1
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Weng WH, Wang CY, Yan ZY, Lee HT, Kao CY, Chang CW. Isolation and characterizations of multidrug-resistant human cancer cells by a biodegradable nano-sensor. Biosens Bioelectron 2024; 249:115985. [PMID: 38219465 DOI: 10.1016/j.bios.2023.115985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/14/2023] [Accepted: 12/27/2023] [Indexed: 01/16/2024]
Abstract
Multidrug resistance (MDR) remains a significant challenge in cancer therapy, with inherent and acquired resistance distinct. While conventional drug selection processes enable the isolation of cancer cells with acquired multidrug resistance, identifying cancer cells with inherent drug resistance remains challenging. Herein, we proposed a molecular beacon (MB)-based strategy to identify and isolate the inherent MDR cancer cells. A lipid/PLGA core-shell nanoparticulate system (DNCP) was designed to deliver MB for intracellular MDR1 mRNA imaging. DNCP-MB - possess a surface potential of -8 mV and a size of 150 nm - demonstrated effective delivery of MB, remarkable selectivity towards the selected intracellular mRNA targets, and low cytotoxicity. Following DNCP transfection, fluorescence-activated cell sorting (FACS) was employed to differentiate MCF-7 cells into two distinct sub-populations: the Top 10 cells with a high level of MDR gene expression and the Bottom 10 cells with a low level of MDR gene expression, which represent inherent drug-resistant and non-drug-resistant cells, respectively. Intriguingly, we observed a positive correlation between elevated MDR1 mRNA expression and increased migration, enhanced proliferation rate, and tighter spheroid formation. Moreover, we conducted RNA sequencing analysis on the Top 10, Bottom 10, and MCF-7/ADR cells. The findings revealed a notable disparity in the gene ontology enrichment analysis of differentially expressed genes between the Top 10 and Bottom 10 cells when compared to the Bottom 10 and MCF-7/ADR cells. This novel approach provides a promising avenue for isolating inherent drug-resistant cells and holds significant potential in unraveling the mechanisms underlying inherent drug resistance.
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Affiliation(s)
- Wei-Han Weng
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC
| | - Chu-Yun Wang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC
| | - Zi-Yu Yan
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC
| | - Hsiang-Tzu Lee
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC
| | - Cheng-Yuan Kao
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan, ROC
| | - Chien-Wen Chang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC.
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2
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Abdolahzadeh A, Ang QR, Caine JR, Panchapakesan SSS, Thio S, Cojocaru R, Unrau PJ. Turn-on RNA Mango Beacons for trans-acting fluorogenic nucleic acid detection. RNA (NEW YORK, N.Y.) 2024; 30:392-403. [PMID: 38282417 PMCID: PMC10946430 DOI: 10.1261/rna.079833.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/03/2024] [Indexed: 01/30/2024]
Abstract
The Mango I and II RNA aptamers have been widely used in vivo and in vitro as genetically encodable fluorogenic markers that undergo large increases in fluorescence upon binding to their ligand, TO1-Biotin. However, while studying nucleic acid sequences, it is often desirable to have trans-acting probes that induce fluorescence upon binding to a target sequence. Here, we rationally design three types of light-up RNA Mango Beacons based on a minimized Mango core that induces fluorescence upon binding to a target RNA strand. Our first design is bimolecular in nature and uses a DNA inhibition strand to prevent folding of the Mango aptamer core until binding to a target RNA. Our second design is unimolecular in nature, and features hybridization arms flanking the core that inhibit G-quadruplex folding until refolding is triggered by binding to a target RNA strand. Our third design builds upon this structure, and incorporates a self-inhibiting domain into one of the flanking arms that deliberately binds to, and precludes folding of, the aptamer core until a target is bound. This design separates G-quadruplex folding inhibition and RNA target hybridization into separate modules, enabling a more universal unimolecular beacon design. All three Mango Beacons feature high contrasts and low costs when compared to conventional molecular beacons, with excellent potential for in vitro and in vivo applications.
