201
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Yang J, Elbaz-Younes I, Primo C, Murungi D, Hirschi KD. Intestinal permeability, digestive stability and oral bioavailability of dietary small RNAs. Sci Rep 2018; 8:10253. [PMID: 29980707 PMCID: PMC6035168 DOI: 10.1038/s41598-018-28207-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022] Open
Abstract
Impactful dietary RNA delivery requires improving uptake and enhancing digestive stability. In mouse feeding regimes, we have demonstrated that a plant-based ribosomal RNA (rRNA), MIR2911, is more bioavailable than synthetic MIR2911 or canonical microRNAs (miRNAs). Here mutagenesis was used to discern if MIR2911 has a distinctive sequence that aids stability and uptake. Various mutations had modest impacts while one scrambled sequence displayed significantly enhanced digestive stability, serum stability, and bioavailability. To assess if small RNA (sRNA) bioavailability in mice could be improved by increasing gut permeability, various diets, genetic backgrounds and pharmacological methods were surveyed. An intraperitoneal injection of anti-CD3 antibody enhanced gut permeability which correlated with improved uptake of the digestively stable scrambled MIR2911 variant. However, the bioavailability of canonical miRNAs was not enhanced. Similarly, interleukin-10 (IL-10)-deficient mice and mice treated with aspirin displayed enhanced gut permeability that did not enhance uptake of most plant-based sRNAs. This work supports a model where dietary RNAs are vulnerable to digestion and altering gut permeability alone will not impact apparent bioavailability. We suggest that some dietary sRNA may be more digestively stable and methods to broadly increase sRNA uptake requires delivery vehicles to optimize gut and serum stability in the consumer.
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Affiliation(s)
- Jian Yang
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Avenue, Houston, TX, 77030, USA
| | - Ismail Elbaz-Younes
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Avenue, Houston, TX, 77030, USA
| | - Cecilia Primo
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Avenue, Houston, TX, 77030, USA
| | - Danna Murungi
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Avenue, Houston, TX, 77030, USA
| | - Kendal D Hirschi
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Avenue, Houston, TX, 77030, USA.
- Vegetable and Fruit Improvement Center, Texas A&M University, College Station, TX, 77845, USA.
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202
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203
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The potential atheroprotective role of plant MIR156a as a repressor of monocyte recruitment on inflamed human endothelial cells. J Nutr Biochem 2018; 57:197-205. [DOI: 10.1016/j.jnutbio.2018.03.026] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 03/21/2018] [Accepted: 03/27/2018] [Indexed: 02/04/2023]
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204
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Zhao Q, Liu Y, Zhang N, Hu M, Zhang H, Joshi T, Xu D. Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples. PLoS One 2018; 13:e0187519. [PMID: 29949574 PMCID: PMC6021041 DOI: 10.1371/journal.pone.0187519] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 05/14/2018] [Indexed: 02/07/2023] Open
Abstract
In recent years, an increasing number of studies have reported the presence of plant miRNAs in human samples, which resulted in a hypothesis asserting the existence of plant-derived exogenous microRNA (xenomiR). However, this hypothesis is not widely accepted in the scientific community due to possible sample contamination and the small sample size with lack of rigorous statistical analysis. This study provides a systematic statistical test that can validate (or invalidate) the plant-derived xenomiR hypothesis by analyzing 388 small RNA sequencing data from human samples in 11 types of body fluids/tissues. A total of 166 types of plant miRNAs were found in at least one human sample, of which 14 plant miRNAs represented more than 80% of the total plant miRNAs abundance in human samples. Plant miRNA profiles were characterized to be tissue-specific in different human samples. Meanwhile, the plant miRNAs identified from microbiome have an insignificant abundance compared to those from humans, while plant miRNA profiles in human samples were significantly different from those in plants, suggesting that sample contamination is an unlikely reason for all the plant miRNAs detected in human samples. This study also provides a set of testable synthetic miRNAs with isotopes that can be detected in situ after being fed to animals.
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Affiliation(s)
- Qi Zhao
- Department of Computer Science and Technology, Jilin University, Changchun, Jilin, China
- Department of Electrical Engineering and Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- Sino-Dutch Biomedical and Information Engineering School, Northeastern University, Shenyang, Liaoning, China
| | - Yuanning Liu
- Department of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Ning Zhang
- MU Informatics Institute, University of Missouri, Columbia, Missouri, United States of America
| | - Menghan Hu
- Department of Biostatistics, Brown University, Providence, Rhode Island, United States of America
| | - Hao Zhang
- Department of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Trupti Joshi
- Department of Electrical Engineering and Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- MU Informatics Institute, University of Missouri, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Dong Xu
- Department of Computer Science and Technology, Jilin University, Changchun, Jilin, China
- Department of Electrical Engineering and Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- MU Informatics Institute, University of Missouri, Columbia, Missouri, United States of America
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205
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Patel M, Patel S, Mangukia N, Patel S, Mankad A, Pandya H, Rawal R. Ocimum basilicum miRNOME revisited: A cross kingdom approach. Genomics 2018; 111:772-785. [PMID: 29775783 DOI: 10.1016/j.ygeno.2018.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/29/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023]
Abstract
O. basilicum is medicinally important herb having inevitable role in human health. However, the mechanism of action is largely unknown. Present study aims to understand the mechanism of regulation of key human target genes that could plausibly modulated by O. basilicum miRNAs in cross kingdom manner using computational and system biology approach. O. basilicum miRNA sequences were retrieved and their corresponding human target genes were identified using psRNA target and interaction analysis of hub nodes. Six O. basilicum derived miRNAs were found to modulate 26 human target genes which were associated `with PI3K-AKTand MAPK signaling pathways with PTPN11, EIF2S2, NOS1, IRS1 and USO1 as top 5 Hub nodes. O. basilicum miRNAs not only regulate key human target genes having a significance in various diseases but also paves the path for future studies that might explore potential of miRNA mediated cross-kingdom regulation, prevention and treatment of various human diseases including cancer.
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Affiliation(s)
- Maulikkumar Patel
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Shanaya Patel
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Naman Mangukia
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Saumya Patel
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Archana Mankad
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Himanshu Pandya
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Rakesh Rawal
- Department of Life Sciences, Food Science and Nutrition, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India.
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206
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The Stability of Medicinal Plant microRNAs in the Herb Preparation Process. Molecules 2018; 23:molecules23040919. [PMID: 29659501 PMCID: PMC6016954 DOI: 10.3390/molecules23040919] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 01/23/2023] Open
Abstract
Herbal medicine is now globally accepted as a valid alternative system of pharmaceutical therapies. Various studies around the world have been initiated to develop scientific evidence-based herbal therapies. Recently, the therapeutic potential of medicinal plant derived miRNAs has attracted great attraction. MicroRNAs have been indicated as new bioactive ingredients in medicinal plants. However, the stability of miRNAs during the herbal preparation process and their bioavailability in humans remain unclear. Viscum album L. (European mistletoe) has been widely used in folk medicine for the treatment of cancer and cardiovascular diseases. Our previous study has indicated the therapeutic potential of mistletoe miRNAs by using bioinformatics tools. To evaluate the stability of these miRNAs, various mistletoe extracts that mimic the clinical medicinal use as well as traditional folk medicinal use were prepared. The mistletoe miRNAs including miR166a-3p, miR159a, miR831-5p, val-miR218 and val-miR11 were quantified by stem-loop qRT-PCR. As a result, miRNAs were detectable in the majority of the extracts, indicating that consumption of medicinal plant preparations might introduce miRNAs into mammals. The factors that might cause miRNA degradation include ultrasonic treatment, extreme heat, especially RNase treatment, while to be associated with plant molecules (e.g., proteins, exosomes) might be an efficient way to protect miRNAs against degradation. Our study confirmed the stability of plant derived miRNAs during herb preparations, suggesting the possibility of functionally intact medicinal plant miRNAs in mammals.
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207
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Tomé-Carneiro J, Fernández-Alonso N, Tomás-Zapico C, Visioli F, Iglesias-Gutierrez E, Dávalos A. Breast milk microRNAs harsh journey towards potential effects in infant development and maturation. Lipid encapsulation can help. Pharmacol Res 2018; 132:21-32. [PMID: 29627443 DOI: 10.1016/j.phrs.2018.04.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/03/2018] [Accepted: 04/03/2018] [Indexed: 12/18/2022]
Abstract
The possibility that diet-derived miRNAs survive the gastrointestinal tract and exert biological effects in target cells is triggering considerable research in the potential abilities of alimentary preventive and therapeutic approaches. Many validation attempts have been carried out and investigators disagree on several issues. The barriers exogenous RNAs must surpass are harsh and adequate copies must reach target cells for biological actions to be carried out. This prospect opened a window for previously unlikely scenarios concerning exogenous non-coding RNAs, such as a potential role for breast milk microRNAs in infants' development and maturation. This review is focused on the thorny path breast milk miRNAs face towards confirmation as relevant role players in infants' development and maturation, taking into consideration the research carried out so far on the uptake, gastrointestinal barriers and potential biological effects of diet-derived miRNAs. We also discuss the future pharmacological and pharma-nutritional consequences of appropriate miRNAs research.
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Affiliation(s)
- João Tomé-Carneiro
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM+CSIC, Madrid 28049, Spain
| | | | - Cristina Tomás-Zapico
- Department of Functional Biology (Physiology), University of Oviedo, Oviedo 33006, Spain; Universidad Autónoma de Chile, Santiago 7500912, Chile
| | - Francesco Visioli
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM+CSIC, Madrid 28049, Spain; Department of Molecular Medicine, University of Padova, Padova 35121, Italy
| | | | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM+CSIC, Madrid 28049, Spain.
