1
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Maltseva D, Kirillov I, Zhiyanov A, Averinskaya D, Suvorov R, Gubani D, Kudriaeva A, Belogurov A, Tonevitsky A. Incautious design of shRNAs for stable overexpression of miRNAs could result in generation of undesired isomiRs. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195046. [PMID: 38876159 DOI: 10.1016/j.bbagrm.2024.195046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
shRNA-mediated strategy of miRNA overexpression based on RNA Polymerase (Pol III) expression cassettes is widely used for miRNA functional studies. For some miRNAs, e.g., encoded in the genome as a part of a polycistronic miRNA cluster, it is most likely the only way for their individual stable overexpression. Here we have revealed that expression of miRNAs longer than 19 nt (e.g. 23 nt in length hsa-miR-93-5p) using such approach could be accompanied by undesired predominant generation of 5' end miRNA isoforms (5'-isomiRs). Extra U residues (up to five) added by Pol III at the 3' end of the transcribed shRNA during transcription termination could cause a shift in the Dicer cleavage position of the shRNA. This results in the formation of 5'-isomiRs, which have a significantly altered seed region compared to the initially encoded canonical hsa-miR-93-5p. We demonstrated that the commonly used qPCR method is insensitive to the formation of 5'-isomiRs and cannot be used to confirm miRNA overexpression. However, the predominant expression of 5'-isomiRs without three or four first nucleotides instead of the canonical isoform could be disclosed based on miRNA-Seq analysis. Moreover, mRNA sequencing data showed that the 5'-isomiRs of hsa-miR-93-5p presumably regulate their own mRNA targets. Thus, omitting miRNA-Seq analysis may lead to erroneous conclusions regarding revealed mRNA targets and possible molecular mechanisms in which studied miRNA is involved. Overall, the presented results show that structures of shRNAs for stable overexpression of miRNAs requires careful design to avoid generation of undesired 5'-isomiRs.
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Affiliation(s)
- Diana Maltseva
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Ivan Kirillov
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Anton Zhiyanov
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Daria Averinskaya
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Roman Suvorov
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Daria Gubani
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Anna Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexey Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; Art Photonics GmbH, Berlin 12489, Germany.
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2
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Ferre A, Santiago L, Sánchez-Herrero JF, López-Rodrigo O, Sánchez-Curbelo J, Sumoy L, Bassas L, Larriba S. 3'IsomiR Species Composition Affects Reliable Quantification of miRNA/isomiR Variants by Poly(A) RT-qPCR: Impact on Small RNA-Seq Profiling Validation. Int J Mol Sci 2023; 24:15436. [PMID: 37895116 PMCID: PMC10607168 DOI: 10.3390/ijms242015436] [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: 09/21/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Small RNA-sequencing (small RNA-seq) has revealed the presence of small RNA-naturally occurring variants such as microRNA (miRNA) isoforms or isomiRs. Due to their small size and the sequence similarity among miRNA isoforms, their validation by RT-qPCR is challenging. We previously identified two miR-31-5p isomiRs-the canonical and a 3'isomiR variant (3' G addition)-which were differentially expressed between individuals with azoospermia of different origin. Here, we sought to determine the discriminatory capacity between these two closely-related miRNA isoforms of three alternative poly(A) based-RT-qPCR strategies in both synthetic and real biological context. We found that these poly(A) RT-qPCR strategies exhibit a significant cross-reactivity between these miR-31-5p isomiRs which differ by a single nucleotide, compromising the reliable quantification of individual miRNA isoforms. Fortunately, in the biological context, given that the two miRNA variants show changes in the same direction, RT-qPCR results were consistent with the findings of small RNA-seq study. We suggest that miRNA selection for RT-qPCR validation should be performed with care, prioritizing those canonical miRNAs that, in small RNA-seq, show parallel/homogeneous expression behavior with their most prevalent isomiRs, to avoid confounding RT-qPCR-based results. This is suggested as the current best strategy for robust biomarker selection to develop clinically useful tests.