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Affiliation(s)
- Amir Abdolahzadeh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Quiana R Ang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Jana R Caine
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | | | - Shinta Thio
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Razvan Cojocaru
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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3
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Anil A, Chaskar J, Pawar AB, Tiwari A, Chaskar AC. Recent advances in DNA-based probes for photoacoustic imaging. J Biotechnol 2024; 382:8-20. [PMID: 38211667 DOI: 10.1016/j.jbiotec.2023.12.019] [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: 03/02/2022] [Revised: 11/29/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024]
Abstract
Photoacoustic imaging(PAI) is a widely developing imaging modality that has seen tremendous evolvement in the last decade. PAI has gained the upper hand in the imaging field as it takes advantage of optical absorption and ultrasound detection that imparts higher resolution, rich contrast and elevated penetration depth. Unlike other imaging techniques, PAI does not use ionising radiation and is a better, cost-effective and healthier alternative to other imaging techniques. It offers greater specificity than conventional ultrasound imaging with the ability to detect haemoglobin, lipids, water and other light-absorbing chromophores. These properties of PAI have led to its extended applications in the biomedical field in the treatment of diseases such as cancer. This paper reviews how DNA probes have been used in PAI, the various techniques by which it has been modified, and their role in the process. We also focus on different nanocomposites containing DNA having PAI and photothermal therapy(PTT) properties for detection, diagnosis and therapy, its constituents and the role of DNA in it.
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Affiliation(s)
- Anusri Anil
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India
| | - Jyotsna Chaskar
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India
| | - Avinash B Pawar
- Department of Chemistry, Bharati Vidyapeeth (Deemed to be University), Yashwantrao Mohite College of Arts, Science & Commerce, Pune 411038, India
| | - Abhishekh Tiwari
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India.
| | - Atul Changdev Chaskar
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India; Department of Chemistry, Institute of Chemical Technology, Mumbai.
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4
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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5
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Weigert N, Schweiger AL, Gross J, Matthes M, Corbacioglu S, Sommer G, Heise T. Detection of a 7SL RNA-derived small non-coding RNA using Molecular Beacons in vitro and in cells. Biol Chem 2023; 404:1123-1136. [PMID: 37632732 DOI: 10.1515/hsz-2023-0185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023]
Abstract
Small non-coding RNAs (sncRNA) are involved in many steps of the gene expression cascade and regulate processing and expression of mRNAs by the formation of ribonucleoprotein complexes (RNP) such as the RNA-induced silencing complex (RISC). By analyzing small RNA Seq data sets, we identified a sncRNA annotated as piR-hsa-1254, which is likely derived from the 3'-end of 7SL RNA2 (RN7SL2), herein referred to as snc7SL RNA. The 7SL RNA is an abundant long non-coding RNA polymerase III transcript and serves as structural component of the cytoplasmic signal recognition particle (SRP). To evaluate a potential functional role of snc7SL RNA, we aimed to define its cellular localization by live cell imaging. Therefore, a Molecular Beacon (MB)-based method was established to compare the subcellular localization of snc7SL RNA with its precursor 7SL RNA. We designed and characterized several MBs in vitro and tested those by live cell fluorescence microscopy. Using a multiplex approach, we show that 7SL RNA localizes mainly to the endoplasmic reticulum (ER), as expected for the SRP, whereas snc7SL RNA predominately localizes to the nucleus. This finding suggests a fundamentally different function of 7SL RNA and its derivate snc7SL RNA.
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Affiliation(s)
- Nina Weigert
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Anna-Lena Schweiger
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Jonas Gross
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Marie Matthes
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Selim Corbacioglu
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Gunhild Sommer
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Tilman Heise
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
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6
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Bühler B, Schokolowski J, Jäschke A, Sunbul M. Programmable, Structure-Switching RhoBAST for Hybridization-Mediated mRNA Imaging in Living Cells. ACS Chem Biol 2023; 18:1838-1845. [PMID: 37530071 DOI: 10.1021/acschembio.3c00258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
The development of fluorescent probes for visualizing endogenous RNAs in living cells is crucial to understand their complex biochemical roles. Recently, we developed RhoBAST, one of the most photostable and brightest fluorescence light-up aptamers (FLAPs), as a genetically encoded tag for imaging messenger RNAs (mRNAs). Here, we describe programmable RhoBAST sequences flanked by target-binding hybridization arms that light up only when bound to the untagged target RNA in trans. As part of the hybridization arm, we introduced a modular transducer sequence that switches the secondary structure of RhoBAST and renders it incapable of binding to its fluorogenic ligand TMR-DN. Only the specific binding of the hybridization arms to the target RNA triggers the correct folding of RhoBAST and fluorescence light-up after binding to TMR-DN. We characterized the structural switching of programmable RhoBAST sequences extensively in vitro and applied them to visualize untagged mRNAs in live bacteria.
