) exposed to the DvSSJ1 dsRNA and the IPD072Aa protein expressed in DP23211 maize was assessed. Worst-case estimated environmental concentrations (EECs) for different NTO functional groups (pollinators and pollen feeders, soil dwelling detritivores, predators and parasitoids, aquatic detritivores, insectivorous birds, and wild mammals) were calculated using worst-case assumptions. Several factors that reduce exposure to NTOs under more realistic environmental conditions were applied, when needed to provide more environmentally relevant EECs. Laboratory bioassays were conducted to assess the activity of DvSSJ1 dsRNA or the IPD072Aa protein against selected surrogate species, and margins of exposure (MOEs) were calculated by comparing the Tier I hazard study results to worst-case or refined EECs. Based on specificity and MOE values, DvSSJ1 dsRNA and the IPD072Aa protein expressed in DP23211 maize are not expected to be harmful to NTO populations at environmentally relevant concentrations.

Multi-omics reveals the anticancer mechanism of asparagus saponin-asparanin A on endometrial cancer Ishikawa cells

Multi-omics reveals that AA not only induced apoptosis, but also triggered autophagy in Ishikawa cells through ER stress and DNA damage-related pathways.

Soybean-derived miRNAs specifically inhibit proliferation and stimulate apoptosis of human colonic Caco-2 cancer cells but not normal mucosal cells in culture

MicroRNAs (miRNAs) are important regulators of gene expression in eukaryotes. Studies have shown that plant-derived miRNAs can be absorbed through diets and regulate gene expression in mammals. Although soybean-derived miRNAs have been reported, their biological functions are still unclear. In this study, we found that soybean-derived small RNAs (sRNAs) significantly inhibited the proliferation and stimulated the apoptosis of Caco-2 cells. Bioinformatics analysis indicated that the target gene set of soybean miRNAs was extensively enriched in cancer pathways. Besides, we obtained 8 target genes, including Transcription factor 7 (TCF7), associated with colon cancer through prediction. Further studies showed that gma-miR159a inhibited the proliferation of Caco-2 cells and played an important role in the inhibitory effect of sRNAs by inhibiting TCF7 protein, which are upregulated in colon cancer cells but not normal mucosal cells in culture. These findings provide a novel molecular mechanism of soybean-derived miRNAs for potential application in tumor prevention.

In silico prediction of human genes as potential targets for rice miRNAs

BACKGROUND

Exogenous microRNAs (miRNAs) enter the human body through food, and their effects on metabolic processes can be considerable. It is important to determine which miRNAs from plants affect the expression of human genes and the extent of their influence.

METHOD

The binding sites of 738Oryza sativa miRNAs (osa-miRNAs) that interact with 17 508 mRNAs of human genes were determined using the MirTarget program.

RESULT

The characteristics of the binding of 46 single osa-miRNAs to 86 mRNAs of human genes with a value of free energy (ΔG) interaction equal 94%-100% from maximum ΔG were established. The findings showed that osa-miR2102-5p, osa-miR5075-3p, osa-miR2097-5p, osa-miR2919 targeted the largest number of genes at 38, 36, 23, 19 sites, respectively. mRNAs of 86 human genes were identified as targets for 93 osa-miRNAs of all family osa-miRNAs with ΔG values equal 94%-98% from maximum ΔG. Each miRNA of the osa-miR156-5p, osa-miR164-5p, osa-miR168-5p, osa-miR395-3p, osa-miR396-3p, osa-miR396-5p, osa-miR444-3p, osa-miR529-3p, osa-miR1846-3p, osa-miR2907-3p families had binding sites in mRNAs of several human target genes. The binding sites of osa-miRNAs in mRNAs of the target genes for each family of osa-miRNAs were conserved when compared to flanking nucleotide sequences.

CONCLUSION

Target mRNA human genes of osa-miRNAs are also candidate genes of cancer, cardiovascular and neurodegenerative diseases.