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Affiliation(s)
- Adriana Ferre
- Human Molecular Genetics Group—Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain; (A.F.); (L.S.)
| | - Lucía Santiago
- Human Molecular Genetics Group—Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain; (A.F.); (L.S.)
| | - José Francisco Sánchez-Herrero
- High Content Genomics and Bioinformatics (HCGB), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain; (J.F.S.-H.); (L.S.)
| | - Olga López-Rodrigo
- Laboratory of Andrology and Sperm Bank, Andrology Service-Puigvert Foundation, 08025 Barcelona, Spain; (O.L.-R.); (J.S.-C.); (L.B.)
| | - Josvany Sánchez-Curbelo
- Laboratory of Andrology and Sperm Bank, Andrology Service-Puigvert Foundation, 08025 Barcelona, Spain; (O.L.-R.); (J.S.-C.); (L.B.)
| | - Lauro Sumoy
- High Content Genomics and Bioinformatics (HCGB), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain; (J.F.S.-H.); (L.S.)
| | - Lluís Bassas
- Laboratory of Andrology and Sperm Bank, Andrology Service-Puigvert Foundation, 08025 Barcelona, Spain; (O.L.-R.); (J.S.-C.); (L.B.)
| | - Sara Larriba
- Human Molecular Genetics Group—Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain; (A.F.); (L.S.)
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3
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Guo L, Ren D, Zhang Y, Wang Q, Yu S, Xu X, Luo L, Yu J, Liang T. A comprehensive pan-cancer analysis reveals cancer-associated robust isomiR expression landscapes in miRNA arm switching. Mol Genet Genomics 2023; 298:521-535. [PMID: 36813858 DOI: 10.1007/s00438-023-01997-4] [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: 10/17/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023]
Abstract
MicroRNAs (miRNAs), important regulators of gene expression, play critical roles in various biological processes and tumorigenesis. To reveal the potential relationships between multiple isomiRs and arm switching, we performed a comprehensive pan-cancer analysis to discuss their roles in tumorigenesis and cancer prognosis. Our results showed that many miR-#-5p and miR-#-3p pairs from the two arms of pre-miRNA may have abundant expression levels, and they are often involved in distinct functional regulatory networks by targeting different mRNAs, although they may also interact with common targets. The two arms may show diverse isomiR expression landscapes, and their expression ratio might vary, mainly depending on tissue type. Dominantly expressed isomiRs can be used to determine distinct cancer subtypes that are associated with clinical outcome, indicating that they may be potential prognostic biomarkers. Our findings indicate robust and flexible isomiR expression landscapes that will enrich the study of miRNAs/isomiRs and aid in revealing the potential roles of multiple isomiRs yielded by arm switching in tumorigenesis.
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Affiliation(s)
- Li Guo
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Dekang Ren
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Yuting Zhang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Qiushi Wang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Shiyi Yu
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Xinru Xu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Lulu Luo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jiafeng Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, China
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing, 210023, China.
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4
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Thomas KT, Vermare A, Egleston SO, Wang YD, Mishra A, Lin T, Peng J, Zakharenko SS. MicroRNA 3' ends shorten during adolescent brain maturation. Front Mol Neurosci 2023; 16:1168695. [PMID: 37122627 PMCID: PMC10140418 DOI: 10.3389/fnmol.2023.1168695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
MicroRNA (miRNA) dysregulation is well-documented in psychiatric disease, but miRNA dynamics remain poorly understood during adolescent and early adult brain maturation, when symptoms often first appear. Here, we use RNA sequencing to examine miRNAs and their mRNA targets in cortex and hippocampus from early-, mid-, and late-adolescent and adult mice. Furthermore, we use quantitative proteomics by tandem mass tag mass spectrometry (TMT-MS) to examine protein dynamics in cortex from the same subjects. We found that ~25% of miRNAs' 3' ends shorten with age due to increased 3' trimming and decreased U tailing. Particularly, shorter but functionally competent isoforms (isomiRs) of miR-338-3p increase up to 10-fold during adolescence and only in brain. MiRNAs that undergo 3' shortening exhibit stronger negative correlations with targets that decrease with age and stronger positive correlations with targets that increase with age, than miRNAs with stable 3' ends. Increased 3' shortening with age was also observed in available mouse and human miRNA-seq data sets, and stronger correlations between miRNAs that undergo shortening and their mRNA targets were observed in two of the three available data sets. We conclude that age-associated miRNA 3' shortening is a well-conserved feature of postnatal brain maturation.