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Affiliation(s)
- Bastian Bühler
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Janin Schokolowski
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
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7
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Gerber A, van Otterdijk S, Bruggeman FJ, Tutucci E. Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. Transcription 2023; 14:105-126. [PMID: 37050882 PMCID: PMC10807504 DOI: 10.1080/21541264.2023.2199669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023] Open
Abstract
Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.
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Affiliation(s)
- Alan Gerber
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Sander van Otterdijk
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J. Bruggeman
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Evelina Tutucci
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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8
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Liang Y, Willey S, Chung YC, Lo YM, Miao S, Rundell S, Tu LC, Bong D. Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA. Nat Commun 2023; 14:2987. [PMID: 37225690 DOI: 10.1038/s41467-023-38579-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
The most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sydney Willey
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Yi-Meng Lo
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Li-Chun Tu
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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9
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Kim SH, Li ITS. Super-Resolution Tension PAINT Imaging with a Molecular Beacon. Angew Chem Int Ed Engl 2023; 62:e202217028. [PMID: 36534951 DOI: 10.1002/anie.202217028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
DNA-PAINT enabled super-resolution imaging through the transient binding of fluorescently-labelled single-stranded DNA (ssDNA) imagers to target ssDNA. However, its performance is constrained by imager background fluorescence, resulting in relatively long image acquisition and potential artifacts. We designed a molecular beacon (MB) as the PAINT imager. Unbound MB in solution reduces the background fluorescence due to its natively quenched state. They are fluorogenic upon binding to target DNA to create individual fluorescence events. We demonstrate that MB-PAINT provides localization precision similar to traditional linear imager DNA-PAINT. We also show that MB-PAINT is ideally suited for fast super-resolution imaging of molecular tension probes in living cells, eliminating the potential of artifacts from free-diffusing imagers in traditional DNA-PAINT at the cell-substrate interface.
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Affiliation(s)
- Seong Ho Kim
- Department of Chemistry, The University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - Isaac T S Li
- Department of Chemistry, The University of British Columbia, Kelowna, BC V1V 1V7, Canada
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10
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Algar WR, Szwarczewski A, Massey M. Are We There Yet? Intracellular Sensing with Luminescent Nanoparticles and FRET. Anal Chem 2023; 95:551-559. [PMID: 36595310 DOI: 10.1021/acs.analchem.2c03751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Combinations of luminescent nanoparticles (LNPs) and Förster resonance energy transfer (FRET) offer properties and features that are advantageous for sensing of biomolecular targets and activity. Despite a multitude of designs for LNP-FRET sensors, intracellular sensing applications are underdeveloped. We introduce readers to this field, summarize essential concepts, meta-analyze the literature, and offer a perspective on the bottleneck in LNP-FRET sensor development.
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Affiliation(s)
- W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Agnes Szwarczewski
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Melissa Massey
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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11
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Lu Y, Li X, Liu Y, Li J, Chen Z, Meng X, Li W, Fang J. Novel Molecular Aptamer Beacon for the Specific Simultaneous Analysis of Circulating Tumor Cells and Exosomes of Colorectal Cancer Patients. Anal Chem 2023; 95:1251-1261. [PMID: 36583760 DOI: 10.1021/acs.analchem.2c04017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Liquid biopsy provides non-invasive and real-time detection for cancer diagnosis, but the lack of specific markers targeted to liquid biopsy components, such as circulating tumor cells (CTCs) and exosomes, has impeded its effective utilization in clinical settings. W3 is an aptamer, and its target has been previously demonstrated to be a predictor of colorectal cancer (CRC) metastasis. Herein, we developed a W3-based molecular beacon (MAB-W3-3G) to specifically detect CTCs and exosomes derived from CRC patients by modifying the W3 sequence and adding a fluorescent group FAM at the 5' end and a quencher group BHQ1 at the 3' end, resulting in a detectable green fluorescence only in the presence of the target. MAB-W3-3G retained features similar to those of the original W3, including high specificity and affinity for metastatic CRC cells, as well as excellent plasma stability. Notably, W3 target-positive CTCs were visualized, positive exosomes were quantified in CRC patients' whole blood without any sample pretreatment, and both detections could be finished in one step without any routine washing procedures. For CRC, the W3 target-positive CTC enumeration in metastasis was higher than that in non-metastasis (p < 0.01), and the quantitation of positive exosomes was correlated with CRC patients (p < 0.0001). Moreover, the MAB-W3-3G-based simultaneous detection of CTCs and exosomes was proven to have the potential for more precise clinical diagnosis. In conclusion, MAB-W3-3G could detect CTCs and exosomes in the blood samples of tumor patients with simple manipulation, rapid analysis, and high specificity, providing an effective liquid biopsy tool for the prediction of CRC.
