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Green D, Singh A, Tippett VL, Tattersall L, Shah KM, Siachisumo C, Ward NJ, Thomas P, Carter S, Jeys L, Sumathi V, McNamara I, Elliott DJ, Gartland A, Dalmay T, Fraser WD. YBX1-interacting small RNAs and RUNX2 can be blocked in primary bone cancer using CADD522. J Bone Oncol 2023; 39:100474. [PMID: 36936386 PMCID: PMC10015236 DOI: 10.1016/j.jbo.2023.100474] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023] Open
Abstract
Primary bone cancer (PBC) comprises several subtypes each underpinned by distinctive genetic drivers. This driver diversity produces novel morphological features and clinical behaviour that serendipitously makes PBC an excellent metastasis model. Here, we report that some transfer RNA-derived small RNAs termed tRNA fragments (tRFs) perform as a constitutive tumour suppressor mechanism by blunting a potential pro-metastatic protein-RNA interaction. This mechanism is reduced in PBC progression with a gradual loss of tRNAGlyTCC cleavage into 5' end tRF-GlyTCC when comparing low-grade, intermediate-grade and high-grade patient tumours. We detected recurrent activation of miR-140 leading to upregulated RUNX2 expression in high-grade patient tumours. Both tRF-GlyTCC and RUNX2 share a sequence motif in their 3' ends that matches the YBX1 recognition site known to stabilise pro-metastatic mRNAs. Investigating some aspects of this interaction network, gain- and loss-of-function experiments using small RNA mimics and antisense LNAs, respectively, showed that ectopic tRF-GlyTCC reduced RUNX2 expression and dispersed 3D micromass architecture in vitro. iCLIP sequencing revealed YBX1 physical binding to the 3' UTR of RUNX2. The interaction between YBX1, tRF-GlyTCC and RUNX2 led to the development of the RUNX2 inhibitor CADD522 as a PBC treatment. CADD522 assessment in vitro revealed significant effects on PBC cell behaviour. In xenograft mouse models, CADD522 as a single agent without surgery significantly reduced tumour volume, increased overall and metastasis-free survival and reduced cancer-induced bone disease. Our results provide insight into PBC molecular abnormalities that have led to the identification of new targets and a new therapeutic.
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Key Words
- CADD522
- CADD522, computer aided drug design molecule 522
- CI, confidence interval
- CNV, copy number variant
- CS, chondrosarcoma
- CTC, circulating tumour cell
- DE, differentially expressed
- ES, Ewing sarcoma
- HD, high definition
- HR, hazard ratio
- OS, osteosarcoma
- RBP, RNA binding protein
- RNU6-1, U6 small nuclear 1
- ROI, region-of-interest
- Rnl, T4 RNA ligase
- SNV, single nucleotide variant
- SV, structural variant
- bone cancer
- iCLIP, individual nucleotide resolution cross-linking and immunoprecipitation
- mRNA, messenger RNA
- miRNA
- miRNA, microRNA
- piRNA, piwi interacting RNA
- sRNA, small RNA
- small RNA
- tRF
- tRF, transfer RNA fragment
- tRNA, transfer RNA
- ysRNA, Y RNA-derived sRNA
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Affiliation(s)
- Darrell Green
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, UK
- Corresponding author.