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Affiliation(s)
- Kristen T. Thomas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Anaïs Vermare
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Suzannah O. Egleston
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Tong Lin
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- *Correspondence: Stanislav S. Zakharenko,
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5
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Moradi A, Whatmore P, Farashi S, Barrero RA, Batra J. IsomiR-eQTL: A Cancer-Specific Expression Quantitative Trait Loci Database of miRNAs and Their Isoforms. Int J Mol Sci 2022; 23:ijms232012493. [PMID: 36293349 PMCID: PMC9604134 DOI: 10.3390/ijms232012493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
The identification of expression quantitative trait loci (eQTL) is an important component in efforts to understand how genetic variants influence disease risk. MicroRNAs (miRNAs) are short noncoding RNA molecules capable of regulating the expression of several genes simultaneously. Recently, several novel isomers of miRNAs (isomiRs) that differ slightly in length and sequence composition compared to their canonical miRNAs have been reported. Here we present isomiR-eQTL, a user-friendly database designed to help researchers find single nucleotide polymorphisms (SNPs) that can impact miRNA (miR-eQTL) and isomiR expression (isomiR-eQTL) in 30 cancer types. The isomiR-eQTL includes a total of 152,671 miR-eQTLs and 2,390,805 isomiR-eQTLs at a false discovery rate (FDR) of 0.05. It also includes 65,733 miR-eQTLs overlapping known cancer-associated loci identified through genome-wide association studies (GWAS). To the best of our knowledge, this is the first study investigating the impact of SNPs on isomiR expression at the genome-wide level. This database may pave the way for researchers toward finding a model for personalised medicine in which miRNAs, isomiRs, and genotypes are utilised.
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Affiliation(s)
- Afshin Moradi
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane 4059, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane 4102, Australia
| | - Paul Whatmore
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane 4000, Australia
| | - Samaneh Farashi
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane 4059, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane 4102, Australia
| | - Roberto A. Barrero
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane 4000, Australia
| | - Jyotsna Batra
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane 4059, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane 4102, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane 4059, Australia
- Correspondence:
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6
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Voss G, Edsjö A, Bjartell A, Ceder Y. Quantification of microRNA editing using two-tailed RT-qPCR for improved biomarker discovery. RNA (NEW YORK, N.Y.) 2021; 27:1412-1424. [PMID: 34433636 PMCID: PMC8522694 DOI: 10.1261/rna.078867.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Even though microRNAs have been viewed as promising biomarkers for years, their clinical implementation is still lagging far behind. This is in part due to the lack of RT-qPCR technologies that can differentiate between microRNA isoforms. For example, A-to-I editing of microRNAs through adenosine deaminase acting on RNA (ADAR) enzymes can affect their expression levels and functional roles, but editing isoform-specific assays are not commercially available. Here, we describe RT-qPCR assays that are specific for editing isoforms, using microRNA-379 (miR-379) as a model. The assays are based on two-tailed RT-qPCR, and we show them to be compatible both with SYBR Green and hydrolysis-based chemistries, as well as with both qPCR and digital PCR. The assays could readily detect different miR-379 editing isoforms in various human tissues as well as changes of editing levels in ADAR-overexpressing cell lines. We found that the miR-379 editing frequency was higher in prostate cancer samples compared to benign prostatic hyperplasia samples. Furthermore, decreased expression of unedited miR-379, but not edited miR-379, was associated with treatment resistance, metastasis, and shorter overall survival. Taken together, this study presents the first RT-qPCR assays that were demonstrated to distinguish A-to-I-edited microRNAs, and shows that they can be useful in the identification of biomarkers that previously have been masked by other isoforms.