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Affiliation(s)
- Yanbing Lu
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, PR China
| | - Xin Li
- Department of Anesthesiology, Cancer Hospital of China Medical University, Shenyang 110042, PR China
| | - Yun Liu
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, PR China
| | - Jiabin Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, PR China
| | - Zhezhou Chen
- Department of Clinical Laboratory, Shenyang First People's Hospital, Shenyang 110041, PR China
| | - Xianmeng Meng
- Department of Pathology and Clinical Laboratory, Liaoning Provincial Corps Hospital of Chinese People's Armed Police Forces, Shenyang 110034, PR China
| | - Wanming Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, PR China
| | - Jin Fang
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, PR China
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12
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Xu C, Ren XH, Han D, Peng Y, Lei JJ, Yu LX, Liu LJ, Xu WC, Cheng SX. Precise Detection on Cell-Cell Fusion by a Facile Molecular Beacon-Based Method. Anal Chem 2022; 94:17334-17340. [PMID: 36456915 DOI: 10.1021/acs.analchem.2c04852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Cell-cell fusion studies provide an experimental platform for evaluating disease progression and investigating cell infection. However, to realize sensitive and quantitative detection on cell-cell fusion is still a challenge. Herein, we report a facile molecular beacon (MB)-based method for precise detection on cell-cell fusion. By transfection of the spike protein (S protein) and enhanced green fluorescent protein (EGFP) in HEK 293 cells, the virus-mimicking fusogenic effector cells 293-S-EGFP cells were constructed to interact with target cells. Before mixing the effector cells with the target cells, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression in 293-S-EGFP cells was silenced, and the MB for GAPDH mRNA detection was delivered into the GAPDH silenced 293-S-EGFP cells. Once cell-cell fusion occurred, MB migrated from the GAPDH silenced effector cells to the target cells and hybridized with GAPDH mRNA in the target cells to induce fluorescence emission. The cell-cell fusion can be easily visualized and quantitated by fluorescence microscopy and flow cytometry. The fluorescence intensity is strongly dependent on the number of fused target cells. This MB-based method can easily identify the differences in the cell fusions for various target cells with different angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) expression levels, resulting in dramatically different fluorescence intensities in fused target cells. Our study provides a convenient and efficient quantitative detection approach to study cell-cell fusion.
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Affiliation(s)
- Chang Xu
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China
| | - Xiao-He Ren
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China
| | - Di Han
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China
| | - Yan Peng
- Department of Pharmacy, The Renmin Hospital of Wuhan University, Wuhan 430060, P. R. China
| | - Jin-Ju Lei
- Cancer Center, The Renmin Hospital of Wuhan University, Wuhan 430060, P. R. China
| | - Luo-Xiao Yu
- Cancer Center, The Renmin Hospital of Wuhan University, Wuhan 430060, P. R. China
| | - Ling-Juan Liu
- Cancer Center, The Renmin Hospital of Wuhan University, Wuhan 430060, P. R. China
| | - Wei-Chao Xu
- Cancer Center, The Renmin Hospital of Wuhan University, Wuhan 430060, P. R. China
| | - Si-Xue Cheng
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China
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13
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Assembly of Biologically Functional Structures by Nucleic Acid Templating: Implementation of a Strategy to Overcome Inhibition by Template Excess. Molecules 2022; 27:molecules27206831. [PMID: 36296424 PMCID: PMC9610079 DOI: 10.3390/molecules27206831] [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: 08/26/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
Delivery of therapeutic molecules to pathogenic cells is often hampered by unintended toxicity to normal cells. In principle, this problem can be circumvented if the therapeutic effector molecule is split into two inactive components, and only assembled on or within the target cell itself. Such an in situ process can be realized by exploiting target-specific molecules as templates to direct proximity-enhanced assembly. Modified nucleic acids carrying inert precursor fragments can be designed to co-hybridize on a target-specific template nucleic acid, such that the enforced proximity accelerates assembly of a functional molecule for antibody recognition. We demonstrate the in vitro feasibility of this adaptation of nucleic acid-templated synthesis (NATS) using oligonucleotides bearing modified peptides (“haplomers”), for templated assembly of a mimotope recognized by the therapeutic antibody trastuzumab. Enforced proximity promotes mimotope assembly via traceless native chemical ligation. Nevertheless, titration of participating haplomers through template excess is a potential limitation of trimolecular NATS. In order to overcome this problem, we devised a strategy where haplomer hybridization can only occur in the presence of target, without being subject to titration effects. This generalizable NATS modification may find future applications in enabling directed targeting of pathological cells.