Anti-inflammatory effects of miRNA-146a induced in adipose and periodontal tissues

MicroRNA (miRNA) plays an important role in diverse cellular biological processes such as inflammatory response, differentiation and proliferation, and carcinogenesis. miR-146a has been suggested as a negative regulator of the inflammatory reaction. Although, it has been reported as expressed in inflamed adipose and periodontal tissues, however, miR-146a's inhibitory effects against inflammatory response in both the tissues, are not well understood. Therefore, in this study, the inhibitory effects of miR-146a on both adipose and periodontal inflammation, was investigated. In vitro study has revealed that miR-146a transfection into either adipocytes or gingival fibroblasts, has resulted in a reduced cytokine gene expression, observed on co-culturing the cells with macrophages in the presence of lipopolysaccharides (LPS), in comparison to the control miRNA transfected. Similarly, miR-146a transfection into macrophages resulted in a reduced expression of TNF-α gene and protein in response to LPS stimulation. In vivo study revealed that a continuous intravenous miR-146a administration into mice via tail vein, protected the mice from developing high-fat diet-induced obesity and the inflammatory cytokine gene expression was down-regulated in both adipose and periodontal tissues. miR-146a appeared to be induced by macrophage-derived inflammatory signals such as TNF-α by negative feed-back mechanism, and it suppressed inflammatory reaction in both adipose and periodontal tissues. Therefore, miR-146a could be suggested as a potential therapeutic molecule and as a common inflammatory regulator for both obesity-induced diabetes and related periodontal diseases.

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miR-146a induced by adipose and periodontal inflammation via macrophage mediators.

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miR-146a is a negative inflammation regulator in adipose and periodontal tissues.

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miR-146a is a potential therapeutic target against obesity and periodontal diseases.

Association of oral dysbiosis with oral cancer development

Oral squamous cell carcinoma (OSCC) is the leading cause of mortality for oral cancer. Numerous risk factors mainly related to unhealthy habits and responsible for chronic inflammation and infections have been recognized as predisposing factors for oral carcinogenesis. Recently, even microbiota alterations have been associated with the development of human cancers. In particular, some specific bacterial strains have been recognized and strongly associated with oral cancer development (Capnocytophaga gingivalis, Fusobacterium spp., Streptococcus spp., Peptostreptococcus spp., Porphyromonas gingivalis and Prevotella spp.). Several hypotheses have been proposed to explain how the oral microbiota could be involved in cancer pathogenesis by mainly paying attention to chronic inflammation, microbial synthesis of cancerogenic substances, and alteration of epithelial barrier integrity. Based on knowledge of the carcinogenic effects of dysbiosis, it was recently suggested that probiotics may have anti-tumoral activity. Nevertheless, few data exist with regard to probiotic effects on oral cancer. On this basis, the association between the development of oral cancer and oral dysbiosis is discussed focusing attention on the potential benefits of probiotics administration in cancer prevention.

Nutritive implications of dietary microRNAs: facts, controversies, and perspectives

As a group of non-coding RNA molecules, microRNAs have recently become more well-known due to their pivotal role in gene regulation. A large number of endogenous microRNAs naturally occur in the human body, and some of them act as regulatory targets of diet and its components. The wide presence of microRNAs in various food materials has inspired food scientists and nutritionists to explore their nutritive and bioactive significance. This article comprehensively reports updated insights into the accessibility, stability, absorbability, and bioactivity of dietary microRNAs by combining the current knowledge into figures and tables for reader's convenience. As one frontier in food science and nutrition, the research platform on dietary microRNAs is imperfect and even defective as indicated by the inconsistent and even contradictory results concluded by different investigations. The pros and cons as well as the limitations of current investigations have been critically discussed with attention chiefly paid to experimental designs and protocols. Moreover, future research directions have been recommended. Thus, this paper may not only provide a quick glance at the state-of-the-art of dietary microRNAs but also guide further research to clarify the present controversies and make the results more credible and persuasive.

