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Everaert C, Verwilt J, Verniers K, Vandamme N, Marcos Rubio A, Vandesompele J, Mestdagh P. Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation. Biol Proced Online 2023; 25:7. [PMID: 36890441 PMCID: PMC9996952 DOI: 10.1186/s12575-023-00193-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/14/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND RNA sequencing has become the gold standard for transcriptome analysis but has an inherent limitation of challenging quantification of low-abundant transcripts. In contrast to microarray technology, RNA sequencing reads are proportionally divided in function of transcript abundance. Therefore, low-abundant RNAs compete against highly abundant - and sometimes non-informative - RNA species. RESULTS We developed an easy-to-use strategy based on high-affinity RNA-binding oligonucleotides to block reverse transcription and PCR amplification of specific RNA transcripts, thereby substantially reducing their abundance in the final sequencing library. To demonstrate the broad application potential of our method, we applied it to different transcripts and library preparation strategies, including YRNAs in small RNA sequencing of human blood plasma, mitochondrial rRNAs in both 3' end sequencing and long-read sequencing, and MALAT1 in single-cell 3' end sequencing. We demonstrate that the blocking strategy is highly efficient, reproducible, specific, and generally results in better transcriptome coverage and complexity. CONCLUSION Our method does not require modifications of the library preparation procedure apart from simply adding blocking oligonucleotides to the RT reaction and can thus be easily integrated into virtually any RNA sequencing library preparation protocol.
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Affiliation(s)
- Celine Everaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Jasper Verwilt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Kimberly Verniers
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Niels Vandamme
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
- VIB Single Cell Core, Vlaams Instituut voor Biotechnologie, Ghent-Leuven, Belgium
| | - Alvaro Marcos Rubio
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.
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2
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Norouzi M, Bakhtiarizadeh MR, Salehi A. Investigation of the transability of dietary small non-coding RNAs to animals. Front Genet 2022; 13:933709. [PMID: 36134021 PMCID: PMC9483711 DOI: 10.3389/fgene.2022.933709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Our daily diet not only provides essential nutrients needed for survival and growth but also supplies bioactive ingredients to promote health and prevent disease. Recent studies have shown that exogenous microRNAs (miRNAs), xenomiRs, may enter the consumer’s body through dietary intake and regulate gene expression. This fascinating phenomenon suggests that xenomiRs can act as a new class of bioactive substances associated with mammalian systems. In contrast, several studies have failed to detect xenomiRs in consumers and reported that the observed diet-derived miRNAs in the previous studies can be related to the false positive effects of experiments. This discrepancy can be attributed to the potential artifacts related to the process of experiments, small sample size, and inefficient bioinformatics pipeline. Since this hypothesis is not generally accepted yet, more studies are required. Here, a stringent and reliable bioinformatics pipeline was used to analyze 133 miRNA sequencing data from seven different studies to investigate this phenomenon. Generally, our results do not support the transfer of diet-derived miRNAs into the animal/human tissues in every situation. Briefly, xenomiRs were absent from most samples, and also, their expressions were very low in the samples where they were present, which is unlikely to be sufficient to regulate cell transcripts. Furthermore, this study showed that the possibility of miRNAs being absorbed through animals’ diets and thus influencing gene expression during specific periods of biological development is not inconceivable. In this context, our results were in agreement with the theory of the transfer of small RNAs under certain conditions and periods as xenomiRs were found in colostrum which may modulate infants’ immune systems via post-transcriptional regulation. These findings provide evidence for the selective absorption of diet-derived small RNAs, which need to be investigated in future studies to shed light on the mechanisms underlying the transference of diet-derived miRNAs.