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14
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Falco N, Garfio CM, Spitalny L, Spitale RC. A Fluorescent Reverse-Transcription Assay to Detect Chemical Adducts on RNA. Biochemistry 2022; 61:1665-1668. [PMID: 35876726 PMCID: PMC10010264 DOI: 10.1021/acs.biochem.2c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we detail a novel reverse-transcription (RT) assay to directly detect chemical adducts on RNA. We optimize a fluorescence quenching assay to detect RT polymerization and employ our approach to detect N1-alkylation of inosine, an important post-transcriptional modification, using a phenylacrylamide as a model compound. We anticipate our approach can be expanded to identify novel reagents that form adducts with RNA and further explored to understand the relationship between RT processivity and natural post-transcriptional modifications in RNA.
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15
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Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A, Saha A, Arantes PR, Ippodrino R, Ricci F, Treglia I, Delibato E, van der Oost J, Palermo G, Perugino G, Porchetta A. Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Res 2022; 50:8377-8391. [PMID: 35822842 PMCID: PMC9371913 DOI: 10.1093/nar/gkac578] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Cas12a due to its improved affinity (Km) for hairpin DNA structures, and provide mechanistic insights of our findings through Molecular Dynamics simulations. Using hairpin DNA probes we significantly enhance FRET-based signal transduction compared to the widely used linear single stranded DNA reporters. Our signal transduction enables faster detection of clinically relevant double stranded DNA targets with improved sensitivity and specificity either in the presence or in the absence of an upstream pre-amplification step.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Danila Moscone
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Aakash Saha
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Rudy Ippodrino
- Ulisse BioMed S.r.l. Area Science Park, 34149 Trieste, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Ida Treglia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.,Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte Sant'Angelo, Ed. 7, Via Cintia 26, 80126 Naples, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
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16
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Yang N, Xu J, Wang F, Yang F, Han D, Xu S. Thermal Probing Techniques for a Single Live Cell. SENSORS 2022; 22:s22145093. [PMID: 35890773 PMCID: PMC9317922 DOI: 10.3390/s22145093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/02/2022] [Accepted: 07/03/2022] [Indexed: 02/01/2023]
Abstract
Temperature is a significant factor in determining and characterizing cellular metabolism and other biochemical activities. In this study, we provide a brief overview of two important technologies used to monitor the local temperatures of individual living cells: fluorescence nano-thermometry and an array of micro-/nano-sized thin-film thermocouples. We explain some key technical issues that must be addressed and optimised for further practical applications, such as in cell biology, drug selection, and novel antitumor therapy. We also offer a method for combining them into a hybrid measuring system.
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Affiliation(s)
- Nana Yang
- School of Microelectronics, Shandong University, Jinan 250100, China; (N.Y.); (F.W.)
- School of Electronics, Peking University, Beijing 100871, China; (F.Y.); (D.H.); (S.X.)
| | - Jingjing Xu
- School of Electronics, Peking University, Beijing 100871, China; (F.Y.); (D.H.); (S.X.)
- Correspondence:
| | - Fan Wang
- School of Microelectronics, Shandong University, Jinan 250100, China; (N.Y.); (F.W.)
| | - Fan Yang
- School of Electronics, Peking University, Beijing 100871, China; (F.Y.); (D.H.); (S.X.)
| | - Danhong Han
- School of Electronics, Peking University, Beijing 100871, China; (F.Y.); (D.H.); (S.X.)
- Beijing Research Institute of Mechanical Equipment, Beijing 100854, China
| | - Shengyong Xu
- School of Electronics, Peking University, Beijing 100871, China; (F.Y.); (D.H.); (S.X.)