| | - Archana Singh
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Victoria L. Tippett
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | - Luke Tattersall
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | - Karan M. Shah
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | | | - Nicole J. Ward
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Paul Thomas
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Henry Wellcome Laboratory for Cell Imaging, Faculty of Science, University of East Anglia, Norwich, UK
| | - Simon Carter
- Orthopaedic Oncology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Lee Jeys
- Orthopaedic Oncology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Vaiyapuri Sumathi
- Musculoskeletal Pathology, University Hospitals Birmingham, Royal Orthopaedic Hospital, Birmingham, UK
| | - Iain McNamara
- Orthopaedics & Trauma, Norfolk and Norwich University Hospital, Norwich, UK
| | | | - Alison Gartland
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - William D. Fraser
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, UK
- Clinical Biochemistry, Diabetes and Endocrinology, Norfolk and Norwich University Hospital, Norwich, UK
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Chorley BN, Carswell GK, Nelson G, Bhat VS, Wood CE. Early microRNA indicators of PPARα pathway activation in the liver. Toxicol Rep 2020; 7:805-15. [PMID: 32642447 DOI: 10.1016/j.toxrep.2020.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/01/2020] [Accepted: 06/19/2020] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNA species that play key roles in post-transcriptional regulation of gene expression. MiRNAs also serve as a promising source of early biomarkers for different environmental exposures and health effects, although there is limited information linking miRNA changes to specific target pathways. In this study, we measured liver miRNAs in male B6C3F1 mice exposed to a known chemical activator of the peroxisome proliferator-activated receptor alpha (PPARα) pathway, di(2-ethylhexyl) phthalate (DEHP), for 7 and 28 days at concentrations of 0, 750, 1500, 3000, or 6000 ppm in feed. At the highest dose tested, DEHP altered 61 miRNAs after 7 days and 171 miRNAs after 28 days of exposure, with 48 overlapping miRNAs between timepoints. Analysis of these 48 common miRNAs indicated enrichment in PPARα–related targets and other pathways related to liver injury and cancer. Four of the 10 miRNAs exhibiting a clear dose trend were linked to the PPARα pathway: mmu-miRs-125a-5p, -182−5p, -20a−5p, and -378a−3p. mmu-miRs-182−5p and -378a−3p were subsequently measured using digital drop PCR across a dose range for DEHP and two related phthalates with weaker PPARα activity, di-n-octyl phthalate and n-butyl benzyl phthalate, following 7-day exposures. Analysis of mmu-miRs-182−5p and -378a−3p by transcriptional benchmark dose analysis correctly identified DEHP as having the greatest potency. However, benchmark dose estimates for DEHP based on these miRNAs (average 163; range 126−202 mg/kg-day) were higher on average than values for PPARα target genes (average 74; range 29−183 mg/kg-day). These findings identify putative miRNA biomarkers of PPARα pathway activity and suggest that early miRNA changes may be used to stratify chemical potency.
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Key Words
- AIC, Akaike Information Criterion
- ALT, alanine aminotransferase
- AOP, adverse outcome pathway
- AST, aspartate aminotransferase
- Acox1, acyl-Coenzyme A oxidase 1
- Adverse outcome pathway (AOP)
- AhR, aryl hydrocarbon receptor
- BBP, n-butyl benzyl phthalate
- BMD, benchmark dose
- BMDA, apical-based benchmark dose
- BMDL, BMD lower confidence interval
- BMDT, transcriptional-based benchmark dose
- BMR, benchmark response
- BROD, benzyloxyresorufin O-debenzylation
- Benchmark dose (BMD)
- Biomarkers
- CAR, constitutive androstane receptor
- DEGs, differentially expressed genes
- DEHP, di (2-thylhexyl) phthalate
- DEmiRs, differentially expressed miRNAs
- DNOP, di-n-octyl phthalate
- EPA, U.S. Environmental Protection Agency
- EROD, ethoxyresorufin O-dealkylation
- GEO, Gene Expression Omnibus
- HCA, hepatocellular adenoma
- HCC, hepatocellular carcinoma
- Hepatocellular carcinoma