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208
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Fan W, Qi Y, Qiu L, He P, Liu C, Li Z. Click Chemical Ligation-Initiated On-Bead DNA Polymerization for the Sensitive Flow Cytometric Detection of 3'-Terminal 2'-O-Methylated Plant MicroRNA. Anal Chem 2018; 90:5390-5397. [PMID: 29600844 DOI: 10.1021/acs.analchem.8b00589] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A versatile flow cytometric strategy is developed for the sensitive detection of plant microRNA (miRNA) by coupling the target-templated click nucleic acid ligation (CNAL) with on-bead terminal enzymatic DNA polymerization (TEP). Unlike ligase-catalyzed ligation reaction, the plant miRNA-templated enzyme-free CNAL between two single-stranded DNA (ssDNA) probes, respectively modified with Aza-dibenzocyclooctyne (Aza-DBCO) and N3, can not only simplify the operation, but also achieve a much higher ligation efficiency. More importantly, the undesirable nonspecific ligation between the Aza-DBCO- and N3-modified ssDNA, can be effectively eliminated by adding Tween-20, which allows the use of cycling CNAL (CCNAL) in a background-free manner. So each plant miRNA can template many rounds of CNAL reaction to produce numerous ligation products, forming efficient signal amplification. The ligated ssDNA can be anchored on the magnetic beads (MBs) with the 3'-OH termini exposed outside. Then terminal deoxynucleotidyl transferase (TdT), a sequence-independent and template-free polymerase, would specifically catalyze the DNA polymerization along these 3'-OH termini on the MBs, forming poly(T) tails up to thousands of nucleotides long. Each poly(T) tail allows specific binding of numerous 6-carboxyfluorescein (FAM)-labeled poly(A)25 oligonucleotides to accumulate a lot of fluorophores on the MBs, leading to the second step of signal amplification. By integrating the advantages of CCNAL-TEP for highly efficient signal amplification and robust MBs signal readout with powerful flow cytometer, high sensitivity is achieved and the detection limit of plant miRNA has been pushed down to a low level of 5 fM with high specificity to well discriminate even single-base difference between miRNA targets.
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Affiliation(s)
- Wenjiao Fan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Yan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Liying Qiu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Pan He
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Chenghui Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
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209
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Zhang W, Li X, Ma L, Urrehman U, Bao X, Zhang Y, Zhang CY, Hou D, Zhou Z. Identification of microRNA-like RNAs in Ophiocordyceps sinensis. SCIENCE CHINA-LIFE SCIENCES 2018; 62:349-356. [DOI: 10.1007/s11427-017-9277-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/29/2017] [Indexed: 01/07/2023]
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210
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Zhao Z, Yu S, Li M, Gui X, Li P. Isolation of Exosome-Like Nanoparticles and Analysis of MicroRNAs Derived from Coconut Water Based on Small RNA High-Throughput Sequencing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2749-2757. [PMID: 29478310 DOI: 10.1021/acs.jafc.7b05614] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
In this study, the presence of microRNAs in coconut water was identified by real-time polymerase chain reaction (PCR) based on the results of high-throughput small RNA sequencing. In addition, the differences in microRNA content between immature and mature coconut water were compared. A total of 47 known microRNAs belonging to 25 families and 14 new microRNAs were identified in coconut endosperm. Through analysis using a target gene prediction software, potential microRNA target genes were identified in the human genome. Real-time PCR showed that the level of most microRNAs was higher in mature coconut water than in immature coconut water. Then, exosome-like nanoparticles were isolated from coconut water. After ultracentrifugation, some particle structures were seen in coconut water samples using 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate fluorescence staining. Subsequent scanning electron microscopy observation and dynamic light scattering analysis also revealed some exosome-like nanoparticles in coconut water, and the mean diameters of the particles detected by the two methods were 13.16 and 59.72 nm, respectively. In conclusion, there are extracellular microRNAs in coconut water, and their levels are higher in mature coconut water than in immature coconut water. Some exosome-like nanoparticles were isolated from coconut water, and the diameter of these particles was smaller than that of animal-derived exosomes.
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Affiliation(s)
- Zhehao Zhao
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology , Tongji University , 1239 Siping Road , Shanghai 200092 , People's Republic of China
| | - Siran Yu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology , Tongji University , 1239 Siping Road , Shanghai 200092 , People's Republic of China
| | - Min Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology , Tongji University , 1239 Siping Road , Shanghai 200092 , People's Republic of China
| | - Xin Gui
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology , Tongji University , 1239 Siping Road , Shanghai 200092 , People's Republic of China
| | - Ping Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology , Tongji University , 1239 Siping Road , Shanghai 200092 , People's Republic of China
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211
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Witwer KW. Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma. F1000Res 2018; 7:244. [PMID: 29744036 PMCID: PMC5904727 DOI: 10.12688/f1000research.14060.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2018] [Indexed: 12/22/2022] Open
Abstract
Background: A 2017 study reported that “Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi”. Analysis of two human blood plasma sequencing datasets was said to provide evidence for uptake of plant miRNAs into human plasma. The results were also purportedly inconsistent with contamination. Methods: Sequences from public datasets and miRNA databases were compared with results downloaded from the website of the reporting journal. Results: Only one putative plant miRNA (“peu-MIR2910) mapped consistently above background, and this sequence is found with 100% identity in a human rRNA. Several other rarer but consistently mapped putative plant miRNAs also have 100% or near 100% matches to human transcripts or genomic sequences, and some do not appear to map to plant genomes at all. Conclusions: Reanalysis of public data suggests that dietary plant xenomiR uptake is not supported, but instead confirms previous findings that detection of rare plant miRNAs in mammalian sequencing datasets is artifactual. Some putative plant miRNAs, including MIR2910 and MIR2911, may represent human sequence contamination or other artifacts in plant studies, emphasizing the need for rigorous controls and data filtering strategies when assessing possible xenomiRNAs.
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Affiliation(s)
- Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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212
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Comparative Study of Withanolide Biosynthesis-Related miRNAs in Root and Leaf Tissues of Withania somnifera. Appl Biochem Biotechnol 2018; 185:1145-1159. [PMID: 29476318 DOI: 10.1007/s12010-018-2702-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022]
Abstract
Withania somnifera, popularly known as Indian ginseng, is one of the most important medicinal plants. The plant is well studied in terms of its pharmaceutical activities and genes involved in biosynthetic pathways. However, not much is known about the regulatory mechanism of genes responsible for the production of secondary metabolites. The idea was to identify miRNA transcriptome responsible for the regulation of withanolide biosynthesis, specifically of root and leaf tissues individually. The transcriptome data of in vitro culture of root and leaf tissues of the plant was considered for miRNA identification. A total of 24 and 39 miRNA families were identified in root and leaf tissues, respectively. Out of these, 15 and 27 miRNA families have shown their involvement in different biological functions in root and leaf tissues, respectively. We report here, specific miRNAs and their corresponding target genes for corresponding root and leaf tissues. The target genes have also been analyzed for their role in withanolide metabolism. Endogenous root-miR5140, root-miR159, leaf-miR477, and leaf-miR530 were reported for regulation of withanolide biosynthesis.
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213
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Abstract
The gut microbiota, as the main member in gut microecology, is an essential mediator in health and disease. The gut microbiota interacts with various organs and systems in the body, including brain, lung, liver, bone, cardiovascular system, and others. Microbiota-derived metabolites such as the short chain fatty acid (SCFA) butyrate are primary signals, which link the gut microbiota and physiology. Recently, the gut microbiota has been identified as the origin of a number of diseases by influencing the related cell signaling pathways such as WNT/beta-catenin pathway in colorectal cancer and T cell receptor signaling in the central nervous system. Moreover, several microRNAs participate in signaling networks through the intervention of the gut microbiota. The interaction between the gut microbiota and miRNAs plays a crucial role in vascular dysfunction and hepatocellular carcinoma (HCC). In this review, we will report and discuss recent findings about the crosstalk between the gut microbiota and physical organs and how the gut microbiota and miRNAs regulate each other while influencing the host via genes, proteins, or metabolites.
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Affiliation(s)
- Qingqing Feng
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Wei-Dong Chen
- Key Laboratory of Receptors-Mediated Gene Regulation and Drug Discovery, School of Medicine, Henan University, Kaifeng, China.,Key Laboratory of Molecular Pathology, School of Basic Medical Science, Inner Mongolia Medical University, Hohhot, China
| | - Yan-Dong Wang
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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214
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Huang H, Davis CD, Wang TTY. Extensive Degradation and Low Bioavailability of Orally Consumed Corn miRNAs in Mice. Nutrients 2018; 10:nu10020215. [PMID: 29462875 PMCID: PMC5852791 DOI: 10.3390/nu10020215] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 01/09/2023] Open
Abstract
The current study seeks to resolve the discrepancy in the literature regarding the cross-kingdom transfer of plant microRNAs (miRNAs) into mammals using an improved miRNA processing and detection method. Two studies utilizing C57BL/6 mice were performed. In the first study, mice were fed an AIN-93M diet and gavaged with water, random deoxynucleotide triphosphates (dNTP) or isolated corn miRNAs for two weeks (n = 10 per group). In the second study, mice were fed an AIN-93M diet, or the diet supplemented with 3% fresh or autoclaved corn powder for two weeks (n = 10 per group). Corn miRNA levels were analyzed in blood and tissue samples by real-time PCR (RT-PCR) following periodate oxidation and β elimination treatments to eliminate artifacts. After removing false positive detections, there were no differences in corn miRNA levels between control and treated groups in cecal, fecal, liver and blood samples. Using an in vitro digestion system, corn miRNAs in AIN-93M diet or in the extracts were found to be extensively degraded. Less than 1% was recovered in the gastrointestinal tract after oral and gastric phases. In conclusion, no evidence of increased levels of corn miRNAs in whole blood or tissues after supplementation of corn miRNAs in the diet was observed in a mouse model.
