1
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Sart S, Liu C, Zeng EZ, Xu C, Li Y. Downstream bioprocessing of human pluripotent stem cell-derived therapeutics. Eng Life Sci 2022; 22:667-680. [PMID: 36348655 PMCID: PMC9635003 DOI: 10.1002/elsc.202100042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/08/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022] Open
Abstract
With the advancement in lineage-specific differentiation from human pluripotent stem cells (hPSCs), downstream cell separation has now become a critical step to produce hPSC-derived products. Since differentiation procedures usually result in a heterogeneous cell population, cell separation needs to be performed either to enrich the desired cell population or remove the undesired cell population. This article summarizes recent advances in separation processes for hPSC-derived cells, including the standard separation technologies, such as magnetic-activated cell sorting, as well as the novel separation strategies, such as those based on adhesion strength and metabolic flux. Specifically, the downstream bioprocessing flow and the identification of surface markers for various cell lineages are discussed. While challenges remain for large-scale downstream bioprocessing of hPSC-derived cells, the rational quality-by-design approach should be implemented to enhance the understanding of the relationship between process and the product and to ensure the safety of the produced cells.
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Affiliation(s)
- Sebastien Sart
- Laboratory of Physical Microfluidics and BioengineeringDepartment of Genome and GeneticsInstitut PasteurParisFrance
| | - Chang Liu
- Department of Chemical and Biomedical EngineeringFAMU‐FSU College of EngineeringFlorida State UniversityTallahasseeFLUSA
| | - Eric Z. Zeng
- Department of Chemical and Biomedical EngineeringFAMU‐FSU College of EngineeringFlorida State UniversityTallahasseeFLUSA
| | - Chunhui Xu
- Department of PediatricsEmory University School of Medicine and Children's Healthcare of AtlantaAtlantaGAUSA
| | - Yan Li
- Department of Chemical and Biomedical EngineeringFAMU‐FSU College of EngineeringFlorida State UniversityTallahasseeFLUSA
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2
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Murata Y, Jo JI, Tabata Y. Intracellular Controlled Release of Molecular Beacon Prolongs the Time Period of mRNA Visualization. Tissue Eng Part A 2019; 25:1527-1537. [DOI: 10.1089/ten.tea.2019.0017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Yuki Murata
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jun-ichiro Jo
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasuhiko Tabata
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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3
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Milliron HYY, Weiland MJ, Kort EJ, Jovinge S. Isolation of Cardiomyocytes Undergoing Mitosis With Complete Cytokinesis. Circ Res 2019; 125:1070-1086. [PMID: 31648614 DOI: 10.1161/circresaha.119.314908] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RATIONALE Adult human cardiomyocytes do not complete cytokinesis despite passing through the S-phase of the cell cycle. As a result, polyploidization and multinucleation occur. To get a deeper understanding of the mechanisms surrounding division of cardiomyocytes, there is a crucial need for a technique to isolate cardiomyocytes that complete cell division/cytokinesis. OBJECTIVE Markers of cell cycle progression based on DNA content cannot distinguish between mitotic cardiomyocytes that fail to complete cytokinesis from those cells that undergo true cell division. With the use of molecular beacons (MBs) targeting specific mRNAs, we aimed to identify truly proliferative cardiomyocytes derived from human induced pluripotent stem cells. METHODS AND RESULTS Fluorescence-activated cell sorting combined with MBs was performed to sort cardiomyocyte populations enriched for mitotic cells. Expressions of cell cycle specific genes were confirmed by means of reverse transcription-quantitative polymerase chain reaction and single-cell RNA sequencing (scRNA-seq) combined with gene signatures of cell cycle progression. We characterized the sorted groups by proliferation assays and time-lapse microscopy which confirmed the proliferative advantage of MB-positive cell populations relative to MB-negative and G2/M populations. Gene expression analysis revealed that the MB-positive cardiomyocyte subpopulation exhibited patterns consistent with the processes of nuclear division, chromosome segregation, and transition from M to G1 phase. The use of dual-MBs targeting CDC20 and SPG20 mRNAs enabled the enrichment of cytokinetic events (CDC20highSPG20high). Interestingly, cells that did not complete cytokinesis and remained binucleated were found to be CDC20lowSPG20high while polyploid cardiomyocytes that replicated DNA but failed to complete karyokinesis were found to be CDC20lowSPG20low. CONCLUSIONS This study demonstrates a novel alternative to existing DNA content-based approaches for sorting cardiomyocytes with true mitotic potential that can be used to study the unique dynamics of cardiomyocyte nuclei during mitosis. Our technique for sorting live cardiomyocytes undergoing cytokinesis would provide a basis for future studies to uncover mechanisms underlying the development and regeneration of heart tissue.
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Affiliation(s)
- Hsiao-Yun Y Milliron
- From the DeVos Cardiovascular Program, Van Andel Research Institute and Fredrik Meijer Heart and Vascular Institute/Spectrum Health, Grand Rapids, MI (H.Y.M., M.J.W., E.J.K., S.J.)
| | - Matthew J Weiland
- From the DeVos Cardiovascular Program, Van Andel Research Institute and Fredrik Meijer Heart and Vascular Institute/Spectrum Health, Grand Rapids, MI (H.Y.M., M.J.W., E.J.K., S.J.)
| | - Eric J Kort
- From the DeVos Cardiovascular Program, Van Andel Research Institute and Fredrik Meijer Heart and Vascular Institute/Spectrum Health, Grand Rapids, MI (H.Y.M., M.J.W., E.J.K., S.J.).,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, East Lansing (E.J.K.)
| | - Stefan Jovinge
- From the DeVos Cardiovascular Program, Van Andel Research Institute and Fredrik Meijer Heart and Vascular Institute/Spectrum Health, Grand Rapids, MI (H.Y.M., M.J.W., E.J.K., S.J.).,Cardiovascular Institute, Stanford University, Palo Alto, CA (S.J.)
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4
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Divide and conquer: two stem cell populations in squamous epithelia, reserves and the active duty forces. Int J Oral Sci 2019; 11:26. [PMID: 31451683 PMCID: PMC6802623 DOI: 10.1038/s41368-019-0061-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/09/2019] [Accepted: 07/22/2019] [Indexed: 12/22/2022] Open
Abstract
Stem cells are of great interest to the scientific community due to their potential role in regenerative and rejuvenative medicine. However, their role in the aging process and carcinogenesis remains unclear. Because DNA replication in stem cells may contribute to the background mutation rate and thereby to cancer, reducing proliferation and establishing a relatively quiescent stem cell compartment has been hypothesized to limit DNA replication-associated mutagenesis. On the other hand, as the main function of stem cells is to provide daughter cells to build and maintain tissues, the idea of a quiescent stem cell compartment appears counterintuitive. Intriguing observations in mice have led to the idea of separated stem cell compartments that consist of cells with different proliferative activity. Some epithelia of short-lived rodents appear to lack quiescent stem cells. Comparing stem cells of different species and different organs (comparative stem cell biology) may allow us to elucidate the evolutionary pressures such as the balance between cancer and longevity that govern stem cell biology (evolutionary stem cell biology). The oral mucosa and its stem cells are an exciting model system to explore the characteristics of quiescent stem cells that have eluded biologists for decades.
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5
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Wu X, Mao S, Yang Y, Rushdi MN, Krueger CJ, Chen AK. A CRISPR/molecular beacon hybrid system for live-cell genomic imaging. Nucleic Acids Res 2019; 46:e80. [PMID: 29718399 PMCID: PMC6061827 DOI: 10.1093/nar/gky304] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/12/2018] [Indexed: 12/20/2022] Open
Abstract
The clustered regularly interspersed short palindromic repeat (CRISPR) gene-editing system has been repurposed for live-cell genomic imaging, but existing approaches rely on fluorescent protein reporters, making sensitive and continuous imaging difficult. Here, we present a fluorophore-based live-cell genomic imaging system that consists of a nuclease-deactivated mutant of the Cas9 protein (dCas9), a molecular beacon (MB), and an engineered single-guide RNA (sgRNA) harboring a unique MB target sequence (sgRNA-MTS), termed CRISPR/MB. Specifically, dCas9 and sgRNA-MTS are first co-expressed to target a specific locus in cells, followed by delivery of MBs that can then hybridize to MTS to illuminate the target locus. We demonstrated the feasibility of this approach for quantifying genomic loci, for monitoring chromatin dynamics, and for dual-color imaging when using two orthogonal MB/MTS pairs. With flexibility in selecting different combinations of fluorophore/quencher pairs and MB/MTS sequences, our CRISPR/MB hybrid system could be a promising platform for investigating chromatin activities.
