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Cabrelle C, Giorgi FM, Mercatelli D. Quantitative and qualitative detection of tRNAs, tRNA halves and tRFs in human cancer samples: Molecular grounds for biomarker development and clinical perspectives. Gene 2024; 898:148097. [PMID: 38128792 DOI: 10.1016/j.gene.2023.148097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 12/04/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Transfer RNAs (tRNAs) are small non-coding RNAs playing a central role during protein synthesis. Besides translation, growing evidence suggests that in many contexts, precursor or mature tRNAs can also be processed into smaller fragments playing many non-canonical regulatory roles in different biological pathways with oncogenic relevance. Depending on the source, these molecules can be classified as tRNA halves (also known as tiRNAs) or tRNA-derived fragments (tRFs), and furtherly divided into 5'-tRNA and 3'-tRNA halves, or tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF, respectively. Unlike DNA and mRNA, high-throughput sequencing of tRNAs is challenging, because of technical limitations of currently developed sequencing methods. In recent years, different sequencing approaches have been proposed allowing the quantification and identification of an increasing number of tRNA fragments with critical functions in distinct physiological and pathophysiological processes. In the present review, we discussed pros and cons of recent advances in different sequencing methods, also introducing the expanding repertoire of bioinformatics tool and resources specifically focused on tRNA research and discussing current issues in the study of these small RNA molecules. Furthermore, we discussed the potential value of tRNA fragments as diagnostic and prognostic biomarkers for different types of cancers.
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Affiliation(s)
- Chiara Cabrelle
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
| | | | - Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
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2
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Yu M, Yi J, Qiu Q, Yao D, Li J, Yang J, Mi C, Zhou L, Lu B, Lu W, Ying K, Chen W, Chen E, Zhang H, Lu Z, Lu Y, Liu P. Pan-cancer tRNA-derived fragment CAT1 coordinates RBPMS to stabilize NOTCH2 mRNA to promote tumorigenesis. Cell Rep 2023; 42:113408. [PMID: 37943661 DOI: 10.1016/j.celrep.2023.113408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/20/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
Transfer RNA-derived fragments (tRFs) are a class of small non-coding regulatory RNAs that are involved in the pathophysiology of many diseases. However, the role of tRFs in cancer progression remains largely elusive. Here, we demonstrate that a pan-cancer 3'-tRF, CAT1 (cancer associated tRF 1), is ubiquitously upregulated in tumors and associated with poor prognosis of a variety of cancers, including lung cancer. The upregulated CAT1 in cancer cells binds to RNA-binding protein with multiple splicing (RBPMS) and displaces NOTCH2 association from RBPMS, thereby inhibiting the subsequent CCR4-NOT deadenylation-complex-mediated NOTCH2 mRNA decay. The CAT1-enhanced NOTCH2 expression promotes lung cancer cell proliferation and metastasis in vitro and in vivo. In addition, plasma CAT1 levels are substantially increased in patients with lung cancer compared to non-cancer control subjects. Our findings reveal an intrinsic connection between cancer-specific upregulation of CAT1 and cancer progression, show the regulation of NOTCH signaling in cancer by a 3'-tRF, and highlight its great clinical potential.
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Affiliation(s)
- Mengqian Yu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Jiani Yi
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Qiongzi Qiu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Dongxia Yao
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Jia Li
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Juze Yang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Chunyi Mi
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Liyuan Zhou
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Bingjian Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Weiguo Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Kejing Ying
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Wantao Chen
- Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200011, China
| | - Enguo Chen
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Honghe Zhang
- Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Zhimin Lu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China.
| | - Yan Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China.
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310013, China; Department of Physiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA.
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3
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U A, Viswam P, Kattupalli D, Eppurathu Vasudevan S. Elucidation of transfer RNAs as stress regulating agents and the experimental strategies to conceive the functional role of tRNA-derived fragments in plants. Crit Rev Biotechnol 2023; 43:275-292. [PMID: 35382663 DOI: 10.1080/07388551.2022.2026288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In plants, the transfer RNAs (tRNAs) exhibit their profound influence in orchestrating diverse physiological activities like cell growth, development, and response to several surrounding stimuli. The tRNAs, which were known to restrict their function solely in deciphering the codons, are now emerging as frontline defenders in stress biology. The plants that are constantly confronted with a huge panoply of stresses rely on tRNA-mediated stress regulation by altering the tRNA abundance, curbing the transport of tRNAs, fragmenting the mature tRNAs during stress. Among them, the studies on the generation of transfer RNA-derived fragments (tRFs) and their biological implication in stress response have attained huge interest. In plants, the tRFs hold stable expression patterns and regulate biological functions under diverse environmental conditions. In this review, we discuss the fate of plant tRNAs upon stress and thereafter how the tRFs are metamorphosed into sharp ammunition to wrestle with stress. We also address the various methods developed to date for uncovering the role of tRFs and their function in plants.
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Affiliation(s)
- Aswathi U
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
| | - Pooja Viswam
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
| | - Divya Kattupalli
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
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Orbán TI. One locus, several functional RNAs-emerging roles of the mechanisms responsible for the sequence variability of microRNAs. Biol Futur 2023:10.1007/s42977-023-00154-7. [PMID: 36847925 DOI: 10.1007/s42977-023-00154-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023]
Abstract
With the development of modern molecular genetics, the original "one gene-one enzyme" hypothesis has been outdated. For protein coding genes, the discovery of alternative splicing and RNA editing provided the biochemical background for the RNA repertoire of a single locus, which also serves as an important pillar for the enormous protein variability of the genomes. Non-protein coding RNA genes were also revealed to produce several RNA species with distinct functions. The loci of microRNAs (miRNAs), encoding for small endogenous regulatory RNAs, were also found to produce a population of small RNAs, rather than a single defined product. This review aims to present the mechanisms contributing to the astonishing variability of miRNAs revealed by the new sequencing technologies. One important source is the careful balance of arm selection, producing sequentially different 5p- or 3p-miRNAs from the same pre-miRNA, thereby broadening the number of regulated target RNAs and the phenotypic response. In addition, the formation of 5', 3' and polymorphic isomiRs, with variable end and internal sequences also leads to a higher number of targeted sequences, and increases the regulatory output. These miRNA maturation processes, together with other known mechanisms such as RNA editing, further increase the potential outcome of this small RNA pathway. By discussing the subtle mechanisms behind the sequence diversity of miRNAs, this review intends to reveal this engaging aspect of the inherited "RNA world", how it contributes to the almost infinite molecular variability among living organisms, and how this variability can be exploited to treat human diseases.
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Affiliation(s)
- Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar Tudósok Körútja 2, Budapest, 1117, Hungary.
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Hecker M, Fitzner B, Putscher E, Schwartz M, Winkelmann A, Meister S, Dudesek A, Koczan D, Lorenz P, Boxberger N, Zettl UK. Implication of genetic variants in primary microRNA processing sites in the risk of multiple sclerosis. EBioMedicine 2022; 80:104052. [PMID: 35561450 PMCID: PMC9111935 DOI: 10.1016/j.ebiom.2022.104052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 12/01/2022] Open
Abstract
Background Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system with a well-established genetic contribution to susceptibility. Over 200 genetic regions have been linked to the inherited risk of developing MS, but the disease-causing variants and their functional effects at the molecular level are still largely unresolved. We hypothesised that MS-associated single-nucleotide polymorphisms (SNPs) affect the recognition and enzymatic cleavage of primary microRNAs (pri-miRNAs). Methods Our study focused on 11 pri-miRNAs (9 primate-specific) that are encoded in genetic risk loci for MS. The levels of mature miRNAs and potential isoforms (isomiRs) produced from those pri-miRNAs were measured in B cells obtained from the peripheral blood of 63 MS patients and 28 healthy controls. We tested for associations between SNP genotypes and miRNA expression in cis using quantitative trait locus (cis-miR-eQTL) analyses. Genetic effects on miRNA stem-loop processing efficiency were verified using luciferase reporter assays. Potential direct miRNA target genes were identified by transcriptome profiling and computational binding site assessment. Findings Mature miRNAs and isomiRs from hsa-mir-26a-2, hsa-mir-199a-1, hsa-mir-4304, hsa-mir-4423, hsa-mir-4464 and hsa-mir-4492 could be detected in all B-cell samples. When MS patient subgroups were compared with healthy controls, a significant differential expression was observed for miRNAs from the 5’ and 3’ strands of hsa-mir-26a-2 and hsa-mir-199a-1. The cis-miR-eQTL analyses and reporter assays pointed to a slightly more efficient Drosha-mediated processing of hsa-mir-199a-1 when the MS risk allele T of SNP rs1005039 is present. On the other hand, the MS risk allele A of SNP rs817478, which substitutes the first C in a CNNC sequence motif, was found to cause a markedly lower efficiency in the processing of hsa-mir-4423. Overexpression of hsa-mir-199a-1 inhibited the expression of 60 protein-coding genes, including IRAK2, MIF, TNFRSF12A and TRAF1. The only target gene identified for hsa-mir-4423 was TMEM47. Interpretation We found that MS-associated SNPs in sequence determinants of pri-miRNA processing can affect the expression of mature miRNAs. Our findings complement the existing literature on the dysregulation of miRNAs in MS. Further studies on the maturation and function of miRNAs in different cell types and tissues may help to gain a more detailed functional understanding of the genetic basis of MS. Funding This study was funded by the Rostock University Medical Center (FORUN program, grant: 889002), Sanofi Genzyme (grant: GZ-2016-11560) and Merck Serono GmbH (Darmstadt, Germany, an affiliate of Merck KGaA, CrossRef Funder ID: 10.13039/100009945, grant: 4501860307). NB was supported by the Stiftung der Deutschen Wirtschaft (sdw) and the FAZIT foundation. EP was supported by the Landesgraduiertenförderung Mecklenburg-Vorpommern.