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17
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Gorbenko DA, Shkodenko LA, Rubel MS, Slita AV, Nikitina EV, Martens EA, Kolpashchikov DM. DNA nanomachine for visual detection of structured RNA and double stranded DNA. Chem Commun (Camb) 2022; 58:5395-5398. [PMID: 35415727 DOI: 10.1039/d2cc00325b] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Visual detection of ssRNA and dsDNA amplicons was achieved at room temperature without the need for a probe-analyte annealing stage. This approach uses a DNA nanostructure equipped with two analyte-binding arms. Highly selective binding of the third arm leads to the formation of a G-quadruplex structure capable of changing the solution color.
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Affiliation(s)
- Daria A Gorbenko
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, Saint-Petersburg, Russia, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation. .,Ioffe Institute, 26 Politekhnicheskaya, St. Petersburg, 194021, Russian Federation
| | - Liubov A Shkodenko
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, Saint-Petersburg, Russia, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation.
| | - Maria S Rubel
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, Saint-Petersburg, Russia, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation.
| | - Aleksandr V Slita
- St. Petersburg Pasteur Institute, 14 Mira Str., St. Petersburg, 197101, Russian Federation
| | - Ekaterina V Nikitina
- Pediatric Research and Clinical Center for Infectious Diseases, 9 Prof. Popova Str, Saint Petersburg, 197022, Russian Federation
| | - Elvira A Martens
- Pediatric Research and Clinical Center for Infectious Diseases, 9 Prof. Popova Str, Saint Petersburg, 197022, Russian Federation
| | - Dmitry M Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, Saint-Petersburg, Russia, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation. .,Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA.,National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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18
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Bustamante-Jaramillo LF, Fingal J, Blondot ML, Rydell GE, Kann M. Imaging of Hepatitis B Virus Nucleic Acids: Current Advances and Challenges. Viruses 2022; 14:v14030557. [PMID: 35336964 PMCID: PMC8950347 DOI: 10.3390/v14030557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/30/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis B virus infections are the main reason for hepatocellular carcinoma development. Current treatment reduces the viral load but rarely leads to virus elimination. Despite its medical importance, little is known about infection dynamics on the cellular level not at least due to technical obstacles. Regardless of infections leading to extreme viral loads, which may reach 1010 virions per mL serum, hepatitis B viruses are of low abundance and productivity in individual cells. Imaging of the infections in cells is thus a particular challenge especially for cccDNA that exists only in a few copies. The review describes the significance of microscopical approaches on genome and transcript detection for understanding hepatitis B virus infections, implications for understanding treatment outcomes, and recent microscopical approaches, which have not been applied in HBV research.
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Affiliation(s)
- Luisa F. Bustamante-Jaramillo
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Joshua Fingal
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Marie-Lise Blondot
- Microbiologie Fondamentale et Pathogénicité (MFP), CNRS UMR 5234, University of Bordeaux, 33076 Bordeaux, France;
| | - Gustaf E. Rydell
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Michael Kann
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
- Region Västra Götaland, Department of Clinical Microbiology, Sahlgrenska University Hospital, 405 30 Gothenburg, Sweden
- Correspondence:
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19
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Han D, Xu C, Ren XH, Peng Y, Xu B, Song JL, Chen J, Cheng SX. In Situ Detection of Nanotoxicity in Living Cells Based on Multiple miRNAs Probed by a Peptide Functionalized Nanoprobe. Anal Chem 2022; 94:2399-2407. [PMID: 35099175 DOI: 10.1021/acs.analchem.1c03950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The potential toxicity of nanoparticles, especially for clinically applicable ones, has become a critical concern. Technologies that can in situ-evaluate the toxicity of nanoparticles with high sensitivity are urgently needed. In this study, a facile strategy was developed for sensitive detection on the nanotoxicity of nanoparticles with low toxicity or a low dose. A functional nanoprobe loaded with molecular beacons was constructed to realize in situ evaluation of the nanotoxicity through probing multiple miRNAs in nanoparticle-exposed living cells. Being composed of protamine complexed with molecular beacons for miRNA detection and decorated by TAT and KALA peptides, the dual-peptide functionalized nanoprobe can efficiently deliver molecular beacons into living cells to realize the real-time monitoring of early biomarkers (miR-21 and miR-221) to evaluate nanotoxicity. Using mesoporous silica nanoparticles (MSNs) with different surface modifications as typical representatives of low toxic nanoparticles, we demonstrate that our nanoprobe can sensitively detect miRNA changes in cells under diverse exposure conditions, that is, MSN-NH2 exhibits the strongest capability to upregulate miR-21 and miR-221, and the upregulation is exposure dose- and time-dependent. Our approach is much more sensitive as compared with conventional methods to study cytotoxicity such as 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, cell morphology observation, and reactive oxygen species (ROS) assay. This study paves a path for effective and facile nanotoxicity evaluation and provides insights into the biological impacts of MSNs.