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Affiliation(s)
- Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,School of Life Sciences, Peking University, Beijing 100871, China
| | - Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Muaz N Rushdi
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
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6
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Atashzar MR, Baharlou R, Karami J, Abdollahi H, Rezaei R, Pourramezan F, Zoljalali Moghaddam SH. Cancer stem cells: A review from origin to therapeutic implications. J Cell Physiol 2019; 235:790-803. [PMID: 31286518 DOI: 10.1002/jcp.29044] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 02/06/2023]
Abstract
Cancer stem cells (CSCs), also known as tumor-initiating cells (TICs), are elucidated as cells that can perpetuate themselves via autorestoration. These cells are highly resistant to current therapeutic approaches and are the main reason for cancer recurrence. Radiotherapy has made a lot of contributions to cancer treatment. However, despite continuous achievements, therapy resistance and tumor recurrence are still prevalent in most patients. This resistance might be partly related to the existence of CSCs. In the present study, recent advances in the investigation of different biological properties of CSCs, such as their origin, markers, characteristics, and targeting have been reviewed. We have also focused our discussion on radioresistance and adaptive responses of CSCs and their related extrinsic and intrinsic influential factors. In summary, we suggest CSCs as the prime therapeutic target for cancer treatment.
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Affiliation(s)
- Mohammad Reza Atashzar
- Department of Immunology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Rasoul Baharlou
- Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran.,Department of Immunology, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Jafar Karami
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Abdollahi
- Department of Radiologic Sciences and Medical Physics, School of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Ramazan Rezaei
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Pourramezan
- Department of Immunology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
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7
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Veronesi F, Tschon M, Visani A, Fini M. Biosensors for real-time monitoring of physiological processes in the musculoskeletal system: A systematic review. J Cell Physiol 2019; 234:21504-21518. [PMID: 31062360 DOI: 10.1002/jcp.28753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/26/2019] [Accepted: 04/11/2019] [Indexed: 11/09/2022]
Abstract
Biosensors are composed of (bio)receptors, transducers, and detection systems and are able to convert the biological stimulus into a measurable signal. This systematic review evaluates the current state of the art of innovation and research in this field, identifying the biosensors that in vitro monitor the musculoskeletal system cellular processes. Two databases found 20 in vitro studies, from January 1, 2008 to December 31, 2017, dealing with musculoskeletal system cells. The biosensors were divided into two groups based on the transduction mechanism: optical or electrochemical. The first group evaluated osteoblasts or mesenchymal stem cell (MSC) biocompatibility, viability, differentiation, alkaline phosphatase, enzyme, and protein detection. The second group detected cell impedance, ATP release, and superoxide concentration in tenocytes, osteoblasts, MSCs, and myoblasts. This review highlighted that the in vitro scenario is still at an early phase and limited for what concerns both the type of bioanalyte and for the type of system detector used.
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Affiliation(s)
- Francesca Veronesi
- Laboratory of Preclinical and Surgical Studies, IRCCS-Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Matilde Tschon
- Laboratory of Preclinical and Surgical Studies, IRCCS-Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Andrea Visani
- Laboratory of Biomechanics and Technology Innovation, IRCCS-Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Milena Fini
- Laboratory of Preclinical and Surgical Studies, IRCCS-Istituto Ortopedico Rizzoli, Bologna, Italy
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8
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Chen M, Mao S, Wu X, Ma Z, Yang Y, Krueger CJ, Chen AK. Single-Molecule Analysis of RNA Dynamics in Living Cells Using Molecular Beacons. Methods Mol Biol 2019; 1870:23-39. [PMID: 30539544 DOI: 10.1007/978-1-4939-8808-2_2] [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] [Indexed: 06/09/2023]
Abstract
Over the past decade, emerging evidence has indicated that long intergenic noncoding RNAs (lincRNAs), a class of RNA transcripts greater than 200 nt in length, function as key regulators of gene expression in cellular physiology and pathogenesis. Greater understanding of lincRNA activities, particularly in the context of subcellular localization and dynamic regulation at the single-molecule level, is expected to provide in-depth understanding of molecular mechanisms that regulate cell behavior and disease evolution. We have recently developed a fluorescence-imaging approach to investigate RNA dynamics in living cells at the single-molecule level. This approach entails the use of molecular beacons (MBs), which are a class of stem-loop forming oligonculeotide-based probes that emit detectable fluorescence upon binding to target sequence, and tandem repeats of MB target sequences integrated to the target RNA sequence. Binding of the MBs to the tandem repeats could illuminate the target RNA as a bright spot when imaged by conventional fluorescence microscopy, making the MB-based imaging approach a versatile tool for RNA analysis across laboratories. In this chapter, we describe the development of the MB-based approach and its application for imaging single NEAT1 lincRNA transcripts in living cells.
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Affiliation(s)
- Mingming Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Zhao Ma
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China.
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9
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Murata Y, Jo JI, Tabata Y. Preparation of cationized gelatin nanospheres incorporating molecular beacon to visualize cell apoptosis. Sci Rep 2018; 8:14839. [PMID: 30287861 PMCID: PMC6172245 DOI: 10.1038/s41598-018-33231-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/17/2018] [Indexed: 12/16/2022] Open
Abstract
The objective of this study is to prepare cationized gelatin nanospheres (cGNS) incorporating a molecular beacon (MB), and visualize cellular apoptosis. Two types of MB to detect the messenger RNA (mRNA) of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (GAP MB), and caspase-3 (casp3 MB) were incorporated in cGNS, respectively. MB incorporated in cGNS showed the DNA sequence specificity in hybridization. The cGNS incorporation enabled MB to enhance the stability against nuclease to a significantly great extent compared with free MB. The cGNS incorporating GAP MB were internalized into the KUM6 of a mouse bone marrow-derived stem cell by an endocytotic pathway. The cGNS were not distributed at the lysosomes. After the incubation with cGNS, the cell apoptosis was induced at different concentrations of camptothecin. No change in the intracellular fluorescence was observed for cGNSGAPMB. On the other hand, for the cGNScasp3MB, the fluorescent intensity significantly enhanced by the apoptosis induction of cells. It is concluded that cGNS incorporating MB is a promising system for the visualization of cellular apoptosis.
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Affiliation(s)
- Yuki Murata
- Laboratory of Biomaterials, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Jun-Ichiro Jo
- Laboratory of Biomaterials, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yasuhiko Tabata
- Laboratory of Biomaterials, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
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10
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Abstract
Conventional molecular beacons (MBs) have been used extensively for imaging specific endogenous RNAs in living cells, but their tendency to generate false-positive signals as a result of nuclease degradation and/or nonspecific binding limits sensitive and accurate imaging of intracellular RNAs. In an attempt to overcome this limitation, MBs have been synthesized with various chemically modified oligonucleotide backbones to confer greater biostability. We have recently developed a new MB architecture composed of 2'-O-methyl RNA (2Me), a fully phosphorothioate (PS) modified loop domain and a phosphodiester stem (2Me/PSLOOP MB). We showed that this new MB exhibits a marginal level of false-positive signals and enables accurate single-molecule imaging of target RNA in living cells. In this chapter, we describe detailed methods that led us to conclude that, among various PS-modified configurations, the 2Me/PSLOOP MB is an optimal design for intracellular RNA analysis.