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He F, Ni N, Wang H, Zeng Z, Zhao P, Shi D, Xia Y, Chen C, Hu D, Qin K, Wagstaff W, Qin D, Hendren-Santiago B, Ho S, Haydon R, Luu H, Reid R, Shen L, Gan H, Fan J, He TC. OUHP: an optimized universal hairpin primer system for cost-effective and high-throughput RT-qPCR-based quantification of microRNA (miRNA) expression. Nucleic Acids Res 2022; 50:e22. [PMID: 34850128 PMCID: PMC8887422 DOI: 10.1093/nar/gkab1153] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are single-stranded, ∼22-nucleotide noncoding RNAs that regulate many cellular processes. While numerous miRNA quantification technologies are available, a recent analysis of 12 commercial platforms revealed high variations in reproducibility, sensitivity, accuracy, specificity and concordance within and/or between platforms. Here, we developed a universal hairpin primer (UHP) system that negates the use of miRNA-specific hairpin primers (MsHPs) for quantitative reverse transcription PCR (RT-qPCR)-based miRNA quantification. Specifically, we analyzed four UHPs that share the same hairpin structure but are anchored with two, three, four and six degenerate nucleotides at 3'-ends (namely UHP2, UHP3, UHP4 and UHP6), and found that the four UHPs yielded robust RT products and quantified miRNAs with high efficiency. UHP-based RT-qPCR miRNA quantification was not affected by long transcripts. By analyzing 14 miRNAs, we demonstrated that UHP4 closely mimicked MsHPs in miRNA quantification. Fine-tuning experiments identified an optimized UHP (OUHP) mix with a molar composition of UHP2:UHP4:UHP6 = 8:1:1, which closely recapitulated MsHPs in miRNA quantification. Using synthetic LET7 isomiRs, we demonstrated that the OUHP-based qPCR system exhibited high specificity and sensitivity. Collectively, our results demonstrate that the OUHP system can serve as a reliable and cost-effective surrogate of MsHPs for RT-qPCR-based miRNA quantification for basic research and precision medicine.
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Affiliation(s)
- Fang He
- Departments of Nephrology, Gastroenterology, Laboratory Diagnostic Medicine, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Na Ni
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Hao Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Zongyue Zeng
- Departments of Nephrology, Gastroenterology, Laboratory Diagnostic Medicine, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Piao Zhao
- Departments of Nephrology, Gastroenterology, Laboratory Diagnostic Medicine, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Orthopaedic Surgery, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Daniel A Hu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Kevin H Qin
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - David Qin
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Bryce Hendren-Santiago
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Sherwin H Ho
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Rex C Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hue H Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Russell R Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Le Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hua Gan
- Departments of Nephrology, Gastroenterology, Laboratory Diagnostic Medicine, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jiaming Fan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
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7
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Yao Y, Zhang H, Tian T, Liu Y, Zhu R, Ji J, Liu B. Iodide-modified Ag nanoparticles coupled with DSN-Assisted cycling amplification for label-free and ultrasensitive SERS detection of MicroRNA-21. Talanta 2021; 235:122728. [PMID: 34517596 DOI: 10.1016/j.talanta.2021.122728] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/17/2021] [Accepted: 07/21/2021] [Indexed: 01/22/2023]
Abstract
With the emergence of microRNA (miRNA) as a key player in early clinical disease diagnosis, development of rapidly sensitive and quantitative miRNA detection methods are imperative. Herein, a label-free SERS assay coupled with duplex-specific nuclease (DSN) signal amplification strategy was proposed for facilely ultrasensitive and quantitative analysis of miRNA-21. Firstly, magnetic beads assembled with excessive capture DNA were utilized to hybridize the target miRNA-21. These DNA-RNA heteroduplexes were cleaved by DSN to generate small nucleotide fragments into the supernatant and the miRNA-21 released and rehybridized another DNA, going to the next DSN cycle. Consequently, numerous of small nucleotide fragments of capture DNA were released from magnetic beads and the miRNA-21 signal was transferred and amplified by the SERS signals of total phosphate backbones which are abundant in nucleotide. Furthermore, iodide-modified Ag nanoparticles (AgINPs) was employed to generate a strong and reproducible SERS signal. The proposed method displayed excellent performance for miRNA-21 detection with the linear range from 0.33 fM to 3.3 pM, and a lower detection limit of 42 aM. Moreover, this strategy exhibited effectively base discrimination capability and was successfully applied for monitoring the expression levels of miRNA-21 in different cancer cell lines and human serum.
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Affiliation(s)
- Yuanyuan Yao
- Department of Chemistry, Shanghai Stomatological Hospital, Institute of Biomedical Sciences, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China; Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Science and Engineering, Jiaxing University, Jiaxing, Zhejiang, 314001, China
| | - Hongding Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, Institute of Biomedical Sciences, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China
| | - Tongtong Tian
- Department of Chemistry, Shanghai Stomatological Hospital, Institute of Biomedical Sciences, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China
| | - Yixin Liu
- Department of Chemistry, Shanghai Stomatological Hospital, Institute of Biomedical Sciences, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China
| | - Rendan Zhu
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Science and Engineering, Jiaxing University, Jiaxing, Zhejiang, 314001, China
| | - Ji Ji
- Department of Chemistry, Shanghai Stomatological Hospital, Institute of Biomedical Sciences, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China.
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, Institute of Biomedical Sciences, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China.
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8
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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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9
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MicroRNA Isoforms Contribution to Melanoma Pathogenesis. Noncoding RNA 2021; 7:ncrna7040063. [PMID: 34698264 PMCID: PMC8544706 DOI: 10.3390/ncrna7040063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022] Open
Abstract
Cutaneous melanoma (CM) is the most lethal tumor among skin cancers, and its incidence is constantly increasing. A deeper understanding of the molecular processes guiding melanoma pathogenesis could improve diagnosis, treatment and prognosis. MicroRNAs play a key role in melanoma biology. Recently, next generation sequencing (NGS) experiments, designed to assess small-RNA expression, revealed the existence of microRNA variants with different length and sequence. These microRNA isoforms are known as isomiRs and provide an additional layer to the complex non-coding RNA world. Here, we collected data from NGS experiments to provide a comprehensive characterization of miRNA and isomiR dysregulation in benign nevi (BN) and early-stage melanomas. We observed that melanoma and BN express different and specific isomiRs and have a different isomiR abundance distribution. Moreover, isomiRs from the same microRNA can have opposite expression trends between groups. Using The Cancer Genome Atlas (TCGA) dataset of skin cancers, we analyzed isomiR expression in primary melanoma and melanoma metastasis and tested their association with NF1, BRAF and NRAS mutations. IsomiRs differentially expressed were identified and catalogued with reference to the canonical form. The reported non-random dysregulation of specific isomiRs contributes to the understanding of the complex melanoma pathogenesis and serves as the basis for further functional studies.
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10
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Wang P, Zhou Y, Richards AM. Effective tools for RNA-derived therapeutics: siRNA interference or miRNA mimicry. Theranostics 2021; 11:8771-8796. [PMID: 34522211 PMCID: PMC8419061 DOI: 10.7150/thno.62642] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022] Open
Abstract
The approval of the first small interfering RNA (siRNA) drug Patisiran by FDA in 2018 marks a new era of RNA interference (RNAi) therapeutics. MicroRNAs (miRNA), an important post-transcriptional gene regulator, are also the subject of both basic research and clinical trials. Both siRNA and miRNA mimics are ~21 nucleotides RNA duplexes inducing mRNA silencing. Given the well performance of siRNA, researchers ask whether miRNA mimics are unnecessary or developed siRNA technology can pave the way for the emergence of miRNA mimic drugs. Through comprehensive comparison of siRNA and miRNA, we focus on (1) the common features and lessons learnt from the success of siRNAs; (2) the unique characteristics of miRNA that potentially offer additional therapeutic advantages and opportunities; (3) key areas of ongoing research that will contribute to clinical application of miRNA mimics. In conclusion, miRNA mimics have unique properties and advantages which cannot be fully matched by siRNA in clinical applications. MiRNAs are endogenous molecules and the gene silencing effects of miRNA mimics can be regulated or buffered to ameliorate or eliminate off-target effects. An in-depth understanding of the differences between siRNA and miRNA mimics will facilitate the development of miRNA mimic drugs.