- IPA, Ingenuity Pathway Analysis
- Liver toxicity
- MOA, mode of action
- MicroRNAs
- Mode of action (MOA)
- Nrf2, nuclear receptor erythroid 2-like 2
- POD, point-of-departure
- PPARα, peroxisome proliferator-activated receptor alpha
- PROD, pentoxyresorufin O-depentylation
- PXR, pregnane X receptor
- Peroxisome proliferator-activated receptor alpha (PPARα)
- Phthalate
- SDH, sorbitol dehydrogenase
- TMM, trimmed mean of M-values
- ddPCR, droplet digital polymerase chain reaction
- mRNA, messenger RNA
- miRNAs, microRNAs
- mtDNA, mitochondrial
- rRNA, ribosomal RNA
- smallRNA-seq, small RNA sequencing
- tRNA, transfer RNA
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Mohanta TK, Mishra AK, Hashem A, Qari SH, Abd Allah EF, Khan AL, Al-Harrasi A. Genome-wide analysis revealed novel molecular features and evolution of Anti-codons in cyanobacterial tRNAs. Saudi J Biol Sci 2019; 27:1195-1200. [PMID: 32346324 PMCID: PMC7182786 DOI: 10.1016/j.sjbs.2019.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/01/2019] [Accepted: 12/11/2019] [Indexed: 11/30/2022] Open
Abstract
Transfer RNAs (tRNAs) play important roles to decode the genetic information contained in mRNA in the process of translation. The tRNA molecules possess conserved nucleotides at specific position to regulate the unique function. However, several nucleotides at different position of the tRNA undergo modification to maintain proper stability and function. The major modifications include the presence of pseudouridine (Ψ) residue instead of uridine and the presence of m5-methylation sites. We found that, Ψ13 is conserved in D-stem, whereas Ψ38 & Ψ39 were conserved in the anti-codon loop (AL) and anti-codon arm (ACA), respectively. Furthermore, Ψ55 found to be conserved in the Ψ loop. Although, fourteen possible methylation sites can be found in the tRNA, cyanobacterial tRNAs were found to possess conserved G9, m3C32, C36, A37, m5C38 and U54 methylation sites. The presence of multiple conserved methylation sites might be responsible for providing necessary stability to the tRNA. The evolutionary study revealed, tRNAMet and tRNAIle were evolved earlier than other tRNA isotypes and their evolution is date back to at least 4000 million years ago. The presence of novel pseudouridination and m5-methylation sites in the cyanobacterial tRNAs are of particular interest for basic biology. Further experimental study can delineate their functional significance in protein translation.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
| | | | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, 11451 Riyadh, Saudi Arabia.,Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, Egypt
| | - Sameer H Qari
- Biology Department, Aljumum University College, Umm Al-Qura University, Holy Makkah, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agriculture Science, King Saud University, 11451 Riyadh, Saudi Arabia
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
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Jiang L, Lim CJ, Jeong JC, Kim CY, Kim DH, Kim SW, Lee J. Whole-genome sequence data and analysis of Saccharibacillus sp. ATSA2 isolated from Kimchi cabbage seeds. Data Brief 2019; 26:104465. [PMID: 31534997 PMCID: PMC6743023 DOI: 10.1016/j.dib.2019.104465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 08/23/2019] [Indexed: 12/03/2022] Open
Abstract
Saccharibacillus sp. ATSA2 was isolated from Kimchi cabbage seeds grown in Gyeongbuk province in the Republic of Korea. Whole-genome sequencing of Saccharibacillus sp. ATSA2 was performed using the PacBio RSII and Illumina HiSeq platforms, and it features a 5,619,468 bp circular chromosome with 58.4% G + C content. The genome includes 4543 protein-coding genes, 104 RNA genes (70 transfer RNA genes, 30 ribosomal RNA genes, and 4 non-coding RNA), and 73 pseudogenes. Multiple gene clusters associated with stress responses, nitrogen and phosphorus metabolism, and plant hormone biosynthesis were annotated in the genome. The genome information will provide fundamental knowledge of this organism as well as insight for understanding microbial activity in the agricultural application. The whole-genome sequence of Saccharibacillus sp. ATSA2 is available at GenBank/EMBL/DDBJ under accession number CP041217.