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Affiliation(s)
- Haiqiu Huang
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD 20705, USA.
- Office of Dietary Supplements, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Cindy D Davis
- Office of Dietary Supplements, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Thomas T Y Wang
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD 20705, USA.
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215
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Chen X, Wu RZ, Zhu YQ, Ren ZM, Tong YL, Yang F, Dai GH. Study on the inhibition of Mfn1 by plant-derived miR5338 mediating the treatment of BPH with rape bee pollen. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 18:38. [PMID: 29382326 PMCID: PMC5791735 DOI: 10.1186/s12906-018-2107-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/19/2018] [Indexed: 01/10/2023]
Abstract
Background Recent studies have found that plant derived microRNA can cross-kingdom regulate the expression of genes in humans and other mammals, thereby resisting diseases. Can exogenous miRNAs cross the blood-prostate barrier and entry prostate then participate in prostate disease treatment? Methods Using HiSeq sequencing and RT-qPCR technology, we detected plant miRNAs that enriched in the prostates of rats among the normal group, BPH model group and rape bee pollen group. To forecast the functions of these miRNAs, the psRobot software and TargetFinder software were used to predict their candidate target genes in rat genome. The qRT-PCR technology was used to validate the expression of candidate target genes. Results Plant miR5338 was enriched in the posterior lobes of prostate gland of rats fed with rape bee pollen, which was accompanied by the improvement of BPH. Among the predicted target genes of miR5338, Mfn1 was significantly lower in posterior lobes of prostates of rats in the rape bee pollen group than control groups. Further experiments suggested that Mfn1 was highly related to BPH. Conclusions These results suggesting that plant-derived miR5338 may involve in treatment of rat BPH through inhibiting Mfn1 in prostate. These results will provide more evidence for plant miRNAs cross-kingdom regulation of animal gene, and will provide preliminary theoretical and experimental basis for development of rape bee pollen into innovative health care product or medicine for the treatment of BPH. Electronic supplementary material The online version of this article (10.1186/s12906-018-2107-y) contains supplementary material, which is available to authorized users.
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216
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Wang L, Sadri M, Giraud D, Zempleni J. RNase H2-Dependent Polymerase Chain Reaction and Elimination of Confounders in Sample Collection, Storage, and Analysis Strengthen Evidence That microRNAs in Bovine Milk Are Bioavailable in Humans. J Nutr 2018; 148:153-159. [PMID: 29378054 PMCID: PMC6251634 DOI: 10.1093/jn/nxx024] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/23/2017] [Indexed: 12/13/2022] Open
Abstract
Background Evidence suggests that dietary microRNAs (miRs) are bioavailable and regulate gene expression across species boundaries. Concerns were raised that the detection of dietary miRs in plasma might have been due to sample contamination or lack of assay specificity. Objectives: The objectives of this study were to assess potential confounders of plasma miR analysis and to detect miRs from bovine milk in human plasma. Methods Potential confounders of plasma miR analysis (circadian rhythm, sample collection and storage, calibration, and erythrocyte hemolysis) were assessed by quantitative reverse transcriptase polymerase chain reaction (PCR) by using blood from healthy adults (7 men, 6 women; aged 23-57 y). Bovine miRs were analyzed by RNase H2-dependent PCR (rhPCR) in plasma collected from a subcohort of 11 participants before and 6 h after consumption of 1.0 L of 1%-fat bovine milk. Results The use of heparin tubes for blood collection resulted in a complete loss of miRs. Circadian variations did not affect the concentrations of 8 select miRs. Erythrocyte hemolysis caused artifacts for some miRs if plasma absorbance at 414 nm was >0.300. The stability of plasma miRs depended greatly on the matrix in which the miRs were stored and whether the plasma was frozen before analysis. Purified miR-16, miR-200c, and cel-miR-39 were stable for ≤24 h at room temperature, whereas losses equaled ≤80% if plasma was frozen, thawed, and stored at room temperature for as little as 4 h. rhPCR distinguished between bovine and human miRs with small variations in the nucleotide sequence; plasma concentrations of Bos taurus (bta)-miR-21-5p and bta-miR-30a-5p were >100% higher 6 h after milk consumption than before milk consumption. Conclusions Confounders in plasma miR analysis include the use of heparin tubes, erythrocyte hemolysis, and storage of thawed plasma at room temperature. rhPCR is a useful tool to detect dietary miRs.
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Affiliation(s)
- Lanfang Wang
- Department of Nutrition and Health Sciences, University of Nebraska–Lincoln,
Lincoln, NE
| | - Mahrou Sadri
- Department of Nutrition and Health Sciences, University of Nebraska–Lincoln,
Lincoln, NE
| | - David Giraud
- Department of Nutrition and Health Sciences, University of Nebraska–Lincoln,
Lincoln, NE
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska–Lincoln,
Lincoln, NE,Address correspondence to JZ (e-mail: )
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General Overviews on Applications of ELISA. SPRINGERBRIEFS IN APPLIED SCIENCES AND TECHNOLOGY 2018. [DOI: 10.1007/978-981-10-6766-2_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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218
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Zhao Y, Wen H, Teotia S, Du Y, Zhang J, Li J, Sun H, Tang G, Peng T, Zhao Q. Suppression of microRNA159 impacts multiple agronomic traits in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2017; 17:215. [PMID: 29162059 PMCID: PMC5699021 DOI: 10.1186/s12870-017-1171-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 11/10/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND microRNAs (miRNAs) are important regulators in plant growth and development. miR159 is a conserved miRNA among different plant species and has various functions in plants. Studies on miR159 are mostly done on model plant, Arabidopsis thaliana. In rice, studies on miR159 were either based upon genome-wide expression analyses focused upon responses to different nitrogen forms and abiotic stress or upon phenotypic studies of transgenic plants overexpressing its precursor. STTM (Short Tandem Target Mimic) is an effective tool to block the activity of endogenous mature miRNA activity in plant. Therefore, specific roles of miR159 in rice could be explored by down regulating miR159 through STTM. RESULTS In this study, expression of mature miR159 was successfully suppressed by STTM which resulted in the increased expressions of its two targets genes, OsGAMYB and OsGAMYBL1 (GAMYB-LIKE 1). Overall, STTM159 plants exhibited short stature along with smaller organ size and reduction in stem diameter, length of flag leaf, main panicle, spikelet hulls and grain size. Histological analysis of stem, leaf and mature spikelet hull showed the reduced number of small vascular bundles (SVB), less number of small veins (SV) between two big veins (LV) and less cell number in outer parenchyma. Gene Ontology (GO) enrichment analysis of differentially expressed genes between wild type plants and STTM159 transgenic plants showed that genes involved in cell division, auxin, cytokinin (CK) and brassinosteroids (BRs) biosynthesis and signaling are significantly down-regulated in STTM159 plants. CONCLUSION Our data suggests that in rice, miR159 positively regulates organ size, including stem, leaf, and grain size due to the promotion of cell division. Further analysis from the RNA-seq data showed that the decreased cell divisions in STTM159 transgenic plants may result, at least partly from the lower expression of the genes involved in cell cycle and hormone homeostasis, which provides new insights of rice miR159-specific functions.
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Affiliation(s)
- Yafan Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002 China
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, 450002 China
| | - Huili Wen
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002 China
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, 450002 China
| | - Sachin Teotia
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002 China
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931 USA
| | - Yanxiu Du
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002 China
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, 450002 China
| | - Jing Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002 China
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, 450002 China
| | - Junzhou Li
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002 China
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, 450002 China
| | - Hongzheng Sun
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002 China
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, 450002 China
| | - Guiliang Tang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002 China
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931 USA
| | - Ting Peng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002 China
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, 450002 China
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002 China
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, 450002 China
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Wang W, Hang C, Zhang Y, Chen M, Meng X, Cao Q, Song N, Itkow J, Shen F, Yu D. Dietary miR-451 protects erythroid cells from oxidative stress via increasing the activity of Foxo3 pathway. Oncotarget 2017; 8:107109-107124. [PMID: 29291015 PMCID: PMC5739800 DOI: 10.18632/oncotarget.22346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 08/26/2017] [Indexed: 11/25/2022] Open
Abstract
One fundamental issue in public health is the safety of food products derived from plants and animals. A recent study raised a concern that microRNAs, which widely exist in everyday foods, may alter consumers' functions. However, some studies have strongly questioned the likelihood of dietary uptake of functional microRNAs in mammals. Here we use a microRNA gene knockout animal model to show that miR-144/451 null mice can orally uptake miR-451 from a daily chow diet, and ingestion of wild type blood, that contains abundant miR-451, also enhances the level of miR-451 in the circulating blood of knockout mice. Moreover, reducing miR-451 level in miR-144/451 knockout blood by consuming food lacking miR-451 reduces the anti-oxidant capacity of miR-144/451 null red blood cells by targeting the 14-3-3ζ/Foxo3 pathway, while increasing miR-451 level via gavage-feeding of wild type blood increases the anti-oxidant capacity of miR-144/451 null red blood cells. We conclude that 1) some miRNAs in food can pass through the gastrointestinal tract into the blood to affect consumers' function and 2) microRNA knockout animals such as miR-144/451 null mice can acquire the deleted genetic information from daily foods, which might alter the results and conclusions from the studies using such animals.