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Affiliation(s)
- Peipei Wang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
| | - Yue Zhou
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
| | - Arthur M. Richards
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
- Christchurch Heart Institute, Department of Medicine, University of Otago Christchurch, New Zealand
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11
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Tomasello L, Distefano R, Nigita G, Croce CM. The MicroRNA Family Gets Wider: The IsomiRs Classification and Role. Front Cell Dev Biol 2021; 9:668648. [PMID: 34178993 PMCID: PMC8220208 DOI: 10.3389/fcell.2021.668648] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are the most characterized class of non-coding RNAs and are engaged in many cellular processes, including cell differentiation, development, and homeostasis. MicroRNA dysregulation was observed in several diseases, cancer included. Epitranscriptomics is a branch of epigenomics that embraces all RNA modifications occurring after DNA transcription and RNA synthesis and involving coding and non-coding RNAs. The development of new high-throughput technologies, especially deep RNA sequencing, has facilitated the discovery of miRNA isoforms (named isomiRs) resulting from RNA modifications mediated by enzymes, such as deaminases and exonucleases, and differing from the canonical ones in length, sequence, or both. In this review, we summarize the distinct classes of isomiRs, their regulation and biogenesis, and the active role of these newly discovered molecules in cancer and other diseases.
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Affiliation(s)
- Luisa Tomasello
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
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12
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Wu J, Tian Y, He L, Zhang J, Huang Z, Luo Z, Duan Y. An efficient localized catalytic hairpin assembly-based DNA nanomachine for miRNA-21 imaging in living cells. Analyst 2021; 146:3041-3051. [PMID: 33949412 DOI: 10.1039/d1an00001b] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
As an enzyme-free isothermal amplification strategy, catalytic hairpin assembly (CHA) is a very promising method for cell imaging. However, the practical application of CHA on intracellular miRNA imaging is limited by slow kinetics, insufficient amplification efficiency and strong interference in living cells. Herein, a localized catalytic hairpin assembly-based DNA nanomachine (LCHA nanomachine) was developed for the rapid, efficient and reliable fluorescence resonance energy transformation (FRET) imaging of miRNA-21 in living cells. The nanomachine was simply constructed by a one-step self-assembly process of a stator strand, a pair of hairpin probes from CHA and an AS1411 aptamer. Benefiting from the spatial-confinement effect, a pair of hairpin probes with high collision frequency was rapidly and efficiently assembled using miRNA-21 as the catalyst on a stator strand in every nanomachine. Compared with the free-CHA nanomachine, the LCHA nanomachine shortened the reaction time by 4.5-fold for reaching a plateau and significant improved the sensitivity by 7.6-fold for miRNA-21 detection in vitro. Importantly, the nanomachine was successfully applied for miRNA-21 imaging in living cells. With the assistance of an AS1411 aptamer and stator strand, the pair of hairpin probes with the ratio of 1 : 1 synchronously transported into a co-site of the cytoplasm, which ensures efficient imaging of trace miRNA-21. The signal output of the ratio of 6-carboxy-fluorescein (FAM) to tetramethyl rhodamine (TAMRA) intensities guaranteed reliability through avoiding the interference from different amounts of the nanomachine that enters into cells. Notably, the nanomachine can distinguish the miRNA-21 expression level in different kinds of cancer cells. By virtue of the advantages of simplicity, efficiency and reliability, the proposed strategy provides a powerful method for exploring the functions of miRNA and diagnosis of disease.
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Affiliation(s)
- Juan Wu
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, Shaanxi, P.R. China.
| | - Yonghui Tian
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, Shaanxi, P.R. China.
| | - Lu He
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, Shaanxi, P.R. China.
| | - Jing Zhang
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, Shaanxi, P.R. China.
| | - Zhijun Huang
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, Shaanxi, P.R. China.
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, Shaanxi, P.R. China.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, Shaanxi, P.R. China.
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13
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Pan X, Geng X, Liu Y, Yu M, Mishra MK, Xu X, Ding X, Liu P, Liang M. Transfer RNA Fragments in the Kidney in Hypertension. Hypertension 2021; 77:1627-1637. [PMID: 33775129 DOI: 10.1161/hypertensionaha.121.16994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Xiaoqing Pan
- Department of Mathematics, Shanghai Normal University, China (X.P.).,Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Xuemei Geng
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.).,Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Mengqian Yu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China (M.Y., P.L.)
| | - Manoj K Mishra
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Xialian Xu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.).,Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China (M.Y., P.L.)
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
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14
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Choi EJ, Wu W, Zhang K, Lee I, Kim IH, Lee YS, Bao X. ELAC2, an Enzyme for tRNA Maturation, Plays a Role in the Cleavage of a Mature tRNA to Produce a tRNA-Derived RNA Fragment During Respiratory Syncytial Virus Infection. Front Mol Biosci 2021; 7:609732. [PMID: 33604354 PMCID: PMC7884774 DOI: 10.3389/fmolb.2020.609732] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/21/2020] [Indexed: 11/24/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection in young children. However, effective treatment against RSV is unavailable. tRNA-derived RNA fragments (tRFs) are a recently discovered family of non-coding RNAs. We made an early observation that RSV infection causes significant induction of tRFs, which are mainly derived from the 5’-end of mature tRNAs (tRF5). However, their functions and biogenesis mechanism are not fully understood. Herein, we identified an enzyme responsible for the induction of a functional tRF5 derived from tRNA-Gln-CTG (tRF5-GlnCTG). We found that tRF5-GlnCTG promotes RSV replication and its induction, assessed by Northern blot and a new qRT-PCR-based method, is regulated by ribonuclease ELAC2. ELAC2-mediated tRF5 induction has never been reported. We also found that ELAC2 is associated with RSV N and NS1 proteins. Given the fact that tRF5-GlnCTG plays a role in RSV replication, the identification of ELAC2 being responsible for tRF5-GlnCTG induction could provide new insights into therapeutic strategy development against RSV infection.
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Affiliation(s)
- Eun-Jin Choi
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Wenzhe Wu
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Ke Zhang
- Department of Chemistry, The University of Houston Clear Lake, Clear Lake, TX, United States
| | - Inhan Lee
- miRcore, Ann Arbor, MI, United States
| | - In-Hoo Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Xiaoyong Bao
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States.,Sealy Center for Molecular Medicine, The University of Texas Medical Branch, Galveston, TX, United States.,The Institute of Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States.,The Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, United States
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15
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Wang B, Kostarelos K, Nelson BJ, Zhang L. Trends in Micro-/Nanorobotics: Materials Development, Actuation, Localization, and System Integration for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2002047. [PMID: 33617105 DOI: 10.1002/adma.202002047] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/24/2020] [Indexed: 05/23/2023]
Abstract
Micro-/nanorobots (m-bots) have attracted significant interest due to their suitability for applications in biomedical engineering and environmental remediation. Particularly, their applications in in vivo diagnosis and intervention have been the focus of extensive research in recent years with various clinical imaging techniques being applied for localization and tracking. The successful integration of well-designed m-bots with surface functionalization, remote actuation systems, and imaging techniques becomes the crucial step toward biomedical applications, especially for the in vivo uses. This review thus addresses four different aspects of biomedical m-bots: design/fabrication, functionalization, actuation, and localization. The biomedical applications of the m-bots in diagnosis, sensing, microsurgery, targeted drug/cell delivery, thrombus ablation, and wound healing are reviewed from these viewpoints. The developed biomedical m-bot systems are comprehensively compared and evaluated based on their characteristics. The current challenges and the directions of future research in this field are summarized.
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Affiliation(s)
- Ben Wang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin N.T., Hong Kong, China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Kostas Kostarelos
- Nanomedicine Lab, Faculty of Biology, Medicine & Health, The University of Manchester, AV Hill Building, Manchester, M13 9PT, UK
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), Campus UAB, Bellaterra, Barcelona, Spain
| | - Bradley J Nelson
- Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, Tannenstrasse 3, Zurich, CH-8092, Switzerland
| | - Li Zhang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin N.T., Hong Kong, China
- CUHK T Stone Robotics Institute, The Chinese University of Hong Kong, Shatin N.T., Hong Kong, China
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16
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Magee R, Rigoutsos I. On the expanding roles of tRNA fragments in modulating cell behavior. Nucleic Acids Res 2020; 48:9433-9448. [PMID: 32890397 PMCID: PMC7515703 DOI: 10.1093/nar/gkaa657] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
The fragments that derive from transfer RNAs (tRNAs) are an emerging category of regulatory RNAs. Known as tRFs, these fragments were reported for the first time only a decade ago, making them a relatively recent addition to the ever-expanding pantheon of non-coding RNAs. tRFs are short, 16-35 nucleotides (nts) in length, and produced through cleavage of mature and precursor tRNAs at various positions. Both cleavage positions and relative tRF abundance depend strongly on context, including the tissue type, tissue state, and disease, as well as the sex, population of origin, and race/ethnicity of an individual. These dependencies increase the urgency to understand the regulatory roles of tRFs. Such efforts are gaining momentum, and comprise experimental and computational approaches. System-level studies across many tissues and thousands of samples have produced strong evidence that tRFs have important and multi-faceted roles. Here, we review the relevant literature on tRF biology in higher organisms, single cell eukaryotes, and prokaryotes.