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Affiliation(s)
- Lingmin Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
- Department of Bioactive Materials, Chonbuk National University, Jeonju, 54896, Republic of Korea
| | - Chan Ju Lim
- Asia Seed Co., Research Institute of Biotechnology Breeding, Icheon, 17414, Republic of Korea
| | - Jae Cheol Jeong
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - Cha Young Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - Dae-Hyuk Kim
- Department of Bioactive Materials, Chonbuk National University, Jeonju, 54896, Republic of Korea
| | - Suk Weon Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
- Corresponding author.
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
- Corresponding author.
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Mohanta TK, Yadav D, Khan A, Hashem A, Abd_Allah EF, Al-Harrasi A. Analysis of genomic tRNA revealed presence of novel genomic features in cyanobacterial tRNA. Saudi J Biol Sci 2019; 27:124-133. [PMID: 31889826 PMCID: PMC6933170 DOI: 10.1016/j.sjbs.2019.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/29/2019] [Accepted: 06/06/2019] [Indexed: 12/17/2022] Open
Abstract
Transfer RNAs (tRNA) are important molecules that involved in protein translation machinery and acts as a bridge between the ribosome and codon of the mRNA. The study of tRNA is evolving considerably in the fields of bacteria, plants, and animals. However, detailed genomic study of the cyanobacterial tRNA is lacking. Therefore, we conducted a study of cyanobacterial tRNA from 61 species. Analysis revealed that; cyanobacteria contain thirty-six to seventy-eight tRNA gens per genome that encodes for 20 tRNA isotypes. The number of iso-acceptors (anti-codons) ranged from thirty-two to forty-three per genome. tRNAIle with anti-codon AAU, GAU, and UAU was reported to be absent from the genome of Gleocapsa PCC 73,106 and Xenococcus sp. PCC 7305. Instead, they were contained anti-codon CAU that is common to tRNAMet and tRNAIle as well. The iso-acceptors ACA (tRNACys), ACC (tRNAGly), AGA, ACU (tRNASer), AAA (tRNAPhe), AGG (tRNAPro), AAC (tRNAVal), GCG (tRNAArg), AUG (tRNAHis), and AUC (tRNAAsp) were absent from the genome of cyanobacterial lineages studied so far. A few of the cyanobacterial species encode suppressor tRNAs, whereas none of the species were found to encode a selenocysteine iso-acceptor. Cyanobacterial species encode a few putative novel tRNAs whose functions are yet to be elucidated.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
- Corresponding author.
| | - Dhananjay Yadav
- Dept. of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Abdullatif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agriculture Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
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Mussack V, Wittmann G, Pfaffl MW. Comparing small urinary extracellular vesicle purification methods with a view to RNA sequencing-Enabling robust and non-invasive biomarker research. Biomol Detect Quantif 2019; 17:100089. [PMID: 31194192 PMCID: PMC6554496 DOI: 10.1016/j.bdq.2019.100089] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/27/2019] [Accepted: 04/10/2019] [Indexed: 01/10/2023]
Abstract
Small extracellular vesicles (EVs) are 50–200 nm sized mediators in intercellular communication that reflect both physiological and pathophysiological changes of their parental cells. Thus, EVs hold great potential for biomarker detection. However, reliable purification methods for the downstream screening of the microRNA (miRNA) cargo carried within urinary EVs by small RNA sequencing have yet to be established. To address this knowledge gap, RNA extracted from human urinary EVs obtained by five different urinary EV purification methods (spin column chromatography, immunoaffinity, membrane affinity, precipitation and ultracentrifugation combined with density gradient) was analyzed by small RNA sequencing. Urinary EVs were further characterized by nanoparticle tracking analysis, Western blot analysis and transmission electron microscopy. Comprehensive EV characterization established significant method-dependent differences in size and concentration as well as variances in protein composition of isolated vesicles. Even though all purification methods captured enough total RNA to allow small RNA sequencing, method-dependent differences were also observed with respect to library sizes, mapping distributions, number of miRNA reads and diversity of transcripts. Whereas EVs obtained by immunoaffinity yielded the purest subset of small EVs, highly comparable with results attained by ultracentrifugation combined with density gradient, precipitation and membrane affinity, sample purification by spin column chromatography indicated a tendency to isolate different subtypes of small EVs, which might also carry a distinct subset of miRNAs. Based on our results, different EV purification methods seem to preferentially isolate different subtypes of EVs with varying efficiencies. As a consequence, sequencing experiments and resulting miRNA profiles were also affected. Hence, the selection of a specific EV isolation method has to satisfy the respective research question and should be well considered. In strict adherence with the MISEV (minimal information for studies of extracellular vesicles) guidelines, the importance of a combined evaluation of biophysical and proteomic EV characteristics alongside transcriptomic results was clearly demonstrated in this present study.