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Affiliation(s)
- Wanchen Wang
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University School of Medicine, Yangzhou 225001, China
| | - Chengwen Hang
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University School of Medicine, Yangzhou 225001, China
| | - Yanqing Zhang
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University School of Medicine, Yangzhou 225001, China
| | - Mingshi Chen
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University School of Medicine, Yangzhou 225001, China
| | - Xinyu Meng
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University School of Medicine, Yangzhou 225001, China
| | - Qing Cao
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University School of Medicine, Yangzhou 225001, China
| | - Nana Song
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University School of Medicine, Yangzhou 225001, China
| | - Jacobi Itkow
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University School of Medicine, Yangzhou 225001, China
| | - Feiyang Shen
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University School of Medicine, Yangzhou 225001, China
| | - Duonan Yu
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University School of Medicine, Yangzhou 225001, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou 225001, China.,Institute of Translational Medicine, Yangzhou University School of Medicine, Yangzhou 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou 225001, China
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Kasiappan R, Rajarajan D. Role of MicroRNA Regulation in Obesity-Associated Breast Cancer: Nutritional Perspectives. Adv Nutr 2017; 8:868-888. [PMID: 29141971 PMCID: PMC5682994 DOI: 10.3945/an.117.015800] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Breast cancer is the most common malignancy diagnosed in women, and the incidence of breast cancer is increasing every year. Obesity has been identified as one of the major risk factors for breast cancer progression. The mechanisms by which obesity contributes to breast cancer development is not yet understood; however, there are a few mechanisms counted as potential producers of breast cancer in obesity, including insulin resistance, chronic inflammation and inflammatory cytokines, adipokines, and sex hormones. Recent emerging evidence suggests that alterations in microRNA (miRNA) expressions are found in several diseases, including breast cancer and obesity; however, miRNA roles in obesity-linked breast cancer are beginning to unravel. miRNAs are thought to be potential noninvasive biomarkers for diagnosis and prognosis of cancer patients with comorbid conditions of obesity as well as therapeutic targets. Recent studies have evidenced that nutrients and other dietary factors protect against cancer and obesity through modulation of miRNA expressions. Herein, we summarize a comprehensive overview of up-to-date information related to miRNAs and their molecular targets involved in obesity-associated breast cancer. We also address the mechanisms by which dietary factors modulate miRNA expression and its protective roles in obesity-associated breast cancer. It is hoped that this review would provide new therapeutic strategies for the treatment of obesity-associated breast cancer to reduce the burden of breast cancer.
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Affiliation(s)
- Ravi Kasiappan
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
| | - Dheeran Rajarajan
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
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221
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Xie W, Adolf J, Melzig MF. Identification of Viscum album L. miRNAs and prediction of their medicinal values. PLoS One 2017; 12:e0187776. [PMID: 29112983 PMCID: PMC5675405 DOI: 10.1371/journal.pone.0187776] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 10/25/2017] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of approximately 22 nucleotides single-stranded non-coding RNA molecules that play crucial roles in gene expression. It has been reported that the plant miRNAs might enter mammalian bloodstream and have a functional role in human metabolism, indicating that miRNAs might be one of the hidden bioactive ingredients in medicinal plants. Viscum album L. (Loranthaceae, European mistletoe) has been widely used for the treatment of cancer and cardiovascular diseases, but its functional compounds have not been well characterized. We considered that miRNAs might be involved in the pharmacological activities of V. album. High-throughput Illumina sequencing was performed to identify the novel and conserved miRNAs of V. album. The putative human targets were predicted. In total, 699 conserved miRNAs and 1373 novel miRNAs have been identified from V. album. Based on the combined use of TargetScan, miRanda, PITA, and RNAhybrid methods, the intersection of 30697 potential human genes have been predicted as putative targets of 29 novel miRNAs, while 14559 putative targets were highly enriched in 33 KEGG pathways. Interestingly, these highly enriched KEGG pathways were associated with some human diseases, especially cancer, cardiovascular diseases and neurological disorders, which might explain the clinical use as well as folk medicine use of mistletoe. However, further experimental validation is necessary to confirm these human targets of mistletoe miRNAs. Additionally, target genes involved in bioactive components synthesis in V. album were predicted as well. A total of 68 miRNAs were predicted to be involved in terpenoid biosynthesis, while two miRNAs including val-miR152 and miR9738 were predicted to target viscotoxins and lectins, respectively, which increased the knowledge regarding miRNA-based regulation of terpenoid biosynthesis, lectin and viscotoxin expressions in V. album.
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Affiliation(s)
- Wenyan Xie
- Institut für Pharmazie, Freie Universität Berlin, Berlin, Germany
- * E-mail:
| | - Jacob Adolf
- Technische Hochschule Wildau, Wildau, Germany
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Yang J, Kongchan N, Primo Planta C, Neilson JR, Hirschi KD. The atypical genesis and bioavailability of the plant-based small RNA MIR2911: Bulking up while breaking down. Mol Nutr Food Res 2017; 61:10.1002/mnfr.201600974. [PMID: 28319645 PMCID: PMC5583006 DOI: 10.1002/mnfr.201600974] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 12/21/2022]
Abstract
SCOPE The uptake of dietary plant small RNAs (sRNAs) in consumers remains controversial, which is mainly due to low dietary content in combination with poor fractional absorption. MIR2911, among all the plant sRNAs including microRNAs, has been shown to be one of the most robustly absorbed sRNAs. Here we analyze the unusual abundance and unique genesis of MIR2911 during vegetable processing. METHODS AND RESULTS Using qRT-PCR, the abundance of MIR2911 increased dramatically in macerated tissues while other microRNAs degraded. The accumulation of MIR2911 correlated with the degradation of the rRNAs, consistent with MIR2911 being derived from the 26S rRNA. Bioinformatic analysis predicts a microRNA-like precursor structure for MIR2911; however, no reciprocal increase in the putative star-strand was noted, and using an Arabidopsis mutation deficient in miRNA processing the accumulation of MIR2911 appeared Dicer independent. MIR2911 was incorporated into the mammalian RNA-induced silencing complex as demonstrated in HEK293T cells, where transfected synthetic MIR2911 modestly suppressed the activity of a cognate luciferase reporter. CONCLUSION The genesis and amplification of MIR2911 post-harvest is atypical, as traditional plant bioactives are less plentiful as vegetables lose freshness. These findings offer an explanation to the disparity in serum detection between MIR2911 and canonical plant-based miRNAs.
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Affiliation(s)
- Jian Yang
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Natee Kongchan
- Department of Molecular Biology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Cecilia Primo Planta
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Joel R Neilson
- Department of Molecular Biology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Kendal D Hirschi
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
- Vegetable and Fruit Improvement Center, Texas A&M University, College Station, TX, USA
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223
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Zhu K, Liu M, Fu Z, Zhou Z, Kong Y, Liang H, Lin Z, Luo J, Zheng H, Wan P, Zhang J, Zen K, Chen J, Hu F, Zhang CY, Ren J, Chen X. Plant microRNAs in larval food regulate honeybee caste development. PLoS Genet 2017; 13:e1006946. [PMID: 28859085 PMCID: PMC5578494 DOI: 10.1371/journal.pgen.1006946] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 07/27/2017] [Indexed: 11/18/2022] Open
Abstract
The major environmental determinants of honeybee caste development come from larval nutrients: royal jelly stimulates the differentiation of larvae into queens, whereas beebread leads to worker bee fate. However, these determinants are not fully characterized. Here we report that plant RNAs, particularly miRNAs, which are more enriched in beebread than in royal jelly, delay development and decrease body and ovary size in honeybees, thereby preventing larval differentiation into queens and inducing development into worker bees. Mechanistic studies reveal that amTOR, a stimulatory gene in caste differentiation, is the direct target of miR162a. Interestingly, the same effect also exists in non-social Drosophila. When such plant RNAs and miRNAs are fed to Drosophila larvae, they cause extended developmental times and reductions in body weight and length, ovary size and fecundity. This study identifies an uncharacterized function of plant miRNAs that fine-tunes honeybee caste development, offering hints for understanding cross-kingdom interaction and co-evolution. How caste has formed in honeybees is an enduring puzzle. The prevailing view is that royal jelly stimulates the differentiation of larvae into queen. Here, we uncover a new mechanism that plant miRNAs in worker bee’s food postpone larval development, thereby inducing sterile worker bees. Thus, the theories about honeybee caste formation need to be re-examined from a new angle besides the traditional focus on royal jelly and its components. Furthermore, since miRNAs are transmitted between species of different kingdoms and can contribute to the phenotype regulation, this new model of horizontal miRNA transfer may open up a new avenue to further study the molecular mechanisms underlying cross-kingdom interaction and co-evolution.
