1
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Lazarski CA, Hanley PJ. Review of flow cytometry as a tool for cell and gene therapy. Cytotherapy 2024; 26:103-112. [PMID: 37943204 PMCID: PMC10872958 DOI: 10.1016/j.jcyt.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Quality control testing and analytics are critical for the development and manufacture of cell and gene therapies, and flow cytometry is a key quality control and analytical assay that is used extensively. However, the technical scope of characterization assays and safety assays must keep apace as the breadth of cell therapy products continues to expand beyond hematopoietic stem cell products into producing novel adoptive immune therapies and gene therapy products. Flow cytometry services are uniquely positioned to support the evolving needs of cell therapy facilities, as access to flow cytometers, new antibody clones and improved fluorochrome reagents becomes more egalitarian. This report will outline the features, logistics, limitations and the current state of flow cytometry within the context of cellular therapy.
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Affiliation(s)
- Christopher A Lazarski
- Program for Cell Enhancement and Technology for Immunotherapy, Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA; The George Washington University, Washington, DC, USA.
| | - Patrick J Hanley
- Program for Cell Enhancement and Technology for Immunotherapy, Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA; The George Washington University, Washington, DC, USA.
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2
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Adampourezare M, Hasanzadeh M, Seidi F. Microfluidic assisted recognition of miRNAs towards point-of-care diagnosis: Technical and analytical overview towards biosensing of short stranded single non-coding oligonucleotides. Biomed Pharmacother 2022; 153:113365. [PMID: 35785705 DOI: 10.1016/j.biopha.2022.113365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/02/2022] Open
Abstract
MiRNAs are short stranded single non-coding oligonucleotides that play an important role in regulating gene expression. MiRNAs are stable in RNase enriched environments such as human body fluids and their dysregulation or abnormal abundance in human body fluids as a diagnostic biomarker has been associated with several diseases. Due to the low concentration of miRNAs, it is difficult to detect using interactive methods (ideal detection limit is femtomolar range). However, clinicians lack sensitive and reliable methods for quantifying miRNA. Microfluidic devices integrated with electrochemical, optical (fluorometric, SERs, FRET, colorimetric), electrochemiluminescence and photoelectrochemical signal readout led to development innovative diagnostic device test, can probably overcome the limitations of the traditional methods. In the present review, microfluid methods for the sensitive and selective recognition of miRNA in various biological matrices are surveyed. Also, advantages and limitation of recognition methods on the performance and efficiency of microfluidic based biosensing of miRNAs are critically investigated. Finally, the future perspectives on the diagnosis of disease based on microfluidic analysis of miRNAs are provided.
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Affiliation(s)
- Mina Adampourezare
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran; Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Farzad Seidi
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
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3
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Sempere LF, Azmi AS, Moore A. microRNA-based diagnostic and therapeutic applications in cancer medicine. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1662. [PMID: 33998154 PMCID: PMC8519065 DOI: 10.1002/wrna.1662] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 01/18/2023]
Abstract
It has been almost two decades since the first link between microRNAs and cancer was established. In the ensuing years, this abundant class of short noncoding regulatory RNAs has been studied in virtually all cancer types. This tremendously large body of research has generated innovative technological advances for detection of microRNAs in tissue and bodily fluids, identified the diagnostic, prognostic, and/or predictive value of individual microRNAs or microRNA signatures as potential biomarkers for patient management, shed light on regulatory mechanisms of RNA-RNA interactions that modulate gene expression, uncovered cell-autonomous and cell-to-cell communication roles of specific microRNAs, and developed a battery of viral and nonviral delivery approaches for therapeutic intervention. Despite these intense and prolific research efforts in preclinical and clinical settings, there are a limited number of microRNA-based applications that have been incorporated into clinical practice. We review recent literature and ongoing clinical trials that highlight most promising approaches and standing challenges to translate these findings into viable microRNA-based clinical tools for cancer medicine. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Lorenzo F. Sempere
- Department of Radiology, Precision Health ProgramMichigan State UniversityEast LansingMichiganUSA
| | - Asfar S. Azmi
- Department of OncologyWayne State University School of MedicineDetroitMichiganUSA
- Karmanos Cancer InstituteDetroitMichiganUSA
| | - Anna Moore
- Departments of Radiology and Physiology, Precision Health ProgramMichigan State UniversityEast LansingMichiganUSA
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4
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Nicolet BP, Zandhuis ND, Lattanzio VM, Wolkers MC. Sequence determinants as key regulators in gene expression of T cells. Immunol Rev 2021; 304:10-29. [PMID: 34486113 PMCID: PMC9292449 DOI: 10.1111/imr.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
T cell homeostasis, T cell differentiation, and T cell effector function rely on the constant fine-tuning of gene expression. To alter the T cell state, substantial remodeling of the proteome is required. This remodeling depends on the intricate interplay of regulatory mechanisms, including post-transcriptional gene regulation. In this review, we discuss how the sequence of a transcript influences these post-transcriptional events. In particular, we review how sequence determinants such as sequence conservation, GC content, and chemical modifications define the levels of the mRNA and the protein in a T cell. We describe the effect of different forms of alternative splicing on mRNA expression and protein production, and their effect on subcellular localization. In addition, we discuss the role of sequences and structures as binding hubs for miRNAs and RNA-binding proteins in T cells. The review thus highlights how the intimate interplay of post-transcriptional mechanisms dictate cellular fate decisions in T cells.