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Key Words
- A, spin column chromatography
- ANOVA, analysis of variance
- Ago2, argonaute-2 protein
- B, immunoaffinity
- Biomarker
- C, membrane affinity
- D, precipitation
- DGE, differential gene expression
- DTT, dithiothreitol
- E, ultracentrifugation combined with density gradient
- EV(s), extracellular vesicle(s)
- Extracellular vesicles
- FM, fluorescent mode
- Human
- MISEV, minimal information for studies of extracellular vesicles
- NTA, nanoparticle tracking analysis
- PC, principal component
- RIN, RNA integrity number
- RNA-Seq, RNA sequencing
- SM, scattering mode
- Small RNA sequencing
- TEM, transmission electron microscopy
- UCrea, urinary creatinine
- Urine
- mIgG, murine immunoglobulin G
- mRNA, messenger RNA
- miRNA, microRNA
- microRNA
- nm, nanometer(s)
- nt, nucleotide(s)
- rRNA, ribosomal RNA
- snRNA, small nuclear RNA
- snoRNA, small nucleolar RNA
- tRNA, transfer RNA
- uEVs, urinary extracellular vesicles
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Affiliation(s)
- Veronika Mussack
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Georg Wittmann
- Department for Transfusion Medicine, Cell therapeutics and Haemostaseology, University Hospital LMU, Marchioninistraße 15, 81377, Munich, Germany
| | - Michael W Pfaffl
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
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Kondratov K, Kurapeev D, Popov M, Sidorova M, Minasian S, Galagudza M, Kostareva A, Fedorov A. Heparinase treatment of heparin-contaminated plasma from coronary artery bypass grafting patients enables reliable quantification of microRNAs. Biomol Detect Quantif 2016; 8:9-14. [PMID: 27335806 PMCID: PMC4906134 DOI: 10.1016/j.bdq.2016.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/12/2016] [Accepted: 03/16/2016] [Indexed: 11/13/2022]
Abstract
Plasma collected before cardiac surgery also contain variable amounts of heparin. Evaluation of RT-qPCR inhibition is recommended for all types of clinical samples. Heparinase treatment completely eliminated widely different levels of inhibition. Heparinase treatment causes different (1.5- to 6.5-fold) decrease in the amount of detected RNA for different targets. Heparinase treatment did not influence the technical variability RNA quantification, neither at high nor at low concentration of targets.
Background microRNAs have recently been identified as powerful biomarkers of human disease. Reliable polymerase chain reaction (PCR)-based quantification of nucleic acids in clinical samples contaminated with polymerase inhibitor heparin requires deheparinization. However, the effects of deheparinization procedure on quantification of nucleic acids remain largely unknown. The aim of this study was to determine whether the deheparinization procedure completely eliminates the inhibition of amplification, while maintaining RNA integrity and technical variability of the measured microRNA levels. Methods Heparinized plasma from 9 patients undergoing coronary artery bypass grafting (CABG) and the heparin-free plasma from 58 rats were spiked with a synthetic RNA oligonucleotide and total RNA was extracted. The RNA solutions were then treated with heparinase I to remove contaminating heparin prior to reverse transcription. Levels of synthetic spike-in RNA oligonucleotide, as well as endogenous hsa-miR-1-3p and hsa-miR-208a-3p, were measured using quantitative reverse transcription PCR (RT-qPCR). The amplification efficiency and presence of inhibitors in individual samples were directly determined using calibration curves. Results In contrast to RNA samples from rat plasma, RNA samples derived from the CABG patient plasma contained inhibitors, which were completely eliminated by treatment with heparinase. The procedure caused a decrease in the amount of detected RNA; however, the technical variability of the measured targets did not change, allowing for the quantification of circulating endogenous hsa-miR-1-3p and hsa-miR-208a-3p in the plasma of CABG patients. Conclusions The heparinase treatment procedure enables utilization of RT-qPCR for reliable microRNA quantification in heparinized plasma.