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Affiliation(s)
- Kegan Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
| | - Minghui Liu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
| | - Zheng Fu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
| | - Zhen Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
| | - Yan Kong
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
| | - Hongwei Liang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
| | - Zheguang Lin
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Jun Luo
- Model Animal Research Center and MOE Key Laboratory of Model Animals for Disease Study, Nanjing University, Nanjing, China
| | - Huoqing Zheng
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Ping Wan
- Model Animal Research Center and MOE Key Laboratory of Model Animals for Disease Study, Nanjing University, Nanjing, China
| | - Junfeng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
| | - Ke Zen
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
| | - Jiong Chen
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
- Model Animal Research Center and MOE Key Laboratory of Model Animals for Disease Study, Nanjing University, Nanjing, China
- * E-mail: (XC); (JR); (CZ); (FH); (JC)
| | - Fuliang Hu
- College of Animal Science, Zhejiang University, Hangzhou, China
- * E-mail: (XC); (JR); (CZ); (FH); (JC)
| | - Chen-Yu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
- * E-mail: (XC); (JR); (CZ); (FH); (JC)
| | - Jie Ren
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- * E-mail: (XC); (JR); (CZ); (FH); (JC)
| | - Xi Chen
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing, China
- * E-mail: (XC); (JR); (CZ); (FH); (JC)
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Yadav S, Shekhawat M, Jahagirdar D, Kumar Sharma N. Natural and artificial small RNAs: a promising avenue of nucleic acid therapeutics for cancer. Cancer Biol Med 2017; 14:242-253. [PMID: 28884041 PMCID: PMC5570601 DOI: 10.20892/j.issn.2095-3941.2017.0038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/22/2017] [Indexed: 01/02/2023] Open
Abstract
Since the failure of traditional therapy, gene therapy using functional DNA sequence and small RNA/DNA molecules (oligonucleotide) has become a promising avenue for cancer treatment. The discovery of RNA molecules has impelled researchers to investigate small regulatory RNA from various natural and artificial sources and determine a cogent target for controlling tumor progression. Small regulatory RNAs are used for therapeutic silencing of oncogenes and aberrant DNA repair response genes. Despite their advantages, therapies based on small RNAs exhibit limitations in terms of stability of therapeutic drugs, precision-based delivery in tissues, precision-based intercellular and intracellular targeting, and tumor heterogeneity-based responses. In this study, we summarize the potential and drawbacks of small RNAs in nucleic acid therapeutics for cancer.
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Affiliation(s)
- Sunny Yadav
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
| | - Mamta Shekhawat
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
| | - Devashree Jahagirdar
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
| | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
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225
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Yang J, Primo C, Elbaz-Younes I, Hirschi KD. Bioavailability of transgenic microRNAs in genetically modified plants. GENES & NUTRITION 2017; 12:17. [PMID: 29507644 PMCID: PMC5831112 DOI: 10.1186/s12263-017-0563-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/18/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Transgenic expression of small RNAs is a prevalent approach in agrobiotechnology for the global enhancement of plant foods. Meanwhile, emerging studies have, on the one hand, emphasized the potential of transgenic microRNAs (miRNAs) as novel dietary therapeutics and, on the other, suggested potential food safety issues if harmful miRNAs are absorbed and bioactive. For these reasons, it is necessary to evaluate the bioavailability of transgenic miRNAs in genetically modified crops. RESULTS As a pilot study, two transgenic Arabidopsis lines ectopically expressing unique miRNAs were compared and contrasted with the plant bioavailable small RNA MIR2911 for digestive stability and serum bioavailability. The expression levels of these transgenic miRNAs in Arabidopsis were found to be comparable to that of MIR2911 in fresh tissues. Assays of digestive stability in vitro and in vivo suggested the transgenic miRNAs and MIR2911 had comparable resistance to degradation. Healthy mice consuming diets rich in Arabidopsis lines expressing these miRNAs displayed MIR2911 in the bloodstream but no detectable levels of the transgenic miRNAs. CONCLUSIONS These preliminary results imply digestive stability and high expression levels of miRNAs in plants do not readily equate to bioavailability. This initial work suggests novel engineering strategies be employed to enhance miRNA bioavailability when attempting to use transgenic foods as a delivery platform.
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Affiliation(s)
- Jian Yang
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030 USA
| | - Cecilia Primo
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030 USA
| | - Ismail Elbaz-Younes
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030 USA
| | - Kendal D. Hirschi
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030 USA
- Vegetable and Fruit Improvement Center, Texas A&M University, College Station, TX 77845 USA
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226
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Chan SY, Snow JW. Formidable challenges to the notion of biologically important roles for dietary small RNAs in ingesting mammals. GENES AND NUTRITION 2017; 12:13. [PMID: 29308096 PMCID: PMC5753850 DOI: 10.1186/s12263-017-0561-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 04/19/2017] [Indexed: 02/07/2023]
Abstract
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.
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Affiliation(s)
- Stephen Y Chan
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, BST 1704.2, 200 Lothrop Street, Pittsburgh, PA 15261 USA
| | - Jonathan W Snow
- Department of Biology, Barnard College, New York, NY 10027 USA
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Hou YH, Jeyaraj A, Zhang X, Wei CL. Absolute quantification of microRNAs in green tea (Camellia sinensis) by stem-loop quantitative real-time PCR. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:2975-2981. [PMID: 27861949 DOI: 10.1002/jsfa.8137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 10/03/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND There are some studies to show that food-derived plant microRNAs (miRNAs) may be detected in mammals. The research evidence has provoked a considerable debate whether plant-derived miRNAs exert the same regulatory functions as endogenous animal miRNAs. To test the hypothesis, methods of highly sensitive absolute quantification miRNAs have been developed. However, absolute miRNA quantification of green tea has not yet been reported. This study is the first to build an absolute quantification method to detect miRNAs level in green tea using stem-loop quantitative real-time PCR (qRT-PCR). RESULTS Two miRNAs, csn-miR164 (a conserved miRNA) and csn-miRn329 (a tea-specific miRNA), were selected as examples for the detection and absolute quantification of miRNAs in green tea samples using stem-loop qRT-PCR. The content of csn-miR164 was significantly higher in the Yuexi Cuilan (YX) samples than in the Shucheng Orchid (SC) samples. The content of csn-miRn329 was found to be high at the start of processing in leaf tissues in both the withering and soaking experiments, after which it gradually decreased with time. CONCLUSION To the best of our knowledge, this is the first report to absolutely quantify the miRNAs present in green tea. This method will help to further investigate the possibility that tea-derived miRNAs may play an important role on defending against various diseases in humans. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Ying-Hui Hou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Anburaj Jeyaraj
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Xiao Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
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228
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Witwer KW, Zhang CY. Diet-derived microRNAs: unicorn or silver bullet? GENES AND NUTRITION 2017; 12:15. [PMID: 28694875 PMCID: PMC5501113 DOI: 10.1186/s12263-017-0564-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 01/09/2023]
Abstract
In ancient lore, a bullet cast from silver is the only effective weapon against monsters. The uptake of active diet-derived microRNAs (miRNAs) in consumers may be the silver bullet long sought after in nutrition and oral therapeutics. However, the majority of scientists consider the transfer and regulation of consumer’s gene activity by these diet-derived miRNAs to be a fantasy akin to spotting a unicorn. Nevertheless, groups like Dr. Chen-Yu Zhang’s lab in Nanjing University have stockpiled breathtaking amounts of data to shoot down these naysayers. Meanwhile, Dr. Ken Witwer at John Hopkins has steadfastly cautioned the field to beware of fallacies caused by contamination, technical artifacts, and confirmation bias. Here, Dr. Witwer and Dr. Zhang share their realities of dietary miRNAs by answering five questions related to this controversial field.
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Affiliation(s)
- Kenneth W Witwer
- Departments of Molecular and Comparative Pathobiology and Neurology, Johns Hopkins University, Baltimore, USA.,School of Life Sciences, Nanjing University, Nanjing, People's Republic of China
| | - Chen-Yu Zhang
- Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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229
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Hirschi KD. Navigating dietary small RNAs. GENES AND NUTRITION 2017; 12:16. [PMID: 28694876 PMCID: PMC5501344 DOI: 10.1186/s12263-017-0565-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 05/19/2017] [Indexed: 11/15/2022]
Abstract
When a novel nutritional concept comes along, scientists become enthusiastic and start new explorations. In 2012, the field was enthralled with a study suggesting plant-based nucleic acid “information” acts as a bioactive to regulate animal metabolism.
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Affiliation(s)
- Kendal D Hirschi
- Children's Nutrition Research Center Baylor College of Medicine, Houston, USA
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230
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Zempleni J. Milk exosomes: beyond dietary microRNAs. GENES AND NUTRITION 2017; 12:12. [PMID: 28694874 PMCID: PMC5501576 DOI: 10.1186/s12263-017-0562-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/19/2017] [Indexed: 12/13/2022]
Abstract
Extracellular vesicles deliver a variety of cargos to recipient cells, including the delivery of cargos in dietary vesicles from bovine milk to non-bovine species. The rate of discovery in this important line of research is slowed by a controversy whether the delivery and bioactivity of a single class of vesicle cargos, microRNAs, are real or not. This opinion paper argues that the evidence in support of the bioavailability of microRNAs encapsulated in dietary exosomes outweighs the evidence produced by scholars doubting that phenomenon is real. Importantly, this paper posits that the time is ripe to look beyond microRNA cargos and pursue innovative pathways through which dietary exosomes alter metabolism. Here, we highlight potentially fruitful lines of exploration.