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Affiliation(s)
- Benoit P. Nicolet
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Nordin D. Zandhuis
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - V. Maria Lattanzio
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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5
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Freen-van Heeren JJ. Flow-FISH as a Tool for Studying Bacteria, Fungi and Viruses. BIOTECH 2021; 10:21. [PMID: 35822795 PMCID: PMC9245478 DOI: 10.3390/biotech10040021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022] Open
Abstract
Many techniques are currently in use to study microbes. These can be aimed at detecting, identifying, and characterizing bacterial, fungal, and viral species. One technique that is suitable for high-throughput analysis is flow cytometry-based fluorescence in situ hybridization, or Flow-FISH. This technique employs (fluorescently labeled) probes directed against DNA or (m)RNA, for instance targeting a gene or microorganism of interest and provides information on a single-cell level. Furthermore, by combining Flow-FISH with antibody-based protein detection, proteins of interest can be measured simultaneously with genetic material. Additionally, depending on the type of Flow-FISH assay, Flow-FISH can also be multiplexed, allowing for the simultaneous measurement of multiple gene targets and/or microorganisms. Together, this allows for, e.g., single-cell gene expression analysis or identification of (sub)strains in mixed cultures. Flow-FISH has been used in mammalian cells but has also been extensively employed to study diverse microbial species. Here, the use of Flow-FISH for studying microorganisms is reviewed. Specifically, the detection of (intracellular) pathogens, studying microorganism biology and disease pathogenesis, and identification of bacterial, fungal, and viral strains in mixed cultures is discussed, with a particular focus on the viruses EBV, HIV-1, and SARS-CoV-2.
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6
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Nielsen MM, Pedersen JS. miRNA activity inferred from single cell mRNA expression. Sci Rep 2021; 11:9170. [PMID: 33911110 PMCID: PMC8080788 DOI: 10.1038/s41598-021-88480-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/08/2021] [Indexed: 01/26/2023] Open
Abstract
High throughput single-cell RNA sequencing (scRNAseq) can provide mRNA expression profiles for thousands of cells. However, miRNAs cannot currently be studied at the same scale. By exploiting that miRNAs bind well-defined sequence motifs and typically down-regulate target genes, we show that motif enrichment analysis can be used to derive miRNA activity estimates from scRNAseq data. Motif enrichment analyses have traditionally been used to derive binding motifs for regulatory factors, such as miRNAs or transcription factors, that have an effect on gene expression. Here we reverse its use. By starting from the miRNA seed site, we derive a measure of activity for miRNAs in single cells. We first establish the approach on a comprehensive set of bulk TCGA cancer samples (n = 9679), with paired mRNA and miRNA expression profiles, where many miRNAs show a strong correlation with measured expression. By downsampling we show that the method can be used to estimate miRNA activity in sparse data comparable to scRNAseq experiments. We then analyze a human and a mouse scRNAseq data set, and show that for several miRNA candidates, including liver specific miR-122 and muscle specific miR-1 and miR-133a, we obtain activity measures supported by the literature. The methods are implemented and made available in the miReact software. Our results demonstrate that miRNA activities can be estimated at the single cell level. This allows insights into the dynamics of miRNA activity across a range of fields where scRNAseq is applied.