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Affiliation(s)
- Rogan Magee
- Computational Medicine Center, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Isidore Rigoutsos
- To whom correspondence should be addressed. Tel: +1 215 503 4219; Fax: +1 215 503 0466;
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17
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Cui Y, Fan S, Yuan Z, Song M, Hu J, Qian D, Zhen D, Li J, Zhu B. Ultrasensitive electrochemical assay for microRNA-21 based on CRISPR/Cas13a-assisted catalytic hairpin assembly. Talanta 2020; 224:121878. [PMID: 33379087 DOI: 10.1016/j.talanta.2020.121878] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are related to many biological processes and regarded as biomarkers of disease. Rapid, sensitive, and specific methods for miRNA assay are very important for early disease diagnostic and therapy. In the present work, an ultrasensitive electrochemical biosensing platform has been developed for miRNA-21 assay by combining CRISPR-Cas13a system and catalytic hairpin assembly (CHA). In the presence of miRNA-21, it would hybridize with the spacer region of Cas13a/crRNA duplex to activate the cleavage activity of CRISPR-Cas13a system, leading to the release of initiator of CHA to generate amplified electrochemical signals. Base on the CRISPR-Cas13a-mediated cascade signal amplification strategy, the developed electrochemical biosensing platform exhibited high sensitivity with a low detection limit of 2.6 fM (S/N = 3), indicating that the platform has great potential for application in early clinical diagnostic.
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Affiliation(s)
- Ying Cui
- Hunan Key Laboratory of Two-Dimensional Materials, Advanced Catalytic Engineering Research Center of the Ministry of Education, and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China; College of Chemistry and Materials Science, Hengyang Normal University, Hengyang, 421001, China
| | - Shanji Fan
- Department of Thyroid Breast Surgery, The First Affiliated Hospital of University of South China, Hengyang, 421001, China
| | - Ze Yuan
- Hunan Key Laboratory of Two-Dimensional Materials, Advanced Catalytic Engineering Research Center of the Ministry of Education, and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Minghui Song
- Hunan Key Laboratory of Two-Dimensional Materials, Advanced Catalytic Engineering Research Center of the Ministry of Education, and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jiawen Hu
- Hunan Key Laboratory of Two-Dimensional Materials, Advanced Catalytic Engineering Research Center of the Ministry of Education, and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Dong Qian
- Hunan Provincial Key Laboratory of Chemical Power Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China
| | - Deshuai Zhen
- Hunan Key Laboratory of Two-Dimensional Materials, Advanced Catalytic Engineering Research Center of the Ministry of Education, and College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Junhua Li
- College of Chemistry and Materials Science, Hengyang Normal University, Hengyang, 421001, China.
| | - Baode Zhu
- College of Chemistry Biology & and Environmental Engineering, Xiangnan University, Chenzhou, 423043, China.
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18
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Sun X, Yang J, Yu M, Yao D, Zhou L, Li X, Qiu Q, Lin W, Lu B, Chen E, Wang P, Chen W, Tao S, Xu H, Williams A, Liu Y, Pan X, Cowley AW, Lu W, Liang M, Liu P, Lu Y. Global identification and characterization of tRNA-derived RNA fragment landscapes across human cancers. NAR Cancer 2020; 2:zcaa031. [PMID: 34316691 PMCID: PMC8210304 DOI: 10.1093/narcan/zcaa031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/24/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Transfer RNA-derived RNA fragments (tRFs) are a class of small non-coding RNAs that are abundant in many organisms, but their role in cancer has not been fully explored. Here, we report a functional genomic landscape of tRFs in 8118 specimens across 15 cancer types from The Cancer Genome Atlas. These tRFs exhibited characteristics of widespread expression, high sequence conservation, cytoplasmic localization, specific patterns of tRNA cleavage and conserved cleavage in tissues. A cross-tumor analysis revealed significant commonality among tRF expression subtypes from distinct tissues of origins, characterized by upregulation of a group of tRFs with similar size and activation of cancer-associated signaling. One of the largest superclusters was composed of 22 nt 3'-tRFs upregulated in 13 cancer types, all of which share the activation of Ras/MAPK, RTK and TSC/mTOR signaling. tRF-based subgrouping provided clinically relevant stratifications and significantly improved outcome prediction by incorporating clinical variables. Additionally, we discovered 11 cancer driver tRFs using an effective approach for accurately exploring cross-tumor and platform trends. As a proof of concept, we performed comprehensive functional assays on a non-microRNA driver tRF, 5'-IleAAT-8-1-L20, and validated its oncogenic roles in lung cancer in vitro and in vivo. Our study also provides a valuable tRF resource for identifying diagnostic and prognostic biomarkers, developing cancer therapy and studying cancer pathogenesis.
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Affiliation(s)
- Xiwei Sun
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Juze Yang
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Mengqian Yu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
| | - Dongxia Yao
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
| | - Liyuan Zhou
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Xufan Li
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Qiongzi Qiu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
| | - Weiqiang Lin
- The First Affiliated Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Bingjian Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
| | - Enguo Chen
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Ping Wang
- The First Affiliated Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Wantao Chen
- Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200011, China
| | - Sifeng Tao
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Haiming Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Anna Williams
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Xiaoqing Pan
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Allen W Cowley
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Weiguo Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Pengyuan Liu
- Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, China
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19
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Navarro-Martín L, Martyniuk CJ, Mennigen JA. Comparative epigenetics in animal physiology: An emerging frontier. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100745. [PMID: 33126028 DOI: 10.1016/j.cbd.2020.100745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 12/19/2022]
Abstract
The unprecedented access to annotated genomes now facilitates the investigation of the molecular basis of epigenetic phenomena in phenotypically diverse animals. In this critical review, we describe the roles of molecular epigenetic mechanisms in regulating mitotically and meiotically stable spatiotemporal gene expression, phenomena that provide the molecular foundation for the intra-, inter-, and trans-generational emergence of physiological phenotypes. By focusing principally on emerging comparative epigenetic roles of DNA-level and transcriptome-level epigenetic mark dynamics in the emergence of phenotypes, we highlight the relationship between evolutionary conservation and innovation of specific epigenetic pathways, and their interplay as a priority for future study. This comparative approach is expected to significantly advance our understanding of epigenetic phenomena, as animals show a diverse array of strategies to epigenetically modify physiological responses. Additionally, we review recent technological advances in the field of molecular epigenetics (single-cell epigenomics and transcriptomics and editing of epigenetic marks) in order to (1) investigate environmental and endogenous factor dependent epigenetic mark dynamics in an integrative manner; (2) functionally test the contribution of specific epigenetic marks for animal phenotypes via genome and transcript-editing tools. Finally, we describe advantages and limitations of emerging animal models, which under the Krogh principle, may be particularly useful in the advancement of comparative epigenomics and its potential translational applications in animal science, ecotoxicology, ecophysiology, climate change science and wild-life conservation, as well as organismal health.
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Affiliation(s)
- Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON K1N6N5, Canada
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20
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Yu M, Lu B, Zhang J, Ding J, Liu P, Lu Y. tRNA-derived RNA fragments in cancer: current status and future perspectives. J Hematol Oncol 2020; 13:121. [PMID: 32887641 PMCID: PMC7487644 DOI: 10.1186/s13045-020-00955-6] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/24/2020] [Indexed: 01/02/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have been the focus of many studies over the last few decades, and their fundamental roles in human diseases have been well established. Transfer RNAs (tRNAs) are housekeeping ncRNAs that deliver amino acids to ribosomes during protein biosynthesis. tRNA fragments (tRFs) are a novel class of small ncRNAs produced through enzymatic cleavage of tRNAs and have been shown to play key regulatory roles similar to microRNAs. Development and application of high-throughput sequencing technologies has provided accumulating evidence of dysregulated tRFs in cancer. Aberrant expression of tRFs has been found to participate in cell proliferation, invasive metastasis, and progression in several human malignancies. These newly identified functional tRFs also have great potential as new biomarkers and therapeutic targets for cancer treatment. In this review, we focus on the major biological functions of tRFs including RNA silencing, translation regulation, and epigenetic regulation; summarize recent research on the roles of tRFs in different types of cancer; and discuss the potential of using tRFs as clinical biomarkers for cancer diagnosis and prognosis and as therapeutic targets for cancer treatment.
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Affiliation(s)
- Mengqian Yu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Bingjian Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Jisong Zhang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Jinwang Ding
- Department of Head and Neck Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, China
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China.,Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.
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21
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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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22
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Point-of-care testing of MicroRNA based on personal glucose meter and dual signal amplification to evaluate drug-induced kidney injury. Anal Chim Acta 2020; 1112:72-79. [DOI: 10.1016/j.aca.2020.03.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022]
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23
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Cherlin T, Magee R, Jing Y, Pliatsika V, Loher P, Rigoutsos I. Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner. BMC Biol 2020; 18:38. [PMID: 32279660 PMCID: PMC7153239 DOI: 10.1186/s12915-020-0763-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/03/2020] [Indexed: 01/02/2023] Open
Abstract
Background The advent of next generation sequencing (NGS) has allowed the discovery of short and long non-coding RNAs (ncRNAs) in an unbiased manner using reverse genetics approaches, enabling the discovery of multiple categories of ncRNAs and characterization of the way their expression is regulated. We previously showed that the identities and abundances of microRNA isoforms (isomiRs) and transfer RNA-derived fragments (tRFs) are tightly regulated, and that they depend on a person’s sex and population origin, as well as on tissue type, tissue state, and disease type. Here, we characterize the regulation and distribution of fragments derived from ribosomal RNAs (rRNAs). rRNAs form a group that includes four (5S, 5.8S, 18S, 28S) rRNAs encoded by the human nuclear genome and two (12S, 16S) by the mitochondrial genome. rRNAs constitute the most abundant RNA type in eukaryotic cells. Results We analyzed rRNA-derived fragments (rRFs) across 434 transcriptomic datasets obtained from lymphoblastoid cell lines (LCLs) derived from healthy participants of the 1000 Genomes Project. The 434 datasets represent five human populations and both sexes. We examined each of the six rRNAs and their respective rRFs, and did so separately for each population and sex. Our analysis shows that all six rRNAs produce rRFs with unique identities, normalized abundances, and lengths. The rRFs arise from the 5′-end (5′-rRFs), the interior (i-rRFs), and the 3′-end (3′-rRFs) or straddle the 5′ or 3′ terminus of the parental rRNA (x-rRFs). Notably, a large number of rRFs are produced in a population-specific or sex-specific manner. Preliminary evidence suggests that rRF production is also tissue-dependent. Of note, we find that rRF production is not affected by the identity of the processing laboratory or the library preparation kit. Conclusions Our findings suggest that rRFs are produced in a regimented manner by currently unknown processes that are influenced by both ubiquitous as well as population-specific and sex-specific factors. The properties of rRFs mirror the previously reported properties of isomiRs and tRFs and have implications for the study of homeostasis and disease.