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Key Words
- Biomarkers
- CABG, coronary artery bypass grafting
- Cq, quantification cycle
- EDTA, ethylenediaminetetraacetic acid
- Heparinized plasma
- PCR, polymerase chain reaction
- RIN, RNA integrity number
- RNase, ribonuclease
- RT, reverse transcription
- RT-qPCR efficiency
- RT-qPCR, reverse transcription quantitative real-time PCR
- TP, time point
- cel-miR-39-3p, 3p strand of mature Caenorhabditis elegans microRNA-39
- hsa-miR-1-3p, 3p strand of mature Homo sapiens microRNA-1
- hsa-miR-208a-3p, 3p strand of mature Homo sapiens microRNA-208a
- microRNA quantification
- qPCR, quantitative real-time PCR
- tRNA, transfer RNA
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Affiliation(s)
- Kirill Kondratov
- Institute of Molecular Biology and Genetics, Almazov Federal North-West Medical Research Centre, Saint-Petersburg, Russia
| | - Dmitry Kurapeev
- Institute of Experimental Medicine, Almazov Federal North-West Medical Research Centre, Saint-Petersburg, Russia
| | - Maxim Popov
- Institute of Experimental Medicine, Almazov Federal North-West Medical Research Centre, Saint-Petersburg, Russia
| | - Marina Sidorova
- Department of Biotechnical Systems, Saint-Petersburg Electrotechnical University LETI, Saint-Petersburg, Russia; Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Sarkis Minasian
- Institute of Experimental Medicine, Almazov Federal North-West Medical Research Centre, Saint-Petersburg, Russia
| | - Michael Galagudza
- Institute of Experimental Medicine, Almazov Federal North-West Medical Research Centre, Saint-Petersburg, Russia
| | - Anna Kostareva
- Institute of Molecular Biology and Genetics, Almazov Federal North-West Medical Research Centre, Saint-Petersburg, Russia; Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden; Institute of Translational Medicine, ITMO University, Saint-Petersburg, Russia
| | - Anton Fedorov
- Institute of Molecular Biology and Genetics, Almazov Federal North-West Medical Research Centre, Saint-Petersburg, Russia
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Kim JJ, Yu J, Bag J, Bakovic M, Cant JP. Translation attenuation via 3' terminal codon usage in bovine csn1s2 is responsible for the difference in αs2- and β-casein profile in milk. RNA Biol 2015; 12:354-67. [PMID: 25826667 DOI: 10.1080/15476286.2015.1017231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The rate of secretion of αs2-casein into bovine milk is approximately 25% of that of β-casein, yet mammary expression of their respective mRNA transcripts (csn1s2 and csn2) is not different. Our objective was to identify molecular mechanisms that explain the difference in translation efficiency between csn1s2 and csn2. Cell-free translational efficiency of csn2 was 5 times that of csn1s2. Transcripts of csn1s2 distributed into heavier polysomes than csn2 transcripts, indicating an attenuation of elongation and/or termination. Stimulatory and inhibitory effects of the 5' and 3' UTRs on translational efficiency were different with luciferase and casein sequences in the coding regions. Substituting the 5' and 3' UTRs from csn2 into csn1s2 did not improve csn1s2 translation, implicating the coding region itself in the translation difference. Deletion of a 28-codon fragment from the 3' terminus of the csn1s2 coding region, which displays codons with low correlations to cell fitness, increased translation to a par with csn2. We conclude that the usage of the last 28 codons of csn1s2 is the main regulatory element that attenuates its expression and is responsible for the differential translational expression of csn1s2 and csn2.