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Affiliation(s)
- Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE USA
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231
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Cross-Kingdom Regulation of Putative miRNAs Derived from Happy Tree in Cancer Pathway: A Systems Biology Approach. Int J Mol Sci 2017; 18:ijms18061191. [PMID: 28587194 PMCID: PMC5486014 DOI: 10.3390/ijms18061191] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/17/2017] [Accepted: 05/27/2017] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are well-known key regulators of gene expression primarily at the post-transcriptional level. Plant-derived miRNAs may pass through the gastrointestinal tract, entering into the body fluid and regulate the expression of endogenous mRNAs. Camptotheca acuminata, a highly important medicinal plant known for its anti-cancer potential was selected to investigate cross-kingdom regulatory mechanism and involvement of miRNAs derived from this plant in cancer-associated pathways through in silico systems biology approach. In this study, total 33 highly stable putative novel miRNAs were predicted from the publically available 53,294 ESTs of C. acuminata, out of which 14 miRNAs were found to be regulating 152 target genes in human. Functional enrichment, gene-disease associations and network analysis of these target genes were carried out and the results revealed their association with prominent types of cancers like breast cancer, leukemia and lung cancer. Pathways like focal adhesion, regulation of lipolysis in adipocytes and mTOR signaling pathways were found significantly associated with the target genes. The regulatory network analysis showed the association of some important hub proteins like GSK3B, NUMB, PEG3, ITGA2 and DLG2 with cancer-associated pathways. Based on the analysis results, it can be suggested that the ingestion of the C. acuminata miRNAs may have a functional impact on tumorigenesis in a cross-kingdom way and may affect the physiological condition at genetic level. Thus, the predicted miRNAs seem to hold potentially significant role in cancer pathway regulation and therefore, may be further validated using in vivo experiments for a better insight into their mechanism of epigenetic action of miRNA.
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232
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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233
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Zhou G, Zhou Y, Chen X. New Insight into Inter-kingdom Communication: Horizontal Transfer of Mobile Small RNAs. Front Microbiol 2017; 8:768. [PMID: 28507539 PMCID: PMC5410588 DOI: 10.3389/fmicb.2017.00768] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 04/13/2017] [Indexed: 12/12/2022] Open
Abstract
Small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs), are conventionally regarded as critical molecular regulators of various intracellular processes. However, recent accumulating evidence indicates that sRNAs can be transferred within cells and tissues and even across species. In plants, nematodes and microbes, these mobile sRNAs can mediate inter-kingdom communication, environmental sensing, gene expression regulation, host-parasite defense and many other biological functions. Strikingly, a recent study by our group suggested that ingested plant miRNAs are transferred to blood, accumulate in tissues and regulate transcripts in consuming animals. While our and other independent groups’ subsequent studies further explored the emerging field of sRNA-mediated crosstalk between species, some groups reported negative results and questioned its general applicability. Thus, further studies carefully evaluating the horizontal transfer of exogenous sRNAs and its potential biological functions are urgently required. Here, we review the current state of knowledge in the field of the horizontal transfer of mobile sRNAs, suggest its future directions and key points for examination and discuss its potential mechanisms and application prospects in nutrition, agriculture and medicine.
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Affiliation(s)
- Geyu Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing UniversityNanjing, China
| | - Yu Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing UniversityNanjing, China
| | - Xi Chen
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing UniversityNanjing, China
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234
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Abstract
Biological processes such as defense mechanisms and microbial offense strategies are regulated through RNA induced interference in eukaryotes. Genetic mutations are modulated through biogenesis of small RNAs which directly impacts upon host development. Plant defense mechanisms are regulated and supported by a diversified group of small RNAs which are involved in streamlining several RNA interference pathways leading toward the initiation of pathogen gene silencing mechanisms. In the similar context, pathogens also utilize the support of small RNAs to launch their offensive attacks. Also there are strong evidences about the active involvement of these RNAs in symbiotic associations. Interestingly, small RNAs are not limited to the individuals in whom they are produced; they also show cross kingdom influences through variable interactions with other species thus leading toward the inter-organismic gene silencing. The phenomenon is understandable in the microbes which utilize these mechanisms to overcome host defense line. Understanding the mechanism of triggering host defense strategies can be a valuable step toward the generation of disease resistant host plants. We think that the cross kingdom trafficking of small RNA is an interesting insight that is needed to be explored for its vitality.
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Affiliation(s)
- Waqar Islam
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Saif Ul Islam
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Muhammad Qasim
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Liande Wang
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
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235
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Huang H, Roh J, Davis CD, Wang TTY. An improved method to quantitate mature plant microRNA in biological matrices using modified periodate treatment and inclusion of internal controls. PLoS One 2017; 12:e0175429. [PMID: 28399134 PMCID: PMC5388493 DOI: 10.1371/journal.pone.0175429] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/24/2017] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs (miRNAs) ubiquitously exist in microorganisms, plants, and animals, and appear to modulate a wide range of critical biological processes. However, no definitive conclusion has been reached regarding the uptake of exogenous dietary small RNAs into mammalian circulation and organs and cross-kingdom regulation. One of the critical issues is our ability to assess and distinguish the origin of miRNAs. Although periodate oxidation has been used to differentiate mammalian and plant miRNAs, validation of treatment efficiency and the inclusion of proper controls for this method were lacking in previous studies. This study aimed to address: 1) the efficiency of periodate treatment in a plant or mammalian RNA matrix, and 2) the necessity of inclusion of internal controls. We designed and tested spike-in synthetic miRNAs in various plant and mammalian matrices and showed that they can be used as a control for the completion of periodate oxidation. We found that overloading the reaction system with high concentration of RNA resulted in incomplete oxidation of unmethylated miRNA. The abundant miRNAs from soy and corn were analyzed in the plasma, liver, and fecal samples of C57BL/6 mice fed a corn and soy-based chow diet using our improved methodology. The improvement resulted in the elimination of the false positive detection in the liver, and we did not detect plant miRNAs in the mouse plasma or liver samples. In summary, an improved methodology was developed for plant miRNA detection that appears to work well in different sample matrices.
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Affiliation(s)
- Haiqiu Huang
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, Maryland, United States of America
- Office of Dietary Supplements, NIH, Bethesda, Maryland, United States of America
| | - Jamin Roh
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, Maryland, United States of America
| | - Cindy D. Davis
- Office of Dietary Supplements, NIH, Bethesda, Maryland, United States of America
| | - Thomas T. Y. Wang
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, Maryland, United States of America
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236
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Luo Y, Wang P, Wang X, Wang Y, Mu Z, Li Q, Fu Y, Xiao J, Li G, Ma Y, Gu Y, Jin L, Ma J, Tang Q, Jiang A, Li X, Li M. Detection of dietetically absorbed maize-derived microRNAs in pigs. Sci Rep 2017; 7:645. [PMID: 28381865 PMCID: PMC5428504 DOI: 10.1038/s41598-017-00488-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/27/2017] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs are a class of small RNAs that are important in post-transcriptional gene regulation in animals and plants. These single-stranded molecules are widely distributed in organisms and influence fundamental biological processes. Interestingly, recent studies have reported that diet-derived plant miRNAs could regulate mammalian gene expression, and these studies have broadened our view of cross-kingdom communication. In the present study, we evaluated miRNA levels in cooked maize-containing chow diets, and found that plant miRNAs were resistant to the harsh cooking conditions to a certain extent. After feeding fresh maize to pigs (7 days), maize-derived miRNAs could be detected in porcine tissues and serum, and the authenticity of these plant miRNAs was confirmed by using oxidization reactions. Furthermore, in vivo and in vitro experiments demonstrated that dietary maize miRNAs could cross the gastrointestinal tract and enter the porcine bloodstream. In the porcine cells, we found that plant miRNAs are very likely to specifically target their endogenous porcine mRNAs and influence gene expression in a fashion similar to that of mammalian miRNAs. Our results indicate that maize-derived miRNAs can cross the gastrointestinal tract and present in pigs, and these exogenous miRNAs have the potential to regulate mammalian gene expression.
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Affiliation(s)
- Yi Luo
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengjun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yuhao Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhiping Mu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Chongqing Three Gorges University, Chongqing, 404000, China
| | - Qingzhi Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- The Fishery Institute of Sichuan Academy of Agricultural Sciences, Chengdu, 611731, China
| | - Yuhua Fu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Juan Xiao
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guojun Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yao Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Anan Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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237
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Du J, Liang Z, Xu J, Zhao Y, Li X, Zhang Y, Zhao D, Chen R, Liu Y, Joshi T, Chang J, Wang Z, Zhang Y, Zhu J, Liu Q, Xu D, Jiang C. Plant-derived phosphocholine facilitates cellular uptake of anti-pulmonary fibrotic HJT-sRNA-m7. SCIENCE CHINA-LIFE SCIENCES 2017; 62:309-320. [PMID: 28378154 DOI: 10.1007/s11427-017-9026-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 02/21/2017] [Indexed: 02/06/2023]
Abstract
Pulmonary fibrosis, a progressive chronic disease with a high mortality rate, has limited treatment options. Currently, lung transplantation remains the only effective treatment. Here we report that a small RNA, HJT-sRNA-m7, from a Chinese herbal medicine Hong Jing Tian (HJT, RHODIOHAE CRENULATAE RADIX ET RHIZOMA, Rhodiola crenulata) can effectively reduce the expressions of fibrotic hallmark genes and proteins both in alveolar in vitro and in mouse lung tissues in vivo. We also discovered over one hundred oil-soluble chemicals from HJT decoctions, most of which are found in lipid extracts from other Chinese herbals decoctions, including Pu Gong Ying (PGY, TARAXACI HERBA, Taraxacum mongolicum), Chuan Xin Lian (CXL, changed to "ANDROGRAPHIS HERBA, Andrographis paniculata"), and Jin Yin Hua (JYH, lonicera japonica or Honeysuckle). We identified the active component in these decoctions as two forms of phosphocholines, PC (18:0/18:2) and PC (16:0/18:2). These PCs potentially could form liposomes with small RNAs to enter human alveolar and gastric cells. Our experimental results suggest an unprecendent lipid complex route through which botanic small RNA can enter human bodies. Our results provide an innovative treatment strategy for oral delivery of siRNAs as therapeutic medication.
