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Moradimotlagh A, Brar HK, Chen S, Moon KM, Foster LJ, Reiner N, Nandan D. Characterization of Argonaute-containing protein complexes in Leishmania-infected human macrophages. PLoS One 2024; 19:e0303686. [PMID: 38781128 PMCID: PMC11115314 DOI: 10.1371/journal.pone.0303686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
The intracellular protozoan parasite Leishmania causes leishmaniasis in humans, leading to serious illness and death in tropical and subtropical areas worldwide. Unfortunately, due to the unavailability of approved vaccines for humans and the limited efficacy of available drugs, leishmaniasis is on the rise. A comprehensive understanding of host-pathogen interactions at the molecular level could pave the way to counter leishmaniasis. There is growing evidence that several intracellular pathogens target RNA interference (RNAi) pathways in host cells to facilitate their persistence. The core elements of the RNAi system are complexes of Argonaute (Ago) proteins with small non-coding RNAs, also known as RNA-induced silencing complexes (RISCs). Recently, we have shown that Leishmania modulates Ago1 protein of host macrophages for its survival. In this study, we biochemically characterize the Ago proteins' interactome in Leishmania-infected macrophages compared to non-infected cells. For this, a quantitative proteomic approach using stable isotope labelling by amino acids in cell culture (SILAC) was employed, followed by purification of host Ago-complexes using a short TNRC6 protein-derived peptide fused to glutathione S-transferase beads as an affinity matrix. Proteomic-based detailed biochemical analysis revealed Leishmania modulated host macrophage RISC composition during infection. This analysis identified 51 Ago-interacting proteins with a broad range of biological activities. Strikingly, Leishmania proteins were detected as part of host Ago-containing complexes in infected cells. Our results present the first report of comprehensive quantitative proteomics of Ago-containing complexes isolated from Leishmania-infected macrophages and suggest targeting the effector complex of host RNAi machinery. Additionally, these results expand knowledge of RISC in the context of host-pathogen interactions in parasitology in general.
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Affiliation(s)
- Atieh Moradimotlagh
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Harsimran Kaur Brar
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Stella Chen
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, B.C, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, B.C, Canada
| | - Neil Reiner
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Devki Nandan
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
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2
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Sahu S, Rao AR, Sahu TK, Pandey J, Varshney S, Kumar A, Gaikwad K. Predictive Role of Cluster Bean ( Cyamopsis tetragonoloba) Derived miRNAs in Human and Cattle Health. Genes (Basel) 2024; 15:448. [PMID: 38674383 PMCID: PMC11049822 DOI: 10.3390/genes15040448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 04/28/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding conserved molecules with lengths varying between 18-25nt. Plants miRNAs are very stable, and probably they might have been transferred across kingdoms via food intake. Such miRNAs are also called exogenous miRNAs, which regulate the gene expression in host organisms. The miRNAs present in the cluster bean, a drought tolerant legume crop having high commercial value, might have also played a regulatory role for the genes involved in nutrients synthesis or disease pathways in animals including humans due to dietary intake of plant parts of cluster beans. However, the predictive role of miRNAs of cluster beans for gene-disease association across kingdoms such as cattle and humans are not yet fully explored. Thus, the aim of the present study is to (i) find out the cluster bean miRNAs (cb-miRs) functionally similar to miRNAs of cattle and humans and predict their target genes' involvement in the occurrence of complex diseases, and (ii) identify the role of cb-miRs that are functionally non-similar to the miRNAs of cattle and humans and predict their targeted genes' association with complex diseases in host systems. Here, we predicted a total of 33 and 15 functionally similar cb-miRs (fs-cb-miRs) to human and cattle miRNAs, respectively. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the participation of targeted genes of fs-cb-miRs in 24 and 12 different pathways in humans and cattle, respectively. Few targeted genes in humans like LCP2, GABRA6, and MYH14 were predicted to be associated with disease pathways of Yesinia infection (hsa05135), neuroactive ligand-receptor interaction (hsa04080), and pathogenic Escherichia coli infection (hsa05130), respectively. However, targeted genes of fs-cb-miRs in humans like KLHL20, TNS1, and PAPD4 are associated with Alzheimer's, malignant tumor of the breast, and hepatitis C virus infection disease, respectively. Similarly, in cattle, targeted genes like ATG2B and DHRS11 of fs-cb-miRs participate in the pathways of Huntington disease and steroid biosynthesis, respectively. Additionally, the targeted genes like SURF4 and EDME2 of fs-cb-miRs are associated with mastitis and bovine osteoporosis, respectively. We also found a few cb-miRs that do not have functional similarity with human and cattle miRNAs but are found to target the genes in the host organisms and as well being associated with human and cattle diseases. Interestingly, a few genes such as NRM, PTPRE and SUZ12 were observed to be associated with Rheumatoid Arthritis, Asthma and Endometrial Stromal Sarcoma diseases, respectively, in humans and genes like SCNN1B associated with renal disease in cattle.
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Affiliation(s)
- Sarika Sahu
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Atmakuri Ramakrishna Rao
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
- Indian Council of Agricultural Research, New Delhi 110001, India
| | - Tanmaya Kumar Sahu
- Indian Grassland and Fodder Research Institute, ICAR, Jhansi 284003, India;
| | - Jaya Pandey
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
| | - Shivangi Varshney
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
| | - Archna Kumar
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Kishor Gaikwad
- National Institute for Plant Biotechnology, ICAR, New Delhi 110012, India;
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3
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Chowdhury S, Sais D, Donnelly S, Tran N. The knowns and unknowns of helminth-host miRNA cross-kingdom communication. Trends Parasitol 2024; 40:176-191. [PMID: 38151361 DOI: 10.1016/j.pt.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 12/29/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that oversee gene modulation. They are integral to cellular functions and can migrate between species, leading to cross-kingdom gene suppression. Recent breakthroughs in helminth genome studies have sparked curiosity about helminth RNA regulators and their ability to regulate genes across species. Growing data indicate that helminth miRNAs have a significant impact on the host's immune system. Specific miRNAs from helminth parasites can merge with the host's miRNA system, implying that parasites could exploit their host's regulatory machinery and function. This review highlights the role of cross-kingdom helminth-derived miRNAs in the interplay between host and parasite, exploring potential routes for their uptake, processing, and consequences in host interaction.
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Affiliation(s)
- Sumaiya Chowdhury
- The School of Life Sciences, University of Technology, Sydney, Australia; School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia
| | - Dayna Sais
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia
| | - Sheila Donnelly
- The School of Life Sciences, University of Technology, Sydney, Australia.
| | - Nham Tran
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia.
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4
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Ajila V, Colley L, Ste-Croix DT, Nissan N, Cober ER, Mimee B, Samanfar B, Green JR. Species-specific microRNA discovery and target prediction in the soybean cyst nematode. Sci Rep 2023; 13:17657. [PMID: 37848601 PMCID: PMC10582106 DOI: 10.1038/s41598-023-44469-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023] Open
Abstract
The soybean cyst nematode (SCN) is a devastating pathogen for economic and food security considerations. Although the SCN genome has recently been sequenced, the presence of any miRNA has not been systematically explored and reported. This paper describes the development of a species-specific SCN miRNA discovery pipeline and its application to the SCN genome. Experiments on well-documented model nematodes (Caenorhabditis elegans and Pristionchus pacificus) are used to tune the pipeline's hyperparameters and confirm its recall and precision. Application to the SCN genome identifies 3342 high-confidence putative SCN miRNA. Prediction specificity within SCN is confirmed by applying the pipeline to RNA hairpins from known exonic regions of the SCN genome (i.e., sequences known to not be miRNA). Prediction recall is confirmed by building a positive control set of SCN miRNA, based on a limited deep sequencing experiment. Interestingly, a number of novel miRNA are predicted to be encoded within the intronic regions of effector genes, known to be involved in SCN parasitism, suggesting that these miRNA may also be involved in the infection process or virulence. Beyond miRNA discovery, gene targets within SCN are predicted for all high-confidence novel miRNA using a miRNA:mRNA target prediction system. Lastly, cross-kingdom miRNA targeting is investigated, where putative soybean mRNA targets are identified for novel SCN miRNA. All predicted miRNA and gene targets are made available in appendix and through a Borealis DataVerse open repository ( https://borealisdata.ca/dataset.xhtml?persistentId=doi:10.5683/SP3/30DEXA ).
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Affiliation(s)
- Victoria Ajila
- Department of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6, Canada
| | - Laura Colley
- Department of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6, Canada
| | - Dave T Ste-Croix
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, J3B 7B5, Canada
| | - Nour Nissan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, K1S 5B6, Canada
| | - Elroy R Cober
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, Canada
| | - Benjamin Mimee
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, J3B 7B5, Canada
| | - Bahram Samanfar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, K1S 5B6, Canada
| | - James R Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6, Canada.
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5
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Wu J, Yang F, Zhao M, Xiao H, Chen Y, Liu X, Zheng D. Antler-derived microRNA PC-5p-1090 inhibits HCC cell proliferation, migration, and invasion by targeting MARCKS, SMARCAD1, and SOX9. Funct Integr Genomics 2023; 23:156. [PMID: 37165199 DOI: 10.1007/s10142-023-01089-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023]
Abstract
The capability of microRNAs (miRNAs) to regulate gene expression across species has opened new avenues for miRNA-based therapeutics. Here, we investigated the potential of PC-5p-1090 (miR-PC-1090), a miRNA found in deer antlers, to control the malignant phenotypes of hepatocellular carcinoma (HCC) cells. Using Cell Counting Kit-8 and transwell assays, we found that heterologous expression of miR-PC-1090 inhibited HCC cell proliferation, migration, and invasion. Bioinformatics analysis indicated that predicted miR-PC-1090 targets, including MARCKS, SMARCAD1, and SOX9, were significantly elevated in HCC tissues, and their high expressions were associated with poor overall survival of HCC patients. Moreover, mechanistic investigations revealed that miR-PC-1090 promoted the degradation of MARCKS and SMARCAD1 mRNAs and hindered the translation of SOX9 mRNA by recognizing their 3' untranslated regions. Subsequent loss-of-function and rescue experiments confirmed the involvement of MARCKS, SMARCAD1, and SOX9 in miR-PC-1090-suppressed HCC cell proliferation, migration, and invasion. Notably, MARCKS knockdown induced the downregulation of phosphorylated MARCKS and a corresponding upregulation of phosphorylated AKT in HCC. Conversely, miR-PC-1090 repressed MARCKS phosphorylation and effectively circumvented the activation of the PI3K/AKT pathway. Furthermore, miR-PC-1090 regulates the Wnt/β-catenin pathway through SMARCAD1- and SOX9-mediated reduction of β-catenin expression. Overall, our results illustrate the tumor-suppressive activity and molecular mechanism of antler-derived miR-PC-1090 in HCC cells, indicating its potential as a multiple-target agent for HCC treatment.