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11
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Ma Z, Wu X, Krueger CJ, Chen AK. Engineering Novel Molecular Beacon Constructs to Study Intracellular RNA Dynamics and Localization. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:279-286. [PMID: 28942262 PMCID: PMC5673673 DOI: 10.1016/j.gpb.2017.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 04/08/2017] [Accepted: 04/17/2017] [Indexed: 11/25/2022]
Abstract
With numerous advancements in novel biochemical techniques, our knowledge of the role of RNAs in the regulation of cellular physiology and pathology has grown significantly over the past several decades. Nevertheless, detailed information regarding RNA processing, trafficking, and localization in living cells has been lacking due to technical limitations in imaging single RNA transcripts in living cells with high spatial and temporal resolution. In this review, we discuss techniques that have shown great promise for single RNA imaging, followed by highlights in our recent work in the development of molecular beacons (MBs), a class of nanoscale oligonucleotide-probes, for detecting individual RNA transcripts in living cells. With further refinement of MB design and development of more sophisticated fluorescence microscopy techniques, we envision that MB-based approaches could promote new discoveries of RNA functions and activities.
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Affiliation(s)
- Zhao Ma
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China; Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
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12
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Xia Y, Zhang R, Wang Z, Tian J, Chen X. Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 2017; 46:2824-2843. [PMID: 28345687 PMCID: PMC5472208 DOI: 10.1039/c6cs00675b] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.
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Affiliation(s)
- Yuqiong Xia
- Engineering Research Center of Molecular-imaging and Neuro-imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China.
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13
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Ban K, Bae S, Yoon YS. Current Strategies and Challenges for Purification of Cardiomyocytes Derived from Human Pluripotent Stem Cells. Theranostics 2017. [PMID: 28638487 PMCID: PMC5479288 DOI: 10.7150/thno.19427] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cardiomyocytes (CMs) derived from human pluripotent stem cells (hPSCs) are considered a most promising option for cell-based cardiac repair. Hence, various protocols have been developed for differentiating hPSCs into CMs. Despite remarkable improvement in the generation of hPSC-CMs, without purification, these protocols can only generate mixed cell populations including undifferentiated hPSCs or non-CMs, which may elicit adverse outcomes. Therefore, one of the major challenges for clinical use of hPSC-CMs is the development of efficient isolation techniques that allow enrichment of hPSC-CMs. In this review, we will discuss diverse strategies that have been developed to enrich hPSC-CMs. We will describe major characteristics of individual hPSC-CM purification methods including their scientific principles, advantages, limitations, and needed improvements. Development of a comprehensive system which can enrich hPSC-CMs will be ultimately useful for cell therapy for diseased hearts, human cardiac disease modeling, cardiac toxicity screening, and cardiac tissue engineering.
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14
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Varma S, Fendyur A, Box A, Voldman J. Multiplexed Cell-Based Sensors for Assessing the Impact of Engineered Systems and Methods on Cell Health. Anal Chem 2017; 89:4663-4670. [DOI: 10.1021/acs.analchem.7b00256] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Andrew Box
- Cytometry
Shared Resource Laboratory, Stowers Institute for Medical Research, Kansas
City, Missouri 64110, United States
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15
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Ban K, Wile B, Cho KW, Kim S, Song MK, Kim SY, Singer J, Syed A, Yu SP, Wagner M, Bao G, Yoon YS. Non-genetic Purification of Ventricular Cardiomyocytes from Differentiating Embryonic Stem Cells through Molecular Beacons Targeting IRX-4. Stem Cell Reports 2016; 5:1239-1249. [PMID: 26651608 PMCID: PMC4682289 DOI: 10.1016/j.stemcr.2015.10.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 10/29/2015] [Accepted: 10/30/2015] [Indexed: 12/15/2022] Open
Abstract
Isolation of ventricular cardiomyocytes (vCMs) has been challenging due to the lack of specific surface markers. Here we show that vCMs can be purified from differentiating mouse embryonic stem cells (mESCs) using molecular beacons (MBs) targeting specific intracellular mRNAs. We designed MBs (IRX4 MBs) to target mRNA encoding Iroquois homeobox protein 4 (Irx4), a transcription factor specific for vCMs. To purify mESC vCMs, IRX4 MBs were delivered into cardiomyogenically differentiating mESCs, and IRX4 MBs-positive cells were FACS-sorted. We found that, of the cells isolated, ∼98% displayed vCM-like action potentials by electrophysiological analyses. These MB-purified vCMs continuously maintained their CM characteristics as verified by spontaneous beating, Ca2+ transient, and expression of vCM-specific proteins. Our study shows the feasibility of isolating pure vCMs via cell sorting without modifying host genes. The homogeneous and functional ventricular CMs generated via the MB-based method can be useful for disease investigation, drug discovery, and cell-based therapies. Molecular beacon (MB)-based method was developed to purify ventricular CMs from ESCs Ventricular CM-specific MBs targeting Irx4 mRNA were successfully generated About 98% of the CMs sorted via Irx4-MB displayed ventricular CM-like phenotypes Irx4-MB-based purified CMs continuously maintained ventricular CM characteristics
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Affiliation(s)
- Kiwon Ban
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Brian Wile
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Kyu-Won Cho
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sangsung Kim
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ming-Ke Song
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sang Yoon Kim
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jason Singer
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Anum Syed
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Shan Ping Yu
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mary Wagner
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA.
| | - Young-Sup Yoon
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA 30322, USA; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Korea.
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16
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Zhao D, Yang Y, Qu N, Chen M, Ma Z, Krueger CJ, Behlke MA, Chen AK. Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons. Biomaterials 2016; 100:172-83. [PMID: 27261815 DOI: 10.1016/j.biomaterials.2016.05.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/10/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022]
Abstract
Molecular Beacons (MBs) composed of 2'-O-methyl RNA (2Me) and phosphorothioate (PS) linkages throughout the backbone (2Me/PSFULL MBs) have enabled long-term imaging of RNA in living cells, but excess PS modification can induce nonspecific binding, causing false-positive signals. In this study, we evaluate the intracellular stability of MBs composed of 2Me with various PS modifications, and found that false-positive signals could be reduced to marginal levels when the MBs possess a fully PS-modified loop domain and a phosphodiester stem (2Me/PSLOOP MB). Additionally, 2Me/PSLOOP MBs exhibited uncompromised hybridization kinetics, prolonged functionality and >88% detection accuracy for single RNA transcripts, and could do so without interfering with gene expression or cell growth. Finally, 2Me/PSLOOP MBs could image the dynamics of single mRNA transcripts in the nucleus and the cytoplasm simultaneously, regardless of whether the MBs targeted the 5'- or the 3'-UTR. Together, these findings demonstrate the effectiveness of loop-domain PS modification in reducing nonspecific signals and the potential for sensitive and accurate imaging of individual RNAs at the single-molecule level. With the growing interest in the role of RNA localization and dynamics in health and disease, 2Me/PSLOOP MBs could enable new discoveries in RNA research.
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Affiliation(s)
- Dan Zhao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Na Qu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Mingming Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Zhao Ma
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA, 52241, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.
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17
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Pellegrino M, Sciambi A, Yates JL, Mast JD, Silver C, Eastburn DJ. RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures. BMC Genomics 2016; 17:361. [PMID: 27189161 PMCID: PMC4869385 DOI: 10.1186/s12864-016-2694-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/04/2016] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Rare cell subtypes can profoundly impact the course of human health and disease, yet their presence within a sample is often missed with bulk molecular analysis. Single-cell analysis tools such as FACS, FISH-FC and single-cell barcode-based sequencing can investigate cellular heterogeneity; however, they have significant limitations that impede their ability to identify and transcriptionally characterize many rare cell subpopulations. RESULTS PCR-activated cell sorting (PACS) is a novel cytometry method that uses single-cell TaqMan PCR reactions performed in microfluidic droplets to identify and isolate cell subtypes with high-throughput. Here, we extend this method and demonstrate that PACS enables high-dimensional molecular profiling on TaqMan-targeted cells. Using a random priming RNA-Seq strategy, we obtained high-fidelity transcriptome measurements following PACS sorting of prostate cancer cells from a heterogeneous population. The sequencing data revealed prostate cancer gene expression profiles that were obscured in the unsorted populations. Single-cell expression analysis with PACS was subsequently used to confirm a number of the differentially expressed genes identified with RNA sequencing. CONCLUSIONS PACS requires minimal sample processing, uses readily available TaqMan assays and can isolate cell subtypes with high sensitivity. We have now validated a method for performing next-generation sequencing on mRNA obtained from PACS isolated cells. This capability makes PACS well suited for transcriptional profiling of rare cells from complex populations to obtain maximal biological insight into cell states and behaviors.