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Affiliation(s)
- Milad Norouzi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | | | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
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3
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Nashimoto M. TRUE Gene Silencing. Int J Mol Sci 2022; 23:5387. [PMID: 35628198 PMCID: PMC9141469 DOI: 10.3390/ijms23105387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
TRUE gene silencing is an RNA-mediated gene expression control technology and is termed after tRNase ZL-utilizing efficacious gene silencing. In this review, I overview the potentiality of small guide RNA (sgRNA) for TRUE gene silencing as novel therapeutics. First, I describe the physiology of tRNase ZL and cellular small RNA, and then sgRNA and TRUE gene silencing. An endoribonuclease, tRNase ZL, which can efficiently remove a 3' trailer from pre-tRNA, is thought to play the role in tRNA maturation in the nucleus and mitochondria. There exist various small RNAs including miRNA and fragments from tRNA and rRNA, which can function as sgRNA, in living cells, and human cells appear to be harnessing cytosolic tRNase ZL for gene regulation together with these small RNAs. By utilizing the property of tRNase ZL to recognize and cleave micro-pre-tRNA, a pre-tRNA-like or micro-pre-tRNA-like complex, as well as pre-tRNA, tRNase ZL can be made to cleave any target RNA at any desired site under the direction of an artificial sgRNA that binds a target RNA and forms the pre-tRNA-like or micro-pre-tRNA-like complex. This general RNA cleavage method underlies TRUE gene silencing. Various examples of the application of TRUE gene silencing are reviewed including the application to several human cancer cells in order to induce apoptosis. Lastly, I discuss the potentiality of sgRNA as novel therapeutics for multiple myeloma.
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Affiliation(s)
- Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
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4
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Nozaki T, Takahashi M, Ishikawa T, Haino A, Seki M, Kikuchi H, Yuan B, Nashimoto M. The heptamer sgRNA targeting the human OCT4 mRNA can upregulate the OCT4 expression. Biochem Biophys Rep 2021; 26:100918. [PMID: 33553691 PMCID: PMC7859166 DOI: 10.1016/j.bbrep.2021.100918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/24/2020] [Accepted: 01/07/2021] [Indexed: 11/17/2022] Open
Abstract
TRUE gene silencing is one of the gene suppression technologies. This technology exploits the enzymatic property of the tRNA 3' processing endoribonuclease tRNase ZL, which is that it can cleave a target RNA under the direction of a small guide RNA (sgRNA). We have been working on the development of therapeutic sgRNAs for hematological malignancies. In the course of an experiment to examine the ability of the heptamer-type sgRNA H15792 targeting the OCT4 mRNA to differentiate human amnion stem cells, we observed unexpectedly that the amnion cells exhibited a morphology resembling initialized cells. Here we investigated the effect of H15792 on human HL60 leukemia cells, and found that H15792 can upregulate the OCT4 expression and the expression of alkaline phosphatase in the cells.
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Affiliation(s)
- Tadasuke Nozaki
- Department of Clinical Molecular Genetics, Faculty of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Horinouchi 1432-1, Hachioji, Tokyo, 192-0392, Japan
| | - Masayuki Takahashi
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata, 956-8603, Japan
| | - Tatsuya Ishikawa
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata, 956-8603, Japan
| | - Arisa Haino
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata, 956-8603, Japan
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata, 956-8603, Japan
| | - Hidetomo Kikuchi
- Department of Clinical Molecular Genetics, Faculty of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Horinouchi 1432-1, Hachioji, Tokyo, 192-0392, Japan
| | - Bo Yuan
- Department of Clinical Molecular Genetics, Faculty of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Horinouchi 1432-1, Hachioji, Tokyo, 192-0392, Japan
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata, 956-8603, Japan
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5
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Ishikawa T, Haino A, Seki M, Kurihara T, Hirose T, Imai Y, Ishiguro T, Chou T, Toshima M, Terada H, Nashimoto M. The 31-nucleotide Y4-RNA fragment in plasma is a potential novel biomarker. Noncoding RNA Res 2020; 5:37-40. [PMID: 32206739 PMCID: PMC7078377 DOI: 10.1016/j.ncrna.2019.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/13/2019] [Accepted: 12/14/2019] [Indexed: 11/17/2022] Open
Abstract
The 31- and 32-nt 5′-fragment of Y4-RNA (Y4RNAfr) exists abundantly in human peripheral blood plasma. Although physiological roles of the plasma Y4RNAfr are not well established, its potential utility as a diagnostic/prognostic marker for acute coronary syndrome was suggested. In this paper, to establish a normal range of the Y4RNAfr level in plasma, we measured plasma Y4RNAfr levels of 40 healthy persons using the method we have developed, and compared them with other blood test data. From the obtained data, we tentatively regarded <0.1 fmol/ng as normal for the Y4RNAfr level in peripheral blood plasma. And the white blood cell count (WBC) and the C-reactive protein (CRP) level showed moderate positive correlations with the Y4RNAfr level, suggesting that Y4RNAfr could be a potential novel inflammatory marker. We also measured the Y4RNAfr level in peripheral blood plasma from four multiple myeloma patients. The plasma Y4RNAfr level was abnormal in all four myeloma patients, and the levels for two patients were far beyond the normal level. The WBC for each patient was normal and the CRP levels for two patients were normal. These observations together suggest that a high level of Y4RNAfr in peripheral blood plasma and a normal WBC could be indicative of multiple myeloma.