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Affiliation(s)
- Jin Wu
- Laboratory of Genetics and Molecular Biology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Fan Yang
- Laboratory of Genetics and Molecular Biology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Mindie Zhao
- Laboratory of Genetics and Molecular Biology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Hui Xiao
- Departments of Central Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215008, Jiangsu, China
| | - Yanxia Chen
- College of Ecology-Environment Engineering, Qinghai University, Xining, 810016, Qinghai, China
| | - Xuedong Liu
- Laboratory of Genetics and Molecular Biology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, China.
| | - Dong Zheng
- Laboratory of Genetics and Molecular Biology, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, Heilongjiang, China.
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6
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Zhao Q, Bae EH, Zhang Y, Shahsavari A, Lotey P, Lee RH, Liu F. Inhibitory Effects of Extracellular Vesicles from iPS-Cell-Derived Mesenchymal Stem Cells on the Onset of Sialadenitis in Sjögren's Syndrome Are Mediated by Immunomodulatory Splenocytes and Improved by Inhibiting miR-125b. Int J Mol Sci 2023; 24:5258. [PMID: 36982329 PMCID: PMC10049013 DOI: 10.3390/ijms24065258] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Extracellular vesicles (EVs) from allogeneic-tissue-derived mesenchymal stem cells (MSCs) are promising to improve Sjögren's syndrome (SS) treatment, but their application is hindered by high variations in and limited expandability of tissue MSCs. We derived standardized and scalable MSCs from iPS cells (iMSCs) and reported that EVs from young but not aging iMSCs (iEVs) inhibited sialadenitis onset in SS mouse models. Here, we aim to determine cellular mechanisms and optimization approaches of SS-inhibitory effects of iEVs. In NOD.B10.H2b mice at the pre-disease stage of SS, we examined the biodistribution and recipient cells of iEVs with imaging, flow cytometry, and qRT-PCR. Intravenously infused iEVs accumulated in the spleen but not salivary glands or cervical lymph nodes and were mainly taken up by macrophages. In the spleen, young but not aging iEVs increased M2 macrophages, decreased Th17 cells, and changed expression of related immunomodulatory molecules. Loading miR-125b inhibitors into aging iEVs significantly improved their effects on repressing sialadenitis onset and regulating immunomodulatory splenocytes. These data indicated that young but not aging iEVs suppress SS onset by regulating immunomodulatory splenocytes, and inhibiting miR-125b in aging iEVs restores such effects, which is promising to maximize production of effective iEVs from highly expanded iMSCs for future clinical application.
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Affiliation(s)
| | | | | | | | | | - Ryang Hwa Lee
- Department of Cell Biology and Genetics, School of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Fei Liu
- Department of Cell Biology and Genetics, School of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
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7
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Ajila V, Colley L, Ste-Croix DT, Nissan N, Golshani A, Cober ER, Mimee B, Samanfar B, Green JR. P-TarPmiR accurately predicts plant-specific miRNA targets. Sci Rep 2023; 13:332. [PMID: 36609461 PMCID: PMC9822942 DOI: 10.1038/s41598-022-27283-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Abstract
microRNAs (miRNAs) are small non-coding ribonucleic acids that post-transcriptionally regulate gene expression through the targeting of messenger RNA (mRNAs). Most miRNA target predictors have focused on animal species and prediction performance drops substantially when applied to plant species. Several rule-based miRNA target predictors have been developed in plant species, but they often fail to discover new miRNA targets with non-canonical miRNA-mRNA binding. Here, the recently published TarDB database of plant miRNA-mRNA data is leveraged to retrain the TarPmiR miRNA target predictor for application on plant species. Rigorous experiment design across four plant test species demonstrates that animal-trained predictors fail to sustain performance on plant species, and that the use of plant-specific training data improves accuracy depending on the quantity of plant training data used. Surprisingly, our results indicate that the complete exclusion of animal training data leads to the most accurate plant-specific miRNA target predictor indicating that animal-based data may detract from miRNA target prediction in plants. Our final plant-specific miRNA prediction method, dubbed P-TarPmiR, is freely available for use at http://ptarpmir.cu-bic.ca . The final P-TarPmiR method is used to predict targets for all miRNA within the soybean genome. Those ranked predictions, together with GO term enrichment, are shared with the research community.
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Affiliation(s)
- Victoria Ajila
- grid.34428.390000 0004 1936 893XDepartment of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6 Canada
| | - Laura Colley
- grid.34428.390000 0004 1936 893XDepartment of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6 Canada
| | - Dave T. Ste-Croix
- grid.55614.330000 0001 1302 4958Saint-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, J3B 7B5 Canada
| | - Nour Nissan
- grid.55614.330000 0001 1302 4958Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6 Canada ,grid.34428.390000 0004 1936 893XDepartment of Biology, Carleton University, Ottawa, K1S 5B6 Canada
| | - Ashkan Golshani
- grid.34428.390000 0004 1936 893XDepartment of Biology, Carleton University, Ottawa, K1S 5B6 Canada
| | - Elroy R. Cober
- grid.55614.330000 0001 1302 4958Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6 Canada
| | - Benjamin Mimee
- grid.55614.330000 0001 1302 4958Saint-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, J3B 7B5 Canada
| | - Bahram Samanfar
- grid.55614.330000 0001 1302 4958Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6 Canada ,grid.34428.390000 0004 1936 893XDepartment of Biology, Carleton University, Ottawa, K1S 5B6 Canada
| | - James R. Green
- grid.34428.390000 0004 1936 893XDepartment of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6 Canada
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8
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Hardin LT, Xiao N. miRNAs: The Key Regulator of COVID-19 Disease. Int J Cell Biol 2022; 2022:1645366. [PMID: 36345541 PMCID: PMC9637033 DOI: 10.1155/2022/1645366] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/30/2022] [Indexed: 01/12/2024] Open
Abstract
As many parts of the world continue to fight the innumerable waves of COVID-19 infection, SARS-CoV-2 continues to sculpt its antigenic determinants to enhance its virulence and evolvability. Several vaccines were developed and used around the world, and oral antiviral medications are being developed against SARS-CoV-2. However, studies showed that the virus is mutating in line with the antibody's neutralization escape; thus, new therapeutic alternatives are solicited. We hereby review the key role that miRNAs can play as epigenetic mediators of the cross-talk between SARS-CoV-2 and the host cells. The limitations resulting from the "virus intelligence" to escape and antagonize the host miRNAs as well as the possible mechanisms that could be used in the viral evasion strategies are discussed. Lastly, we suggest new therapeutic approaches based on viral miRNAs.
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Affiliation(s)
- Leyla Tahrani Hardin
- Department of Biomedical Sciences at the Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, 94103 CA, USA
| | - Nan Xiao
- Department of Biomedical Sciences at the Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, 94103 CA, USA
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9
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Li S, Lei Z, Sun T. The role of microRNAs in neurodegenerative diseases: a review. Cell Biol Toxicol 2022; 39:53-83. [PMID: 36125599 PMCID: PMC9486770 DOI: 10.1007/s10565-022-09761-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 08/26/2022] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are non-coding RNAs which are essential post-transcriptional gene regulators in various neuronal degenerative diseases and playact a key role in these physiological progresses. Neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, multiple sclerosis, and, stroke, are seriously threats to the life and health of all human health and life kind. Recently, various studies have reported that some various miRNAs can regulate the development of neurodegenerative diseases as well as act as biomarkers to predict these neuronal diseases conditions. Endogenic miRNAs such as miR-9, the miR-29 family, miR-15, and the miR-34 family are generally dysregulated in animal and cell models. They are involved in regulating the physiological and biochemical processes in the nervous system by targeting regulating different molecular targets and influencing a variety of pathways. Additionally, exogenous miRNAs derived from homologous plants and defined as botanmin, such as miR2911 and miR168, can be taken up and transferred by other species to be and then act analogously to endogenic miRNAs to regulate the physiological and biochemical processes. This review summarizes the mechanism and principle of miRNAs in the treatment of some neurodegenerative diseases, as well as discusses several types of miRNAs which were the most commonly reported in diseases. These miRNAs could serve as a study provided some potential biomarkers in neurodegenerative diseases might be an ideal and/or therapeutic targets for neurodegenerative diseases. Finally, the role accounted of the prospective exogenous miRNAs involved in mammalian diseases is described.
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Affiliation(s)
- Shijie Li
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
| | - Zhixin Lei
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China.
| | - Taolei Sun
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China. .,State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China.
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10
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Wang Y, Gong W, Zhou H, Hu Y, Wang L, Shen Y, Yu G, Cao J. A Novel miRNA From Egg-Derived Exosomes of Schistosoma japonicum Promotes Liver Fibrosis in Murine Schistosomiasis. Front Immunol 2022; 13:860807. [PMID: 35572578 PMCID: PMC9094574 DOI: 10.3389/fimmu.2022.860807] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Schistosomiasis caused by Schistosoma japonicum is a serious public health problem in China. Granuloma and hepatic fibrosis are the main pathological features of schistosomiasis japonica. The role and mechanism of egg-derived exosomes of S. japonicum in liver fibrosis remain unclear. In this study, we found that egg-derived exosomes of S. japonicum carry a new type of microRNA (miRNA-33). In vitro, this novel miRNA upregulated the expression of smooth muscle actin (α-SMA) and collagen 1 α1 (Col 1 α1) in the human hepatic stellate cell (LX-2) line at both mRNA and protein levels. In vivo, this novel miRNA was upregulated in the serum of infected mice, and when injected into mice through the tail vein using miRNA agomir, α-SMA, Col 1 α1, and Col 3 α1 were upregulated in liver tissue at both mRNA and protein levels. In addition, this novel miRNA downregulated the expression of α-SMA and Col 1 α1 in liver tissue at mRNA and protein levels in mice infected with S. japonicum and treated with miRNA antagomir. The novel miRNA-33 upregulated TGF-β Receptor I (TGF-β RI) at both mRNA and protein levels in LX-2 cells. Our results suggest that this novel miRNA from egg-derived exosomes of S. japonicum can promote liver fibrosis in the host in a cross-species manner, and the degree of fibrosis can be decreased by inhibiting the expression of this miRNA.
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Affiliation(s)
- Yiluo Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, World Health Organization Collaborating Center for Tropical Diseases, Shanghai, China.,State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Wenci Gong
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, World Health Organization Collaborating Center for Tropical Diseases, Shanghai, China
| | - Hao Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, World Health Organization Collaborating Center for Tropical Diseases, Shanghai, China.,State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Yuan Hu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, World Health Organization Collaborating Center for Tropical Diseases, Shanghai, China.,The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lan Wang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Yujuan Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, World Health Organization Collaborating Center for Tropical Diseases, Shanghai, China.,The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Jianping Cao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, World Health Organization Collaborating Center for Tropical Diseases, Shanghai, China.,The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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11
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Shivaprasad S, Sarnow P. Cross-species microRNA transmission modulates flavivirus growth in mosquitoes. Trends Parasitol 2022; 38:349-350. [PMID: 35246384 DOI: 10.1016/j.pt.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 11/18/2022]
Abstract
Mosquitoes can be infected with a variety of RNA viruses. Recently,Zhu et al. demonstrated that human microRNA hsa-miR-150-5p is acquired by mosquitoes during blood meals and protects the Dengue virus by downregulation of chymotrypsin AaCT-1 mRNA. This finding suggests the use of microRNA antagomirs as an antiviral approach in mosquitoes.