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Key Words
- 40S, small ribosomal subunit
- 60S, large ribosomal subunit
- AA, amino acid
- ARE, AU-rich element
- Apaf-1, apoptosis protease activating factor 1
- DLG1, disc large 1 ncosuppressor
- FMR1, fragile X mental retardation 1
- HRP, horseradish eroxidase
- IE, inhibitory element
- IRE, iron-responsive element
- IRES, nternal ribosome entry site
- IRP, iron-regulatory protein
- MACT, bovine mammary epithelial cell
- PABP, poly(A) binding protein
- PAGE, polyacrylamide gel electrophoresis
- PCR, polymerase chain reaction
- PVDF, polyvinylidene fluoride
- RACE, rapid amplification of cDNA ends
- RBP, RNA-binding protein
- RRL, rabbit reticulocyte lysate
- RT, reverse transcription
- SDS, sodium dodecyl sulfate
- SE, standard error
- STR, single-stranded nucleic acid binding protein
- TBS-T, Tris-buffered saline containing 0.5%
- TfR, transferrin receptor
- Tween 20
- UTR, untranslated region
- aa-tRNA, aminoacyl-tRNA
- aaRS, aminoacyl-tRNA synthetase
- bovine casein
- cDNA, complementary DNA
- cell-free translation
- coding region
- codon usage
- eEF, eukaryotic elongation factor
- eIF, eukaryotic initiation factor
- eRF, eukaryotic termination factor
- m7G, 7-methylated uanidine
- mRNA, messenger RNA
- qPCR, real-time polymerase chain reaction
- sAUG, start codon
- tRNA, transfer RNA
- translational efficiency
- uAUG, upstream start codon
- uORF, open reading frame
- untranslated region
- ΔG, free energy
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Affiliation(s)
- Julie J Kim
- a Animal and Poultry Science; University of Guelph ; Guelph , Ontario , Canada
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Hattori H, Janky R, Nietfeld W, Aerts S, Madan Babu M, Venkitaraman AR. p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response. Cell Cycle 2014; 13:2572-86. [PMID: 25486198 PMCID: PMC4601526 DOI: 10.4161/15384101.2015.942209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The human DNA damage response (DDR) triggers profound changes in gene expression, whose nature and regulation remain uncertain. Although certain micro-(mi)RNA species including miR34, miR-18, miR-16 and miR-143 have been implicated in the DDR, there is as yet no comprehensive description of genome-wide changes in the expression of miRNAs triggered by DNA breakage in human cells. We have used next-generation sequencing (NGS), combined with rigorous integrative computational analyses, to describe genome-wide changes in the expression of miRNAs during the human DDR. The changes affect 150 of 1523 miRNAs known in miRBase v18 from 4-24 h after the induction of DNA breakage, in cell-type dependent patterns. The regulatory regions of the most-highly regulated miRNA species are enriched in conserved binding sites for p53. Indeed, genome-wide changes in miRNA expression during the DDR are markedly altered in TP53-/- cells compared to otherwise isogenic controls. The expression levels of certain damage-induced, p53-regulated miRNAs in cancer samples correlate with patient survival. Our work reveals genome-wide and cell type-specific alterations in miRNA expression during the human DDR, which are regulated by the tumor suppressor protein p53. These findings provide a genomic resource to identify new molecules and mechanisms involved in the DDR, and to examine their role in tumor suppression and the clinical outcome of cancer patients.