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Affiliation(s)
- Jianchao Du
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Zhu Liang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Jiantao Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Yan Zhao
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Xiaoyun Li
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Yanli Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Dandan Zhao
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Ruxuan Chen
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
- Department of Internal Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yang Liu
- Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Trupti Joshi
- Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
- Department of Health Management and Informatics and Office of Medical Research, School of Medicine, University of Missouri, Columbia, MO, 65212, USA
| | - Jiahui Chang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Zhiqing Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Yanxu Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Jindong Zhu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Qiang Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Dong Xu
- Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Chengyu Jiang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China.
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, 610000, China.
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238
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Abstract
Background Emerging evidence indicates that plant miRNAs can present within human circulating system through dietary intake and regulate human gene expression. Hence we deduced that comestible plants miRNAs can be identified in the public available small RNA sequencing data sets. Results In this study, we identified abundant plant miRNAs sequences from 410 human plasma small RNA sequencing data sets. One particular plant miRNA miR2910, conserved in fruits and vegetables, was found to present in high relative amount in the plasma samples. This miRNA, with same 6mer and 7mer-A1 target seed sequences as hsa-miR-4259 and hsa-miR-4715-5p, was predicted to target human JAK-STAT signaling pathway gene SPRY4 and transcription regulation genes. Conclusions Through analysis of public available plasma small RNA sequencing data, we found the supporting evidence for the plant miRNAs cross kingdom RNAi within human circulating system. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3502-3) contains supplementary material, which is available to authorized users.
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239
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Zheng LL, Deng KW, Deng AC, Wu J, Yang JH, Lun ZR, Qu LH. Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs. Front Microbiol 2017; 8:126. [PMID: 28203233 PMCID: PMC5285362 DOI: 10.3389/fmicb.2017.00126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 01/18/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs that play important roles in animals, plants, and viruses. Deep-sequencing technology has been widely adopted in miRNA investigations. However, it is still a big mysterious why nearly all sequencing data contain miRNA sequences from exogenous species, called exo-miRNAs. In this study, we developed a novel platform, exo-miRExplorer, for mining and identifying exo-miRNAs from high-throughput small RNA sequencing experiments which originated from tissues and cell lines of multiple organisms. Thousands of exo-miRNAs are characterized with their expression abundance, the RNA families, original organisms and the sequencing platforms presented in exo-miRExplorer. Subsequently, we used exo-miRExplorer to perform further analysis. Comparative analysis of the exo-miRNAs between different sequencing datasets revealed significant correlation of exo-miRNAs between experiments in the same study. The plant-derived exo-miRNAs analysis provided robust evidence for non-diet source of exo-miRNAs. Virus-derived exo-miRNA analysis showed that pathogen RNAs could transfer to host cells and exist in deep-sequencing result at abundance level. In conclusion, exo-miRExplorer provides users with an integrative resource to facilitate detection and analysis of exo-miRNAs. exo-miRExplorer is available at the following URL: http://rna.sysu.edu.cn/exomiRDB/.
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Affiliation(s)
- Ling-Ling Zheng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - Kai-Wen Deng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - An-Cheng Deng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - Jie Wu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - Zhao-Rong Lun
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, RNA Information Center, School of Life Sciences, Sun Yat-sen University Guangzhou, China
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240
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Zempleni J, Aguilar-Lozano A, Sadri M, Sukreet S, Manca S, Wu D, Zhou F, Mutai E. Biological Activities of Extracellular Vesicles and Their Cargos from Bovine and Human Milk in Humans and Implications for Infants. J Nutr 2017; 147:3-10. [PMID: 27852870 PMCID: PMC5177735 DOI: 10.3945/jn.116.238949] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/19/2016] [Accepted: 10/20/2016] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) in milk harbor a variety of compounds, including lipids, proteins, noncoding RNAs, and mRNAs. Among the various classes of EVs, exosomes are of particular interest, because cargo sorting in exosomes is a regulated, nonrandom process and exosomes play essential roles in cell-to-cell communication. Encapsulation in exosomes confers protection against enzymatic and nonenzymatic degradation of cargos and provides a pathway for cellular uptake of cargos by endocytosis of exosomes. Compelling evidence suggests that exosomes in bovine milk are transported by intestinal cells, vascular endothelial cells, and macrophages in human and rodent cell cultures, and bovine-milk exosomes are delivered to peripheral tissues in mice. Evidence also suggests that cargos in bovine-milk exosomes, in particular RNAs, are delivered to circulating immune cells in humans. Some microRNAs and mRNAs in bovine-milk exosomes may regulate the expression of human genes and be translated into protein, respectively. Some exosome cargos are quantitatively minor in the diet compared with endogenous synthesis. However, noncanonical pathways have been identified through which low concentrations of dietary microRNAs may alter gene expression, such as the accumulation of exosomes in the immune cell microenvironment and the binding of microRNAs to Toll-like receptors. Phenotypes observed in infant-feeding studies include higher Mental Developmental Index, Psychomotor Development Index, and Preschool Language Scale-3 scores in breastfed infants than in those fed various formulas. In mice, supplementation with plant-derived MIR-2911 improved the antiviral response compared with controls. Porcine-milk exosomes promote the proliferation of intestinal cells in mice. This article discusses the above-mentioned advances in research concerning milk exosomes and their cargos in human nutrition. Implications for infant nutrition are emphasized, where permitted, but data in infants are limited.
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Affiliation(s)
- Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Ana Aguilar-Lozano
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Mahrou Sadri
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Sonal Sukreet
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Sonia Manca
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Di Wu
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Fang Zhou
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Ezra Mutai
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE
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241
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Abstract
MicroRNAs (miRs) hybridize with complementary sequences in mRNA and silence genes by destabilizing mRNA or preventing translation of mRNA. Over 60% of human protein-coding genes are regulated by miRs, and 1881 high-confidence miRs are encoded in the human genome. Evidence suggests that miRs not only are synthesized endogenously, but also might be obtained from dietary sources, and that food compounds alter the expression of endogenous miR genes. The main food matrices for studies of biological activity of dietary miRs include plant foods and cow milk. Encapsulation of miRs in exosomes and exosome-like particles confers protection against RNA degradation and creates a pathway for intestinal and vascular endothelial transport by endocytosis, as well as delivery to peripheral tissues. Evidence suggests that the amount of miRs absorbed from nutritionally relevant quantities of foods is sufficient to elicit biological effects, and that endogenous synthesis of miRs is insufficient to compensate for dietary miR depletion and rescue wild-type phenotypes. In addition, nutrition alters the expression of endogenous miR genes, thereby compounding the effects of nutrition-miR interactions in gene regulation and disease diagnosis in liquid biopsies. For example, food components and dietary preferences may modulate serum miR profiles that may influence biological processes. The complex crosstalk between nutrition, miRs, and gene targets poses a challenge to gene network analysis and studies of human disease. Novel pipelines and databases have been developed recently, including a dietary miR database for archiving reported miRs in 15 dietary resources. miRs derived from diet and endogenous synthesis have been implicated in physiologic and pathologic conditions, including those linked with nutrition and metabolism. In fact, several miRs are actively regulated in response to overnutrition and tissue inflammation, and are involved in facilitating the development of chronic inflammation by modulating tissue-infiltrated immune cell function.
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Affiliation(s)
- Juan Cui
- Department of Computer Science and Engineering and
| | - Beiyan Zhou
- Department of Immunology, University of Connecticut Health Center, Farmington, CT; and
| | - Sharon A Ross
- Nutritional Science Research Group, Division of Cancer Prevention, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda, MD
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE;
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242
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Lukasik A, Zielenkiewicz P. Plant MicroRNAs-Novel Players in Natural Medicine? Int J Mol Sci 2016; 18:ijms18010009. [PMID: 28025496 PMCID: PMC5297644 DOI: 10.3390/ijms18010009] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/14/2016] [Accepted: 12/16/2016] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) represent a class of small non-coding RNAs that act as efficient gene expression regulators and thus play many important roles in living organisms. Due to their involvement in several known human pathological and pathogenic states, miRNA molecules have become an important issue in medicine and gained the attention of scientists from the pharmaceutical industry. In recent few years, a growing number of studies have provided evidence that miRNAs may be transferred from one species to another and regulate gene expression in the recipients’ cells. The most intriguing results revealed that stable miRNAs derived from food plants may enter the mammals’ circulatory system and, after reaching the target, inhibit the production of specific mammalian protein. Part of the scientific community has perceived this as an attractive hypothesis that may provide a foundation for novel therapeutic approaches. In turn, others are convinced about the “false positive” effect of performed experiments from which the mentioned results were achieved. In this article, we review the recent literature that provides evidence (from both fronts) of dietary, plant miRNA uptake and functionality in various consumers. Additionally, we discuss possible miRNA transport mechanisms from plant food sources to human cells.