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Affiliation(s)
| | - Adam Sciambi
- Mission Bio, Inc., 953 Indiana St., San Francisco, California, 94107, USA
| | - Jamie L Yates
- Mission Bio, Inc., 953 Indiana St., San Francisco, California, 94107, USA
| | - Joshua D Mast
- Mission Bio, Inc., 953 Indiana St., San Francisco, California, 94107, USA
| | - Charles Silver
- Mission Bio, Inc., 953 Indiana St., San Francisco, California, 94107, USA
| | - Dennis J Eastburn
- Mission Bio, Inc., 953 Indiana St., San Francisco, California, 94107, USA.
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18
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Rumman M, Dhawan J, Kassem M. Concise Review: Quiescence in Adult Stem Cells: Biological Significance and Relevance to Tissue Regeneration. Stem Cells 2015; 33:2903-12. [DOI: 10.1002/stem.2056] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 04/10/2015] [Accepted: 04/20/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Mohammad Rumman
- Institute for Stem Cell Biology and Regenerative Medicine (inStem); Bangalore Karnataka India
- Manipal University; Manipal Karnataka India
| | - Jyotsna Dhawan
- Institute for Stem Cell Biology and Regenerative Medicine (inStem); Bangalore Karnataka India
- CSIR-Center for Cell and Molecular Biology (CCMB); Hyderabad Telangana India
| | - Moustapha Kassem
- Laboratory for Molecular Endocrinology (KMEB), Department of Endocrinology and Metabolism; University Hospital of Odense; Odense Denmark
- Danish Stem Cell Center (DanStem), Panum Institute; University of Copenhagen; Copenhagen Denmark
- Stem cell Unit, Department of Anatomy, College of Medicine; King Saud University; Kingdom of Saudi Arabia
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19
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Giraldo-Vela JP, Kang W, McNaughton RL, Zhang X, Wile BM, Tsourkas A, Bao G, Espinosa HD. Single-cell detection of mRNA expression using nanofountain-probe electroporated molecular beacons. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:2386-91. [PMID: 25641752 PMCID: PMC6016387 DOI: 10.1002/smll.201401137] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Indexed: 05/18/2023]
Abstract
New techniques for single-cell analysis enable new discoveries in gene expression and systems biology. Time-dependent measurements on individual cells are necessary, yet the common single-cell analysis techniques used today require lysing the cell, suspending the cell, or long incubation times for transfection, thereby interfering with the ability to track an individual cell over time. Here a method for detecting mRNA expression in live single cells using molecular beacons that are transfected into single cells by means of nanofountain probe electroporation (NFP-E) is presented. Molecular beacons are oligonucleotides that emit fluorescence upon binding to an mRNA target, rendering them useful for spatial and temporal studies of live cells. The NFP-E is used to transfect a DNA-based beacon that detects glyceraldehyde 3-phosphate dehydrogenase and an RNA-based beacon that detects a sequence cloned in the green fluorescence protein mRNA. It is shown that imaging analysis of transfection and mRNA detection can be performed within seconds after electroporation and without disturbing adhered cells. In addition, it is shown that time-dependent detection of mRNA expression is feasible by transfecting the same single cell at different time points. This technique will be particularly useful for studies of cell differentiation, where several measurements of mRNA expression are required over time.
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Affiliation(s)
- Juan P Giraldo-Vela
- iNfinitesimal LLC, Skokie, IL, 60077, USA
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Wonmo Kang
- iNfinitesimal LLC, Skokie, IL, 60077, USA
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Rebecca L McNaughton
- iNfinitesimal LLC, Skokie, IL, 60077, USA
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Xuemei Zhang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Brian M Wile
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Horacio D Espinosa
- iNfinitesimal LLC, Skokie, IL, 60077, USA
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
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20
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Guo Y, Lu Z, Cohen IS, Scarlata S. Development of a universal RNA beacon for exogenous gene detection. Stem Cells Transl Med 2015; 4:476-82. [PMID: 25769653 DOI: 10.5966/sctm.2014-0166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 01/22/2015] [Indexed: 01/29/2023] Open
Abstract
Stem cell therapy requires a nontoxic and high-throughput method to achieve a pure cell population to prevent teratomas that can occur if even one cell in the implant has not been transformed. A promising method to detect and separate cells expressing a particular gene is RNA beacon technology. However, developing a successful, specific beacon to a particular transfected gene can take months to develop and in some cases is impossible. Here, we report on an off-the-shelf universal beacon that decreases the time and cost of applying beacon technology to select any living cell population transfected with an exogenous gene.
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Affiliation(s)
- Yuanjian Guo
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Zhongju Lu
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Ira Stephen Cohen
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Suzanne Scarlata
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
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21
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Molecular beacon-based detection and isolation of working-type cardiomyocytes derived from human pluripotent stem cells. Biomaterials 2015; 50:176-85. [PMID: 25736507 DOI: 10.1016/j.biomaterials.2015.01.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 01/07/2023]
Abstract
Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) provide a potential source of cells to repair injured ventricular myocardium. CM differentiation cultures contain non-cardiac cells and CMs of both nodal and working subtypes. Direct application of such cultures in clinical studies could induce arrhythmias; thus, further purification of working-type CMs from heterogeneous cultures is desirable. Here, we designed 10 molecular beacons (MBs) targeting NPPA mRNA, a marker associated with working-type CMs and highly up-regulated during differentiation. We examined these MBs by solution assays and established their specificity using NPPA-overexpressing CHO cells as well as hPSC-CMs. We selected one MB for subsequent CM subtype isolation using fluorescence-activated cell sorting because the signal-to-background ratio was the highest for this MB in solution assays and a linear correlation was observed between MB signals and the CM purity in differentiation cultures. Compared with cells with low MB signals, cells positively selected based on MB signal had higher expression levels of genes associated with working-type CMs and lower expression levels of genes associated with nodal-type CMs. Therefore, the MB-based method is capable of separating working-type CMs from nodal-type CMs with high specificity and throughput, potentially providing working-type CMs for biomedical applications.
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22
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Wile BM, Ban K, Yoon YS, Bao G. Molecular beacon-enabled purification of living cells by targeting cell type-specific mRNAs. Nat Protoc 2014; 9:2411-24. [PMID: 25232937 PMCID: PMC4326061 DOI: 10.1038/nprot.2014.154] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular beacons (MBs) are dual-labeled oligonucleotides that fluoresce only in the presence of complementary mRNA. The use of MBs to target specific mRNAs allows sorting of specific cells from a mixed cell population. In contrast to existing approaches that are limited by available surface markers or selectable metabolic characteristics, the MB-based method enables the isolation of a wide variety of cells. For example, the ability to purify specific cell types derived from pluripotent stem cells (PSCs) is important for basic research and therapeutics. In addition to providing a general protocol for MB design, validation and nucleofection into cells, we describe how to isolate a specific cell population from differentiating PSCs. By using this protocol, we have successfully isolated cardiomyocytes differentiated from mouse or human PSCs (hPSCs) with ∼ 97% purity, as confirmed by electrophysiology and immunocytochemistry. After designing MBs, their ordering and validation requires 2 weeks, and the isolation process requires 3 h.
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Affiliation(s)
- Brian M. Wile
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Kiwon Ban
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Young-Sup Yoon
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
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23
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Soltanian S, Dehghani H, Matin MM, Bahrami AR. Expression analysis of BORIS during pluripotent, differentiated, cancerous, and non-cancerous cell states. Acta Biochim Biophys Sin (Shanghai) 2014; 46:647-58. [PMID: 24928684 DOI: 10.1093/abbs/gmu045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BORIS/CTCFL is an 11 zinc finger protein, which is the paralog of CTCF, a ubiquitously expressed protein with diverse roles in gene expression and chromatin organization. Several studies have shown that the expression of BORIS is restricted to normal adult testis, pluripotent cells, and diverse cancer cell lines. Thus, it is known as a cancer-testis (CT) gene that has been hypothesized to exhibit oncogenic properties and to be involved in cancer cell proliferation. On the contrary, other reports have shown that its expression is more widespread and can be detected in differentiated and normal somatic cells; hence, it might have roles in general cellular functions. The present study was aimed to analyze the expression of BORIS in different cell states of pluripotent, differentiated, cancerous and non-cancerous.We found that the two cell states of pluripotency and differentiation are not accompanied with significant variations of BORIS expression. Furthermore, Boris transcripts were detected at approximately the same level in cancer and non-cancer cell lines. These findings suggest that, in contrast to some previous reports, the expression of mouse BORIS is not limited to only cancerous cells or pluripotent cell states.