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Affiliation(s)
- Tatsuya Ishikawa
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Arisa Haino
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Taro Kurihara
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Niigata, 951-8566, Japan
| | - Takayuki Hirose
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Niigata, 951-8566, Japan
| | - Yosuke Imai
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Niigata, 951-8566, Japan
| | - Takuro Ishiguro
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Niigata, 951-8566, Japan
| | - Takaaki Chou
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Niigata, 951-8566, Japan
| | - Muneatsu Toshima
- Niitsu Medical Center Hospital, Niigata, Niigata, 956-0025, Japan
| | - Hiroshi Terada
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
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6
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Ninomiya S, Ishikawa T, Takahashi M, Seki M, Nashimoto M. Potential physiological roles of the 31/32-nucleotide Y4-RNA fragment in human plasma. Noncoding RNA Res 2019; 4:135-140. [PMID: 32072081 PMCID: PMC7012775 DOI: 10.1016/j.ncrna.2019.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 11/29/2022] Open
Abstract
The 31- and 32-nt 5′-fragments of Y4-RNA (Y4RNAfr) exist abundantly in human plasma. The Y4RNAfr can function as 5′-half-tRNA-type sgRNA for tRNase ZL, although we do not know yet what its physiological roles are and what cellular RNAs are its genuine targets. In this paper, we analyzed the effects of the Y4RNAfr on cell viability and transcriptomes using HL60, RPMI-8226, and HEK293 cells, and Y4RNAfr-binding RNAs in A549 cells. Although the Y4RNAfr hardly affected the viability of HL60, RPMI-8226, and HEK293 cells, it significantly affected their transcriptome. The DAVID analysis for > 2-fold upregulated and downregulated genes suggested that the Y4RNAfr may affect various KEGG pathways. We obtained 108 Y4RNAfr-binding RNAs in A549 cells, searched potential secondary structures of complexes between theY4RNAfr and its binding RNAs for the pre-tRNA-like structure, and found many such structures. One of the five best fitted structures was for the MKI67 mRNA, suggesting that the Y4RNAfr can decrease the cellular MKI67 level through guiding the cleavage of the MKI67 mRNA by tRNase ZL. This may be one of the underlying mechanisms for the reported observation that the Y4RNAfr suppresses the proliferation of A549 cells.
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Affiliation(s)
- Sho Ninomiya
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Tatsuya Ishikawa
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Masayuki Takahashi
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
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7
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Ishikawa T, Haino A, Ichiyanagi T, Seki M, Nashimoto M. Evaluation of double heptamer-type sgRNA as a potential therapeutic agent against multiple myeloma. Blood Cells Mol Dis 2019; 79:102341. [PMID: 31226499 DOI: 10.1016/j.bcmd.2019.102341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 06/11/2019] [Indexed: 12/21/2022]
Abstract
Emergence of drug-resistant mutations in the course of myeloma cell evolution and subsequent relapse of myeloma appears to be currently inevitable in most patients. To remedy this situation, we are trying to develop therapeutic small guide RNAs (sgRNAs) based on tRNase ZL-utilizing efficacious gene silencing (TRUE gene silencing), an RNA-mediated gene expression control technology. We designed two sets of double heptamer-type sgRNA, which target the human BCL2 mRNA. Both sets of double heptamer-type sgRNA reduced viability of human myeloma cell lines, RPMI-8226 and KMM-1. We also performed a mouse xenograft experiment to examine how the double heptamer-type sgRNA DHa1(BCL2)/DHa2(BCL2) can reduce the growth of KMM-1 cells in vivo. Median survival periods of the sgRNA cohorts were greater than that of the control cohort by 11-43 days. Furthermore, we designed two sets of double heptamer-type sgRNA, which target the human CCND1 mRNA, and both sets synergistically reduced RPMI-8226 cell viability.