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Affiliation(s)
- Shwetha Shivaprasad
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, CA 94305, USA
| | - Peter Sarnow
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, CA 94305, USA.
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12
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Zhou Y, Li Q, Pan R, Wang Q, Zhu X, Yuan C, Cai F, Gao Y, Cui Y. Regulatory roles of three miRNAs on allergen mRNA expression in Tyrophagus putrescentiae. Allergy 2022; 77:469-482. [PMID: 34570913 DOI: 10.1111/all.15111] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Tyrophagus putresecentiae is an important mite species in rural and urban environments, causing sensitization and allergic disease. While evidence suggests that microRNAs (miRNAs) may regulate the expression of allergen-encoding genes, no study has directly investigated this possibility. Here, this gap was addressed by profiling miRNAs and elucidating their target allergen messenger RNAs (mRNAs) in this mite species. METHODS Small RNA and transcriptome libraries were constructed for eggs, larvae, nymphs, and adults. After deep miRNA and whole-transcriptome sequencing were performed, the miRNA and allergen-encoding mRNA regulatory networks were explored. RESULTS A total of 540 miRNAs were identified, including 155 with expression levels differing significantly across the four mite developmental stages (p < .01), 59 of which were novel. The mRNA expression for allergens was higher for Tyr p 1 in adults than in other developmental stages; Tyr p 2-5, 7, 10, 13, 33, and 34 in immature stages; and Tyr p 28, 35, and 36 in eggs and adults. A combined miRNA and transcriptome bioinformatics analysis showed that allergen Tyr p 3 was regulated by miRNA PC-5p-5698441_1, Tyr p 4 was regulated by PC-5p-7050653_1, and Tyr p 34 was regulated by PC-5p-5534223_1 and PC-5p-5698441_1. These three allergen mRNA and three miRNAs were identified using qRT-PCR, and their regulatory roles were confirmed by double-fluorescent reporter gene system and site-directed mutagenesis technology. CONCLUSIONS For the first time, allergen mRNA expression and miRNAs were profiled throughout the life cycle for an allergen-producing mite, and the results showed that miRNAs bind to target allergen mRNAs to regulate their expression.
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Affiliation(s)
- Ying Zhou
- Department of Pediatrics Laboratory The Affiliated Wuxi Children's Hospital of Nanjing Medical University Wuxi China
| | - Qingqing Li
- Department of Clinical Laboratory The Affiliated Wuxi People's Hospital of Nanjing Medical University Wuxi China
| | - Ruilin Pan
- Department of Clinical Laboratory The Affiliated Wuxi People's Hospital of Nanjing Medical University Wuxi China
| | - Qiong Wang
- Department of Clinical Laboratory The Affiliated Wuxi People's Hospital of Nanjing Medical University Wuxi China
| | - Xuming Zhu
- Department of Clinical Laboratory The Affiliated Wuxi People's Hospital of Nanjing Medical University Wuxi China
| | - Cunyin Yuan
- Department of Clinical Laboratory The Affiliated Wuxi People's Hospital of Nanjing Medical University Wuxi China
| | - Fangfang Cai
- Department of Clinical Laboratory The Affiliated Wuxi People's Hospital of Nanjing Medical University Wuxi China
| | - Ya‐dong Gao
- Department of Allergology Zhongnan Hospital of Wuhan University Wuhan China
| | - Yubao Cui
- Department of Clinical Laboratory The Affiliated Wuxi People's Hospital of Nanjing Medical University Wuxi China
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13
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Luan X, Zhou X, Fallah P, Pandya M, Lyu H, Foyle D, Burch D, Diekwisch TGH. MicroRNAs: Harbingers and shapers of periodontal inflammation. Semin Cell Dev Biol 2021; 124:85-98. [PMID: 34120836 DOI: 10.1016/j.semcdb.2021.05.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/03/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023]
Abstract
Periodontal disease is an inflammatory reaction of the periodontal tissues to oral pathogens. In the present review we discuss the intricate effects of a regulatory network of gene expression modulators, microRNAs (miRNAs), as they affect periodontal morphology, function and gene expression during periodontal disease. These miRNAs are small RNAs involved in RNA silencing and post-transcriptional regulation and affect all stages of periodontal disease, from the earliest signs of gingivitis to the regulation of periodontal homeostasis and immunity and to the involvement in periodontal tissue destruction. MiRNAs coordinate periodontal disease progression not only directly but also through long non-coding RNAs (lncRNAs), which have been demonstrated to act as endogenous sponges or decoys that regulate the expression and function of miRNAs, and which in turn suppress the targeting of mRNAs involved in the inflammatory response, cell proliferation, migration and differentiation. While the integrity of miRNA function is essential for periodontal health and immunity, miRNA sequence variations (genetic polymorphisms) contribute toward an enhanced risk for periodontal disease progression and severity. Several polymorphisms in miRNA genes have been linked to an increased risk of periodontitis, and among those, miR-146a, miR-196, and miR-499 polymorphisms have been identified as risk factors for periodontal disease. The role of miRNAs in periodontal disease progression is not limited to the host tissues but also extends to the viruses that reside in periodontal lesions, such as herpesviruses (human herpesvirus, HHV). In advanced periodontal lesions, HHV infections result in the release of cytokines from periodontal tissues and impair antibacterial immune mechanisms that promote bacterial overgrowth. In turn, controlling the exacerbation of periodontal disease by minimizing the effect of periodontal HHV in periodontal lesions may provide novel avenues for therapeutic intervention. In summary, this review highlights multiple levels of miRNA-mediated control of periodontal disease progression, (i) through their role in periodontal inflammation and the dysregulation of homeostasis, (ii) as a regulatory target of lncRNAs, (iii) by contributing toward periodontal disease susceptibility through miRNA polymorphism, and (iv) as periodontal microflora modulators via viral miRNAs.
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Affiliation(s)
- Xianghong Luan
- Texas A&M Center for Craniofacial Research and Diagnosis and Department of Periodontics, TAMU College of Dentistry, 75246 Dallas, TX USA
| | - Xiaofeng Zhou
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL 60612, USA
| | - Pooria Fallah
- Texas A&M Center for Craniofacial Research and Diagnosis and Department of Periodontics, TAMU College of Dentistry, 75246 Dallas, TX USA
| | - Mirali Pandya
- Texas A&M Center for Craniofacial Research and Diagnosis and Department of Periodontics, TAMU College of Dentistry, 75246 Dallas, TX USA
| | - Huling Lyu
- Texas A&M Center for Craniofacial Research and Diagnosis and Department of Periodontics, TAMU College of Dentistry, 75246 Dallas, TX USA; Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou 510140, China
| | - Deborah Foyle
- Texas A&M Center for Craniofacial Research and Diagnosis and Department of Periodontics, TAMU College of Dentistry, 75246 Dallas, TX USA
| | - Dan Burch
- Department of Pedodontics, TAMU College of Dentistry, 75246 Dallas, TX, USA
| | - Thomas G H Diekwisch
- Texas A&M Center for Craniofacial Research and Diagnosis and Department of Periodontics, TAMU College of Dentistry, 75246 Dallas, TX USA.
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14
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Exogenous miRNA: A Perspective Role as Therapeutic in Rheumatoid Arthritis. Curr Rheumatol Rep 2021; 23:43. [PMID: 33939021 DOI: 10.1007/s11926-021-01009-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2021] [Indexed: 12/15/2022]
Abstract
Rheumatoid arthritis (RA) is an autoimmune and chronic inflammatory disease that causes joint deformation. Till now several studies has been carried out promising its cure, but curing has not yet achieved to the satisfactory levels. Herbal approach to treat disease by a cross-kingdom mechanism via exogenous miRNA is an emerging trend to target associated genes with RA pathogenesis as a therapeutic potential. The concept of acquired/exogenous miRNA into pathophysiological prospect provides an opportunity to explore inter-species kingdom like regulation of plant miRNAs on human health. The change in gene expression was attributed by a short 22-24 nucleotide long sequence that binds to its complementary region to suppress/silence the gene expression. This makes exogenous miRNA a novel approach for targeted therapy to treat complex chronic inflammatory diseases. Here, aim of the review was to address significance of plant derived miRNA based targeted therapy to regulate inflammation in RA.
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15
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Fontana JE, Wang G, Sun R, Xue H, Li Q, Liu J, Davis KE, Thornburg TE, Zhang B, Zhang Z, Pan X. Impact of potassium deficiency on cotton growth, development and potential microRNA-mediated mechanism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 153:72-80. [PMID: 32480238 DOI: 10.1016/j.plaphy.2020.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 05/24/2023]
Abstract
The goal of this study was to investigate the impact of potassium deficiency on cotton seedling growth and development at the individual, physiological, biochemical, and molecular levels. Potassium is an important plant nutrient; our results show that potassium deficiency significantly affected cotton seedling growth and development, evidenced by reduced plant height, and total areas of the leaves and roots as well as further reduced both fresh and dry biomass of the entire plants. Potassium deficiency also significantly inhibited root and leaf respiration and leaf photosynthesis. Compared with the controls, potassium deficiency significantly inhibited root elongation and total root surface areas that further inhibited cotton seedlings to uptake nutrients from the medium. Potassium deficiency induced aberrant expression of both microRNAs (miRNAs) and their protein-coding targets. These miRNAs regulate plant root development as well as response to abiotic stresses. Potassium deficiency altered the expression of miRNAs that regulate the expression of protein-coding genes controlling root development and response to potassium deficiency. miRNAs regulate root development and further control plant development in cotton seedlings under potassium deficiency. In summary, potassium deficiency significantly affected the cotton seedling photosynthesis and respiration that resulted in inhibition of cotton seedling growth and development potentially due to the miRNA-mediated mechanism.
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Affiliation(s)
- Julia Elise Fontana
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China; Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Guo Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Runrun Sun
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Huiyun Xue
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Qian Li
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Jia Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Kyle E Davis
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China; Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Thomas Elliott Thornburg
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China; Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Zhiyong Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China.
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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16
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Huang H, Pham Q, Davis CD, Yu L, Wang TT. Delineating effect of corn microRNAs and matrix, ingested as whole food, on gut microbiota in a rodent model. Food Sci Nutr 2020; 8:4066-4077. [PMID: 32884688 PMCID: PMC7455949 DOI: 10.1002/fsn3.1672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/25/2020] [Accepted: 04/20/2020] [Indexed: 11/30/2022] Open
Abstract
Dietary microRNAs (miRNAs) are thought to regulate a wide range of biological processes, including the gut microbiota. However, it is difficult to separate specific effect(s) of miRNA from that of the food matrix. This study aims to elucidate the specific effect(s) of dietary corn miRNAs, ingested as a whole food, on the gut microbiota. We developed an autoclave procedure to remove 98% of miRNA from corn. A mouse feeding study was conducted comparing autoclaved corn to nonautoclaved corn and purified corn miRNA. Compared to nonspecific nucleotides and corn devoid of miRNAs, feeding purified corn miRNAs or corn to C57BL/6 mice via gavage or diet supplementation for two weeks lead to a decrease in total bacteria in the cecum. The effect appeared to be due to changes in Firmicutes. Additionally, corn matrix minus miRNA and processing also affected gut bacteria. In silico analysis identified corn miRNAs that aligned to Firmicutes genome sequences lending further support to the interaction between corn miRNAs and this bacterium. These data support interactions between plant food miRNA, as well as matrix, and the gut microbiota exist but complex. However, it provides additional support for mechanism by which bioactive dietary components interact with the gut microbiota.