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Affiliation(s)
- Gjendine Voss
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, 22381 Lund, Sweden
| | - Anders Edsjö
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Region Skåne, 22185 Lund, Sweden
| | - Anders Bjartell
- Department of Urology, Skåne University Hospital, 20502 Malmö, Sweden
| | - Yvonne Ceder
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, 22381 Lund, Sweden
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7
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Guo L, Li Y, Cirillo KM, Marick RA, Su Z, Yin X, Hua X, Mills GB, Sahni N, Yi SS. mi-IsoNet: systems-scale microRNA landscape reveals rampant isoform-mediated gain of target interaction diversity and signaling specificity. Brief Bioinform 2021; 22:6225086. [PMID: 33855356 DOI: 10.1093/bib/bbab091] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/23/2022] Open
Abstract
MicroRNA (miRNA) is not a single sequence, but a series of multiple variants (also termed isomiRs) with sequence and expression heterogeneity. Whether and how these isoforms contribute to functional variation and complexity at the systems and network levels remain largely unknown. To explore this question systematically, we comprehensively analyzed the expression of small RNAs and their target sites to interrogate functional variations between novel isomiRs and their canonical miRNA sequences. Our analyses of the pan-cancer landscape of miRNA expression indicate that multiple isomiRs generated from the same miRNA locus often exhibit remarkable variation in their sequence, expression and function. We interrogated abundant and differentially expressed 5' isomiRs with novel seed sequences via seed shifting and identified many potential novel targets of these 5' isomiRs that would expand interaction capabilities between small RNAs and mRNAs, rewiring regulatory networks and increasing signaling circuit complexity. Further analyses revealed that some miRNA loci might generate diverse dominant isomiRs that often involved isomiRs with varied seeds and arm-switching, suggesting a selective advantage of multiple isomiRs in regulating gene expression. Finally, experimental validation indicated that isomiRs with shifted seed sequences could regulate novel target mRNAs and therefore contribute to regulatory network rewiring. Our analysis uncovers a widespread expansion of isomiR and mRNA interaction networks compared with those seen in canonical small RNA analysis; this expansion suggests global gene regulation network perturbations by alternative small RNA variants or isoforms. Taken together, the variations in isomiRs that occur during miRNA processing and maturation are likely to play a far more complex and plastic role in gene regulation than previously anticipated.
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Affiliation(s)
- Li Guo
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongsheng Li
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kara M Cirillo
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Robert A Marick
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Zhe Su
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xing Yin
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xu Hua
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Cell, Developmental and Cancer Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97201, USA.,Precision Oncology, Knight Cancer Institute, Portland, OR 97201, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - S Stephen Yi
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.,Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX 78712, USA.,Interdisciplinary Life Sciences Graduate Programs (ILSGP), College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA.,Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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8
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Xie X, Cong L, Liu S, Xiang L, Fu X. Genistein alleviates chronic vascular inflammatory response via the miR‑21/NF‑κB p65 axis in lipopolysaccharide‑treated mice. Mol Med Rep 2021; 23:192. [PMID: 33495831 PMCID: PMC7809901 DOI: 10.3892/mmr.2021.11831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022] Open
Abstract
Chronic vascular inflammatory response is an important pathological basis of cardiovascular disease. Genistein (GEN), a natural compound, exhibits anti‑inflammatory effects. The aim of the present study was to investigate the effects of GEN on lipopolysaccharide (LPS)‑induced chronic vascular inflammatory response in mice and explore the underlying anti‑inflammatory mechanisms. C57BL/6 mice were fed with a high‑fat diet combined with intraperitoneal injection of LPS to induce chronic vascular inflammation. The expression levels of TNF‑α, IL‑6 and microRNA (miR)‑21 in the vasculature were detected via reverse transcription‑quantitative (RT‑q)PCR. The protein levels of inducible nitric oxide synthase (iNOS) and NF‑κB p65 were detected via western blotting. NF‑κB p65 was also analyzed via immunohistochemistry and immunofluorescence (IF). In addition, after transfection with miR‑21 mimic or inhibitor for 24 h, vascular endothelial cells (VECs) were treated with GEN and LPS. RT‑qPCR and western blot analyses were performed to detect the expression of TNF‑α, IL‑6, miR‑21 and iNOS, and the protein levels of iNOS and NF‑κB p65, respectively. IF was used to measure NF‑κB p65 nuclear translocation. The results revealed that GEN significantly decreased the expression of inflammation‑associated vascular factors in LPS‑treated C57BL/6 mice, including TNF‑α, IL‑6, iNOS, NF‑κB p65 and miR‑21. Furthermore, miR‑21 antagomir enhanced the anti‑inflammatory effects of GEN. In LPS‑induced VECs, miR‑21 mimic increased inflammation‑associated factor expression and attenuated the anti‑inflammatory effects of GEN, whereas miR‑21 inhibitor induced opposing effects. Therefore, the results of the present study suggested that GEN inhibited chronic vascular inflammatory response in mice, which may be associated with the inhibition of VEC inflammatory injury via the miR‑21/NF‑κB p65 pathway.