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Affiliation(s)
- Tess Cherlin
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Rogan Magee
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Yi Jing
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Venetia Pliatsika
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Phillipe Loher
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
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24
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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25
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Huang X, Xu Z, Liu JH, Yu BY, Tian J. Dual signal amplification for microRNA-21 detection based on duplex-specific nuclease and invertase. RSC Adv 2020; 10:11257-11262. [PMID: 35495318 PMCID: PMC9050473 DOI: 10.1039/c9ra10657j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/02/2020] [Indexed: 01/09/2023] Open
Abstract
MicroRNA-21 (miRNA-21) is a significant biomarker which is closely related to some kinds of diseases, such as cancer, cardiovascular disease and kidney disease. Therefore, the detection of miRNA-21 is of great importance and can provide essential information for disease diagnosis. In this study, we report a facile, sensitive assay for miRNA-21 detection using personal glucose meters (PGM). Biotinylated DNA strand linked invertase (Inv) is conjugated on the surface of streptavidin-coated magnetic beads (MBs) to form a MBs-DNA-Inv complex. Target miRNA-21 in the detection system is captured by the MBs-DNA-Inv probe through DNA/RNA hybridization. The duplex-specific nuclease (DSN) enzyme specifically cleaves the DNA to recycle the target miRNA and release invertase, thereby triggering the dual signal amplification and ensuring high sensitivity. Besides, we establish a linear relationship between PGM and different concentrations of miRNA-21 in the range of 10 to 200 pM. The limit of detection is 1.8 pM, which is more sensitive than some of the previous reports. In addition, the biosensor exhibits excellent sequence selectivity and single-base mutation can be discriminated. Moreover, the expression of miRNA-21 is confirmed in urine from mice by our method, which is in good accordance with the qRT-PCR result. Therefore, a dependable, low-cost strategy for the detection of miRNA has been established and it meets the latest analytical demands for miRNA determination that is suitable for the public.
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Affiliation(s)
- Xitong Huang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University Nanjing 211198 P. R. China
| | - Zhiming Xu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University Nanjing 211198 P. R. China
| | - Ji-Hua Liu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University Nanjing 211198 P. R. China
| | - Bo-Yang Yu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University Nanjing 211198 P. R. China
| | - Jiangwei Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, School of Traditional Chinese Pharmacy, China Pharmaceutical University Nanjing 211198 P. R. China
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26
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Wang J, Bing T, Zhang N, Liu X, Shangguan D. FnCas12a/crRNA assisted dumbbell-PCR detection of IsomiRs with terminal and inner sequence variants. Chem Commun (Camb) 2020; 56:10038-10041. [DOI: 10.1039/d0cc04348f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A new FnCas12a/crRNA assisted Dumbbell-PCR (Cas-Db-PCR) method is developed for the detection of isomiR heterogeneity in length and/or sequence variants with high specificity and sensitivity.
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Affiliation(s)
- Junyan Wang
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS, Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS, Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS, Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS, Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- CAS, Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
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27
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van der Kwast RVCT, Woudenberg T, Quax PHA, Nossent AY. MicroRNA-411 and Its 5'-IsomiR Have Distinct Targets and Functions and Are Differentially Regulated in the Vasculature under Ischemia. Mol Ther 2019; 28:157-170. [PMID: 31636041 DOI: 10.1016/j.ymthe.2019.10.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/24/2019] [Accepted: 10/02/2019] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are posttranscriptional regulators of gene expression. As microRNAs can target many genes simultaneously, microRNAs can regulate complex multifactorial processes, including post-ischemic neovascularization, a major recovery pathway in cardiovascular disease. MicroRNAs select their target mRNAs via full complementary binding with their seed sequence, i.e., nucleotides 2-8 from the 5' end of a microRNA. The exact sequence of a mature microRNA, and thus of its 5' and 3' ends, is determined by two sequential cleavage steps of microRNA precursors, Drosha/DGCR8 and Dicer. When these cleavage steps result in nucleotide switches at the 5' end, forming a so-called 5'-isomiR, this results in a shift in the mature microRNA's seed sequence. The role of 5'-isomiRs in cardiovascular diseases is still unknown. Here, we characterize the expression and function of the 5'-isomiR of miR-411 (ISO-miR-411). ISO-miR-411 is abundantly expressed in human primary vascular cells. ISO-miR-411 has a different "targetome" from WT-miR-411, with only minor overlap. The ISO-miR-411/WT-miR-411 ratio is downregulated under acute ischemia, both in cells and a murine ischemia model, but is upregulated instead in chronically ischemic human blood vessels. ISO-miR-411 negatively influences vascular cell migration, whereas WT-miR-411 does not. Our data demonstrate that isomiR formation is a functional pathway that is actively regulated during ischemia.
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Affiliation(s)
- Reginald V C T van der Kwast
- Department of Surgery, Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Tamar Woudenberg
- Department of Surgery, Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Paul H A Quax
- Department of Surgery, Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - A Yaël Nossent
- Department of Surgery, Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden 2333ZA, the Netherlands; Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria; Department of Internal Medicine II, Medical University of Vienna, Vienna 1090, Austria.
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28
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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: 67] [Impact Index Per Article: 13.4] [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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29
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Zhang D, Lee H, Wang X, Groot M, Sharma L, Dela Cruz CS, Jin Y. A potential role of microvesicle-containing miR-223/142 in lung inflammation. Thorax 2019; 74:865-874. [PMID: 31331947 PMCID: PMC7036165 DOI: 10.1136/thoraxjnl-2018-212994] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND Uncontrolled lung inflammation is one of the prominent features in the pathogenesis of lung infection- associated acute lung injury (ALI). Microvesicles (MVs) are extracellular nanovesicles that are generated via direct membrane budding. METHODS Bronchoalveolar lavage fluid (BALF) samples were collected from mice with or without intratracheal lipopolysaccharide (LPS) instillation. BALF MVs were characterised and MV-containing microRNA (miRNA) profiles were assessed and confirmed. Secretion and function of MV-containing miR-223/142 (MV-miR-223/142) were analysed in vivo. RESULTS In BALF, MVs are mainly derived from macrophages in response to LPS. After intratracheal instillation (i.t.) of LPS or Klebsiella pneumoniae, MV-containing miR-223/142 are dramatically induced in both BALF and serum. Mechanistically, miRNA 3' end uridylation mediates the packing of miR-223/142 into MVs. To investigate the functional role of MV-miR-223/142, we loaded miR-223/142 mimics into unstimulated MVs and delivered them into the murine lungs via i.t. The miR-223/142 mimics-enriched MVs selectively targeted lung macrophages and suppressed the inflammatory lung responses that were triggered by LPS or K. pneumoniae. Mechanistically, miR-223 and miR-142 synergistically suppress Nlrp3 inflammasome activation in macrophages via inhibition of Nlrp3 and Asc, respectively. CONCLUSIONS In the pathogenesis of lung macrophage-mediated inflammatory responses, MV-miR-223/142 secretion is robustly enhanced and detectable in BALF and serum. Furthermore, restoration of intracellular miR-223/142 via vesicle-mediated delivery suppresses macrophage activation and lung inflammation via inhibition of Nlrp3 inflammasome activation.
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Affiliation(s)
- Duo Zhang
- Department of Medicine, Boston University Medical Campus, Boston, Massachusetts, USA
| | - Heedoo Lee
- Department of Medicine, Boston University Medical Campus, Boston, Massachusetts, USA
| | - Xiaoyun Wang
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Michael Groot
- Department of Medicine, Boston University Medical Campus, Boston, Massachusetts, USA
| | - Lokesh Sharma
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Charles S Dela Cruz
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yang Jin
- Department of Medicine, Boston University Medical Campus, Boston, Massachusetts, USA
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30
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Rigoutsos I, Londin E, Kirino Y. Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities. Curr Opin Biotechnol 2019; 58:202-210. [PMID: 31323485 DOI: 10.1016/j.copbio.2019.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/09/2019] [Accepted: 05/27/2019] [Indexed: 01/03/2023]
Abstract
We herein provide a brief review of the trajectory that the field of short RNA research followed in the last 25 years. We place emphasis on the unexpected discoveries and the ramifications of these discoveries for the field, as well as offer some thoughts about what the next 25 years may bring. Arguably, the uncovered dependence of different types of short RNAs on individual attributes such as a person's sex, population origin, race, and on tissue type, tissue state, and disease was most unexpected. This dependence has important ramifications in that it will provide a boost to our understanding of the molecular mechanisms of health disparities as well as pave the way for novel approaches to designing improved and personalized diagnostics and therapeutics.