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Affiliation(s)
- Haiqiu Huang
- Diet, Genomics and Immunology LaboratoryBeltsville Human Nutrition Research CenterUSDA‐ARSBeltsvilleMarylandUSA
- Office of Dietary SupplementsNIHBethesdaMarylandUSA
| | - Quynhchi Pham
- Diet, Genomics and Immunology LaboratoryBeltsville Human Nutrition Research CenterUSDA‐ARSBeltsvilleMarylandUSA
| | | | - Liangli Yu
- Department of Nutrition and Food ScienceUniversity of MarylandCollege ParkMarylandUSA
| | - Thomas T.Y. Wang
- Diet, Genomics and Immunology LaboratoryBeltsville Human Nutrition Research CenterUSDA‐ARSBeltsvilleMarylandUSA
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17
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Zhang X, Gong W, Cao S, Yin J, Zhang J, Cao J, Shen Y. Comprehensive Analysis of Non-coding RNA Profiles of Exosome-Like Vesicles From the Protoscoleces and Hydatid Cyst Fluid of Echinococcus granulosus. Front Cell Infect Microbiol 2020; 10:316. [PMID: 32793506 PMCID: PMC7387405 DOI: 10.3389/fcimb.2020.00316] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/25/2020] [Indexed: 12/31/2022] Open
Abstract
Cystic echinococcosis is a worldwide chronic zoonotic disease that threatens human health and animal husbandry. Exosome-like vesicles (ELVs) have emerged recently as mediators in the parasite-parasite intercommunication and parasite-host interactions. Exosome-like vesicles from parasites can transfer non-coding RNAs (ncRNAs) into host cells to regulate their gene expression; however, the ncRNAs profiles of the ELVs from Echinococcus granulosus remain unknown. Here, we isolated protoscolece (PSC)-ELVs and hydatid fluid (HF)-ELVs from the culture medium for E. granulosus PSCs in vitro and the HF of fertile sheep cysts, respectively. The microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) profiles of the two types of ELVs were analyzed using high-throughput sequencing, and their functions were predicted using Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis. In PSC-ELVs and HF-ELVs, 118 and 58 miRNAs were identified, respectively, among which 53 miRNAs were present in both ELVs, whereas 65 and 5 miRNAs were unique to PSC-ELVs and HF-ELVs, respectively; 2,361 and 1,254 lncRNAs were identified in PSC-ELVs and HF-ELVs, respectively, among which 1,004 lncRNAs were present in both ELVs, whereas 1,357 and 250 lncRNAs were unique to PSC-ELVs and HF-ELVs, respectively. Intriguingly, the spilled PSCs from cysts excrete ELVs with higher numbers of and higher expression levels of miRNAs and circRNAs than HF-ELVs. The miRNA sequencing data were validated by quantitative reverse transcription-polymerase chain reaction. Furthermore, the target lncRNAs and mRNAs regulated by the 20 most abundant miRNAs were screened, and a ceRNA regulatory network containing 5 miRNAs, 41 lncRNAs, and 23 mRNAs was constructed, which provided new ideas and the molecular basis for further clarification of the function and mechanism of E. granulosus ELVs ncRNAs in the parasite-host interactions. Egr-miR-125-5p and egr-miR-10a-5p, sharing identical seed sites with host miRNAs, were predicted to mediate inflammatory response, collagen catabolic process, and mitogen-activated protein kinase cascade during parasite infections. In conclusion, for the first time, we identified the ncRNAs profiles in PSC-ELVs and HF-ELVs that might be involved in host immunity and pathogenesis, and enriched the ncRNAs data of E. granulosus. These results provided valuable resources for further analysis of the regulatory potential of ncRNAs, especially miRNAs, in both types of ELVs at the parasite-host interface.
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Affiliation(s)
- Xiaofan Zhang
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Wenci Gong
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Shengkui Cao
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Jianhai Yin
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Jing Zhang
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Jianping Cao
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Yujuan Shen
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
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18
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Du J, Zhang W, Li XH, Li YJ. Bioinformatics analysis of small RNAs in Helicobacter pylori and the role of NAT‑67 under tinidazole treatment. Mol Med Rep 2020; 22:1227-1234. [PMID: 32626984 PMCID: PMC7339756 DOI: 10.3892/mmr.2020.11232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/30/2020] [Indexed: 11/27/2022] Open
Abstract
Helicobacter pylori (Hp) infection is a major cause of gastrointestinal disease. However, the pathogenesis of gastric mucosa injury by Hp has remained elusive. Small non-coding RNA (sRNA) is a type of widespread RNA in prokaryotic organisms and regulates bacterial growth, reproduction and virulence. In the present study, Hp sRNA profiles were generated to reveal the sequences and possible functions of sRNA by bioinformatics analysis. The role of sRNA in tinidazole (TNZ) treatment was also explored. Total sRNAs of HP26695 were sequenced using an Illumina HiSeq2000. Detected Tags were then compared with a known sRNA database to build an sRNA profile. Reverse transcription-quantitative (RT-q)PCR products were sequenced directly and agarose gel electrophoresis was used to identify NAT-67 and 5′ureB-sRNA in HP. Furthermore, HP was treated with TNZ for 6, 12 and 24 h. The bacterial concentration was measured, the expression of NAT-67, 5′ureB-sRNA and ceuE was determined by RT-qPCR and superoxide dismutase (SOD) activity and reactive oxygen species (ROS) production were detected. A total of 163 sRNA tags were predicted in Hp through bioinformatics analysis. Among them, 35 tags were evolutionarily aconserved in different Hp strains. By target prediction, it was indicated that certain candidate sRNAs were associated with bacterial oxidative stress, virulence and chemotaxis. It was also observed that NAT-67 and 5′ureB-sRNA were downregulated in TNZ-treated HP. TNZ treatment inhibited the growth of Hp, which was accompanied by downregulation of ceuE and SOD activity, as well as upregulation of ROS. RNA sequencing and bioinformatics are valuable in predicting the expression profile and function of sRNA in HP. sRNA-targeted genes may be associated with virulence, oxidative stress and chemokines. Downregulation of NAT-67 by TNZ may be involved in Hp oxidative stress regulation, which may comprise one of the mechanisms of the antibacterial effects of TNZ.
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Affiliation(s)
- Jie Du
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Wang Zhang
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Xiao-Hui Li
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Yuan-Jian Li
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
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19
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Rakhmetullina A, Pyrkova A, Aisina D, Ivashchenko A. In silico prediction of human genes as potential targets for rice miRNAs. Comput Biol Chem 2020; 87:107305. [PMID: 32570176 DOI: 10.1016/j.compbiolchem.2020.107305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Exogenous microRNAs (miRNAs) enter the human body through food, and their effects on metabolic processes can be considerable. It is important to determine which miRNAs from plants affect the expression of human genes and the extent of their influence. METHOD The binding sites of 738Oryza sativa miRNAs (osa-miRNAs) that interact with 17 508 mRNAs of human genes were determined using the MirTarget program. RESULT The characteristics of the binding of 46 single osa-miRNAs to 86 mRNAs of human genes with a value of free energy (ΔG) interaction equal 94%-100% from maximum ΔG were established. The findings showed that osa-miR2102-5p, osa-miR5075-3p, osa-miR2097-5p, osa-miR2919 targeted the largest number of genes at 38, 36, 23, 19 sites, respectively. mRNAs of 86 human genes were identified as targets for 93 osa-miRNAs of all family osa-miRNAs with ΔG values equal 94%-98% from maximum ΔG. Each miRNA of the osa-miR156-5p, osa-miR164-5p, osa-miR168-5p, osa-miR395-3p, osa-miR396-3p, osa-miR396-5p, osa-miR444-3p, osa-miR529-3p, osa-miR1846-3p, osa-miR2907-3p families had binding sites in mRNAs of several human target genes. The binding sites of osa-miRNAs in mRNAs of the target genes for each family of osa-miRNAs were conserved when compared to flanking nucleotide sequences. CONCLUSION Target mRNA human genes of osa-miRNAs are also candidate genes of cancer, cardiovascular and neurodegenerative diseases.
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Affiliation(s)
- Aizhan Rakhmetullina
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan
| | - Anna Pyrkova
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan
| | - Dana Aisina
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan
| | - Anatoliy Ivashchenko
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan.
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20
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Terrinoni A, Calabrese C, Basso D, Aita A, Caporali S, Plebani M, Bernardini S. The circulating miRNAs as diagnostic and prognostic markers. Clin Chem Lab Med 2020; 57:932-953. [PMID: 30838832 DOI: 10.1515/cclm-2018-0838] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/23/2018] [Indexed: 02/07/2023]
Abstract
A large portion of the human genome transcribes RNA sequences that do not code for any proteins. The first of these sequences was identified in 1993, and the best known noncoding RNAs are microRNA (miRNAs). It is now fully established that miRNAs regulate approximately 30% of the known genes that codify proteins. miRNAs are involved in several biological processes, like cell proliferation, differentiation, apoptosis and metastatization. These RNA products regulate gene expression at the post-transcriptional level, modulating or inhibiting protein expression by interacting with specific sequences of mRNAs. Mature miRNAs can be detected in blood plasma, serum and also in a wide variety of biological fluids. They can be found associated with proteins, lipids as well as enclosed in exosome vesicles. We know that circulating miRNAs (C-miRNAs) can regulate several key cellular processes in tissues different from the production site. C-miRNAs behave as endogenous mediators of RNA translation, and an extraordinary knowledge on their function has been obtained in the last years. They can be secreted in different tissue cells and associated with specific pathological conditions. Significant evidence indicates that the initiation and progression of several pathologies are "highlighted" by the presence of specific C-miRNAs, underlining their potential diagnostic relevance as clinical biomarkers. Here we review the current literature on the possible use of this new class of molecules as clinical biomarkers of diseases.
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Affiliation(s)
- Alessandro Terrinoni
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier, 1, 00133 Rome, Italy
| | - Cosimo Calabrese
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Daniela Basso
- Department of Medicine - DIMED; Department of Laboratory Medicine, University-Hospital of Padova, Padova, Italy
| | - Ada Aita
- Department of Medicine - DIMED; Department of Laboratory Medicine, University-Hospital of Padova, Padova, Italy
| | - Sabrina Caporali
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Mario Plebani
- Department of Medicine - DIMED; Department of Laboratory Medicine, University-Hospital of Padova, Padova, Italy
| | - Sergio Bernardini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
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21
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Gurwitz D. Genomics and the future of psychopharmacology: MicroRNAs offer novel therapeutics
. DIALOGUES IN CLINICAL NEUROSCIENCE 2020. [PMID: 31636487 PMCID: PMC6787538 DOI: 10.31887/dcns.2019.21.2/dgurwitz] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
MicroRNAs (miRNAs) are short, noncoding RNAs functioning as regulators of the
transcription of protein-coding genes in eukaryotes. During the last two decades,
studies on miRNAs indicate that they have potential as diagnostic and prognostic
biomarkers for a wide range of cancers. Research interest in miRNAs has moved to
embrace further medical disciplines, including neuropsychiatric disorders, comparing
miRNA expression and mRNA targets between patient and control blood samples and
postmortem brain tissues, as well as in animal models of neuropsychiatric disorders.