Tuscany Sangiovese grape juice imparts cardioprotection by regulating gene expression of cardioprotective C-type natriuretic peptide

PURPOSE

A regular intake of red grape juice has cardioprotective properties, but its role on the modulation of natriuretic peptides (NPs), in particular of C-type NP (CNP), has not yet been proven. The aims were to evaluate: (1) in vivo the effects of long-term intake of Tuscany Sangiovese grape juice (SGJ) on the NPs system in a mouse model of myocardial infarction (MI); (2) in vitro the response to SGJ small RNAs of murine MCEC-1 under physiological and ischemic condition; (3) the activation of CNP/NPR-B/NPR-C in healthy human subjects after 7 days' SGJ regular intake.

METHODS

(1) C57BL/6J male and female mice (n = 33) were randomly subdivided into: SHAM (n = 7), MI (n = 15) and MI fed for 4 weeks with a normal chow supplemented with Tuscany SGJ (25% vol/vol, 200 µl/per day) (MI + SGJ, n = 11). Echocardiography and histological analyses were performed. Myocardial NPs transcriptional profile was investigated by Real-Time PCR. (2) MCEC-1 were treated for 24 h with a pool of SGJ small RNAs and cell viability under 24 h exposure to H₂O₂ was evaluated by MTT assay. (3) Human blood samples were collected from seven subjects before and after the 7 days' intake of Tuscany SGJ. NPs and miRNA transcriptional profile were investigated by Real-Time PCR in MCEC-1 and human blood.

RESULTS

Our experimental data, obtained in a multimodal pipeline, suggest that the long-term intake of SGJ promotes an adaptive response of the myocardium to the ischemic microenvironment through the modulation of the cardiac CNP/NPR-B/NPR-C system.

CONCLUSIONS

Our results open new avenue in the development of functional foods aimed at enhancing cardioprotection of infarcted hearts through action on the myocardial epigenome.

Role of microRNA (miRNA) and Viroids in Lethal Diseases of Plants and Animals. Potential Contribution to Human Neurodegenerative Disorders

Both plants and animals have adopted a common strategy of using ~18-25-nucleotide small non-coding RNAs (sncRNAs), known as microRNAs (miRNAs), to transmit DNA-based epigenetic information. miRNAs (i) shape the total transcriptional output of individual cells; (ii) regulate and fine-tune gene expression profiles of cell clusters, and (iii) modulate cell phenotype in response to environmental stimuli and stressors. These miRNAs, the smallest known carriers of gene-encoded post-transcriptional regulatory information, not only regulate cellular function in healthy cells but also act as important mediators in the development of plant and animal diseases. Plants possess their own specific miRNAs; at least 32 plant species have been found to carry infectious sncRNAs called viroids, whose mechanisms of generation and functions are strikingly similar to those of miRNAs. This review highlights recent remarkable and sometimes controversial findings in miRNA signaling in plants and animals. Special attention is given to the intriguing possibility that dietary miRNAs and/or sncRNAs can function as mobile epigenetic and/or evolutionary linkers between different species and contribute to both intra- and interkingdom signaling. Wherever possible, emphasis has been placed on the relevance of these miRNAs to the development of human neurodegenerative diseases, such as Alzheimer's disease. Based on the current available data, we suggest that such xeno-miRNAs may (i) contribute to the beneficial properties of medicinal plants, (ii) contribute to the negative properties of disease-causing or poisonous plants, and (iii) provide cross-species communication between kingdoms of living organisms involving multiple epigenetic and/or potentially pathogenic mechanisms associated with the onset and pathogenesis of various diseases.