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Affiliation(s)
- Di Han
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China
| | - Chang Xu
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China
| | - Xiao-He Ren
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China
| | - Yan Peng
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan 430060, P. R. China
| | - Bin Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, P. R. China
| | - Jun-Long Song
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, P. R. China
| | - Jing Chen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, P. R. China
| | - Si-Xue Cheng
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China
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20
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Li S, Wang C, Xu Y, Wang W, Zhao X, Qian Q, Mi X. A designer DNA tetrahedron-based molecular beacon for tumor-related microRNA fluorescence imaging in living cells. Analyst 2022; 147:2231-2237. [DOI: 10.1039/d2an00418f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A designer nanoprobe of tetrahedral DNA framework (TDF) combined with MB (termed TDFM nanoprobe) for the efficient fluorescence imaging of tumor-related miRNA-214 in living cells.
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Affiliation(s)
- Shuainan Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenguang Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Xu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Wei Wang
- Shanghai Pudong New District Zhoupu Hospital (Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital), Shanghai 201318, China
| | - Xiaoshuang Zhao
- Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Qiuling Qian
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianqiang Mi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Shanghai 200050, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, China
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21
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Qu N, Ying Y, Qin J, Chen AK. Rational design of self-assembled RNA nanostructures for HIV-1 virus assembly blockade. Nucleic Acids Res 2021; 50:e44. [PMID: 34967412 PMCID: PMC9071489 DOI: 10.1093/nar/gkab1282] [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: 09/28/2021] [Revised: 11/16/2021] [Accepted: 12/15/2021] [Indexed: 11/14/2022] Open
Abstract
Many pathological processes are driven by RNA-protein interactions, making such interactions promising targets for molecular interventions. HIV-1 assembly is one such process, in which the viral genomic RNA interacts with the viral Gag protein and serves as a scaffold to drive Gag multimerization that ultimately leads to formation of a virus particle. Here, we develop self-assembled RNA nanostructures that can inhibit HIV-1 virus assembly, achieved through hybridization of multiple artificial small RNAs with a stem-loop structure (STL) that we identify as a prominent ligand of Gag that can inhibit virus particle production via STL-Gag interactions. The resulting STL-decorated nanostructures (double and triple stem-loop structures denoted as Dumbbell and Tribell, respectively) can elicit more pronounced viral blockade than their building blocks, with the inhibition arising as a result of nanostructures interfering with Gag multimerization. These findings could open up new avenues for RNA-based therapy.
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Affiliation(s)
- Na Qu
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, Peking University, Beijing 100871, China
| | - Jinshan Qin
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, Peking University, Beijing 100871, China
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22
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Ranjan S, Jain S, Bhargava A, Shandilya R, Srivastava RK, Mishra PK. Lateral flow assay-based detection of long non-coding RNAs: A point-of-care platform for cancer diagnosis. J Pharm Biomed Anal 2021; 204:114285. [PMID: 34333453 DOI: 10.1016/j.jpba.2021.114285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022]
Abstract
Lateral flow assay (LFA) is a flexible, simple, low-costpoint-of-care platform for rapid detection of disease-specific biomarkers. Importantly, the ability of the assay to capture the circulating bio-molecules has gained significant attention, as it offers a potential minimal invasive system for early disease diagnosis and prognosis. In the present article, we review an innovative concept of LFA-based detection of circulating long non-coding RNAs (lncRNAs), one of the key regulators of fundamental biological processes. In addition, their disease-specific expression pattern and presence in biological fluids at differential levels make them excellent biomarker candidates for cancer detection. Our article also provides an update on the requirements for developing and improving such systems and discusses the key aspects of material selection, operational concepts, principles and conceptual design. We assume that the reviewed points will be helpful to improve the diagnostic applicability of LFA based lncRNA detection in cancer diagnosis.
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Affiliation(s)
- Shashi Ranjan
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Surbhi Jain
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Ruchita Shandilya
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | | | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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