This manuscript reviews recent findings on miRNAs implicated in the pathology of mood
disorders, schizophrenia, and autism, as well as their diagnostic potential, and
their potential as tentative targets for future therapeutics. The plausible
contribution of X chromosome miRNAs to the larger prevalence of major depression
among women is also evaluated.
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Affiliation(s)
- David Gurwitz
- Author affiliations: Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine; Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel. Address for correspondence: David Gurwitz, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978 Israel.
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22
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One Small RNA of Fusarium graminearum Targets and Silences CEBiP Gene in Common Wheat. Microorganisms 2019; 7:microorganisms7100425. [PMID: 31600909 PMCID: PMC6843203 DOI: 10.3390/microorganisms7100425] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/04/2019] [Accepted: 10/06/2019] [Indexed: 12/24/2022] Open
Abstract
The pathogenic fungus Fusarium graminearum (F. graminearum), causing Fusarium head blight (FHB) or scab, is one of the most important cereal killers worldwide, exerting great economic and agronomic losses on global grain production. To repress pathogen invasion, plants have evolved a sophisticated innate immunity system for pathogen recognition and defense activation. Simultaneously, pathogens continue to evolve more effective means of invasion to conquer plant resistance systems. In the process of co-evolution of plants and pathogens, several small RNAs (sRNAs) have been proved in regulating plant immune response and plant-microbial interaction. In this study, we report that a F. graminearum sRNA (Fg-sRNA1) can suppress wheat defense response by targeting and silencing a resistance-related gene, which codes a Chitin Elicitor Binding Protein (TaCEBiP). Transcriptional level evidence indicates that Fg-sRNA1 can target TaCEBiP mRNA and trigger silencing of TaCEBiP in vivo, and in Nicotiana benthamiana (N. benthamiana) plants, Western blotting experiments and YFP Fluorescence observation proofs show that Fg-sRNA1 can suppress the accumulation of protein coding by TaCEBiP gene in vitro. F. graminearum PH-1 strain displays a weakening ability to invasion when Barley stripe mosaic virus (BSMV) vector induces effective silencing Fg-sRNA1 in PH-1 infected wheat plants. Taken together, our results suggest that a small RNA from F. graminearum can target and silence the wheat TaCEBiP gene to enhance invasion of F. graminearum.
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23
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Recent progress in microRNA-based delivery systems for the treatment of human disease. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s41544-019-0024-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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24
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Zhang L, Chen T, Yin Y, Zhang CY, Zhang YL. Dietary microRNA-A Novel Functional Component of Food. Adv Nutr 2019; 10:711-721. [PMID: 31120095 PMCID: PMC6628849 DOI: 10.1093/advances/nmy127] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/26/2018] [Accepted: 12/17/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs are a class of small RNAs that play essential roles in various biological processes by silencing genes. Evidence emerging in recent years suggests that microRNAs in food can be absorbed into the circulatory system and organs of humans and other animals, where they regulate gene expression and biological processes. These food-derived dietary microRNAs may serve as a novel functional component of food, a role that has been neglected to date. However, a significant amount of evidence challenges this new concept. The absorption, stability, and physiological effects of dietary microRNA in recipients, especially in mammals, are currently under heavy debate. In this review, we summarize our current understanding of the unique characteristics of dietary microRNAs and concerns about both the mechanistic and methodological basis for studying the biological significance of dietary microRNAs. Such efforts will benefit continuing investigations and offer new perspectives for the interpretation of the roles of dietary microRNA with respect to the health and disease of humans and animals.
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Affiliation(s)
- Lin Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ting Chen
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yulong Yin
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China,Hunan Polytechnic of Environment and Biology, Hengyang, China
| | - Chen-Yu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, China,Address correspondence to C-YZ (e-mail: )
| | - Yong-Liang Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China,Address correspondence to Y-LZ (e-mail: )
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25
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Li M, Chen T, Wang R, Luo JY, He JJ, Ye RS, Xie MY, Xi QY, Jiang QY, Sun JJ, Zhang YL. Plant MIR156 regulates intestinal growth in mammals by targeting the Wnt/β-catenin pathway. Am J Physiol Cell Physiol 2019; 317:C434-C448. [PMID: 31166713 DOI: 10.1152/ajpcell.00030.2019] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are important negative regulators of genes involved in physiological and pathological processes in plants and animals. Recent studies have shown that miRNAs might regulate gene expression among different species in a cross-kingdom manner. However, the specific roles of plant miRNAs in animals remain poorly understood and somewhat. Herein, we found that plant MIR156 regulates proliferation of intestinal cells both in vitro and in vivo. Continuous administration of a high plant miRNA diet or synthetic MIR156 elevated MIR156 levels and inhibited the Wnt/β-catenin signaling pathway in mouse intestine. Bioinformatics predictions and luciferase reporter assays indicated that MIR156 targets Wnt10b. In vitro, MIR156 suppressed proliferation by downregulating the Wnt10b protein and upregulating β-catenin phosphorylation in the porcine jejunum epithelial (IPEC-J2) cell line. Lithium chloride and an MIR156 inhibitor relieved this inhibition. This research is the first to demonstrate that plant MIR156 inhibits intestinal cell proliferation by targeting Wnt10b. More importantly, plant miRNAs may represent a new class of bioactive molecules that act as epigenetic regulators in humans and other animals.
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Affiliation(s)
- Meng Li
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ting Chen
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ran Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Jun-Yi Luo
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jia-Jian He
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Rui-Song Ye
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Mei-Ying Xie
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qian-Yun Xi
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qing-Yan Jiang
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jia-Jie Sun
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yong-Liang Zhang
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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26
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Lu Q, Li L, Huang A, Cui L, Zhang Y, Liu Q, Wang X, Wang Y, Liu Z, Yuan Z, Dai M. Molecular Characterization and Biological Function of a Novel LncRNA CRNG in Swine. Front Pharmacol 2019; 10:539. [PMID: 31178726 PMCID: PMC6537671 DOI: 10.3389/fphar.2019.00539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/29/2019] [Indexed: 12/22/2022] Open
Abstract
Our previous study has showed that a novel gene is differentially expressed in the liver of cyadox-fed piglets, but its sequence and function are unknown. Here, rapid amplification of cDNA ends (RACE) and bioinformatics analysis showed that the novel gene is 953 bp without protein-coding ability and locates in chromosome 11. Hence, we identified the novel gene as long non-coding RNA (lncRNA) and named it cyadox-related novel gene (CRNG). Fluorescence in situ hybridization (FISH) showed that CRNG mainly distributes in cytoplasm. Moreover, microarray assay in combination with CRNG interference and overexpression showed that the differential genes such as ANPEP, KITLG, STAT5A, FOXP3, miR-451, IL-2, IL-10, IL-6, and TNF-α are mainly involved in viral and pathogens infection and the immune-inflammatory responses in PK-15 cells. This work reveals that CRNG might play a role in preventing the host from being infected by pathogens and viruses and exerting immune regulatory effects in the cytoplasm, which may be involved in prophylaxis of cyadox in piglets.
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Affiliation(s)
- Qirong Lu
- National Reference Laboratory of Veterinary Drug Residues and Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, China.,Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Li Li
- National Reference Laboratory of Veterinary Drug Residues and Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, China
| | - Aixin Huang
- National Reference Laboratory of Veterinary Drug Residues and Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, China
| | - Luqing Cui
- Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Yinfeng Zhang
- Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Qianying Liu
- National Reference Laboratory of Veterinary Drug Residues and Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, China
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues and Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, China.,Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Yulian Wang
- Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Zhenli Liu
- Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Zonghui Yuan
- National Reference Laboratory of Veterinary Drug Residues and Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, China.,Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Menghong Dai
- National Reference Laboratory of Veterinary Drug Residues and Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, China.,Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
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Zhang H, Zhan M, Chang H, Song S, Zhang C, Liu Y. Research Progress of Exogenous Plant MiRNAs in Cross-Kingdom Regulation. Curr Bioinform 2019. [DOI: 10.2174/1574893613666181113142414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background:Studies have shown that exogenous miRNAs have cross-kingdom regulatory effects on bacteria and viruses, but whether exogenous plant miRNAs are stable in human body or participate in cross-kingdom regulation is still controversial.Objective:This study aims to propose a new method for the presence and cross-kingdom regulation pathway of exogenous Plant miRNA, which combines biological calculations and biological experiments.Method:Based on the high-throughput sequencing data of human health tissue, the tissue specificity model of exogenous plant miRNA can be constructed and the absorption characteristics will be excavated and analyzed. Then screening the exogenous Plant miRNA based on the crosskingdom regulation model of plant-human miRNA, and isotope labeling can be used to verify the presence and regulation pathway of exogenous plant miRNA.Results:Only based on a comprehensive analysis to human high-throughput miRNA data, establishing cross-kingdom regulation model and designing effective biological experiments, can we reveal the existence, access pathways and regulation of exogenous plant miRNAs.Conclusion:Here, we reviewed the most recent advances in the presence and pathway of exogenous plant miRNAs into human and their cross-kingdom regulation.
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Affiliation(s)
- Hao Zhang
- Computer Science and Technology Department, College of Software, Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Mengping Zhan
- Computer Science and Technology Department, College of Software, Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Haowu Chang
- Computer Science and Technology Department, College of Software, Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Shizeng Song
- Computer Science and Technology Department, College of Software, Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Chunhe Zhang
- Computer Science and Technology Department, College of Software, Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Yuanning Liu
- Computer Science and Technology Department, College of Software, Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
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28
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Yang X, Kang N, Toyofuku WM, Scott MD. Enhancing the pro-inflammatory anti-cancer T cell response via biomanufactured, secretome-based, immunotherapeutics. Immunobiology 2019; 224:270-284. [PMID: 30711357 DOI: 10.1016/j.imbio.2018.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/24/2022]
Abstract
T lymphocytes play a critical role in the pro-inflammatory anti-cancer response; hence, significant pharmacologic efforts have been made to enhance the endogenous T cell response. Unfortunately, significant toxicity arises consequent to pan T cell activation. In contrast, the less robust T cell alloresponse has also demonstrated an anti-cancer effect, but poses an inherent risk of GvHD. To overcome the GvHD risk, an acellular pro-inflammatory agent (IA1) has been biomanufactured from the secretome of the allorecognition response. To assess IA1's immunomodulatory activity, T cell proliferation and differentiation were determined in vitro. The pro-inflammatory properties of the IA1 therapeutic were mediated by the miRNA-enriched fractions. Moreover, cross-species efficacy was observed consequent to the evolutionary conservation of miRNA. IA1 exerted no toxicity to resting PBMC but induced significant proliferation of resting CD3+ (CD4+ and CD8+) T cells and skewed the response towards a pro-inflammatory state (i.e., increased Teff:Treg ratio). Crucially, IA1-activated PBMC demonstrated a potent inhibition of cancer cell (HeLa and SH-4 melanoma) proliferation relative to the resting PBMC. The anti-proliferation effect of IA1-activated PBMC was noted within ˜12 h versus 4-5 days for resting cells. A second biomanufactured therapeutic (IA2; produced using HeLa cells) surprisingly demonstrated direct toxicity to cancer cells but was less effective than IA1 in inducing a cell-mediated response. This study demonstrates that miRNA-enriched therapeutics can be biomanufactured from the secretome and can induce a potent pro-inflammatory, anti-cancer, effect on resting lymphocytes.