Apple-Derived Nanoparticles Modulate Expression of Organic-Anion-Transporting Polypeptide (OATP) 2B1 in Caco-2 Cells

Interaction of foods with intestinal transporters has generally been ascribed to small molecules, but recently, edible-plant-derived nanoparticles (NPs) have been suggested to affect intestinal function. Here, we examined the effects of NPs contained in edible fruits on intestinal transporters. Apple-derived NPs (APNPs) were isolated by ultracentrifugation and characterized by measurement of particle size distribution and electron microscopy. Human epithelial colorectal adenocarcinoma (Caco-2) cells internalized fluorescently labeled APNPs, suggesting that fruit-derived NPs would be internalized into intestinal epithelial cells in vivo. We found that the mRNA expression levels of several transporters, including organic-anion-transporting polypeptide (OATP) 2B1, were changed in APNP-treated Caco-2 cells. The protein expression and activity of OATP2B1 were also decreased by APNP exposure, as determined by Western blotting and measurements of [³H]estrone-3-sulfate uptake by Caco-2 cells, respectively. These actions required intact APNPs, because sonication or boiling abrogated the effects. Since the content of apple-derived small molecules in APNPs was negligible, the observed decrease of OATP2B1 expression appears to be mediated by large molecules in the APNPs. We further found that the 3'-untranslated region of the OATP2B1 gene was required for the response to APNPs, suggesting that microRNA in the APNPs might be involved. These results propose a novel mechanism, in which large molecules such as microRNA in food could affect intestinal transporters through food-derived NPs, which also demonstrates that food-derived NPs should be useful for delivery of biologically active large molecules to intestinal tissues.

High degradation and no bioavailability of artichoke miRNAs assessed using an in vitro digestion/Caco-2 cell model

Although the cross-kingdom transfer of vegetable miRNAs (miRNAs) in mammalian species, including humans, is still controversial, recent studies have rejected this theory. Based on these recent studies, we hypothesized that artichoke-derived miRNAs (cca-miRNAs) are not adsorbed into human intestinal cells after cooking and in vitro digestion. In order to test this hypothesis, we evaluated miRNA (cca-miRNAs) in the edible part of globe artichokes (head portion), after cooking and digestion by an in vitro digestion system. The cca-miRNA levels were analyzed by real-time PCR (RT-qPCR), and those that withstood cooking and digestion conditions were further analyzed for their bioavailability using an in vitro system (Caco-2/TC7 cell clone). We detected 20 cca-miRNAs after cooking, 5 of which were statistically down-regulated in comparison with uncooked samples. Only 4 cca-miRNAs were found after in vitro digestion. By using scanning electron microscopy (SEM), we also evaluated the extracellular vesicles (EVs) in homogenized artichoke as possible miRNA transporters. However, approximately 81% were degraded after cooking, while the remaining EVs had changed shape from round to elliptical. Finally, we detected no cell-free cca-miRNAs, miRNAs bound to protein complex, and no cca-miRNAs encapsulated in EVs inside Caco-2 cells or in basolateral medium after bioavailability experiments. In conclusion, the data from the present study agrees with recent findings that the human small intestine does not uptake dietary miRNAs from raw or cooked artichoke heads.

Pleiotropic functions of miR107 in cancer networks

MicroRNAs are short regulatory RNAs that posttranscriptionally modulate gene expression and thus play crucial roles in controlling cancer-onset, growth, and progression processes. miR107, a highly conserved microRNA that maps to intron 5 of the PANK1 gene, contributes to the regulation of normal and tumor biological processes. Studies have reported that miR107 has oncogenic or tumor-suppressor functions in different human tumors. The pleiotropic functions of miR107 in various cancers are achieved via its targeting different genes that are involved in tumor proliferation, invasiveness, metastasis, angiogenesis, and chemotherapy-response pathways. The carcinogenicity or cancer-suppressor effects of miR107 occur in a tissue- and cell-specific manner, and the expression level of miR107 can be affected by various factors, including epigenetic and genetic factors, treatment exposure, and daily diet. A comprehensive analysis of the current literature suggests that miR107 functions as a central element in the regulation of cancer networks and can be used as a potential diagnostic and prognostic biomarker and drug target for therapeutic intervention.

Theobromine Does Not Affect Fasting and Postprandial HDL Cholesterol Efflux Capacity, While It Decreases Fasting miR-92a Levels in Humans

SCOPE

Chocolate consumption lowers cardiovascular disease risk, which might be attributed to the methylxanthine theobromine. These effects may be mediated through effects on HDL-mediated cholesterol efflux, which may be affected by microRNA (miRNA) levels in the HDL particles. Therefore, the aim of this study is to investigate effects of theobromine consumption on fasting and postprandial cholesterol efflux and miRNAs levels.