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Affiliation(s)
- Tatsuya Ishikawa
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan
| | - Arisa Haino
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan
| | - Takashi Ichiyanagi
- Department of Orthoptist Training, Niigata College of Medical Technology, Kamishineicho 5-13-3, Nishiku, Niigata, Niigata 950-2076, Japan
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan.
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8
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Isidoro-García M, García-Sánchez A, Sanz C, Estravís M, Marcos-Vadillo E, Pascual M, Roa S, Marques-García F, Triviño JC, Dávila I. YRNAs overexpression and potential implications in allergy. World Allergy Organ J 2019; 12:100047. [PMID: 31384359 PMCID: PMC6664241 DOI: 10.1016/j.waojou.2019.100047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 06/10/2019] [Accepted: 06/18/2019] [Indexed: 02/08/2023] Open
Abstract
Background Small non-coding RNAs (snRNAs) develop important functions related to epigenetic regulation. YRNAs are snRNAs involved in the initiation of DNA replication and RNA stability that regulate gene expression. They have been related to autoimmune, cancer and inflammatory diseases but never before to allergy. In this work we described for the first time in allergic patients the differential expression profile of YRNAs, their regulatory mechanisms and their potential as new diagnostic and therapeutic targets. Methods From a previous whole RNAseq study in B cells of allergic patients, differential expression profiles of coding and non-coding transcripts were obtained. To select the most differentially expressed non coding transcripts, fold change and p-values were analyzed. A validation of the expression differences detected was developed in an independent cohort of 304 individuals, 208 allergic patients and 96 controls by using qPCR. Potential binding and retrotransponibility capacity were characterized by in silico structural analysis. Using a novel bioinformatics approach, RNA targets identification, functional enrichment and network analyses were performed. Results We found that almost 70% of overexpressed non-coding transcripts in allergic patients corresponded to YRNAs. From the three more differentially overexpressed candidates, increased expression was independently confirmed in the peripheral blood of allergic patients. Structural analysis suggested a protein binding capacity decrease and an increase in retrotransponibility. Studies of RNA targets allowed the identification of sequences related to the immune mechanisms underlying allergy. Conclusions Overexpression of YRNAs is observed for the first time in allergic patients. Structural and functional information points to their implication on regulatory mechanisms of the disease.
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Affiliation(s)
- María Isidoro-García
- Department of Clinical Biochemistry, University Hospital of Salamanca, Spain.,Institute for Biomedical Research of Salamanca, Spain.,Department of Medicine, University of Salamanca, Spain.,Asthma, Allergic and Adverse Reactions (ARADyAL) Network for Cooperative Research in Health of Instituto de Salud Carlos III
| | - Asunción García-Sánchez
- Institute for Biomedical Research of Salamanca, Spain.,Department of Biomedical Sciences and Diagnostics, University of Salamanca, Spain.,Asthma, Allergic and Adverse Reactions (ARADyAL) Network for Cooperative Research in Health of Instituto de Salud Carlos III
| | - Catalina Sanz
- Institute for Biomedical Research of Salamanca, Spain.,Department of Microbiology and Genetics, University of Salamanca, Spain.,Asthma, Allergic and Adverse Reactions (ARADyAL) Network for Cooperative Research in Health of Instituto de Salud Carlos III
| | - Miguel Estravís
- Institute for Biomedical Research of Salamanca, Spain.,Department of Biomedical Sciences and Diagnostics, University of Salamanca, Spain.,Asthma, Allergic and Adverse Reactions (ARADyAL) Network for Cooperative Research in Health of Instituto de Salud Carlos III
| | - Elena Marcos-Vadillo
- Department of Clinical Biochemistry, University Hospital of Salamanca, Spain.,Institute for Biomedical Research of Salamanca, Spain
| | - Marien Pascual
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Sergio Roa
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Fernando Marques-García
- Department of Clinical Biochemistry, University Hospital of Salamanca, Spain.,Institute for Biomedical Research of Salamanca, Spain
| | | | - Ignacio Dávila
- Institute for Biomedical Research of Salamanca, Spain.,Department of Biomedical Sciences and Diagnostics, University of Salamanca, Spain.,Department of Allergy, University Hospital of Salamanca, Spain.,Asthma, Allergic and Adverse Reactions (ARADyAL) Network for Cooperative Research in Health of Instituto de Salud Carlos III
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9
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Driedonks TAP, van der Grein SG, Ariyurek Y, Buermans HPJ, Jekel H, Chow FWN, Wauben MHM, Buck AH, 't Hoen PAC, Nolte-'t Hoen ENM. Immune stimuli shape the small non-coding transcriptome of extracellular vesicles released by dendritic cells. Cell Mol Life Sci 2018; 75:3857-3875. [PMID: 29808415 PMCID: PMC6154026 DOI: 10.1007/s00018-018-2842-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/19/2018] [Accepted: 05/14/2018] [Indexed: 01/01/2023]
Abstract