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Affiliation(s)
- Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
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31
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Wright C, Rajpurohit A, Burke EE, Williams C, Collado-Torres L, Kimos M, Brandon NJ, Cross AJ, Jaffe AE, Weinberger DR, Shin JH. Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods. BMC Genomics 2019; 20:513. [PMID: 31226924 PMCID: PMC6588940 DOI: 10.1186/s12864-019-5870-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapter ligation bias with limited evaluation of reverse transcription bias or amplification bias. Furthermore, evaluations of the quantification of isomiRs (miRNA isoforms) or the influence of starting amount on performance have been very limited. No study had yet evaluated the quantification of isomiRs of altered length or compared the consistency of results derived from multiple moderate starting inputs. We therefore evaluated quantifications of miRNA and isomiRs using four library preparation kits, with various starting amounts, as well as quantifications following removal of duplicate reads using unique molecular identifiers (UMIs) to mitigate reverse transcription and amplification biases. RESULTS All methods resulted in false isomiR detection; however, the adapter-free method tested was especially prone to false isomiR detection. We demonstrate that using UMIs improves accuracy and we provide a guide for input amounts to improve consistency. CONCLUSIONS Our data show differences and limitations of current methods, thus raising concerns about the validity of quantification of miRNA and isomiRs across studies. We advocate for the use of UMIs to improve accuracy and reliability of miRNA quantifications.
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Affiliation(s)
- Carrie Wright
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.,AstraZeneca Postdoc Program, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Anandita Rajpurohit
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Emily E Burke
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Courtney Williams
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Martha Kimos
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Nicholas J Brandon
- AstraZeneca Neuroscience, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Alan J Cross
- AstraZeneca Neuroscience, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA. .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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32
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Cheng K, An R, Cui Y, Zhang Y, Han X, Sui Z, Chen H, Liang X, Komiyama M. RNA ligation of very small pseudo nick structures by T4 RNA ligase 2, leading to efficient production of versatile RNA rings. RSC Adv 2019; 9:8620-8627. [PMID: 35518706 PMCID: PMC9061723 DOI: 10.1039/c9ra01513b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 01/07/2023] Open
Abstract
T4 RNA ligase 2 catalyses two types of reactions: (i) sealing of a nick structure in double-stranded RNA and (ii) connection of two single-stranded RNA strands. In order to obtain comprehensive views on these two types of reactions and widen the application scope of this RNA ligase, we here systematically analysed the connection of single-stranded RNA strands having different secondary structures. It has been found that the ligation is enormously promoted when a stem of only 4-bp or longer is formed in the 3′-OH side of the joining site. Additional placement of a stem in the 5′-phosphate side further facilitates the ligation. In contrast, perturbation of the stem structures in RNA substrates suppresses the ligation. These results indicate that ligation of two single-stranded RNA strands by T4 RNA ligase 2 is greatly promoted by forming a “nick-like intermediate”. Even the unstable intermediate, formed only temporarily in the solution, is sufficiently effective. By designing the synthetic systems in terms of this finding, short single-stranded RNA rings of versatile sizes, which are otherwise hard to be obtained, are efficiently prepared in high selectivity and yield. T4 Rnl2 ligates ssRNA via nick-like structures, leading to efficient production of versatile RNA rings for various applications.![]()
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Affiliation(s)
- Kai Cheng
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Ran An
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
| | - Yixiao Cui
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Yaping Zhang
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Xutiange Han
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Zhe Sui
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Hui Chen
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Xingguo Liang
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
| | - Makoto Komiyama
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
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33
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Shigematsu M, Kawamura T, Kirino Y. Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome. Front Genet 2018; 9:562. [PMID: 30538719 PMCID: PMC6277466 DOI: 10.3389/fgene.2018.00562] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/06/2018] [Indexed: 01/03/2023] Open
Abstract
Cellular RNA molecules contain phosphate or hydroxyl ends. A 2′,3′-cyclic phosphate (cP) is one of the 3′-terminal forms of RNAs mainly generated from RNA cleavage by ribonucleases. Although transcriptome profiling using RNA-seq has become a ubiquitous tool in biological and medical research, cP-containing RNAs (cP-RNAs) form a hidden transcriptome layer, which is infrequently recognized and characterized, because standard RNA-seq is unable to capture them. Despite cP-RNAs’ invisibility in RNA-seq data, increasing evidence indicates that they are not accumulated simply as non-functional degradation products; rather, they have physiological roles in various biological processes, designating them as noteworthy functional molecules. This review summarizes our current knowledge of cP-RNA biogenesis pathways and their catalytic enzymatic activities, discusses how the cP-RNA generation affects biological processes, and explores future directions to further investigate cP-RNA biology.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
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34
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Li D, Wu Y, Gan C, Yuan R, Xiang Y. Bio-cleavable nanoprobes for target-triggered catalytic hairpin assembly amplification detection of microRNAs in live cancer cells. NANOSCALE 2018; 10:17623-17628. [PMID: 30204195 DOI: 10.1039/c8nr05229h] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The monitoring and imaging of intracellular microRNAs (miRNAs) with specific sequences plays a vital role in cell biology as it can potentially elucidate many cellular processes and diseases related to miRNAs in living cells with accurate information. However, the detection of trace amounts of under-expressed intracellular miRNAs in living cells represents one of the current major challenges. In an effort to address this issue, we describe the establishment of an in cell catalytic hairpin assembly (CHA) signal amplification strategy for imaging under-expressed intracellular miRNAs in this work. Gold nanoparticles functionalized with FAM- and TAMRA-labeled hairpins with disulfide bonds in the stems are readily delivered into cells via endocytosis. Glutathione with evaluated concentrations in cancer cells cleaves the disulfide bonds in the hairpins by reduction to release the hairpins, and the target miRNAs further trigger CHA between the two hairpins to form many DNA duplexes, which bring the FAM and TAMRA labels into close proximity to generate apparently enhanced fluorescence resonance energy transfer (FRET) for the sensitive monitoring of low amounts of under-expressed miRNAs in live cancer cells. Using CHA to amplify the signal output and FRET to reduce the background noise, a significantly enhanced signal-to-noise ratio, thereby high sensitivity, over conventional fluorescence imaging can be realized, making our method particularly suitable for monitoring low levels of intracellular species.
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Affiliation(s)
- Daxiu Li
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
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35
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Shigematsu M, Honda S, Kirino Y. Dumbbell-PCR for Discriminative Quantification of a Small RNA Variant. Methods Mol Biol 2018; 1680:65-73. [PMID: 29030841 DOI: 10.1007/978-1-4939-7339-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Cellular RNAs are often expressed as multiple isoforms of complex heterogeneity in both length and terminal sequences. IsomiRs, the isoforms of microRNAs, are such an example. Distinct quantification of each RNA variant is necessary to unravel the biogenesis mechanism and biological significance of heterogenetic RNA expression. Here we describe Dumbbell-PCR (Db-PCR), a TaqMan RT-PCR-based method that distinctively quantifies a specific small RNA variant with single-nucleotide resolution at terminal sequences. Db-PCR enables the quantitative analysis of RNA terminal heterogeneity without performing Next-Generation Sequencing.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, JAH Suite #M77, Philadelphia, PA, 19107, USA.
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36
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Gu Y, Zhang TT, Huang ZF, Hu SW, Zhao W, Xu JJ, Chen HY. An exploration of nucleic acid liquid biopsy using a glucose meter. Chem Sci 2018; 9:3517-3522. [PMID: 29780482 PMCID: PMC5934745 DOI: 10.1039/c8sc00627j] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/28/2018] [Indexed: 01/01/2023] Open
Abstract
The development of non-invasive techniques for the diagnosis of cancer, characterization of mutation and monitoring treatment response could greatly reduce the morbidity and mortality caused by cancer. Nevertheless, the extremely low amount of cell free nucleic acids makes liquid biopsy a very challenging task. Herein, taking advantage of the pocket size, reliable quantitative results and simple operation of the pocket-sized personal glucose meter (PGM), we report an approach of circulating microRNA-21 (miR-21) detection with high precision and low cost. Via target-induced release of invertase from the DNA-invertase conjugate, which could convert sucrose into glucose, the detection of miR-21 in serum was linked to PGM readings. Combining the DNAzyme feedback amplification (DFA) program and highly efficient enzymatic turnover, an ultralow detection limit of 7 × 10-16 M for miR-21 was achieved using a PGM as the reporter. The high sensitivity and selectivity of the proposed method meets the requirement of quantifying cell free nucleic acids in serum. In addition, this approach fills the shortage of quantitative RT-PCR and next-generation sequencing in quantifying miRNAs with a short length and greatly reduces the cost of detection. We believe that widely used personal diagnosis devices could hold an important place in the booming area of liquid biopsy.