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24
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Klemm S, Semrau S, Wiebrands K, Mooijman D, Faddah DA, Jaenisch R, van Oudenaarden A. Transcriptional profiling of cells sorted by RNA abundance. Nat Methods 2014; 11:549-551. [PMID: 24681693 PMCID: PMC4174458 DOI: 10.1038/nmeth.2910] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 02/20/2014] [Indexed: 11/09/2022]
Abstract
We have developed a quantitative technique for sorting cells based on endogenous RNA abundance with a molecular resolution of 10-20 transcripts. We demonstrate efficient and unbiased RNA extraction from transcriptionally sorted cells and report a high fidelity transcriptome measurement of (mouse) induced pluripotent stem cells (iPSCs) isolated from a heterogeneous reprogramming culture. This method is broadly applicable to profiling transcriptionally distinct cellular states without requiring antibodies or transgenic fluorescent proteins.
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Affiliation(s)
- Sandy Klemm
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Stefan Semrau
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Kay Wiebrands
- Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.,University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dylan Mooijman
- Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.,University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dina A Faddah
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States
| | - Rudolf Jaenisch
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States
| | - Alexander van Oudenaarden
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States.,Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.,University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
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25
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Kummer S, Knoll A, Herrmann A, Seitz O. Sequence-specific imaging of influenza A mRNA in living infected cells using fluorescent FIT-PNA. Methods Mol Biol 2014; 1039:291-301. [PMID: 24026704 DOI: 10.1007/978-1-62703-535-4_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Significant efforts have been devoted to the development of techniques allowing the investigation of viral mRNA progression during the replication cycle. We herein describe the use of sequence-specific FIT-PNA (Forced Intercalation Peptide Nucleic Acids) probes which contain a single intercalator serving as an artificial fluorescent nucleobase. FIT-PNA probes are not degraded by enzymes, neither by nucleases nor by proteases, and provide for both high sensitivity and high target specificity under physiological conditions inside the infected living host cell.
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26
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Desai HV, Voruganti IS, Jayasuriya C, Chen Q, Darling EM. Live-cell, temporal gene expression analysis of osteogenic differentiation in adipose-derived stem cells. Tissue Eng Part A 2014; 20:899-907. [PMID: 24367991 PMCID: PMC3938923 DOI: 10.1089/ten.tea.2013.0761] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 11/12/2022] Open
Abstract
Adipose-derived stem cells (ASCs) are a widely investigated type of mesenchymal stem cells with great potential for musculoskeletal regeneration. However, the use of ASCs is complicated by their cellular heterogeneity, which exists at both the population and single-cell levels. This study demonstrates a live-cell assay to investigate gene expression in ASCs undergoing osteogenesis using fluorescently tagged DNA hybridization probes called molecular beacons. A molecular beacon was designed to target the mRNA sequence for alkaline phosphatase (ALPL), a gene characteristically expressed during early osteogenesis. The percentage of cells expressing this gene in a population was monitored daily to quantify the uniformity of the differentiation process. Differentiating ASC populations were repeatedly measured in a nondestructive fashion over a 10-day period to obtain temporal gene expression data. Results showed consistent expression patterns for the investigated osteogenic genes in response to induction medium. Peak signal level, indicating when the most cells expressed ALPL at once, was observed on days 3-5. The differentiation response of sample populations was generally uniform when assessed on a well-by-well basis over time. The expression of alkaline phosphatase is consistent with previous studies of osteogenic differentiation, suggesting that molecular beacons are a viable means of monitoring the spatiotemporal gene expression of live, differentiating ASCs.
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Affiliation(s)
- Hetal V. Desai
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island
| | - Indu S. Voruganti
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island
| | - Chathuraka Jayasuriya
- Molecular Biology Laboratory, Department of Orthopaedics, Brown University, Providence, Rhode Island
| | - Qian Chen
- Molecular Biology Laboratory, Department of Orthopaedics, Brown University, Providence, Rhode Island
| | - Eric M. Darling
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Center for Biomedical Engineering, Department of Orthopaedics, School of Engineering, Brown University, Providence, Rhode Island
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27
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Zhang X, Zajac AL, Huang L, Behlke MA, Tsourkas A. Imaging the directed transport of single engineered RNA transcripts in real-time using ratiometric bimolecular beacons. PLoS One 2014; 9:e85813. [PMID: 24454933 PMCID: PMC3893274 DOI: 10.1371/journal.pone.0085813] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/02/2013] [Indexed: 11/26/2022] Open
Abstract
The relationship between RNA expression and cell function can often be difficult to decipher due to the presence of both temporal and sub-cellular processing of RNA. These intricacies of RNA regulation can often be overlooked when only acquiring global measurements of RNA expression. This has led to development of several tools that allow for the real-time imaging of individual engineered RNA transcripts in living cells. Here, we describe a new technique that utilizes an oligonucleotide-based probe, ratiometric bimolecular beacon (RBMB), to image RNA transcripts that were engineered to contain 96-tandem repeats of the RBMB target sequence in the 3′-untranslated region. Binding of RBMBs to the target RNA resulted in discrete bright fluorescent spots, representing individual transcripts, that could be imaged in real-time. Since RBMBs are a synthetic probe, the use of photostable, bright, and red-shifted fluorophores led to a high signal-to-background. RNA motion was readily characterized by both mean squared displacement and moment scaling spectrum analyses. These analyses revealed clear examples of directed, Brownian, and subdiffusive movements.
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Affiliation(s)
- Xuemei Zhang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Allison L. Zajac
- Cell Biology and Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lingyan Huang
- Integrated DNA Technologies, Inc., Coralville, Iowa, United States of America
| | - Mark A. Behlke
- Integrated DNA Technologies, Inc., Coralville, Iowa, United States of America
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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28
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Wang K, Huang J, Yang X, He X, Liu J. Recent advances in fluorescent nucleic acid probes for living cell studies. Analyst 2014; 138:62-71. [PMID: 23154215 DOI: 10.1039/c2an35254k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Living cell studies can offer tremendous opportunities for biological and disease studies. Due to their high sensitivity and selectivity, minimum interference with living biological systems, ease of design and synthesis, fluorescent nucleic acid probes (FNAPs) have been widely used in living cell studies, such as for intracellular detection, cell detection, and cell-to-cell communication. Here, we review the general requirements and the recent developments in FNAPs for living cell studies. We broadly classify these designs as hybridization probes and aptamer probes. For hybridization probes, we describe recently developed designs, such as nanomaterial-based and amplification-based hybridization probes. For aptamer probes, we discuss four general paradigms that have appeared most frequently in the literature: nanomaterial-based, nanomachine-based, cell surface-anchored and activatable aptamer probe designs in vivo. FNAPs promise to open up new and exciting opportunities in biological marks detection for a wide range of biological and medical applications.
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Affiliation(s)
- Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Changsha 410082, China.
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29
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Ilieva M, Della Vedova P, Hansen O, Dufva M. Tracking neuronal marker expression inside living differentiating cells using molecular beacons. Front Cell Neurosci 2013; 7:266. [PMID: 24431988 PMCID: PMC3883158 DOI: 10.3389/fncel.2013.00266] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/03/2013] [Indexed: 01/14/2023] Open
Abstract
Monitoring gene expression is an important tool for elucidating mechanisms of cellular function. In order to monitor gene expression during nerve cell development, molecular beacon (MB) probes targeting markers representing different stages of neuronal differentiation were designed and synthesized as 2'-O-methyl RNA backbone oligonucleotides. MBs were transfected into human mesencephalic cells (LUHMES) using streptolysin-O-based membrane permeabilization. Mathematical modeling, simulations and experiments indicated that MB concentration was equal to the MB in the transfection medium after 10 min transfection. The cells will then each contain about 60,000 MBs. Gene expression was detected at different time points using fluorescence microscopy. Nestin and NeuN mRNA were expressed in approximately 35% of the LUHMES cells grown in growth medium, and in 80–90% of cells after differentiation. MAP2 and tyrosine hydroxylase mRNAs were expressed 2 and 3 days post induction of differentiation, respectively. Oct 4 was not detected with MB in these cells and signal was not increased over time suggesting that MB are generally stable inside the cells. The gene expression changes measured using MBs were confirmed using qRT-PCR. These results suggest that MBs are simple to use sensors inside living cell, and particularly useful for studying dynamic gene expression in heterogeneous cell populations.