METHODS AND RESULTS

Thirty overweight and 14 obese healthy men and women participated in this randomized, double-blind crossover study. Participants consumed 500 mg d-1 of theobromine or placebo for 4 weeks. ABCA1-mediated cholesterol efflux was measured using J774 macrophages. MiRNAs levels (miR-92a, miR-223, miR-135a*) were quantified in apolipoprotein B-depleted serum. Theobromine consumption did not affect fasting and postprandial cholesterol efflux. Fasting miR-223 and miR-135a levels were unchanged, while miR-92a levels were decreased (-0.21; p < 0.05). The high-fat meal increased postprandial cholesterol efflux capacity (+4.3 percentage points; p ≤ 0.001), miR-92a (+1.21; p < 0.001), and miR-223 (+1.79; p < 0.001) levels, while a trend was found for miR-135a (+1.08; p = 0.06).

CONCLUSION

Theobromine did not improve fasting and postprandial ABCA1-mediated cholesterol efflux capacity, but decreased fasting miR-92a levels. High-fat meal intake increased postprandial cholesterol efflux and the three selected miRNAs levels.

Nutrimiromics: Role of microRNAs and Nutrition in Modulating Inflammation and Chronic Diseases

Nutrimiromics studies the influence of the diet on the modification of gene expression due to epigenetic processes related to microRNAs (miRNAs), which may affect the risk for the development of chronic diseases. miRNAs are a class of non-coding endogenous RNA molecules that are usually involved in post-transcriptional gene silencing by inducing mRNA degradation or translational repression by binding to a target messenger RNA. They can be controlled by environmental and dietary factors, particularly by isolated nutrients or bioactive compounds, indicating that diet manipulation may hold promise as a therapeutic approach in modulating the risk of chronic diseases. This review summarizes the evidence regarding the influence of nutrients and bioactive compounds on the expression of miRNAs related to inflammation and chronic disease in several models (cell culture, animal models, and human trials).

Wilson disease: At the crossroads between genetics and epigenetics-A review of the evidence

Environmental factors, including diet, exercise, stress, and toxins, profoundly impact disease phenotypes. This review examines how Wilson disease (WD), an autosomal recessive genetic disorder, is influenced by genetic and environmental inputs. WD is caused by mutations in the copper-transporter gene ATP7B, leading to the accumulation of copper in the liver and brain, resulting in hepatic, neurological, and psychiatric symptoms. These symptoms range in severity and can first appear anytime between early childhood and old age. Over 300 disease-causing mutations in ATP7B have been identified, but attempts to link genotype to the phenotypic presentation have yielded little insight, prompting investigators to identify alternative mechanisms, such as epigenetics, to explain the highly varied clinical presentation. Further, WD is accompanied by structural and functional abnormalities in mitochondria, potentially altering the production of metabolites that are required for epigenetic regulation of gene expression. Notably, environmental exposure affects the regulation of gene expression and mitochondrial function. We present the "multi-hit" hypothesis of WD progression, which posits that the initial hit is an environmental factor that affects fetal gene expression and epigenetic mechanisms and subsequent "hits" are environmental exposures that occur in the offspring after birth. These environmental hits and subsequent changes in epigenetic regulation may impact copper accumulation and ultimately WD phenotype. Lifestyle changes, including diet, increased physical activity, stress reduction, and toxin avoidance, might influence the presentation and course of WD, and therefore may serve as potential adjunctive or replacement therapies.