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Affiliation(s)
- Yu Gu
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
| | - Ting-Ting Zhang
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
| | - Zhi-Feng Huang
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
| | - Shan-Wen Hu
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China . ;
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37
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Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap. Methods Mol Biol 2018; 1680:237-255. [PMID: 29030853 DOI: 10.1007/978-1-4939-7339-2_16] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
There is an increasing interest within the scientific community in identifying tRNA-derived fragments (tRFs) and elucidating the roles they play in the cell. Such endeavors can be greatly facilitated by mining the numerous datasets from many cellular contexts that exist publicly. However, the standard mapping tools cannot be used for the purpose. Several factors complicate this endeavor including: the presence of multiple identical or nearly identical isodecoders at various genomic locations; the presence of identical sequence segments that are shared by isodecoders of the same or even different anticodons; the existence of numerous partial tRNA sequences across the genome; the existence of hundreds of "lookalike" sequences that resemble true tRNAs; and others. This is generating a need for specialized tools that can mine deep sequencing data to identify and quantify tRFs. We discuss the various complicating factors and their ramifications, and how to use and run MINTmap, a tool that addresses these considerations.
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38
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Androvic P, Valihrach L, Elling J, Sjoback R, Kubista M. Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification. Nucleic Acids Res 2017; 45:e144. [PMID: 28911110 PMCID: PMC5587787 DOI: 10.1093/nar/gkx588] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/28/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs are a class of small non-coding RNAs that serve as important regulators of gene expression at the posttranscriptional level. They are stable in body fluids and pose great potential to serve as biomarkers. Here, we present a highly specific, sensitive and cost-effective system to quantify miRNA expression based on two-step RT-qPCR with SYBR-green detection chemistry called Two-tailed RT-qPCR. It takes advantage of novel, target-specific primers for reverse transcription composed of two hemiprobes complementary to two different parts of the targeted miRNA, connected by a hairpin structure. The introduction of a second probe ensures high sensitivity and enables discrimination of highly homologous miRNAs irrespectively of the position of the mismatched nucleotide. Two-tailed RT-qPCR has a dynamic range of seven logs and a sensitivity sufficient to detect down to ten target miRNA molecules. It is capable to capture the full isomiR repertoire, leading to accurate representation of the complete miRNA content in a sample. The reverse transcription step can be multiplexed and the miRNA profiles measured with Two-tailed RT-qPCR show excellent correlation with the industry standard TaqMan miRNA assays (r2 = 0.985). Moreover, Two-tailed RT-qPCR allows for rapid testing with a total analysis time of less than 2.5 hours.
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Affiliation(s)
- Peter Androvic
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic.,Laboratory of Growth Regulators, Faculty of Science, Palacky University, Olomouc 783 71, Czech Republic
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic
| | | | | | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic.,TATAA Biocenter AB, Gothenburg 411 03, Sweden
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39
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Shigematsu M, Honda S, Loher P, Telonis AG, Rigoutsos I, Kirino Y. YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs. Nucleic Acids Res 2017; 45:e70. [PMID: 28108659 PMCID: PMC5605243 DOI: 10.1093/nar/gkx005] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 01/03/2017] [Indexed: 11/18/2022] Open
Abstract
Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To unravel the emerging complexities of tRNA biology and molecular mechanisms underlying them, an efficient tRNA sequencing method is required. However, the rigid structure of tRNA has been presenting a challenge to the development of such methods. We report the development of Y-shaped Adapter-ligated MAture TRNA sequencing (YAMAT-seq), an efficient and convenient method for high-throughput sequencing of mature tRNAs. YAMAT-seq circumvents the issue of inefficient adapter ligation, a characteristic of conventional RNA sequencing methods for mature tRNAs, by employing the efficient and specific ligation of Y-shaped adapter to mature tRNAs using T4 RNA Ligase 2. Subsequent cDNA amplification and next-generation sequencing successfully yield numerous mature tRNA sequences. YAMAT-seq has high specificity for mature tRNAs and high sensitivity to detect most isoacceptors from minute amount of total RNA. Moreover, YAMAT-seq shows quantitative capability to estimate expression levels of mature tRNAs, and has high reproducibility and broad applicability for various cell lines. YAMAT-seq thus provides high-throughput technique for identifying tRNA profiles and their regulations in various transcriptomes, which could play important regulatory roles in translation and other biological processes.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
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40
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Abstract
We sought to determine whether commercial quantitative polymerase chain reaction (qPCR) methods are capable of distinguishing isomiRs: variants of mature microRNAs (miRNAs) with sequence endpoint differences. We used two commercially available miRNA qPCR methods to quantify miR-21-5p in both synthetic and real cell contexts. We find that although these miRNA qPCR methods possess high sensitivity for specific sequences, they also pick up background signals from closely related isomiRs, which influences the reliable quantification of individual isomiRs. We conclude that these methods do not possess the requisite specificity for reliable isomiR quantification.
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41
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Shigematsu M, Kirino Y. 5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves. RNA (NEW YORK, N.Y.) 2017; 23:161-168. [PMID: 27879434 PMCID: PMC5238791 DOI: 10.1261/rna.058024.116] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
Transfer RNAs (tRNAs) are fundamental adapter components of translational machinery. tRNAs can further serve as a source of tRNA-derived noncoding RNAs that play important roles in various biological processes beyond translation. Among all species of tRNAs, tRNAHisGUG has been known to uniquely contain an additional guanosine residue at the -1 position (G-1) of its 5'-end. To analyze this -1 nucleotide in detail, we developed a TaqMan qRT-PCR method that can distinctively quantify human mature cytoplasmic tRNAHisGUG containing G-1, U-1, A-1, or C-1 or lacking the -1 nucleotide (starting from G1). Application of this method to the mature tRNA fraction of BT-474 breast cancer cells revealed the presence of tRNAHisGUG containing U-1 as well as the one containing G-1 Moreover, tRNA lacking the -1 nucleotide was also detected, thus indicating the heterogeneous expression of 5'-tRNAHisGUG variants. A sequence library of sex hormone-induced 5'-tRNA halves (5'-SHOT-RNAs), identified via cP-RNA-seq of a BT-474 small RNA fraction, also demonstrated the expression of 5'-tRNAHisGUG halves containing G-1, U-1, or G1 as 5'-terminal nucleotides. Although the detected 5'-nucleotide species were identical, the relative abundances differed widely between mature tRNA and 5'-half from the same BT-474 cells. The majority of mature tRNAs contained the -1 nucleotide, whereas the majority of 5'-halves lacked this nucleotide, which was biochemically confirmed using a primer extension assay. These results reveal the novel identities of tRNAHisGUG molecules and provide insights into tRNAHisGUG maturation and the regulation of tRNA half production.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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42
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Li CY, Cao D, Song CY, Xu CM, Ma XY, Zhang ZL, Pang DW, Tang HW. Integrating optical tweezers with up-converting luminescence: a non-amplification analytical platform for quantitative detection of microRNA-21 sequences. Chem Commun (Camb) 2017; 53:4092-4095. [DOI: 10.1039/c7cc01133d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We report a single-microsphere based imaging assay for detecting microRNA-21 sequences with a detection limit of 12 fM.
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Affiliation(s)
- Cheng-Yu Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
- P. R. China
| | - Di Cao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
- P. R. China
| | - Chong-Yang Song
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
- P. R. China
| | - Chun-Miao Xu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
- P. R. China
| | - Xu-Yan Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
- P. R. China
| | - Zhi-Ling Zhang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
- P. R. China
| | - Dai-Wen Pang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
- P. R. China
| | - Hong-Wu Tang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
- P. R. China
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43
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Tomassi AH, Gagliardi D, Cambiagno DA, Manavella PA. Nonradioactive Detection of Small RNAs Using Digoxigenin-Labeled Probes. Methods Mol Biol 2017; 1640:199-210. [PMID: 28608344 DOI: 10.1007/978-1-4939-7165-7_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Small RNAs have been traditionally detected and quantified using small RNA blots, a modified Northern blot technique. The small RNAs are size-fractionated from the rest of the cellular RNA molecules by polyacrylamide gel electrophoresis and transferred by blotting onto a positively charged membrane. A radiolabeled probe was then traditionally used to detect a specific small RNA in the cellular pool. Small RNA blotting is a relatively simple, inexpensive approach to visualize small RNAs without artifacts. However, the radioactive labeling of the probe is sometimes an impediment, especially due to the requirement of specialized facilities. Here we describe a sensitive and simple method to detect and quantify small RNAs using digoxigenin-based nonradioactive RNA blots.
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Affiliation(s)
- Ariel H Tomassi
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET-FBCB), Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Delfina Gagliardi
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET-FBCB), Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET-FBCB), Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET-FBCB), Paraje El Pozo, 3000, Santa Fe, Argentina.