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Affiliation(s)
- Mirolyuba Ilieva
- Department of Micro- and Nanotechnology, Technical University of Denmark Kgs. Lyngby, Denmark
| | - Paolo Della Vedova
- Department of Micro- and Nanotechnology, Technical University of Denmark Kgs. Lyngby, Denmark
| | - Ole Hansen
- Department of Micro- and Nanotechnology, Technical University of Denmark Kgs. Lyngby, Denmark ; Center for Individual Nanoparticle Functionality, Technical University of Denmark Kgs. Lyngby, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology, Technical University of Denmark Kgs. Lyngby, Denmark
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30
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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A quencher-free molecular beacon design based on pyrene excimer fluorescence using pyrene-labeled UNA (unlocked nucleic acid). Bioorg Med Chem 2013; 21:6186-90. [DOI: 10.1016/j.bmc.2013.04.062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/08/2013] [Accepted: 04/16/2013] [Indexed: 11/18/2022]
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Ban K, Wile B, Kim S, Park HJ, Byun J, Cho KW, Saafir T, Song MK, Yu SP, Wagner M, Bao G, Yoon YS. Purification of cardiomyocytes from differentiating pluripotent stem cells using molecular beacons that target cardiomyocyte-specific mRNA. Circulation 2013; 128:1897-909. [PMID: 23995537 DOI: 10.1161/circulationaha.113.004228] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Although methods for generating cardiomyocytes from pluripotent stem cells have been reported, current methods produce heterogeneous mixtures of cardiomyocytes and noncardiomyocyte cells. Here, we report an entirely novel system in which pluripotent stem cell-derived cardiomyocytes are purified by cardiomyocyte-specific molecular beacons (MBs). MBs are nanoscale probes that emit a fluorescence signal when hybridized to target mRNAs. METHOD AND RESULTS Five MBs targeting mRNAs of either cardiac troponin T or myosin heavy chain 6/7 were generated. Among 5 MBs, an MB that targeted myosin heavy chain 6/7 mRNA (MHC1-MB) identified up to 99% of HL-1 cardiomyocytes, a mouse cardiomyocyte cell line, but <3% of 4 noncardiomyocyte cell types in flow cytometry analysis, which indicates that MHC1-MB is specific for identifying cardiomyocytes. We delivered MHC1-MB into cardiomyogenically differentiated pluripotent stem cells through nucleofection. The detection rate of cardiomyocytes was similar to the percentages of cardiac troponin T- or cardiac troponin I-positive cardiomyocytes, which supports the specificity of MBs. Finally, MHC1-MB-positive cells were sorted by fluorescence-activated cell sorter from mouse and human pluripotent stem cell differentiating cultures, and ≈97% cells expressed cardiac troponin T or cardiac troponin I as determined by flow cytometry. These MB-based sorted cells maintained their cardiomyocyte characteristics, which was verified by spontaneous beating, electrophysiological studies, and expression of cardiac proteins. When transplanted in a myocardial infarction model, MB-based purified cardiomyocytes improved cardiac function and demonstrated significant engraftment for 4 weeks without forming tumors. CONCLUSIONS We developed a novel cardiomyocyte selection system that allows production of highly purified cardiomyocytes. These purified cardiomyocytes and this system can be valuable for cell therapy and drug discovery.
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Affiliation(s)
- Kiwon Ban
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Brian Wile
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA
| | - Sangsung Kim
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Hun-Jun Park
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA.,Division of Cardiology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jaemin Byun
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Kyu-Won Cho
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Talib Saafir
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA
| | - Ming-Ke Song
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA
| | - Shan Ping Yu
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA
| | - Mary Wagner
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA
| | - Young-Sup Yoon
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
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Ilieva M, Dufva M. SOX2 and OCT4 mRNA-expressing cells, detected by molecular beacons, localize to the center of neurospheres during differentiation. PLoS One 2013; 8:e73669. [PMID: 24013403 PMCID: PMC3754928 DOI: 10.1371/journal.pone.0073669] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/19/2013] [Indexed: 12/26/2022] Open
Abstract
Neurospheres are used as in vitro assay to measure the properties of neural stem cells. To investigate the molecular and phenotypic heterogeneity of neurospheres, molecular beacons (MBs) targeted against the stem cell markers OCT4 and SOX2 were designed, and synthesized with a 2'-O-methyl RNA backbone. OCT4 and SOX2 MBs were transfected into human embryonic mesencephalon derived cells, which spontaneously form neurospheres when grown on poly-L-ornitine/fibronectin matrix and medium complemented with bFGF. OCT4 and SOX2 gene expression were tracked in individual cell using the MBs. Quantitative image analysis every day for seven days showed that the OCT4 and SOX2 mRNA-expressing cells clustered in the centre of the neurospheres cultured in differentiation medium. By contrast, cells at the periphery of the differentiating spheres developed neurite outgrowths and expressed the tyrosine hydroxylase protein, indicating terminal differentiation. Neurospheres cultured in growth medium contained OCT4 and SOX2-positive cells distributed throughout the entire sphere, and no differentiating neurones. Gene expression of SOX2 and OCT4 mRNA detected by MBs correlated well with gene and protein expression measured by qRT-PCR and immunostaining, respectively. These experimental data support the theoretical model that stem cells cluster in the centre of neurospheres, and demonstrate the use of MBs for the spatial localization of specific gene-expressing cells within heterogeneous cell populations.
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Affiliation(s)
- Mirolyuba Ilieva
- Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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Tosun Z, McFetridge PS. Improved recellularization of ex vivo vascular scaffolds using directed transport gradients to modulate ECM remodeling. Biotechnol Bioeng 2013; 110:2035-45. [PMID: 23613430 PMCID: PMC4438987 DOI: 10.1002/bit.24934] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 12/16/2012] [Accepted: 12/18/2012] [Indexed: 01/09/2023]
Abstract
The regeneration of functional, clinically viable, tissues from acellular ex vivo tissues has been problematic largely due to poor nutrient transport conditions that limit cell migration and integration. Compounding these issues are subcellular pore sizes that necessarily requires extracellular matrix (ECM) remodeling in order for cells to migrate and regenerate the tissue. The aim of the present work was to create a directed growth environment that allows cells to fully populate an ex vivo-derived vascular scaffold and maintain viability over extended periods. Three different culture conditions using single (one nutrient source) or dual perfusion bioreactor systems (two nutrients sources) were designed to assess the effect of pressure and nutrient gradients under either low (50/30 mmHg) or high (120/80) relative pressure conditions. Human myofibroblasts were seeded to the ablumenal periphery of an ex vivo-derived vascular scaffold using a collagen/hydrogel cell delivery system. After 30 days culture, total cell density was consistent between groups; however, significant variation was noted in cell distribution and construct mechanics as a result of differing perfusion conditions. The most aggressive transport gradient was developed by the single perfusion low-pressure circuits and resulted in a higher proportion of cells migrating across the scaffold toward the vessel lumen (nutrient source). These investigations illustrate the influence of directed nutrient gradients where precisely controlled perfusion conditions significantly affects cell migration, distribution and function, resulting in pronounced effects on construct mechanics during early remodeling events.