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Affiliation(s)
- Morten Muhlig Nielsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark. .,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark. .,Bioinformatics Research Centre, C.F. Møllers Allé 8, Aarhus University, 8000, Aarhus C, Denmark.
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7
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Deng C, Naler LB, Lu C. Microfluidic epigenomic mapping technologies for precision medicine. LAB ON A CHIP 2019; 19:2630-2650. [PMID: 31338502 PMCID: PMC6697104 DOI: 10.1039/c9lc00407f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Epigenomic mapping of tissue samples generates critical insights into genome-wide regulations of gene activities and expressions during normal development and disease processes. Epigenomic profiling using a low number of cells produced by patient and mouse samples presents new challenges to biotechnologists. In this review, we first discuss the rationale and premise behind profiling epigenomes for precision medicine. We then examine the existing literature on applying microfluidics to facilitate low-input and high-throughput epigenomic profiling, with emphasis on technologies enabling interfacing with next-generation sequencing. We detail assays on studies of histone modifications, DNA methylation, 3D chromatin structures and non-coding RNAs. Finally, we discuss what the future may hold in terms of method development and translational potential.
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Affiliation(s)
- Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
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8
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Wang N, Lu Y, Chen Z, Fan R. Multiplexed PCR-Free Detection of MicroRNAs in Single Cancer Cells Using a DNA-Barcoded Microtrough Array Chip. MICROMACHINES 2019; 10:mi10040215. [PMID: 30934734 PMCID: PMC6523668 DOI: 10.3390/mi10040215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 01/01/2023]
Abstract
MicroRNAs are a class of small RNA molecules that regulate the expression of mRNAs in a wide range of biological processes and are implicated in human health and disease such as cancers. How to measure microRNA profiles in single cells with high throughput is essential to the development of cell-based assays for interrogating microRNA-mediated intratumor heterogeneity and the design of new lab tests for diagnosis and monitoring of cancers. Here, we report on an in situ hybridization barcoding workflow implemented in a sub-nanoliter microtrough array chip for high-throughput and multiplexed microRNA detection at the single cell level. The microtroughs are used to encapsulate single cells that are fixed, permeabilized, and pre-incubated with microRNA detection probes, each of which consists of a capture strand complementary to specific microRNA and a unique reporter strand that can be photocleaved in the microtroughs and subsequently detected by an array of DNA barcodes patterned on the bottom of the microtroughs. In this way, the measurement of reporter strands released from single cells is a surrogate for detecting single-cell microRNA profiles. This approach permits direct measurement of microRNAs without PCR amplification owing to the small volume (<1 nL) of microtroughs. It offers high throughput and high multiplexing capability for evaluating microRNA heterogeneity in single cells, representing a new approach toward microRNA-based diagnosis and monitoring of complex human diseases.
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Affiliation(s)
- Nayi Wang
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
| | - Yao Lu
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
| | - Zhuo Chen
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA.
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA.
- Human and Translational Immunology Program, Yale University School of Medicine, New Haven, CT 06520, USA.
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9
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Abstract
Single-cell omics studies provide unique information regarding cellular heterogeneity at various levels of the molecular biology central dogma. This knowledge facilitates a deeper understanding of how underlying molecular and architectural changes alter cell behavior, development, and disease processes. The emerging microchip-based tools for single-cell omics analysis are enabling the evaluation of cellular omics with high throughput, improved sensitivity, and reduced cost. We review state-of-the-art microchip platforms for profiling genomics, epigenomics, transcriptomics, proteomics, metabolomics, and multi-omics at single-cell resolution. We also discuss the background of and challenges in the analysis of each molecular layer and integration of multiple levels of omics data, as well as how microchip-based methodologies benefit these fields. Additionally, we examine the advantages and limitations of these approaches. Looking forward, we describe additional challenges and future opportunities that will facilitate the improvement and broad adoption of single-cell omics in life science and medicine.
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Affiliation(s)
- Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Amanda Finck
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
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10
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Liu J, Wen Y, He H, Chen HY, Liu Z. Probing cytoplasmic and nuclear microRNAs in single living cells via plasmonic affinity sandwich assay. Chem Sci 2018; 9:7241-7246. [PMID: 30288244 PMCID: PMC6148463 DOI: 10.1039/c8sc02533a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/25/2018] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) regulate the expression of mRNAs in cells. The determination of subcellular miRNAs in single living cells is essential for understanding the subcellular localizations and functions of miRNAs as well as the microheterogeneity of cells.