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Affiliation(s)
- Xiaolin Xie
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, Hunan Normal University, Changsha, Hunan 410013, P.R. China
- Department of Basic Medicine, School of Medicine, Hunan Normal University, Changsha, Hunan 410013, P.R. China
| | - Li Cong
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, Hunan Normal University, Changsha, Hunan 410013, P.R. China
| | - Sujuan Liu
- Department of Basic Medicine, School of Medicine, Hunan Normal University, Changsha, Hunan 410013, P.R. China
| | - Liping Xiang
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Xiaohua Fu
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, Hunan Normal University, Changsha, Hunan 410013, P.R. China
- Department of Basic Medicine, School of Medicine, Hunan Normal University, Changsha, Hunan 410013, P.R. China
- Correspondence to: Professor Xiaohua Fu, Department of Basic Medicine, School of Medicine, Hunan Normal University, 371 Tongzipo Road, Changsha, Hunan 410013, P.R. China, E-mail:
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9
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Akbal Vural O, Yaman YT, Bolat G, Abaci S. Human Serum Albumin−Gold Nanoparticle Based Impedimetric Sensor for Sensitive Detection of miRNA‐200c. ELECTROANAL 2020. [DOI: 10.1002/elan.202060342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Oznur Akbal Vural
- Advanced Technologies Application and Research Center Hacettepe University Ankara Turkey
| | - Yesim Tugce Yaman
- Advanced Technologies Application and Research Center Hacettepe University Ankara Turkey
- Analytical Chemistry Division, Department of Chemistry Hacettepe University Ankara Turkey
| | - Gulcin Bolat
- Analytical Chemistry Division, Department of Chemistry Hacettepe University Ankara Turkey
| | - Serdar Abaci
- Advanced Technologies Application and Research Center Hacettepe University Ankara Turkey
- Analytical Chemistry Division, Department of Chemistry Hacettepe University Ankara Turkey
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10
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Zarnack K, Balasubramanian S, Gantier MP, Kunetsky V, Kracht M, Schmitz ML, Sträßer K. Dynamic mRNP Remodeling in Response to Internal and External Stimuli. Biomolecules 2020; 10:biom10091310. [PMID: 32932892 PMCID: PMC7565591 DOI: 10.3390/biom10091310] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
Signal transduction and the regulation of gene expression are fundamental processes in every cell. RNA-binding proteins (RBPs) play a key role in the post-transcriptional modulation of gene expression in response to both internal and external stimuli. However, how signaling pathways regulate the assembly of RBPs with mRNAs remains largely unknown. Here, we summarize observations showing that the formation and composition of messenger ribonucleoprotein particles (mRNPs) is dynamically remodeled in space and time by specific signaling cascades and the resulting post-translational modifications. The integration of signaling events with gene expression is key to the rapid adaptation of cells to environmental changes and stress. Only a combined approach analyzing the signal transduction pathways and the changes in post-transcriptional gene expression they cause will unravel the mechanisms coordinating these important cellular processes.