The release and uptake of nano-sized extracellular vesicles (EV) is a highly conserved means of intercellular communication. The molecular composition of EV, and thereby their signaling function to target cells, is regulated by cellular activation and differentiation stimuli. EV are regarded as snapshots of cells and are, therefore, in the limelight as biomarkers for disease. Although research on EV-associated RNA has predominantly focused on microRNAs, the transcriptome of EV consists of multiple classes of small non-coding RNAs with potential gene-regulatory functions. It is not known whether environmental cues imposed on cells induce specific changes in a broad range of EV-associated RNA classes. Here, we investigated whether immune-activating or -suppressing stimuli imposed on primary dendritic cells affected the release of various small non-coding RNAs via EV. The small RNA transcriptomes of highly pure EV populations free from ribonucleoprotein particles were analyzed by RNA sequencing and RT-qPCR. Immune stimulus-specific changes were found in the miRNA, snoRNA, and Y-RNA content of EV from dendritic cells, whereas tRNA and snRNA levels were much less affected. Only part of the changes in EV-RNA content reflected changes in cellular RNA, which urges caution in interpreting EV as snapshots of cells. By comprehensive analysis of RNA obtained from highly purified EV, we demonstrate that multiple RNA classes contribute to genetic messages conveyed via EV. The identification of multiple RNA classes that display cell stimulation-dependent association with EV is the prelude to unraveling the function and biomarker potential of these EV-RNAs.
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Affiliation(s)
- Tom A P Driedonks
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Susanne G van der Grein
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Henk P J Buermans
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Henrike Jekel
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Franklin W N Chow
- School of Biological Sciences, Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Marca H M Wauben
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Amy H Buck
- School of Biological Sciences, Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Centre for Biomolecular and Molecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, The Netherlands
| | - Esther N M Nolte-'t Hoen
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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10
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Witwer KW. Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma. F1000Res 2018; 7:244. [PMID: 29744036 PMCID: PMC5904727 DOI: 10.12688/f1000research.14060.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2018] [Indexed: 12/22/2022] Open
Abstract
Background: A 2017 study reported that “Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi”. Analysis of two human blood plasma sequencing datasets was said to provide evidence for uptake of plant miRNAs into human plasma. The results were also purportedly inconsistent with contamination. Methods: Sequences from public datasets and miRNA databases were compared with results downloaded from the website of the reporting journal. Results: Only one putative plant miRNA (“peu-MIR2910) mapped consistently above background, and this sequence is found with 100% identity in a human rRNA. Several other rarer but consistently mapped putative plant miRNAs also have 100% or near 100% matches to human transcripts or genomic sequences, and some do not appear to map to plant genomes at all. Conclusions: Reanalysis of public data suggests that dietary plant xenomiR uptake is not supported, but instead confirms previous findings that detection of rare plant miRNAs in mammalian sequencing datasets is artifactual. Some putative plant miRNAs, including MIR2910 and MIR2911, may represent human sequence contamination or other artifacts in plant studies, emphasizing the need for rigorous controls and data filtering strategies when assessing possible xenomiRNAs.
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Affiliation(s)
- Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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The Y4-RNA fragment, a potential diagnostic marker, exists in saliva. Noncoding RNA Res 2017; 2:122-128. [PMID: 30159430 PMCID: PMC6096425 DOI: 10.1016/j.ncrna.2017.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 01/07/2023] Open
Abstract
The 94-nt full-length Y4-RNA is thought to have roles in the initiation of DNA replication and RNA quality control. Although its 31/32-nt fragment also exists abundantly in plasma, little is known about its physiological role. Since the 31/32-nt Y4-RNA fragment in sera is reported to be more abundant in patients with coronary artery disease than healthy persons, the fragment may have a potential for a diagnostic and/or prognostic biomarker for some diseases regardless of its functionality. As a step toward further investigation of its potential utility, we examined if the 31/32-nt Y4-RNA fragment also exists in saliva that can be obtained noninvasively, and showed that, in addition to the 31/32-nt fragment, 14- and 11-nt Y4-RNA fragments are present in all saliva RNA samples from four healthy persons. We established a PCR method to accurately quantitate the amount of the 31/32-nt Y4-RNA fragment, and estimated its amount in saliva of healthy persons to be 0.06 ± 0.04 fmol per nanogram of saliva RNA. We also tried to develop an easier quantitation method using a DNA molecular beacon.