MicroRNAs (miRNAs) regulate the expression of mRNAs in cells. The determination of subcellular miRNAs in single living cells is essential for understanding the subcellular localizations and functions of miRNAs as well as the microheterogeneity of cells. However, current approaches fail either to keep the cells alive or maintain their original cellular composition or are unable to provide subcellular resolution. Herein, we presented a new approach, called plasmonic affinity sandwich assay (PASA), for rapid and ultrasensitive probing of trace cytoplasmic and nuclear miRNAs in single living cells. It combined efficient in vivo subcellular extraction with ultrasensitive plasmon-enhanced Raman scattering (PERS) detection. By virtue of a micromanipulator, target miRNAs in the cytoplasm and nucleus were first specifically extracted from single living cells by gold thinlayer-coated glass microprobes modified with a half complementary sequence to the target miRNA and then, they were labelled with silver nanotags modified with a Raman reporter and the other half complement. Sandwich-like complexes of extraction sequence-target miRNA-labelling sequence were formed on the extraction microprobe, which were subjected to PERS detection. The subcellular resolution of this approach was confirmed with miR-29b (predominantly localized in the nuclei) and miR-29a (mainly located in the cytoplasm), whereas the quantitative capability was verified with three cytoplasmic miRNAs including miR-21, miR-155 and miR-203. This approach obviated tedious steps such as subcellular fractionation and enzymatic amplification, and it required only 10 min. It could be a promising tool to provide insights into subcellular localizations, functions and microheterogeneity of miRNAs.
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Affiliation(s)
- Jia Liu
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China .
| | - Yanrong Wen
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China .
| | - Hui He
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China .
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China .
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China .
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11
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Fan Y, Dong D, Li Q, Si H, Pei H, Li L, Tang B. Fluorescent analysis of bioactive molecules in single cells based on microfluidic chips. LAB ON A CHIP 2018; 18:1151-1173. [PMID: 29541737 DOI: 10.1039/c7lc01333g] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Single-cell analysis of bioactive molecules is an essential strategy for a better understanding of cell biology, exploring cell heterogeneity, and improvement of the ability to detect early diseases. In single-cell analysis, highly efficient single-cell manipulation techniques and high-sensitive detection schemes are in urgent need. The rapid development of fluorescent analysis techniques combined with microfluidic chips have offered a widely applicable solution. Thus, in this review, we mainly focus on the application of fluorescence methods in components analysis on microchips at a single-cell level. By targeting different types of biological molecules in cells such as nucleic acids, proteins, and active small molecules, we specially introduce and comment on their corresponding fluorescent probes, fluorescence labelling and sensing strategies, and different fluorescence detection instruments used in single-cell analysis on a microfluidic chip. We hope that through this review, readers will have a better understanding of single-cell fluorescence analysis, especially for single-cell component fluorescence analysis based on microfluidic chips.
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Affiliation(s)
- Yuanyuan Fan
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
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12
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Shrirao AB, Fritz Z, Novik EM, Yarmush GM, Schloss RS, Zahn JD, Yarmush ML. Microfluidic flow cytometry: The role of microfabrication methodologies, performance and functional specification. TECHNOLOGY 2018; 6:1-23. [PMID: 29682599 PMCID: PMC5907470 DOI: 10.1142/s2339547818300019] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Flow cytometry is an invaluable tool utilized in modern biomedical research and clinical applications requiring high throughput, high resolution particle analysis for cytometric characterization and/or sorting of cells and particles as well as for analyzing results from immunocytometric assays. In recent years, research has focused on developing microfluidic flow cytometers with the motivation of creating smaller, less expensive, simpler, and more autonomous alternatives to conventional flow cytometers. These devices could ideally be highly portable, easy to operate without extensive user training, and utilized for research purposes and/or point-of-care diagnostics especially in limited resource facilities or locations requiring on-site analyses. However, designing a device that fulfills the criteria of high throughput analysis, automation and portability, while not sacrificing performance is not a trivial matter. This review intends to present the current state of the field and provide considerations for further improvement by focusing on the key design components of microfluidic flow cytometers. The recent innovations in particle focusing and detection strategies are detailed and compared. This review outlines performance matrix parameters of flow cytometers that are interdependent with each other, suggesting trade offs in selection based on the requirements of the applications. The ongoing contribution of microfluidics demonstrates that it is a viable technology to advance the current state of flow cytometry and develop automated, easy to operate and cost-effective flow cytometers.