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Affiliation(s)
- Zehra Tosun
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences Building, JG-56, Gainesville, FL 32611, USA
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35
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Zhang X, Song Y, Shah AY, Lekova V, Raj A, Huang L, Behlke MA, Tsourkas A. Quantitative assessment of ratiometric bimolecular beacons as a tool for imaging single engineered RNA transcripts and measuring gene expression in living cells. Nucleic Acids Res 2013; 41:e152. [PMID: 23814183 PMCID: PMC3753654 DOI: 10.1093/nar/gkt561] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recently, we developed an oligonucleotide-based probe, ratiometric bimolecular beacon (RBMB), which generates a detectable fluorescent signal in living cells that express the target RNA. Here, we show that RBMBs can also be used to image single RNA transcripts in living cells, when the target RNA is engineered to contain as few as four hybridization sites. Moreover, comparison with single-molecule fluorescence in situ hybridization confirmed that RBMBs could be used to accurately quantify the number of RNA transcripts within individual cells. Measurements of gene expression could be acquired within 30 min and using a wide range of RBMB concentrations. The ability to acquire accurate measurements of RNA copy number in both HT-1080 cells and CHO cells also suggests that RBMBs can be used to image and quantify single RNA transcripts in a wide range of cell lines. Overall, these findings highlight the robustness and versatility of RBMBs as a tool for imaging RNA in live cells. We envision that the unique capabilities of RBMBs will open up new avenues for RNA research.
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Affiliation(s)
- Xuemei Zhang
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA, Department of Biology, University of Pennsylvania, 433 S. University Ave, 102 Leidy Laboratories, Philadelphia, PA 19104, USA and Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA
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36
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Oligonucleotide optical switches for intracellular sensing. Anal Bioanal Chem 2013; 405:6181-96. [PMID: 23793395 DOI: 10.1007/s00216-013-7086-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/16/2013] [Accepted: 05/17/2013] [Indexed: 12/16/2022]
Abstract
Fluorescence imaging coupled with nanotechnology is making possible the development of powerful tools in the biological field for applications such as cellular imaging and intracellular messenger RNA monitoring and detection. The delivery of fluorescent probes into cells and tissues is currently receiving growing interest because such molecules, often coupled to nanodimensional materials, can conveniently allow the preparation of small tools to spy on cellular mechanisms with high specificity and sensitivity. The purpose of this review is to provide an exhaustive overview of current research in oligonucleotide optical switches for intracellular sensing with a focus on the engineering methods adopted for these oligonucleotides and the more recent and fascinating techniques for their internalization into living cells. Oligonucleotide optical switches can be defined as specifically designed short nucleic acid molecules capable of turning on or modifying their light emission on molecular interaction with well-defined molecular targets. Molecular beacons, aptamer beacons, hybrid molecular probes, and simpler linear oligonucleotide switches are the most promising optical nanosensors proposed in recent years. The intracellular targets which have been considered for sensing are a plethora of messenger-RNA-expressing cellular proteins and enzymes, or, directly, proteins or small molecules in the case of sensing through aptamer-based switches. Engineering methods, including modification of the oligonucleotide itself with locked nucleic acids, peptide nucleic acids, or L-DNA nucleotides, have been proposed to enhance the stability of nucleases and to prevent false-negative and high background optical signals. Conventional delivery techniques are treated here together with more innovative methods based on the coupling of the switches with nano-objects.
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Desai HV, Voruganti IS, Jayasuriya C, Chen Q, Darling EM. Live-cell, temporal gene expression analysis of osteogenic differentiation in adipose-derived stem cells. Tissue Eng Part A 2013; 19:40-8. [PMID: 22840182 PMCID: PMC3530940 DOI: 10.1089/ten.tea.2012.0127] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 07/16/2012] [Indexed: 12/25/2022] Open
Abstract
Adipose-derived stem cells (ASCs) are a widely investigated type of mesenchymal stem cell with great potential for musculoskeletal regeneration. However, use of ASCs is complicated by their cellular heterogeneity, which exists at both the population and single-cell levels. This study demonstrates a live-cell assay to investigate gene expression in ASCs undergoing osteogenesis using fluorescently tagged DNA hybridization probes called molecular beacons. Three molecular beacons were designed to target mRNA sequences for alkaline phosphatase, type I collagen, and osteocalcin (ALPL, COL1A1, and BGLAP), genes characteristically expressed during osteogenesis. The percentage of cells expressing these genes in a population was monitored daily to quantify the uniformity of the differentiation process. Differentiating ASC populations were repeatedly measured in a nondestructive fashion over a 21-day period to obtain temporal gene expression data. Results showed consistent expression patterns for the investigated osteogenic genes in response to induction medium. Peak expression was observed at days 3-4 for ALPL, day 14 for COL1A1, and day 21 for BGLAP. Additionally, the differentiation response of sample populations became more uniform after 2 weeks in osteogenic induction medium, suggesting a syncing of ASCs occurs over time. These findings are consistent with previous studies of osteogenic differentiation and suggest that molecular beacons are a viable means to monitor the spatiotemporal gene expression of live, differentiating ASCs.
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Affiliation(s)
- Hetal V. Desai
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island
| | - Indu S. Voruganti
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island
| | - Chathuraka Jayasuriya
- Molecular Biology Laboratory, Department of Orthopaedics, Brown University, Providence, Rhode Island
| | - Qian Chen
- Molecular Biology Laboratory, Department of Orthopaedics, Brown University, Providence, Rhode Island
| | - Eric M. Darling
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island
- Department of Orthopaedics, Brown University, Providence, Rhode Island
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island
- School of Engineering, Brown University, Providence, Rhode Island
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Larsson HM, Lee ST, Roccio M, Velluto D, Lutolf MP, Frey P, Hubbell JA. Sorting live stem cells based on Sox2 mRNA expression. PLoS One 2012; 7:e49874. [PMID: 23209609 PMCID: PMC3507951 DOI: 10.1371/journal.pone.0049874] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/15/2012] [Indexed: 01/08/2023] Open
Abstract
While cell sorting usually relies on cell-surface protein markers, molecular beacons (MBs) offer the potential to sort cells based on the presence of any expressed mRNA and in principle could be extremely useful to sort rare cell populations from primary isolates. We show here how stem cells can be purified from mixed cell populations by sorting based on MBs. Specifically, we designed molecular beacons targeting Sox2, a well-known stem cell marker for murine embryonic (mES) and neural stem cells (NSC). One of our designed molecular beacons displayed an increase in fluorescence compared to a nonspecific molecular beacon both in vitro and in vivo when tested in mES and NSCs. We sorted Sox2-MB+SSEA1+ cells from a mixed population of 4-day retinoic acid-treated mES cells and effectively isolated live undifferentiated stem cells. Additionally, Sox2-MB+ cells isolated from primary mouse brains were sorted and generated neurospheres with higher efficiency than Sox2-MB− cells. These results demonstrate the utility of MBs for stem cell sorting in an mRNA-specific manner.
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Affiliation(s)
- Hans M. Larsson
- Laboratory for Regenerative Medicine and Pharmacobiology, Institute for Bioengineering, School of Life Sciences and School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Seung Tae Lee
- Laboratory for Regenerative Medicine and Pharmacobiology, Institute for Bioengineering, School of Life Sciences and School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Laboratory of Stem Cell Biomodulation, Department of Animal Biotechnology, Kangwon National University, Chuncheon, Korea
| | - Marta Roccio
- Laboratory of Stem Cell Bioengineering, Institute for Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Diana Velluto
- Laboratory for Regenerative Medicine and Pharmacobiology, Institute for Bioengineering, School of Life Sciences and School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Matthias P. Lutolf
- Laboratory of Stem Cell Bioengineering, Institute for Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Peter Frey
- Laboratory for Regenerative Medicine and Pharmacobiology, Institute for Bioengineering, School of Life Sciences and School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Laboratory of Experimental Pediatric Urology, Department of Pediatric Urology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Jeffrey A. Hubbell
- Laboratory for Regenerative Medicine and Pharmacobiology, Institute for Bioengineering, School of Life Sciences and School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail:
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Hellebust A, Richards-Kortum R. Advances in molecular imaging: targeted optical contrast agents for cancer diagnostics. Nanomedicine (Lond) 2012; 7:429-45. [PMID: 22385200 DOI: 10.2217/nnm.12.12] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Over the last three decades, our understanding of the molecular changes associated with cancer development and progression has advanced greatly. This has led to new cancer therapeutics targeted against specific molecular pathways; such therapies show great promise to reduce mortality, in part by enabling physicians to tailor therapy for patients based on a molecular profile of their tumor. Unfortunately, the tools for definitive cancer diagnosis - light microscopic examination of biopsied tissue stained with nonspecific dyes - remain focused on the analysis of tissue ex vivo. There is an important need for new clinical tools to support the molecular diagnosis of cancer. Optical molecular imaging is emerging as a technique to help meet this need. Targeted, optically active contrast agents can specifically label extra- and intracellular biomarkers of cancer. Optical images can be acquired in real time with high spatial resolution to image-specific molecular targets, while still providing morphologic context. This article reviews recent advances in optical molecular imaging, highlighting the advances in technology required to improve early cancer detection, guide selection of targeted therapy and rapidly evaluate therapeutic efficacy.