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Haino A, Ishikawa T, Seki M, Nashimoto M. TRUE Gene Silencing: Screening of a Heptamer-type Small Guide RNA Library for Potential Cancer Therapeutic Agents. J Vis Exp 2016:53879. [PMID: 27285342 PMCID: PMC4927757 DOI: 10.3791/53879] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
TRUE gene silencing (termed after tRNase Z(L)-utilizing efficacious gene silencing) is one of the RNA-directed gene silencing technologies, which utilizes an artificial small guide RNA (sgRNA) to guide tRNA 3' processing endoribonuclease, tRNase Z(L), to recognize a target RNA. sgRNAs can be taken up by cells without any transfection reagents and can downregulate their target RNA levels and/or induce apoptosis in human cancer cells. We have screened an sgRNA library containing 156 heptamer-type sgRNAs for the effect on viability of human myeloma and leukemia cells, and found that 20 of them can efficiently induce apoptosis in at least one of the cancer cell lines. Here we present a protocol for screening of a heptamer-type sgRNA library for potential therapeutic drugs against blood cancers. The protocol includes how to construct the sgRNA library, how to assess the effect of each sgRNA on cell viability, and how to further evaluate the effective sgRNAs by flow cytometry. Around 2,000 hits would be expected to be obtained by screening the full-scale sgRNA library composed of 16,384 heptamers.
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Affiliation(s)
- Arisa Haino
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences
| | - Tatsuya Ishikawa
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences;
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Kaudewitz D, Skroblin P, Bender LH, Barwari T, Willeit P, Pechlaner R, Sunderland NP, Willeit K, Morton AC, Armstrong PC, Chan MV, Lu R, Yin X, Gracio F, Dudek K, Langley SR, Zampetaki A, de Rinaldis E, Ye S, Warner TD, Saxena A, Kiechl S, Storey RF, Mayr M. Association of MicroRNAs and YRNAs With Platelet Function. Circ Res 2015; 118:420-432. [PMID: 26646931 DOI: 10.1161/circresaha.114.305663] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 12/08/2015] [Indexed: 12/21/2022]
Abstract
RATIONALE Platelets shed microRNAs (miRNAs). Plasma miRNAs change on platelet inhibition. It is unclear whether plasma miRNA levels correlate with platelet function. OBJECTIVE To link small RNAs to platelet reactivity. METHODS AND RESULTS Next-generation sequencing of small RNAs in plasma revealed 2 peaks at 22 to 23 and 32 to 33 nucleotides corresponding to miRNAs and YRNAs, respectively. Among YRNAs, predominantly, fragments of RNY4 and RNY5 were detected. Plasma miRNAs and YRNAs were measured in 125 patients with a history of acute coronary syndrome who had undergone detailed assessment of platelet function 30 days after the acute event. Using quantitative real-time polymerase chain reactions, 92 miRNAs were assessed in patients with acute coronary syndrome on different antiplatelet therapies. Key platelet-related miRNAs and YRNAs were correlated with platelet function tests. MiR-223 (rp=0.28; n=121; P=0.002), miR-126 (rp=0.22; n=121; P=0.016), and other abundant platelet miRNAs and YRNAs showed significant positive correlations with the vasodilator-stimulated phosphoprotein phosphorylation assay. YRNAs, miR-126, and miR-223 were also among the small RNAs showing the greatest dependency on platelets and strongly correlated with plasma levels of P-selectin, platelet factor 4, and platelet basic protein in the population-based Bruneck study (n=669). A single-nucleotide polymorphism that facilitates processing of pri-miR-126 to mature miR-126 accounted for a rise in circulating platelet activation markers. Inhibition of miR-126 in mice reduced platelet aggregation. MiR-126 directly and indirectly affects ADAM9 and P2Y12 receptor expression. CONCLUSIONS Levels of platelet-related plasma miRNAs and YRNAs correlate with platelet function tests in patients with acute coronary syndrome and platelet activation markers in the general population. Alterations in miR-126 affect platelet reactivity.