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Affiliation(s)
- Xining Yang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; University of British Columbia Centre for Blood Research, Canada
| | - Ning Kang
- University of British Columbia Centre for Blood Research, Canada; Canadian Blood Services, Canada
| | - Wendy M Toyofuku
- University of British Columbia Centre for Blood Research, Canada; Canadian Blood Services, Canada
| | - Mark D Scott
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; University of British Columbia Centre for Blood Research, Canada; Canadian Blood Services, Canada.
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29
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Gurwitz D. Genomics and the future of psychopharmacology: MicroRNAs offer novel therapeutics
. DIALOGUES IN CLINICAL NEUROSCIENCE 2019; 21:131-148. [PMID: 31636487 PMCID: PMC6787538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/26/2024]
Abstract
MicroRNAs (miRNAs) are short, noncoding RNAs functioning as regulators of the transcription of protein-coding genes in eukaryotes. During the last two decades, studies on miRNAs indicate that they have potential as diagnostic and prognostic biomarkers for a wide range of cancers. Research interest in miRNAs has moved to embrace further medical disciplines, including neuropsychiatric disorders, comparing miRNA expression and mRNA targets between patient and control blood samples and postmortem brain tissues, as well as in animal models of neuropsychiatric disorders. This manuscript reviews recent findings on miRNAs implicated in the pathology of mood disorders, schizophrenia, and autism, as well as their diagnostic potential, and their potential as tentative targets for future therapeutics. The plausible contribution of X chromosome miRNAs to the larger prevalence of major depression among women is also evaluated.
.
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Affiliation(s)
- David Gurwitz
- Author affiliations: Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine; Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel. Address for correspondence: David Gurwitz, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978 Israel.
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30
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Cong L, Zhao Y, Pogue AI, Lukiw WJ. Role of microRNA (miRNA) and Viroids in Lethal Diseases of Plants and Animals. Potential Contribution to Human Neurodegenerative Disorders. BIOCHEMISTRY (MOSCOW) 2018; 83:1018-1029. [PMID: 30472940 DOI: 10.1134/s0006297918090031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Both plants and animals have adopted a common strategy of using ~18-25-nucleotide small non-coding RNAs (sncRNAs), known as microRNAs (miRNAs), to transmit DNA-based epigenetic information. miRNAs (i) shape the total transcriptional output of individual cells; (ii) regulate and fine-tune gene expression profiles of cell clusters, and (iii) modulate cell phenotype in response to environmental stimuli and stressors. These miRNAs, the smallest known carriers of gene-encoded post-transcriptional regulatory information, not only regulate cellular function in healthy cells but also act as important mediators in the development of plant and animal diseases. Plants possess their own specific miRNAs; at least 32 plant species have been found to carry infectious sncRNAs called viroids, whose mechanisms of generation and functions are strikingly similar to those of miRNAs. This review highlights recent remarkable and sometimes controversial findings in miRNA signaling in plants and animals. Special attention is given to the intriguing possibility that dietary miRNAs and/or sncRNAs can function as mobile epigenetic and/or evolutionary linkers between different species and contribute to both intra- and interkingdom signaling. Wherever possible, emphasis has been placed on the relevance of these miRNAs to the development of human neurodegenerative diseases, such as Alzheimer's disease. Based on the current available data, we suggest that such xeno-miRNAs may (i) contribute to the beneficial properties of medicinal plants, (ii) contribute to the negative properties of disease-causing or poisonous plants, and (iii) provide cross-species communication between kingdoms of living organisms involving multiple epigenetic and/or potentially pathogenic mechanisms associated with the onset and pathogenesis of various diseases.
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Affiliation(s)
- L Cong
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112-2272, USA.,Department of Neurology, Shengjing Hospital, China Medical University, Heping District, Shenyang, Liaoning Province, China
| | - Y Zhao
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112-2272, USA.,Department of Anatomy and Cell Biology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112-2272, USA
| | - A I Pogue
- Alchem Biotech Research, Toronto, ON M5S 1A8, Canada
| | - W J Lukiw
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112-2272, USA. .,Department Neurology, Louisiana State University School of Medicine, New Orleans, LA 70112-2272, USA.,Department Ophthalmology, Louisiana State University School of Medicine, New Orleans, LA 70112-2272, USA
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31
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Sanchita, Trivedi R, Asif MH, Trivedi PK. Dietary plant miRNAs as an augmented therapy: cross-kingdom gene regulation. RNA Biol 2018; 15:1433-1439. [PMID: 30474479 PMCID: PMC6333437 DOI: 10.1080/15476286.2018.1551693] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/23/2018] [Accepted: 11/02/2018] [Indexed: 01/08/2023] Open
Abstract
Cross-kingdom gene regulation by microRNAs (miRNAs) initiated a hot debate on the effective role of orally acquired plant miRNAs on human gene expression. It resulted in the expansion of gene regulation theories and role of plant miRNAs in cross-kingdom regulation of gene expression. This opened up the discussion that 'Whether we really get what we eat?' and 'Whether the orally acquired miRNAs really have a biologically important consequences after entering our digestive and circulatory system?' The reports of orally acquired plant miRNAs inside human alimentary canal have been a topic of discussion in the scientific community. The cross-kingdom gene regulations have raised our hopes to explore the exciting world of plant miRNAs as therapeutic potential and dietary supplements. However, there are reports which have raised concerns over any such cross-kingdom regulation and argued that technical flaws in the experiments might have led to such hypothesis. This review will give the complete understanding of exogenous application and cross-kingdom regulation of plant miRNAs on human health. Here, we provide update and discuss the consequences of plant miRNA mediated cross-kingdom gene regulation and possibilities for this exciting regulatory mechanism as an augmented therapy against various diseases.
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Affiliation(s)
- Sanchita
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Ritu Trivedi
- Endocrinology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, Uttar Pradesh, India
| | - Mehar Hasan Asif
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Prabodh Kumar Trivedi
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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32
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Fujita D, Arai T, Komori H, Shirasaki Y, Wakayama T, Nakanishi T, Tamai I. Apple-Derived Nanoparticles Modulate Expression of Organic-Anion-Transporting Polypeptide (OATP) 2B1 in Caco-2 Cells. Mol Pharm 2018; 15:5772-5780. [PMID: 30359033 DOI: 10.1021/acs.molpharmaceut.8b00921] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Interaction of foods with intestinal transporters has generally been ascribed to small molecules, but recently, edible-plant-derived nanoparticles (NPs) have been suggested to affect intestinal function. Here, we examined the effects of NPs contained in edible fruits on intestinal transporters. Apple-derived NPs (APNPs) were isolated by ultracentrifugation and characterized by measurement of particle size distribution and electron microscopy. Human epithelial colorectal adenocarcinoma (Caco-2) cells internalized fluorescently labeled APNPs, suggesting that fruit-derived NPs would be internalized into intestinal epithelial cells in vivo. We found that the mRNA expression levels of several transporters, including organic-anion-transporting polypeptide (OATP) 2B1, were changed in APNP-treated Caco-2 cells. The protein expression and activity of OATP2B1 were also decreased by APNP exposure, as determined by Western blotting and measurements of [3H]estrone-3-sulfate uptake by Caco-2 cells, respectively. These actions required intact APNPs, because sonication or boiling abrogated the effects. Since the content of apple-derived small molecules in APNPs was negligible, the observed decrease of OATP2B1 expression appears to be mediated by large molecules in the APNPs. We further found that the 3'-untranslated region of the OATP2B1 gene was required for the response to APNPs, suggesting that microRNA in the APNPs might be involved. These results propose a novel mechanism, in which large molecules such as microRNA in food could affect intestinal transporters through food-derived NPs, which also demonstrates that food-derived NPs should be useful for delivery of biologically active large molecules to intestinal tissues.
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Affiliation(s)
- Daichi Fujita
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences , Kanazawa University , Kakuma-machi, Kanazawa 920-1192 , Japan
| | - Toshiki Arai
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences , Kanazawa University , Kakuma-machi, Kanazawa 920-1192 , Japan
| | - Hisakazu Komori
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences , Kanazawa University , Kakuma-machi, Kanazawa 920-1192 , Japan
| | - Yuma Shirasaki
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences , Kanazawa University , Kakuma-machi, Kanazawa 920-1192 , Japan
| | - Tomohiko Wakayama
- Faculty of Life Science , Kumamoto University , Kumamoto 860-8555 , Japan
| | - Takeo Nakanishi
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences , Kanazawa University , Kakuma-machi, Kanazawa 920-1192 , Japan
| | - Ikumi Tamai
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences , Kanazawa University , Kakuma-machi, Kanazawa 920-1192 , Japan
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Agapito-Tenfen SZ, Vilperte V, Traavik TI, Nodari RO. Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism. ENVIRONMENTAL SCIENCES EUROPE 2018; 30:37. [PMID: 30294516 PMCID: PMC6153861 DOI: 10.1186/s12302-018-0168-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND While some genetically modified organisms (GMOs) are created to produce new double-stranded RNA molecules (dsRNA), in others, such molecules may occur as an unintended effect of the genetic engineering process. Furthermore, GMOs might produce naturally occurring dsRNA molecules in higher or lower quantities than its non-transgenic counterpart. This study is the first to use high-throughput technology to characterize the miRNome of commercialized GM maize events and to investigate potential alterations in miRNA regulatory networks. RESULTS Thirteen different conserved miRNAs were found to be dys-regulated in GM samples. The insecticide Bt GM variety had the most distinct miRNome. These miRNAs target a range of endogenous transcripts, such as transcription factors and nucleic acid binding domains, which play key molecular functions in basic genetic regulation. In addition, we have identified 20 potential novel miRNAs with target transcripts involved in lipid metabolism in maize. isomiRs were also found in 96 conserved miRNAs sequences, as well as potential transgenic miRNA sequences, which both can be a source of potential off-target effects in the plant genome. We have also provided information on technical limitations and when to carry on additional in vivo experimental testing. CONCLUSIONS These findings do not reveal hazards per se but show that robust and reproducible miRNA profiling technique can strengthen the assessment of risk by detecting any new intended and unintended dsRNA molecules, regardless of the outcome, at any stage of GMO development.