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Affiliation(s)
- Anne Hellebust
- Rice University, Bioengineering Department, 6100 Main Street, Bioengineering, MS 142, Houston, TX 77005-1892, USA
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40
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Greve B, Kelsch R, Spaniol K, Eich HT, Götte M. Flow cytometry in cancer stem cell analysis and separation. Cytometry A 2012; 81:284-93. [PMID: 22311742 DOI: 10.1002/cyto.a.22022] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 12/21/2011] [Accepted: 01/07/2012] [Indexed: 12/19/2022]
Abstract
In recent years, a special type of cancer cell--the cancer stem cell (CSC)--has been identified and characterized for different tumors. CSCs may be responsible for the recurrence of a tumor following a primarily successful therapy and are thought to bear a high metastatic potential. For the development of efficient treatment strategies, the establishment of reliable methods for the identification and effective isolation of CSCs is imperative. Similar to their stem cell counterparts in bone marrow or small intestine, different cluster of differentiation surface antigens have been characterized, thus enabling researchers to identify them within the tumor bulk and to determine their degree of differentiation. In addition, functional properties characteristic of stem cells can be measured. Side population analysis is based on the stem cell-specific activity of certain ATP-binding cassette transporter proteins, which are able to transport fluorescent dyes out of the cells. Furthermore, the stem cell-specific presence of aldehyde dehydrogenase isoform 1 can be used for CSC labeling. However, the flow cytometric analysis of these CSC functional features requires specific technical adjustments. This review focuses on the principles and strategies of the flow cytometric analysis of CSCs and provides an overview of current protocols as well as technical requirements and pitfalls. A special focus is set on side population analysis and analysis of ALDH activity. Flow cytometry-based sorting principles and future flow cytometric applications for CSC analysis are also discussed.
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Affiliation(s)
- Burkhard Greve
- Department of Radiotherapy, University Hospital, 48149 Münster, Germany.
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41
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Beksac M, Preffer F. Is it time to revisit our current hematopoietic progenitor cell quantification methods in the clinic? Bone Marrow Transplant 2011; 47:1391-6. [PMID: 22139068 DOI: 10.1038/bmt.2011.240] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In the clinical practice of hematopoietic SCT, the minimum numbers of cells required for a successful engraftment are defined on the basis of their CD45 and CD34 expression profiles. However, the quantity of earlier progenitors or CD34-positive cells at different differentiation stages within stem cell grafts is not generally taken into consideration. During the last decade, various teams have quantified the number of cells expressing various combinations of CD34, CD38, CD133, CD90 co-expression and/or aldehyde dehydrogenase functional capacity using flow cytometry. Some of these studies resulted in the greater appreciation that combinations of these Ags were associated with varied myeloid, erythroid and platelet engraftment rates whereas others showed that the relative absence or presence of these markers could define cells responsible for either short- or long-term engraftment. These findings were also extended to differences between progenitor cell populations found within BM vs peripheral or cord-blood grafts. Cells harvested from donors are also generally frozen and stored; thawed cells have variable levels of viability and functional capacity based on the time tested post thaw, which also can be assessed by flow cytometry. Finally, flow cytometry has the potential for analysis of cells carrying a mesenchymal stem cell phenotype, which may be quiescent within some of the stem cell products. This review will address the need for stem cell subpopulation quantification and summarize existing published data to identify some Ags and functional characteristics that can be applicable to daily clinical practice.
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Affiliation(s)
- M Beksac
- Ankara University School of Medicine, Department of Hematology, Ankara, Turkey.
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42
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Chen AK, Rhee WJ, Bao G, Tsourkas A. Delivery of molecular beacons for live-cell imaging and analysis of RNA. Methods Mol Biol 2011; 714:159-74. [PMID: 21431740 DOI: 10.1007/978-1-61779-005-8_10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the past decade, a variety of oligonucleotide-based probes have been developed that allow for direct visualization of RNA molecules in living cells. Of these, molecular beacons have garnered a particularly high degree of interest due to their simple yet exquisite unimolecular stem-loop design that allows for the efficient conversion of target recognition into a specific fluorescent signal. As a result of their favorable fluorescent enhancement and their high specificity, molecular beacons have been used for a wide range of applications, including the monitoring of RNA expression and localization in living cells, cancer cell detection, and the study of viral infections. In this chapter we describe a general methodology that can be followed for the imaging and analysis of RNA in living cells using molecular beacons. Several commonly employed methods for delivering molecular beacons into the cytosol are discussed including toxin-based cell membrane permeabilization, microinjection, and microporation. Strategies for acquiring ratiometric measurements are also described.
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Affiliation(s)
- Antony K Chen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
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Chen AK, Davydenko O, Behlke MA, Tsourkas A. Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells. Nucleic Acids Res 2010; 38:e148. [PMID: 20507905 PMCID: PMC2919734 DOI: 10.1093/nar/gkq436] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Numerous studies have utilized molecular beacons (MBs) to image RNA expression in living cells; however, there is growing evidence that the sensitivity of RNA detection is significantly hampered by their propensity to emit false-positive signals. To overcome these limitations, we have developed a new RNA imaging probe called ratiometric bimolecular beacon (RBMB), which combines functional elements of both conventional MBs and siRNA. Analogous to MBs, RBMBs elicit a fluorescent reporter signal upon hybridization to complementary RNA. In addition, an siRNA-like double-stranded domain is used to facilitate nuclear export. Accordingly, live-cell fluorescent imaging showed that RBMBs are localized predominantly in the cytoplasm, whereas MBs are sequestered into the nucleus. The retention of RBMBs within the cytoplasmic compartment led to >15-fold reduction in false-positive signals and a significantly higher signal-to-background compared with MBs. The RBMBs were also designed to possess an optically distinct reference fluorophore that remains unquenched regardless of probe confirmation. This reference dye not only provided a means to track RBMB localization, but also allowed single cell measurements of RBMB fluorescence to be corrected for variations in probe delivery. Combined, these attributes enabled RBMBs to exhibit an improved sensitivity for RNA detection in living cells.
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Affiliation(s)
- Antony K Chen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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44
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Chen AK, Behlke MA, Tsourkas A. Sub-cellular trafficking and functionality of 2'-O-methyl and 2'-O-methyl-phosphorothioate molecular beacons. Nucleic Acids Res 2010; 37:e149. [PMID: 19820111 PMCID: PMC2794186 DOI: 10.1093/nar/gkp837] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Molecular beacons (MBs) have shown great potential for the imaging of RNAs within single living cells; however, the ability to perform accurate measurements of RNA expression can be hampered by false-positives resulting from nonspecific interactions and/or nuclease degradation. These false-positives could potentially be avoided by introducing chemically modified oligonucleotides into the MB design. In this study, fluorescence microscopy experiments were performed to elucidate the subcellular trafficking, false-positive signal generation, and functionality of 2′-O-methyl (2Me) and 2′-O-methyl-phosphorothioate (2MePS) MBs. The 2Me MBs exhibited rapid nuclear sequestration and a gradual increase in fluorescence over time, with nearly 50% of the MBs being opened nonspecifically within 24 h. In contrast, the 2MePS MBs elicited an instantaneous increase in false-positives, corresponding to ∼5–10% of the MBs being open, but little increase was observed over the next 24 h. Moreover, trafficking to the nucleus was slower. After 24 h, both MBs were localized in the nucleus and lysosomal compartments, but only the 2MePS MBs were still functional. When the MBs were retained in the cytoplasm, via conjugation to NeutrAvidin, a significant reduction in false-positives and improvement in functionality was observed. Overall, these results have significant implications for the design and applications of MBs for intracellular RNA measurement.
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Affiliation(s)
- Antony K Chen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 and Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
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