Formidable challenges to the notion of biologically important roles for dietary small RNAs in ingesting mammals

The notion of uptake of active diet-derived small RNAs (sRNAs) in recipient organisms could have significant implications for our understanding of oral therapeutics and nutrition, for the safe use of RNA interference (RNAi) in agricultural biotechnology, and for ecological relationships. Yet, the transfer and subsequent regulation of gene activity by diet-derived sRNAs in ingesting mammals are still heavily debated. Here, we synthesize current information based on multiple independent studies of mammals, invertebrates, and plants. Rigorous assessment of these data emphasize that uptake of active dietary sRNAs is neither a robust nor a prevalent mechanism to maintain steady-state levels in higher organisms. While disagreement still continues regarding whether such transfer may occur in specialized contexts, concerns about technical difficulties and a lack of consensus on appropriate methods have led to questions regarding the reproducibility and biologic significance of some seemingly positive results. For any continuing investigations, concerted efforts should be made to establish a strong mechanistic basis for potential effects of dietary sRNAs and to agree on methodological guidelines for realizing such proof. Such processes would ensure proper interpretation of studies aiming to prove dietary sRNA activity in mammals and inform potential for application in therapeutics and agriculture.

Uptake and impact of natural diet-derived small RNA in invertebrates: Implications for ecology and agriculture

The putative transfer and gene regulatory activities of diet-derived small RNAs (sRNAs) in ingesting animals are still debated. The existence of natural uptake of diet-derived sRNA by invertebrate species could have significant implication for our understanding of ecological relationships and could synergize with efforts to use RNA interference (RNAi) technology in agriculture. Here, we synthesize information gathered from studies in invertebrates using natural or artificial dietary delivery of sRNA and from studies of sRNA in vertebrate animals and plants to review our current understanding of uptake and impact of natural diet-derived sRNA on invertebrates. Our understanding has been influenced and sometimes confounded by the diversity of invertebrates and ingested plants studied, our limited insights into how gene expression may be modulated by dietary sRNAs at the mechanistic level, and the paucity of studies focusing directly on natural uptake of sRNA. As such, we suggest 2 strategies to investigate this phenomenon more comprehensively and thus facilitate the realization of its potentially broad impact on ecology and agriculture in the future.

MapReduce Algorithms for Inferring Gene Regulatory Networks from Time-Series Microarray Data Using an Information-Theoretic Approach

Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections are known as gene regulatory networks (GRNs). Elucidating GRNs is crucial to understand the inner workings of the cell and the complexity of gene interactions. To date, numerous algorithms have been developed to infer gene regulatory networks. However, as the number of identified genes increases and the complexity of their interactions is uncovered, networks and their regulatory mechanisms become cumbersome to test. Furthermore, prodding through experimental results requires an enormous amount of computation, resulting in slow data processing. Therefore, new approaches are needed to expeditiously analyze copious amounts of experimental data resulting from cellular GRNs. To meet this need, cloud computing is promising as reported in the literature. Here, we propose new MapReduce algorithms for inferring gene regulatory networks on a Hadoop cluster in a cloud environment. These algorithms employ an information-theoretic approach to infer GRNs using time-series microarray data. Experimental results show that our MapReduce program is much faster than an existing tool while achieving slightly better prediction accuracy than the existing tool.

Nutrigenomics of extra-virgin olive oil: A review

Nutrigenomics data on the functional components of olive oil are still sparse, but rapidly increasing. Olive oil is the main source of fat and health-promoting component of the Mediterranean diet. Positive effects have been observed on genes involved in the pathobiology of most prevalent age- and lifestyle-related human conditions, such as cancer, cardiovascular disease and neurodegeneration. Other effects on health-promoting genes have been identified for bioactive components of olives and olive leafs. Omics technologies are offering unique opportunities to identify nutritional and health biomarkers associated with these gene responses, the use of which in personalized and even predictive protocols of investigation, is a main breakthrough in modern medicine and nutrition. Gene regulation properties of the functional components of olive oil, such as oleic acid, biophenols and vitamin E, point to a role for these molecules as natural homeostatic and even hormetic factors with applications as prevention agents in conditions of premature and pathologic aging. Therapeutic applications can be foreseen in conditions of chronic inflammation, and particularly in cancer, which will be discussed in detail in this review paper as major clinical target of nutritional interventions with olive oil and its functional components. © 2016 BioFactors, 43(1):17-41, 2017.