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Affiliation(s)
- Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt a.M., Germany;
| | | | - Michael P. Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia;
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
| | - Vladislav Kunetsky
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - M. Lienhard Schmitz
- Institute of Biochemistry, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
- Correspondence:
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11
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Avendaño-Vázquez SE, Flores-Jasso CF. Stumbling on elusive cargo: how isomiRs challenge microRNA detection and quantification, the case of extracellular vesicles. J Extracell Vesicles 2020; 9:1784617. [PMID: 32944171 PMCID: PMC7480573 DOI: 10.1080/20013078.2020.1784617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- S Eréndira Avendaño-Vázquez
- Consorcio de Metabolismo de RNA y Vesículas Extracelulares, Instituto Nacional de Medicina Genómica, INMEGEN, Ciudad de México, México
| | - C Fabián Flores-Jasso
- Consorcio de Metabolismo de RNA y Vesículas Extracelulares, Instituto Nacional de Medicina Genómica, INMEGEN, Ciudad de México, México
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12
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Emerging isothermal amplification technologies for microRNA biosensing: Applications to liquid biopsies. Mol Aspects Med 2020; 72:100832. [DOI: 10.1016/j.mam.2019.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/06/2019] [Accepted: 11/10/2019] [Indexed: 02/07/2023]
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13
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Alles J, Fehlmann T, Fischer U, Backes C, Galata V, Minet M, Hart M, Abu-Halima M, Grässer FA, Lenhof HP, Keller A, Meese E. An estimate of the total number of true human miRNAs. Nucleic Acids Res 2019; 47:3353-3364. [PMID: 30820533 PMCID: PMC6468295 DOI: 10.1093/nar/gkz097] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/30/2019] [Accepted: 02/07/2019] [Indexed: 02/06/2023] Open
Abstract
While the number of human miRNA candidates continuously increases, only a few of them are completely characterized and experimentally validated. Toward determining the total number of true miRNAs, we employed a combined in silico high- and experimental low-throughput validation strategy. We collected 28 866 human small RNA sequencing data sets containing 363.7 billion sequencing reads and excluded falsely annotated and low quality data. Our high-throughput analysis identified 65% of 24 127 mature miRNA candidates as likely false-positives. Using northern blotting, we experimentally validated miRBase entries and novel miRNA candidates. By exogenous overexpression of 108 precursors that encode 205 mature miRNAs, we confirmed 68.5% of the miRBase entries with the confirmation rate going up to 94.4% for the high-confidence entries and 18.3% of the novel miRNA candidates. Analyzing endogenous miRNAs, we verified the expression of 8 miRNAs in 12 different human cell lines. In total, we extrapolated 2300 true human mature miRNAs, 1115 of which are currently annotated in miRBase V22. The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNAs.
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Affiliation(s)
- Julia Alles
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Ulrike Fischer
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Marie Minet
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany.,Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Martin Hart
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Masood Abu-Halima
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Friedrich A Grässer
- Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
| | - Hans-Peter Lenhof
- Chair for Bioinformatics, Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
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14
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Forero DA, González-Giraldo Y, Castro-Vega LJ, Barreto GE. qPCR-based methods for expression analysis of miRNAs. Biotechniques 2019; 67:192-199. [PMID: 31560239 DOI: 10.2144/btn-2019-0065] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Several approaches for miRNA expression analysis have been developed in recent years. In this article, we provide an updated and comprehensive review of available qPCR-based methods for miRNA expression analysis and discuss their advantages and disadvantages. Existing techniques involve the use of stem-loop reverse transcriptase-PCR, polyadenylation of RNAs, ligation of adapters or RT with complex primers, using universal or miRNA-specific qPCR primers and/or probes. Many of these methods are oriented towards the expression analysis of mature miRNAs and few are designed for the study of pre-miRNAs and pri-miRNAs. We also discuss findings from articles that compare results from existing methods. Finally, we suggest key points for the improvement of available techniques and for the future development of additional methods.
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Affiliation(s)
- Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,PhD Program in Health Sciences, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luis J Castro-Vega
- INSERM, UMR970, Paris-Cardiovascular Research Center, Equipe Labellisée par la Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
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15
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Kresoja-Rakic J, Szpechcinski A, Kirschner MB, Ronner M, Minatel B, Martinez VD, Lam WL, Weder W, Stahel R, Früh M, Cerciello F, Felley-Bosco E. miR-625-3p and lncRNA GAS5 in Liquid Biopsies for Predicting the Outcome of Malignant Pleural Mesothelioma Patients Treated with Neo-Adjuvant Chemotherapy and Surgery. Noncoding RNA 2019; 5:E41. [PMID: 31212997 PMCID: PMC6631473 DOI: 10.3390/ncrna5020041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/14/2019] [Accepted: 06/15/2019] [Indexed: 02/07/2023] Open
Abstract
Combining neo-adjuvant chemotherapy and surgery is part of multimodality treatment of malignant pleural mesothelioma (MPM), but not all patients benefit from this approach. In this exploratory analysis, we investigated the prognostic value of circulating miR-625-3p and lncRNA GAS5 after neo-adjuvant chemotherapy. 36 MPM patients from the SAKK 17/04 trial (NCT00334594), whose blood was available before and after chemotherapy were investigated. RNA was isolated from plasma and reverse transcribed into cDNA. miR-16-5p and β-actin were used as a reference gene for miR-625-3p and GAS5, respectively. After exclusion of samples due to hemolysis or RNA degradation, paired plasma samples from 32 patients before and after chemotherapy were further analyzed. Quantification of miR-625-3p levels in all 64 samples revealed a bimodal distribution and cloning and sequencing of miR-625-3p qPCR product revealed the presence of miR-625-3p isomiRs. Relative change of the circulating miR-625-3p and GAS5 levels after chemotherapy showed that increased circulating miR-625-3p and decreased GAS5 was significantly associated with disease progression (Fisher's test, p = 0.0393). In addition, decreased levels of circulating GAS5 were significantly associated with shorter overall and progression-free survival. Our exploratory analysis revealed a potential value of circulating non-coding RNA for selection of patients likely to benefit from surgery after platinum-based adjuvant chemotherapy.