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Affiliation(s)
| | - Vinicius Vilperte
- Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, 88034000 Brazil
- Present Address: Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz University of Hannover, 30419 Hannover, Germany
| | - Terje Ingemar Traavik
- GenØk–Centre for Biosafety, Forskningsparken i Breivika, Sykehusveien 23, 9294 Tromsø, Norway
| | - Rubens Onofre Nodari
- Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, 88034000 Brazil
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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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Cohen A, Zinger A, Tiberti N, Grau GER, Combes V. Differential plasma microvesicle and brain profiles of microRNA in experimental cerebral malaria. Malar J 2018; 17:192. [PMID: 29747626 PMCID: PMC5946432 DOI: 10.1186/s12936-018-2330-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 04/20/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Cerebral malaria (CM) is a fatal complication of Plasmodium infection, mostly affecting children under the age of five in the sub-Saharan African region. CM pathogenesis remains incompletely understood, although sequestered infected red blood cells, inflammatory cells aggregating in the cerebral blood vessels, and the microvesicles (MV) that they release in the circulation, have been implicated. Plasma MV numbers increase in CM patients and in the murine model, where blocking their release, genetically or pharmacologically, protects against brain pathology, suggesting a role of MV in CM neuropathogenesis. In this work, the microRNA (miRNA) cargo of MV is defined for the first time during experimental CM with the overarching hypothesis that this characterization could help understand CM pathogenesis. RESULTS The change in abundance of miRNA was studied following infection of CBA mice with Plasmodium berghei ANKA strain (causing experimental CM), and Plasmodium yoelii, which causes severe malaria without cerebral complications, termed non-CM (NCM). miRNA expression was analyzed using microarrays to compare MV from healthy (NI) and CM mice, yielding several miRNA of interest. The differential expression profiles of these selected miRNA (miR-146a, miR-150, miR-193b, miR-205, miR-215, miR-467a, and miR-486) were analyzed in mouse MV, MV-free plasma, and brain tissue by quantitative reverse transcription PCR (RT-qPCR). Two miRNA-miR-146a and miR-193b-were confirmed as differentially abundant in MV from CM mice, compared with NCM and NI mice. These miRNA have been shown to play various roles in inflammation, and their dysregulation during CM may be critical for triggering the neurological syndrome via regulation of their potential downstream targets. CONCLUSIONS These data suggest that, in the mouse model at least, miRNA may have a regulatory role in the pathogenesis of severe malaria.
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Affiliation(s)
- Amy Cohen
- Vascular Immunology Unit, Department of Pathology, The University of Sydney, Sydney, Australia
| | - Anna Zinger
- Vascular Immunology Unit, Department of Pathology, The University of Sydney, Sydney, Australia
| | - Natalia Tiberti
- Vascular Immunology Unit, Department of Pathology, The University of Sydney, Sydney, Australia
- School of Life Sciences, Faculty of Sciences, University of Technology, Sydney, Australia
| | - Georges E R Grau
- Vascular Immunology Unit, Department of Pathology, The University of Sydney, Sydney, Australia
- La Jolla Infectious Diseases Institute, San Diego, CA, USA
| | - Valery Combes
- School of Life Sciences, Faculty of Sciences, University of Technology, Sydney, Australia.
- La Jolla Infectious Diseases Institute, San Diego, CA, USA.
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Mal C, Aftabuddin M, Kundu S. IIKmTA: Inter and Intra Kingdom miRNA-Target Analyzer. Interdiscip Sci 2018; 10:538-543. [PMID: 29549628 DOI: 10.1007/s12539-018-0291-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 03/07/2018] [Accepted: 03/10/2018] [Indexed: 01/23/2023]
Abstract
BACKGROUND Growing evidences suggest that microRNAs (miRNAs) can efficiently regulate gene expression at intracellular and extracellular levels. It has been previously reported that plant/food-derived miRNAs are highly enriched in human serum or serum from phytophagous animals, and they are responsible for regulating mammalian gene expression. Thus, miRNAs could function as active signaling molecules, which carry information across distinct species or even kingdoms. However, the mode of miRNA shuttling among various organisms is still a mystery to unravel. The intra and inter kingdom miRNA transfer has boosted up the hypothesis about the potential impact of plant or animal miRNAs on each other. To our knowledge, the software for analyzing cross-kingdom miRNA-targets is lacking. RESULTS We have developed a web-tool "IIKmTA: Inter and Intra Kingdom miRNA-Target Analyzer" utilizing a database; the data of which have been collected from another web server. Here, user can analyze the targeting potential of (i) plant miRNAs on animal UTRs (Untranslated regions), and vice versa (i.e., inter kingdom), (ii) plant miRNAs on plant UTRs and animal miRNAs on animal UTRs (i.e., intra kingdom). Further, user can analyze (i) miRNAs to targets, (ii) targets to miRNAs, and (iii) miRNA sets targeting sets of targets. For a wide variety of animal and plant species, IIKmTA can identify the miRNA binding sites in the probable target UTRs. Moreover, GC% and AU% of miRNAs will be calculated. All the results can be saved as .csv file. CONCLUSIONS Recent researches identified miRNAs in plants and human secretions and their role in regulating the human genes. Such findings indicate the therapeutic role of secretory miRNAs of such plants which exhibits medicinal value and in near future many diseases may be treated by consumption of these plant miRNAs through food. Using our newly developed database and analyzing tool, one can easily determine the different relationships between miRNAs and their targets across kingdoms. IIKmTA is freely available at http://www.bioinformatics.org/iikmta/ .
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Affiliation(s)
- Chittabrata Mal
- Amity Institute of Biotechnology, Amity University Kolkata, Major Arterial Road(North-South), AA II, Newtown, Rajarhat, West Bengal, 700135, India.
| | - Md Aftabuddin
- Maulana Abul Kalam Azad University of Technology, West Bengal, BF-142, Salt Lake, Sector-I, Kolkata, 700064, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India
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37
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Zhao Y, Cong L, Lukiw WJ. Plant and Animal microRNAs (miRNAs) and Their Potential for Inter-kingdom Communication. Cell Mol Neurobiol 2017; 38:133-140. [DOI: 10.1007/s10571-017-0547-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/31/2017] [Indexed: 12/22/2022]
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38
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Exosomal microRNAs in giant panda (Ailuropoda melanoleuca) breast milk: potential maternal regulators for the development of newborn cubs. Sci Rep 2017; 7:3507. [PMID: 28615713 PMCID: PMC5471263 DOI: 10.1038/s41598-017-03707-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 05/03/2017] [Indexed: 11/09/2022] Open
Abstract
The physiological role of miRNAs is widely understood to include fine-tuning the post-transcriptional regulation of a wide array of biological processes. Extensive studies have indicated that exosomal miRNAs in the bodily fluids of various organisms can be transferred between living cells for the delivery of gene silencing signals. Here, we illustrated the expression characteristics of exosomal miRNAs in giant panda breast milk during distinct lactation periods and highlighted the enrichment of immune- and development-related endogenous miRNAs in colostral and mature giant panda milk. These miRNAs are stable, even under certain harsh conditions, via the protection of extracellular vesicles. These findings indicate that breast milk may facilitate the dietary intake of maternal miRNAs by infants for the regulation of postnatal development. We also detected exogenous plant miRNAs from the primary food source of the giant panda (bamboo) in the exosomes of giant panda breast milk that were associated with regulatory roles in basic metabolism and neuron development. This result suggested that dietary plant miRNAs are absorbed by host cells and subsequently secreted into bodily fluids as potential cross-kingdom regulators. In conclusion, exosomal miRNAs in giant panda breast milk may be crucial maternal regulators for the development of intrinsic 'slink' newborn cubs.
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39
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Zhang H, Li Y, Liu Y, Liu H, Wang H, Jin W, Zhang Y, Zhang C, Xu D. Role of plant MicroRNA in cross-species regulatory networks of humans. BMC SYSTEMS BIOLOGY 2016; 10:60. [PMID: 27502923 PMCID: PMC4977847 DOI: 10.1186/s12918-016-0292-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/22/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND It has been found that microRNAs (miRNAs) can function as a regulatory factor across species. For example, food-derived plant miRNAs may pass through the gastrointestinal (GI) tract, enter into the plasma and serum of mammals, and interact with endogenous RNAs to regulate their expression. Although this new type of regulatory mechanism is not well understood, it provides a fresh look at the relationship between food consumption and physiology. To investigate this new type of mechanism, we conducted a systematic computational study to analyze the potential functions of these dietary miRNAs in the human body. RESULTS In this paper, we predicted human and plant target genes using RNAhybrid and set some criteria to further filter them. Then we built the cross-species regulatory network according to the filtered targets, extracted central nodes by PageRank algorithm and built core modules. We summarized the functions of these modules to three major categories: ion transport, metabolic process and stress response, and especially some target genes are highly related to ion transport, polysaccharides and the lipid metabolic process. Through functional analysis, we found that human and plants have similar functions such as ion transport and stress response, so our study also indicates the existence of a close link between exogenous plant miRNA targets and digestive/urinary organs. CONCLUSIONS According to our analysis results, we suggest that the ingestion of these plant miRNAs may have a functional impact on consuming organisms in a cross-kingdom way, and the dietary habit may affect the physiological condition at a genetic level. Our findings may be useful for discovering cross-species regulatory mechanism in further study.
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Affiliation(s)
- Hao Zhang
- Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Missouri, USA
| | - Yanpu Li
- Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Yuanning Liu
- Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Missouri, USA
| | - Haiming Liu
- Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Hongyu Wang
- Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Wen Jin
- Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Yanmei Zhang
- Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Chao Zhang
- Institute of Computational Biomedicine, Weill Cornell Medical College, New York, USA
| | - Dong Xu
- Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Missouri, USA
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40
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Shchennikova AV, Beletsky AV, Shulga OA, Mazur AM, Prokhortchouk EB, Kochieva EZ, Ravin NV, Skryabin KG. Deep-sequence profiling of miRNAs and their target prediction in Monotropa hypopitys. PLANT MOLECULAR BIOLOGY 2016; 91:441-458. [PMID: 27097902 DOI: 10.1007/s11103-016-0478-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
Myco-heterotroph Monotropa hypopitys is a widely spread perennial herb used to study symbiotic interactions and physiological mechanisms underlying the development of non-photosynthetic plant. Here, we performed, for the first time, transcriptome-wide characterization of M. hypopitys miRNA profile using high throughput Illumina sequencing. As a result of small RNA library sequencing and bioinformatic analysis, we identified 55 members belonging to 40 families of known miRNAs and 17 putative novel miRNAs unique for M. hypopitys. Computational screening revealed 206 potential mRNA targets for known miRNAs and 31 potential mRNA targets for novel miRNAs. The predicted target genes were described in Gene Ontology terms and were found to be involved in a broad range of metabolic and regulatory pathways. The identification of novel M. hypopitys-specific miRNAs, some with few target genes and low abundances, suggests their recent evolutionary origin and participation in highly specialized regulatory mechanisms fundamental for non-photosynthetic biology of M. hypopitys. This global analysis of miRNAs and their potential targets in M. hypopitys provides a framework for further investigation of miRNA role in the evolution and establishment of non-photosynthetic myco-heterotrophs.
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Affiliation(s)
- Anna V Shchennikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Olga A Shulga
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Alexander M Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Egor B Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Elena Z Kochieva
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Nikolay V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Konstantin G Skryabin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071.