Circulating plant miRNAs can regulate human gene expression in vitro

While Brassica oleracea vegetables have been linked to cancer prevention, the exact mechanism remains unknown. Regulation of gene expression by cross-species microRNAs has been previously reported; however, its link to cancer suppression remains unexplored. In this study we address both issues. We confirm plant microRNAs in human blood in a large nutrigenomics study cohort and in a randomized dose-controlled trial, finding a significant positive correlation between the daily amount of broccoli consumed and the amount of microRNA in the blood. We also demonstrate that Brassica microRNAs regulate expression of human genes and proteins in vitro, and that microRNAs cooperate with other Brassica-specific compounds in a possible cancer-preventive mechanism. Combined, we provide strong evidence and a possible multimodal mechanism for broccoli in cancer prevention.

Environmental control of microRNAs in the nervous system: Implications in plasticity and behavior

The discovery of microRNAs (miRNAs) a little over 20 years ago was revolutionary given that miRNAs are essential to numerous physiological and physiopathological processes. Currently, several aspects of the biogenic process of miRNAs and of the translational repression mechanism exerted on their targets mRNAs are known in detail. In fact, the development of bioinformatics tools for predicting miRNA targets has established that miRNAs have the potential to regulate almost all known biological processes. Therefore, the identification of the signals and molecular mechanisms that regulate miRNA function is relevant to understanding the role of miRNAs in both pathological and adaptive processes. Recently, a series of studies has focused on miRNA expression in the brain, establishing that their levels are altered in response to various environmental factors (EFs), such as light, sound, odorants, nutrients, drugs and stress. In this review, we discuss how exposure to various EFs modulates the expression and function of several miRNAs in the nervous system and how this control determines adaptation to their environment, behavior and disease state.

MicroRNA expression profiles of bovine milk exosomes in response to Staphylococcus aureus infection

BACKGROUND

Milk exosomes are a rich source of microRNAs (miRNAs) that are protected from degradation. Ingestion of milk and subsequent absorption of miRNAs into recipient cells by endocytosis may play a role in the regulation of neonatal innate and adaptive immunity. In contrast, the miRNA content of milk exosomes may also be indicative of a lactating animal's health; whereby, the presence or absence of specific miRNAs could serve as biomarkers for early detection of bacterial infection that can lead to mastitis. In the present study, we therefore analyzed and compared miRNA expression profiles of milk exosomes from four Holstein cows obtained during mid-lactation prior to and after infection (48 h) of the mammary gland with Staphylococcus aureus.

METHODS

Milk exosomes, purified from control and S. aureus infected cows, were extracted for RNA. Following preparation indexed libraries from both groups the samples were subjected to next generation sequencing.

RESULTS

Next generation sequencing of eight, unpooled small RNA libraries derived from milk exosomes produced about 60.5 million high-quality, bovine-specific sequence reads for comparison of miRNA expression between treatments. Sequence identity analysis showed the miRNAs make up about 13 % of the average RNA content of these exosomes. Although 417 known bovine miRNAs were identified, miRNAs represented the least diverse class of RNA accounting for only 1 % of all unique sequences. The 20 most prevalent unique sequences within this class accounted for about 90 % of the total miRNA-associated reads across samples. Non-annotated, unique reads provided evidence for another 303 previously unknown bovine miRNAs. Expression analyses found 14 known bovine microRNAs significantly differed in frequency between exosomes from infected and control animals.

CONCLUSIONS

Our survey of miRNA expression from uninfected milk exosomes and those produced in response to infection provides new and comprehensive information supporting a role for delivery into milk of specific miRNAs involved in immune response. In particular, bta-miR-142-5p, and -223 are potential biomarkers for early detection of bacterial infection of the mammary gland. Additionally, 22 mammary-expressed genes involved in regulation of host immune processes and response to inflammation were identified as potential binding targets of the differentially expressed miRNAs.