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44
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Lu W, Chen Y, Liu Z, Tang W, Feng Q, Sun J, Jiang X. Quantitative Detection of MicroRNA in One Step via Next Generation Magnetic Relaxation Switch Sensing. ACS NANO 2016; 10:6685-92. [PMID: 27348259 DOI: 10.1021/acsnano.6b01903] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
One-step, quantitative and rapid detection of microRNA (miRNA) in tumor cells or tissues can provide critical information for clinical diagnosis and cancer treatment. In this work, we develop a magnetic relaxation switch sensing (MRS)-based miRNA sensor using magnetic microparticle (1 μm in diameter, MM1000)-DNA probe-magnetic nanoparticle (30 nm in diameter, MN30) conjugates (MM1000-DNA-MN30). In the presence of target miRNA, DSN enzyme selectively cleaves the DNA tether after miRNA/DNA hybridization to release MN30 and leaves the miRNA intact to lead to the declustering of more MN30 than before. In contrast to conventional MRS by measuring the change of transverse relaxation time (ΔT2) induced by the aggregation or dissociation of magnetic particles in the presence of target, we use the cleaved MN30 from conjugates as the direct readout of ΔT2, which is more sensitive and stable. This MRS-based assay allows for one-step detection of 5 fM of miR-21 in urine samples, quantification of miR-21 from 100 cancer cells, and differentiation of the expression of miR-21 in tumor and surrounding tissues. The merits of this assay, rapidity, ability for quantitation, high sensitivity, and one-step operation, ensure a promising future in diagnostic technology.
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Affiliation(s)
- Wenjing Lu
- Beijing Engineering Research Center for BioNanotechnology & CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology , Beijing 100190, China
| | - Yiping Chen
- Beijing Engineering Research Center for BioNanotechnology & CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology , Beijing 100190, China
| | - Zhong Liu
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences (CAMS)/Peking Union Medical College (PUMC) , Beijing 100730, China
| | - Wenbo Tang
- The Department of Hepatopancreaticobiliary Surgical Oncology, Chinese PLA General Hospital , Beijing 100853, China
| | - Qiang Feng
- Beijing Engineering Research Center for BioNanotechnology & CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology , Beijing 100190, China
| | - Jiashu Sun
- Beijing Engineering Research Center for BioNanotechnology & CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology , Beijing 100190, China
| | - Xingyu Jiang
- Beijing Engineering Research Center for BioNanotechnology & CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology , Beijing 100190, China
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45
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Telonis AG, Loher P, Honda S, Jing Y, Palazzo J, Kirino Y, Rigoutsos I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget 2016; 6:24797-822. [PMID: 26325506 PMCID: PMC4694795 DOI: 10.18632/oncotarget.4695] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/20/2015] [Indexed: 12/21/2022] Open
Abstract
We analyzed transcriptomic data from 452 healthy men and women representing five different human populations and two races, and, 311 breast cancer samples from The Cancer Genome Atlas. Our studies revealed numerous constitutive, distinct fragments with overlapping sequences and quantized lengths that persist across dozens of individuals and arise from the genomic loci of all nuclear and mitochondrial human transfer RNAs (tRNAs). Surprisingly, we discovered that the tRNA fragments' length, starting and ending points, and relative abundance depend on gender, population, race and also on amino acid identity, anticodon, genomic locus, tissue, disease, and disease subtype. Moreover, the length distribution of mitochondrially-encoded tRNAs differs from that of nuclearly-encoded tRNAs, and the specifics of these distributions depend on tissue. Notably, tRNA fragments from the same anticodon do not have correlated abundances. We also report on a novel category of tRNA fragments that significantly contribute to the differences we observe across tissues, genders, populations, and races: these fragments, referred to as i-tRFs, are abundant in human tissues, wholly internal to the respective mature tRNA, and can straddle the anticodon. HITS-CLIP data analysis revealed that tRNA fragments are loaded on Argonaute in a cell-dependent manner, suggesting cell-dependent functional roles through the RNA interference pathway. We validated experimentally two i-tRF molecules: the first was found in 21 of 22 tested breast tumor and adjacent normal samples and was differentially abundant between health and disease whereas the second was found in all eight tested breast cancer cell lines.
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Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Yi Jing
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Juan Palazzo
- Department of Pathology Anatomy and Cell Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
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46
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Koppers-Lalic D, Hackenberg M, de Menezes R, Misovic B, Wachalska M, Geldof A, Zini N, de Reijke T, Wurdinger T, Vis A, van Moorselaar J, Pegtel M, Bijnsdorp I. Non‑invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles. Oncotarget 2016; 7:22566-78. [PMID: 26992225 PMCID: PMC5008382 DOI: 10.18632/oncotarget.8124] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/24/2016] [Indexed: 12/26/2022] Open
Abstract
In many cancer types, the expression and function of ~22 nucleotide-long microRNAs (miRNA) is deregulated. Mature miRNAs can be stably detected in extracellular vesicles (EVs) in biofluids, therefore they are considered to have great potential as biomarkers. In the present study, we investigated whether miRNAs have a distinct expression pattern in urine-EVs of prostate cancer (PCa) patients compared to control males. By next generation sequencing, we determined the miRNA expression in a discovery cohort of 4 control men and 9 PCa patients. miRNAs were validated by using a stemloop RT-PCR in an independent cohort of 74 patients (26 control and 48 PCa-patients). Whereas standard mapping protocols identified > 10 PCa associated miRNAs in urinary EVs, miR-21, miR-375 and miR-204 failed to robustly discriminate for disease in a validation study with RT-PCR-detection of mature miRNA sequences. In contrast, we observed that miRNA isoforms (isomiRs) with 3' end modifications were highly discriminatory between samples from control men and PCa patients. Highly differentially expressed isomiRs of miR-21, miR-204 and miR-375 were subsequently validated in an independent group of 74 patients. Receiver-operating characteristic analysis was performed to evaluate the diagnostic performance of three isomiRs, resulting in a 72.9% sensitivity with a high (88%) specificity and an area under the curve (AUC) of 0.866. In comparison, prostate specific antigen had an AUC of 0.707 and measuring the mature form of these miRNAs yielded a lower 70.8% sensitivity and 72% specificity (AUC 0.766). We propose that isomiRs may carry discriminatory information which is useful to generate stronger biomarkers.
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Affiliation(s)
- Danijela Koppers-Lalic
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
- Department of Neurosurgery, Neuro-Oncology Research Group, VU University Medical Center, Amsterdam, The Netherlands
- Exbiome B.V., 1016 PL Amsterdam, The Netherlands
| | - Michael Hackenberg
- Department of Genetics, Computational Genomics and Bioinformatics Group, University of Granada, Granada Spain
| | - Renee de Menezes
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - Branislav Misovic
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Magda Wachalska
- Department of Urology, VU University Medical Center, Amsterdam, The Netherlands
| | - Albert Geldof
- CNR-National Research Council of Italy, IGM, Bologna, Italy
| | - Nicoletta Zini
- CNR-National Research Council of Italy, IGM, Bologna, Italy
- SC Laboratory of Musculoskeletal Cell Biology, IOR-IRCCS, Bologna, Italy
| | - Theo de Reijke
- Department of Urology, Academic Medical Centre, Amsterdam, The Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, Neuro-Oncology Research Group, VU University Medical Center, Amsterdam, The Netherlands
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Andre Vis
- Department of Urology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Michiel Pegtel
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Irene Bijnsdorp
- Department of Urology, VU University Medical Center, Amsterdam, The Netherlands
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Esteban-Fernández de Ávila B, Martín A, Soto F, Lopez-Ramirez MA, Campuzano S, Vásquez-Machado GM, Gao W, Zhang L, Wang J. Single Cell Real-Time miRNAs Sensing Based on Nanomotors. ACS NANO 2015; 9:6756-64. [PMID: 26035455 DOI: 10.1021/acsnano.5b02807] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A nanomotor-based strategy for rapid single-step intracellular biosensing of a target miRNA, expressed in intact cancer cells, at the single cell level is described. The new concept relies on the use of ultrasound (US) propelled dye-labeled single-stranded DNA (ssDNA)/graphene-oxide (GO) coated gold nanowires (AuNWs) capable of penetrating intact cancer cells. Once the nanomotor is internalized into the cell, the quenched fluorescence signal (produced by the π-π interaction between GO and a dye-labeled ssDNA) is recovered due to the displacement of the dye-ssDNA probe from the motor GO-quenching surface upon binding with the target miRNA-21, leading to an attractive intracellular "OFF-ON" fluorescence switching. The faster internalization process of the US-powered nanomotors and their rapid movement into the cells increase the likelihood of probe-target contacts, leading to a highly efficient and rapid hybridization. The ability of the nanomotor-based method to screen cancer cells based on the endogenous content of the target miRNA has been demonstrated by measuring the fluorescence signal in two types of cancer cells (MCF-7 and HeLa) with significantly different miRNA-21 expression levels. This single-step, motor-based miRNAs sensing approach enables rapid "on the move" specific detection of the target miRNA-21, even in single cells with an extremely low endogenous miRNA-21 content, allowing precise and real-time monitoring of intracellular miRNA expression.
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Affiliation(s)
| | - Aída Martín
- †Department of Nanoengineering, University of California, San Diego, La Jolla, California 92093, United States
- ‡Department of Analytical Chemistry, University of Alcalá de Henares, E-28871 Madrid, Spain
| | - Fernando Soto
- †Department of Nanoengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Miguel Angel Lopez-Ramirez
- †Department of Nanoengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Susana Campuzano
- §Department of Analytical Chemistry, Complutense University of Madrid, E-28040 Madrid, Spain
| | | | - Weiwei Gao
- †Department of Nanoengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Liangfang Zhang
- †Department of Nanoengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Joseph Wang
- †Department of Nanoengineering, University of California, San Diego, La Jolla, California 92093, United States
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