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41
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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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42
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Ferguson JF, Allayee H, Gerszten RE, Ideraabdullah F, Kris-Etherton PM, Ordovás JM, Rimm EB, Wang TJ, Bennett BJ. Nutrigenomics, the Microbiome, and Gene-Environment Interactions: New Directions in Cardiovascular Disease Research, Prevention, and Treatment: A Scientific Statement From the American Heart Association. CIRCULATION. CARDIOVASCULAR GENETICS 2016; 9:291-313. [PMID: 27095829 PMCID: PMC7829062 DOI: 10.1161/hcg.0000000000000030] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cardiometabolic diseases are the leading cause of death worldwide and are strongly linked to both genetic and nutritional factors. The field of nutrigenomics encompasses multiple approaches aimed at understanding the effects of diet on health or disease development, including nutrigenetic studies investigating the relationship between genetic variants and diet in modulating cardiometabolic risk, as well as the effects of dietary components on multiple "omic" measures, including transcriptomics, metabolomics, proteomics, lipidomics, epigenetic modifications, and the microbiome. Here, we describe the current state of the field of nutrigenomics with respect to cardiometabolic disease research and outline a direction for the integration of multiple omics techniques in future nutrigenomic studies aimed at understanding mechanisms and developing new therapeutic options for cardiometabolic disease treatment and prevention.
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43
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Singh NK. microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations. Interdiscip Sci 2016; 9:357-377. [PMID: 27021491 DOI: 10.1007/s12539-016-0166-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/08/2016] [Accepted: 03/11/2016] [Indexed: 12/31/2022]
Abstract
microRNA (miRNA) is an endogenous and evolutionary conserved non-coding RNA, involved in post-transcriptional process as gene repressor and mRNA cleavage through RNA-induced silencing complex (RISC) formation. In RISC, miRNA binds in complementary base pair with targeted mRNA along with Argonaut proteins complex, causes gene repression or endonucleolytic cleavage of mRNAs and results in many diseases and syndromes. After the discovery of miRNA lin-4 and let-7, subsequently large numbers of miRNAs were discovered by low-throughput and high-throughput experimental techniques along with computational process in various biological and metabolic processes. The miRNAs are important non-coding RNA for understanding the complex biological phenomena of organism because it controls the gene regulation. This paper reviews miRNA databases with structural and functional annotations developed by various researchers. These databases contain structural and functional information of animal, plant and virus miRNAs including miRNAs-associated diseases, stress resistance in plant, miRNAs take part in various biological processes, effect of miRNAs interaction on drugs and environment, effect of variance on miRNAs, miRNAs gene expression analysis, sequence of miRNAs, structure of miRNAs. This review focuses on the developmental methodology of miRNA databases such as computational tools and methods used for extraction of miRNAs annotation from different resources or through experiment. This study also discusses the efficiency of user interface design of every database along with current entry and annotations of miRNA (pathways, gene ontology, disease ontology, etc.). Here, an integrated schematic diagram of construction process for databases is also drawn along with tabular and graphical comparison of various types of entries in different databases. Aim of this paper is to present the importance of miRNAs-related resources at a single place.
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Affiliation(s)
- Nagendra Kumar Singh
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, M.P., 462003, India.
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44
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Abstract
Be it their pervasiveness, experimental tractability or their impact on human health and agriculture, nematode–bacterium associations are far-reaching research subjects. Although the omics hype did not spare them and helped reveal mechanisms of communication and exchange between the associated partners, a huge amount of knowledge still awaits to be harvested from their study. Here, I summarize and compare the kind of research that has been already performed on the model nematode Caenorhabditis elegans and on symbiotic nematodes, both marine and entomopathogenic ones. The emerging picture highlights how complementing genetic studies with ecological ones (in the case of well-established genetic model systems such as C. elegans) and vice versa (in the case of the yet uncultured Stilbonematinae) will deepen our understanding of how microbial symbioses evolved and how they impact our environment. Nematode–bacterium associations are major research subjects. Complementing genetic studies with ecological ones is necessary to boost our understanding of how microbial symbioses evolved and how they impact the environment.
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Affiliation(s)
- Silvia Bulgheresi
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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45
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Weiberg A, Bellinger M, Jin H. Conversations between kingdoms: small RNAs. Curr Opin Biotechnol 2015. [PMID: 25622136 DOI: 10.1016/j.copbio.2014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Humans, animals, and plants are constantly under attack from pathogens and pests, resulting in severe consequences on global human health and crop production. Small RNA (sRNA)-mediated RNA interference (RNAi) is a conserved regulatory mechanism that is involved in almost all eukaryotic cellular processes, including host immunity and pathogen virulence. Recent evidence supports the significant contribution of sRNAs and RNAi to the communication between hosts and some eukaryotic pathogens, pests, parasites, or symbiotic microorganisms. Mobile silencing signals—most likely sRNAs—are capable of translocating from the host to its interacting organism, and vice versa. In this review, we will provide an overview of sRNA communications between different kingdoms, with a primary focus on the advances in plant-pathogen interaction systems.
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Affiliation(s)
- Arne Weiberg
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Marschal Bellinger
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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46
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Cohen A, Combes V, Grau GER. MicroRNAs and Malaria - A Dynamic Interaction Still Incompletely Understood. JOURNAL OF NEUROINFECTIOUS DISEASES 2015; 6:165. [PMID: 26005686 PMCID: PMC4441219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Malaria is a mosquito-borne infectious disease caused by parasitic protozoa of the genus Plasmodium. It remains a major problem affecting humans today, especially children. However, the pathogenesis of malaria, especially severe malaria, remains incompletely understood, hindering our ability to treat this disease. Of recent interest is the role that small, non-coding RNAs play in the progression, pathogenesis of, and resistance to, malaria. Independent studies have now revealed the presence of microRNA (miRNA) in the malaria parasite, vector, and host, though these studies are relatively few. Here, we review these studies, focusing on the roles specific miRNA have in the disease, and how they may be harnessed for therapeutic purposes.
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Affiliation(s)
| | | | - Georges ER Grau
- Corresponding author: Grau GER, Medical Foundation Building (K25), 92-94 Parramatta Rd, Camperdown NSW 2050, Australia, Tel: +61 2 9036 3260;
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47
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Weiberg A, Bellinger M, Jin H. Conversations between kingdoms: small RNAs. Curr Opin Biotechnol 2015; 32:207-215. [PMID: 25622136 DOI: 10.1016/j.copbio.2014.12.025] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 12/22/2014] [Accepted: 12/30/2014] [Indexed: 12/30/2022]
Abstract
Humans, animals, and plants are constantly under attack from pathogens and pests, resulting in severe consequences on global human health and crop production. Small RNA (sRNA)-mediated RNA interference (RNAi) is a conserved regulatory mechanism that is involved in almost all eukaryotic cellular processes, including host immunity and pathogen virulence. Recent evidence supports the significant contribution of sRNAs and RNAi to the communication between hosts and some eukaryotic pathogens, pests, parasites, or symbiotic microorganisms. Mobile silencing signals—most likely sRNAs—are capable of translocating from the host to its interacting organism, and vice versa. In this review, we will provide an overview of sRNA communications between different kingdoms, with a primary focus on the advances in plant-pathogen interaction systems.
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Affiliation(s)
- Arne Weiberg
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Marschal Bellinger
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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Cheng G. Circulating miRNAs: roles in cancer diagnosis, prognosis and therapy. Adv Drug Deliv Rev 2015; 81:75-93. [PMID: 25220354 DOI: 10.1016/j.addr.2014.09.001] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/28/2014] [Accepted: 09/03/2014] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) belong to a class of small non-coding RNAs that regulate numerous biological processes by targeting a broad set of messenger RNAs. Recently, miRNAs have been detected in remarkably stable forms in many types of body fluids. A comparison between cancer patients and healthy individuals has clearly shown that certain types of circulating miRNAs are associated with cancer initiation and progression. Research on miRNA-based biomarkers has witnessed phenomenal growth, owing to the non-invasive nature of miRNA-based screening assays and their sensitivity and specificity in detecting cancers. Consequently, a considerable effort has been devoted to identify suitable miRNAs for cancer diagnosis and also decode the information carried by circulating miRNAs. This review highlights the current studies that focus on the identification of circulating miRNA-based diagnostic and prognostic markers, for the most prevalent types of cancer. Additionally, the review also provides an insight into the putative functions of miRNAs, and attempts to delineate the mechanisms through which they are released into the bloodstream. Moreover, methodologies and strategies for identification of circulating miRNAs in cancers are summarized. Finally, potential strategies for circulating miRNA-based cancer therapies are proposed.
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Inal B, Türktaş M, Eren H, Ilhan E, Okay S, Atak M, Erayman M, Unver T. Genome-wide fungal stress responsive miRNA expression in wheat. PLANTA 2014; 240:1287-98. [PMID: 25156489 DOI: 10.1007/s00425-014-2153-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/12/2014] [Indexed: 05/02/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding class of RNAs. They were identified in many plants with their diverse regulatory roles in several cellular and metabolic processes. A number of miRNAs were involved in biotic and abiotic stress responses. Here, fungal stress responsive wheat miRNAs were analyzed by using miRNA-microarray strategy. Two different fungi (Fusarium culmorum and Bipolaris sorokiniana) were inoculated on resistant and sensitive wheat cultivars. A total of 87 differentially regulated miRNAs were detected in the 8 × 15 K array including all of the available plant miRNAs. Using bioinformatics tools, the target transcripts of responsive miRNAs were predicted, and related biological processes and mechanisms were assessed. A number of the miRNAs such as miR2592s, miR869.1, miR169b were highly differentially regulated showing more than 200-fold change upon fungal-inoculation. Some of the miRNAs were identified as fungal-inoculation responsive for the first time. The analyses showed that some of the differentially regulated miRNAs targeted resistance-related genes such as LRR, glucuronosyl transferase, peroxidase and Pto kinase. The comparison of the two miRNA-microarray analyses indicated that fungal-responsive wheat miRNAs were differentially regulated in pathogen- and cultivar-specific manners.
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Affiliation(s)
- Behçet Inal
- Department of Biology, Faculty of Science, Cankiri Karatekin University, 18100, Cankiri, Turkey
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Abstract
This review focuses on the mobility of small RNA (sRNA) molecules from the perspective of trans-kingdom gene silencing. Mobility of sRNA molecules within organisms is a well-known phenomenon, facilitating gene silencing between cells and tissues. sRNA signals are also transmitted between organisms of the same species and of different species. Remarkably, in recent years many examples of RNA-signal exchange have been described to occur between organisms of different kingdoms. These examples are predominantly found in interactions between hosts and their pathogens, parasites, and symbionts. However, they may only represent the tip of the iceberg, since the emerging picture suggests that organisms in biological niches commonly exchange RNA-silencing signals. In this case, we need to take this into account fully to understand how a given biological equilibrium is obtained. Despite many observations of trans-kingdom RNA signal transfer, several mechanistic aspects of these signals remain unknown. Such RNA signal transfer is already being exploited for practical purposes, though. Pathogen genes can be silenced by plant-produced sRNAs designed to affect these genes. This is also known as Host-Induced Genes Silencing (HIGS), and it has the potential to become an important disease-control method in the future.
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Affiliation(s)
- Marijn Knip
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Maria E. Constantin
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Hans Thordal-Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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