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Key Words
- AP-1, activator protein-1
- DDR, DNA damage response
- DNA damage response
- E2F1, transcription factor E2F1
- FoxM1, forkhead box protein M1
- NF-k B, nuclear factor-k B
- NGS, next-generation sequencing
- TF, transcription factor
- TP53, tumour protein p53
- clinical outcome
- computational analysis
- double stranded DNA breaks, DSBs
- ionizing radiation, IR
- miRNA, micro-RNA
- micro-RNA
- misc RNA, miscellaneous RNA
- next-generation sequencing
- p53
- scRNA, small cytoplasmic RNA
- snRNA, small nuclear RNA
- snoRNA, small nucleolar RNA
- tRNA, transfer RNA
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Affiliation(s)
- Hiroyoshi Hattori
- University of Cambridge; Medical Research Council Cancer Unit; Hutchison/MRC Research Center; Cambridge, UK,These authors contributed equally to the work.,Present address: Laboratory of Advanced Therapy; Clinical Research Center; National Hospital Organization; Nagoya Medical Center; Aichi, Japan
| | - Rekin’s Janky
- Medical Research Council Laboratory of Molecular Biology; Cambridge, UK,Center for Human Genetics; KU Leuven; Campus Gasthuisberg; Leuven, Belgium,These authors contributed equally to the work.
| | | | - Stein Aerts
- Center for Human Genetics; KU Leuven; Campus Gasthuisberg; Leuven, Belgium
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology; Cambridge, UK
| | - Ashok R Venkitaraman
- University of Cambridge; Medical Research Council Cancer Unit; Hutchison/MRC Research Center; Cambridge, UK,Correspondence to: Ashok R Venkitaraman;
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Abstract
Box H/ACA ribonucleoproteins (RNPs), each consisting of one unique guide RNA and 4 common core proteins, constitute a family of complex enzymes that catalyze, in an RNA-guided manner, the isomerization of uridines to pseudouridines (Ψs) in RNAs, a reaction known as pseudouridylation. Over the years, box H/ACA RNPs have been extensively studied revealing many important aspects of these RNA modifying machines. In this review, we focus on the composition, structure, and biogenesis of H/ACA RNPs. We explain the mechanism of how this enzyme family recognizes and specifies its target uridine in a substrate RNA. We discuss the substrates of box H/ACA RNPs, focusing on rRNA (rRNA) and spliceosomal small nuclear RNA (snRNA). We describe the modification product Ψ and its contribution to RNA function. Finally, we consider possible mechanisms of the bone marrow failure syndrome dyskeratosis congenita and of prostate and other cancers linked to mutations in H/ACA RNPs.
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Key Words
- DC, dyskeratosis congenita
- H/ACA
- HH, hoyeraal-hreidarsson syndrome
- PIKK, phosphatidylinositol 3-kinase-related kinase
- PUA, pseudouridylase and archaeosine transglycosylase
- RNA modification
- RNA-guided
- RNP, ribonucleoprotein
- SMN, survival of motor neuron protein
- SSD, SHQ1 specific domain
- U, uridine
- X-DC, X-linked dyskeratosis congenita
- dyskeratosis congenita
- prostate cancer
- pseudouridine
- rRNA
- rRNA, ribosomal RNA
- ribonucleoproteins
- sca, small Cajal body
- snRNA, small nuclear RNA
- sno, small nucleolar
- snoRNA
- snoRNA, small nucleolar RNA
- spliceosomal small nuclear RNA
- tRNA, transfer RNA
- ψ, pseudouridine, 5-ribosyluracil
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MESH Headings
- Dyskeratosis Congenita/genetics
- Dyskeratosis Congenita/metabolism
- Dyskeratosis Congenita/pathology
- Humans
- Isomerism
- Male
- Mutation
- Nucleic Acid Conformation
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Pseudouridine/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Uridine/metabolism
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Yi-Tao Yu
- University of Rochester Medical Center; Department of Biochemistry and Biophysics; Center for RNA Biology; Rochester, NY USA
| | - U Thomas Meier
- Albert Einstein College of Medicine; Department of Anatomy and Structural Biology; Bronx, NY USA
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