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Affiliation(s)
- Jelena Kresoja-Rakic
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zürich, 8091 Zürich, Switzerland.
| | - Adam Szpechcinski
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zürich, 8091 Zürich, Switzerland.
| | - Michaela B Kirschner
- Department of Thoracic Surgery, University Hospital Zürich, 8091 Zürich, Switzerland.
| | - Manuel Ronner
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zürich, 8091 Zürich, Switzerland.
| | - Brenda Minatel
- BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
| | - Victor D Martinez
- BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- IWK Health Centre, Halifax, NS B3K 6R8, Canada.
| | - Wan L Lam
- BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
| | - Walter Weder
- Department of Thoracic Surgery, University Hospital Zürich, 8091 Zürich, Switzerland.
| | - Rolf Stahel
- Comprehensive Cancer Center Zürich, University Hospital Zürich, 8091 Zürich, Switzerland.
| | - Martin Früh
- Cantonal Hospital of St. Gallen, 9007 St. Gallen, Switzerland.
- Department of Medical Oncology/Hematology, University of Bern, CH-3000 Bern, Switzerland.
| | | | - Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zürich, 8091 Zürich, Switzerland.
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16
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Pillman KA, Goodall GJ, Bracken CP, Gantier MP. miRNA length variation during macrophage stimulation confounds the interpretation of results: implications for miRNA quantification by RT-qPCR. RNA (NEW YORK, N.Y.) 2019; 25:232-238. [PMID: 30487268 PMCID: PMC6348984 DOI: 10.1261/rna.069047.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
Most microRNAs (miRNAs) are expressed as a mix of length isoforms (referred to as isomiRs). IsomiR stoichiometry can be differentially impacted upon cell stimulation, as recently evidenced by our group in the context of immune responses induced by type-I interferon (IFN). Here, we revisit published RNA-seq data sets of human and mouse macrophages stimulated with bacterial products at the isomiR level. We demonstrate that for several miRNAs, macrophage stimulation induces changes in isomiR stoichiometry. Critically, we find that changes in miRNA expression can be misinterpreted when miRNAs are quantified by RT-qPCR, as primers directed against canonical miRNA sequences may not equally target the different isomiRs that are regulated endogenously. Beyond the case of phagocyte stimulation, our analyses reinforce the concept that analysis of miRNA expression at the isoform level should become standard practice.
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Affiliation(s)
- Katherine A Pillman
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia 5000, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Department of Medicine, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Department of Medicine, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
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17
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Nejad C, Stunden HJ, Gantier MP. A guide to miRNAs in inflammation and innate immune responses. FEBS J 2018; 285:3695-3716. [DOI: 10.1111/febs.14482] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/08/2018] [Accepted: 04/18/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Charlotte Nejad
- Centre for Innate Immunity and Infectious Diseases Hudson Institute of Medical Research Clayton Australia
- Department of Molecular and Translational Science Monash University Clayton Australia
| | - H. James Stunden
- Institute of Innate Immunity Biomedical Center University Hospitals Bonn Bonn Germany
| | - Michael P. Gantier
- Centre for Innate Immunity and Infectious Diseases Hudson Institute of Medical Research Clayton Australia
- Department of Molecular and Translational Science Monash University Clayton Australia
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