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Affiliation(s)
- Anna Lukasik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
- Department of Plant Molecular Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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243
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Chen Q, Yan W, Duan E. Epigenetic inheritance of acquired traits through sperm RNAs and sperm RNA modifications. Nat Rev Genet 2016; 17:733-743. [PMID: 27694809 PMCID: PMC5441558 DOI: 10.1038/nrg.2016.106] [Citation(s) in RCA: 306] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Once deemed heretical, emerging evidence now supports the notion that the inheritance of acquired characteristics can occur through ancestral exposures or experiences and that certain paternally acquired traits can be 'memorized' in the sperm as epigenetic information. The search for epigenetic factors in mammalian sperm that transmit acquired phenotypes has recently focused on RNAs and, more recently, RNA modifications. Here, we review insights that have been gained from studying sperm RNAs and RNA modifications, and their roles in influencing offspring phenotypes. We discuss the possible mechanisms by which sperm become acquisitive following environmental-somatic-germline interactions, and how they transmit paternally acquired phenotypes by shaping early embryonic development.
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Affiliation(s)
- Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89512, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89512, USA
| | - Enkui Duan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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244
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Zhang X, Cozen AE, Liu Y, Chen Q, Lowe TM. Small RNA Modifications: Integral to Function and Disease. Trends Mol Med 2016; 22:1025-1034. [PMID: 27840066 DOI: 10.1016/j.molmed.2016.10.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/14/2016] [Indexed: 02/07/2023]
Abstract
Small RNAs have the potential to store a secondary layer of labile biological information in the form of modified nucleotides. Emerging evidence has shown that small RNAs including microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs) and tRNA-derived small RNAs (tsRNAs) harbor a diversity of RNA modifications. These findings highlight the importance of RNA modifications in the modulation of basic properties such as RNA stability and other complex physiological processes involved in stress responses, metabolism, immunity, and epigenetic inheritance of environmentally acquired traits, among others. High-resolution, high-throughput methods for detecting, mapping and screening these small RNA modifications now provide opportunities to uncover their diagnostic potential as sensitive disease markers.
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Affiliation(s)
- Xudong Zhang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Aaron E Cozen
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ying Liu
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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245
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Perge P, Nagy Z, Decmann Á, Igaz I, Igaz P. Potential relevance of microRNAs in inter-species epigenetic communication, and implications for disease pathogenesis. RNA Biol 2016; 14:391-401. [PMID: 27791594 DOI: 10.1080/15476286.2016.1251001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are short non-protein coding RNA molecules involved in the epigenetic regulation of gene expression. Recently, extracellular microRNAs have been described in body fluids that might enable epigenetic communication between distant tissues. Being highly conserved molecules, exogenous xeno-microRNAs from different species could affect gene expression in the host even in a cross-kingdom fashion. Several data underline the relevance of microRNA-mediated communication between virus and host, and there are some experimental data showing that plant- or animal-derived dietary microRNAs might have gene expression modulating activity in humans. Milk-derived microRNAs might be involved in the "epigenetic priming" of the baby. Exogenous microRNAs might be hypothesized to be implicated in disease pathogenesis, e.g. in tumors. Major questions remain to be addressed including the amount of xeno-microRNAs needed for biological action or routes for microRNA delivery. In this brief review, experimental data and hypotheses on the potential pathogenic inter-species relevance of microRNA are presented.
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Affiliation(s)
- Pál Perge
- a 2nd Department of Medicine, Faculty of Medicine , Semmelweis University , Budapest , Hungary
| | - Zoltán Nagy
- a 2nd Department of Medicine, Faculty of Medicine , Semmelweis University , Budapest , Hungary
| | - Ábel Decmann
- a 2nd Department of Medicine, Faculty of Medicine , Semmelweis University , Budapest , Hungary
| | - Ivan Igaz
- b Department of Gastroenterology , Szent Imre Teaching Hospital , Budapest , Hungary
| | - Peter Igaz
- a 2nd Department of Medicine, Faculty of Medicine , Semmelweis University , Budapest , Hungary
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246
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Witwer KW, Halushka MK. Toward the promise of microRNAs - Enhancing reproducibility and rigor in microRNA research. RNA Biol 2016; 13:1103-1116. [PMID: 27645402 DOI: 10.1080/15476286.2016.1236172] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The fields of applied and translational microRNA research have exploded in recent years as microRNAs have been implicated across a spectrum of diseases. MicroRNA biomarkers, microRNA therapeutics, microRNA regulation of cellular physiology and even xenomiRs have stimulated great interest, which have brought many researchers into the field. Despite many successes in determining general mechanisms of microRNA generation and function, the application of microRNAs in translational areas has not had as much success. It has been a challenge to localize microRNAs to a given cell type within tissues and assay them reliably. At supraphysiologic levels, microRNAs may regulate hosts of genes that are not the physiologic biochemical targets. Thus the applied and translational microRNA literature is filled with pitfalls and claims that are neither scientifically rigorous nor reproducible. This review is focused on increasing awareness of the challenges of working with microRNAs in translational research and recommends better practices in this area of discovery.
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Affiliation(s)
- Kenneth W Witwer
- a Department of Molecular and Comparative Pathobiology , The Johns Hopkins University School of Medicine , Baltimore , MD , USA.,b Department of Neurology , The Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Marc K Halushka
- c Department of Pathology , The Johns Hopkins University School of Medicine , Baltimore , MD , USA
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247
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Circulating plant miRNAs can regulate human gene expression in vitro. Sci Rep 2016; 6:32773. [PMID: 27604570 PMCID: PMC5015063 DOI: 10.1038/srep32773] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 08/15/2016] [Indexed: 12/04/2022] Open
Abstract
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.
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248
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Identification of Dietetically Absorbed Rapeseed (Brassica campestris L.) Bee Pollen MicroRNAs in Serum of Mice. BIOMED RESEARCH INTERNATIONAL 2016; 2016:5413849. [PMID: 27597967 PMCID: PMC5002473 DOI: 10.1155/2016/5413849] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/05/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNA that, through mediating posttranscriptional gene regulation, play a critical role in nearly all biological processes. Over the last decade it has become apparent that plant miRNAs may serve as a novel functional component of food with therapeutic effects including anti-influenza and antitumor. Rapeseed bee pollen has good properties in enhancing immune function as well as preventing and treating disease. In this study, we identified the exogenous miRNAs from rapeseed bee pollen in mice blood using RNA-seq technology. We found that miR-166a was the most highly enriched exogenous plant miRNAs in the blood of mice fed with rapeseed bee pollen, followed by miR-159. Subsequently, RT-qPCR results confirmed that these two miRNAs also can be detected in rapeseed bee pollen. Our results suggested that food-derived exogenous miRNAs from rapeseed bee pollen could be absorbed in mice and the abundance of exogenous miRNAs in mouse blood is dependent on their original levels in the rapeseed bee pollen.
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249
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Pirrò S, Minutolo A, Galgani A, Potestà M, Colizzi V, Montesano C. Bioinformatics Prediction and Experimental Validation of MicroRNAs Involved in Cross-Kingdom Interaction. J Comput Biol 2016; 23:976-989. [PMID: 27428722 DOI: 10.1089/cmb.2016.0059] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that act as efficient post-transcriptional regulators of gene expression. In 2012, the first cross-kingdom miRNA-based interaction had been evidenced, demonstrating that exogenous miRNAs act in a manner of mammalian functional miRNAs. Starting from this evidence, we defined the concept of cross-kingdom functional homology between plant and mammalian miRNAs as a needful requirement for vegetal miRNA to explicit a regulation mechanism into the host mammalian cell, comparable to the endogenous one. Then, we proposed a new dedicated algorithm to compare plant and mammalian miRNAs, searching for functional sequence homologies between them, and we developed a web software called MirCompare. We also predicted human genes regulated by the selected plant miRNAs, and we determined the role of exogenous miRNAs in the perturbation of intracellular interaction networks. Finally, as already performed by Pirrò and coworkers, the ability of MirCompare to select plant miRNAs with functional homologies with mammalian ones has been experimentally confirmed by evaluating the ability of mol-miR168a to downregulate the protein expression of SIRT1, when its mimic is transfected into human hepatoma cell line G2 (HEPG2) cells. This tool is implemented into a user-friendly web interface, and the access is free to public through the website http://160.80.35.140/MirCompare.
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Affiliation(s)
- Stefano Pirrò
- 1 Department of Biology, University of Rome "Tor Vergata ," Rome, Italy .,2 Mir-Nat s.r.l. , Rome, Italy
| | | | - Andrea Galgani
- 1 Department of Biology, University of Rome "Tor Vergata ," Rome, Italy .,2 Mir-Nat s.r.l. , Rome, Italy
| | - Marina Potestà
- 1 Department of Biology, University of Rome "Tor Vergata ," Rome, Italy
| | - Vittorio Colizzi
- 1 Department of Biology, University of Rome "Tor Vergata ," Rome, Italy .,2 Mir-Nat s.r.l. , Rome, Italy
| | - Carla Montesano
- 1 Department of Biology, University of Rome "Tor Vergata ," Rome, Italy
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250
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Sharma A, Sahu S, Kumari P, Gopi SR, Malhotra R, Biswas S. Genome-wide identification and functional annotation of miRNAs in anti-inflammatory plant and their cross-kingdom regulation in Homo sapiens. J Biomol Struct Dyn 2016; 35:1389-1400. [DOI: 10.1080/07391102.2016.1185381] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ankita Sharma
- Department of Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Delhi, India
| | - Sarika Sahu
- School of Biotechnology, Shobhit University, Meerut, Uttar Pradesh, India
| | - Pooja Kumari
- Department of Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Delhi, India
| | - Soundhara Rajan Gopi
- Department of Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Delhi, India
| | - Rajesh Malhotra
- Department of Orthopaedics, All India Institute of Medical Science, New Delhi, India
| | - Sagarika Biswas
- Department of Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Delhi, India
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