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Affiliation(s)
| | - Philipp Skroblin
- King's British Heart Foundation Centre, King's College London, UK
| | - Lukas H Bender
- King's British Heart Foundation Centre, King's College London, UK
| | - Temo Barwari
- King's British Heart Foundation Centre, King's College London, UK
| | - Peter Willeit
- Department of Public Health and Primary Care, University of Cambridge, UK.,Department of Neurology, Medical University Innsbruck, Austria
| | | | | | - Karin Willeit
- Department of Neurology, Medical University Innsbruck, Austria
| | - Allison C Morton
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Paul C Armstrong
- William Harvey Research Institute, Queen Mary University of London, UK
| | - Melissa V Chan
- William Harvey Research Institute, Queen Mary University of London, UK
| | - Ruifang Lu
- King's British Heart Foundation Centre, King's College London, UK
| | - Xiaoke Yin
- King's British Heart Foundation Centre, King's College London, UK
| | - Filipe Gracio
- Biomedical Research Centre, King's College London, UK
| | - Katarzyna Dudek
- King's British Heart Foundation Centre, King's College London, UK
| | - Sarah R Langley
- King's British Heart Foundation Centre, King's College London, UK
| | - Anna Zampetaki
- King's British Heart Foundation Centre, King's College London, UK
| | | | - Shu Ye
- Department of Cardiovascular Sciences, University of Leicester, UK
| | - Timothy D Warner
- William Harvey Research Institute, Queen Mary University of London, UK
| | - Alka Saxena
- Biomedical Research Centre, King's College London, UK
| | - Stefan Kiechl
- Department of Neurology, Medical University Innsbruck, Austria
| | - Robert F Storey
- Department of Cardiovascular Science, University of Sheffield, UK
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, UK
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Cui L, Kwong J, Wang CC. Prognostic value of circulating tumor cells and disseminated tumor cells in patients with ovarian cancer: a systematic review and meta-analysis. J Ovarian Res 2015; 8:38. [PMID: 26077676 PMCID: PMC4479068 DOI: 10.1186/s13048-015-0168-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/05/2015] [Indexed: 01/02/2023] Open
Abstract
Recent studies have shown diagnostic and prognostic values of circulating tumor cells (CTCs) and disseminated tumor cells (DTCs) in various cancers, including ovarian cancer. We aimed to evaluate the association of CTCs and/or DTCs with the clinical outcomes of ovarian cancer. Clinical studies of CTCs/DTCs of ovarian cancer were included for systematic review and meta-analysis. A total of 236 studies were screened but only 16 qualified studies with 1623 subjects were included. Odds ratio (OR) showed CTCs/DTCs were not significantly associated with serous carcinoma (OR = 0.71 [0.49, 1.05]), lymph node metastasis (OR 1.14 [0.67, 1.93]), and residual disease (OR 1.45 [0.90, 2.34]); but significantly associated with advanced tumor staging (OR = 1.90 [1.02, 3.56]). The overall pooled hazard ratio (HR) of CTCs/DTCs on OS and PFS/DFS was 1.94 [1.56- 2.40] and 1.99 [1.59-2.50], respectively. Subgroup analyses revealed that CTCs were significantly associated OS (HR 1.97 [1.50-2.58]) and PFS/DFS (HR 2.52 [1.83-3.48]), while DTCs was significantly associated OS (HR 1.89 [1.33, 2.68]) and PFS/DFS (HR 1.60 [1.17, 2.19]). Meta-analysis showed strong relationship of CTCs/DTCs with advanced staging, treatment response and poor prognosis in patients with ovarian cancer.
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Affiliation(s)
- Long Cui
- Department of Obstetrics and Gynecology, Prince of Wales Hospital, The Chinese University of Hongkong, Shatin, Hong Kong, China.
| | - Joseph Kwong
- Department of Obstetrics and Gynecology, Prince of Wales Hospital, The Chinese University of Hongkong, Shatin, Hong Kong, China
| | - Chi Chiu Wang
- Department of Obstetrics and Gynecology, Prince of Wales Hospital, The Chinese University of Hongkong, Shatin, Hong Kong, China
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