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Affiliation(s)
- Anil B Shrirao
- Department of Biomedical Engineering, Rutgers University, 599, Taylor Road, Piscataway, NJ 08854
| | - Zachary Fritz
- Department of Biomedical Engineering, Rutgers University, 599, Taylor Road, Piscataway, NJ 08854
| | - Eric M Novik
- Hurel Corporation, 671, Suite B, U.S. Highway 1, North Brunswick, NJ 08902
| | - Gabriel M Yarmush
- Department of Biomedical Engineering, Rutgers University, 599, Taylor Road, Piscataway, NJ 08854
| | - Rene S Schloss
- Department of Biomedical Engineering, Rutgers University, 599, Taylor Road, Piscataway, NJ 08854
| | - Jeffrey D Zahn
- Department of Biomedical Engineering, Rutgers University, 599, Taylor Road, Piscataway, NJ 08854
| | - Martin L Yarmush
- Department of Biomedical Engineering, Rutgers University, 599, Taylor Road, Piscataway, NJ 08854
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13
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Xie H, Norman I, Hjerpe A, Vladic T, Larsson C, Lui WO, Östensson E, Andersson S. Evaluation of microRNA-205 expression as a potential triage marker for patients with low-grade squamous intraepithelial lesions. Oncol Lett 2017; 13:3586-3598. [PMID: 28529583 PMCID: PMC5431461 DOI: 10.3892/ol.2017.5909] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/26/2017] [Indexed: 12/16/2022] Open
Abstract
High-risk human papillomavirus (HPV) testing is a recommended triage approach for females with atypical squamous cells of undetermined significance (ASCUS), but due to its poor specificity this approach is not recommended for patients with low-grade squamous intraepithelial lesions (LSIL). The objective of the current study was to determine microRNA (miR)-205 expression levels in liquid-based cytology (LBC) samples, and evaluate their ability to predict cervical intraepithelial neoplasia grade 2/3 or worse (CIN2/3+) in females with minor cytological abnormalities. LBC samples were obtained from patients attending the Swedish Cervical Cancer Screening Program. The Mann-Whitney U test, one-way analysis of variance, Kruskal-Wallis test, Spearman rank order correlation analysis, and Pearson's χ2 test were used to assess the results. Accuracy analyses indicated that high miR-205 expression had a significantly higher specificity to high-risk HPV testing, and a sensitivity similar to that of high-risk HPV testing to predict CIN2+ and CIN3+ in women with LSIL, but not those with high-grade squamous intraepithelial lesions. Although further research is required for females with LSIL, miR-205 expression in LBC samples may be a novel triage marker for, or a beneficial supplement to high-risk-HPV testing in these patients.
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Affiliation(s)
- Hong Xie
- Tianjin Life Science Research Center and Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P.R. China.,Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden
| | - Ingrid Norman
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Anders Hjerpe
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Tomislav Vladic
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden
| | - Catharina Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden
| | - Weng-Onn Lui
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden
| | - Ellinor Östensson
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sonia Andersson
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden
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14
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Microfluidics-assisted fluorescence in situ hybridization for advantageous human epidermal growth factor receptor 2 assessment in breast cancer. J Transl Med 2017; 97:93-103. [PMID: 27892928 DOI: 10.1038/labinvest.2016.121] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 11/08/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is one of the recommended techniques for human epidermal growth factor receptor 2 (HER2) status assessment on cancer tissues. Here we develop microfluidics-assisted FISH (MA-FISH), in which hybridization of the FISH probes with their target DNA strands is obtained by applying square-wave oscillatory flows of diluted probe solutions in a thin microfluidic chamber of 5 μl volume. By optimizing the experimental parameters, MA-FISH decreases the consumption of the expensive probe solution by a factor 5 with respect to the standard technique, and reduces the hybridization time to 4 h, which is four times faster than in the standard protocol. To validate the method, we blindly conducted HER2 MA-FISH on 51 formalin-fixed paraffin-embedded tissue slides of 17 breast cancer samples, and compared the results with standard HER2 FISH testing. HER2 status classification was determined according to published guidelines, based on average number of HER2 copies per cell and average HER2/CEP17 ratio. Excellent agreement was observed between the two methods, supporting the validity of MA-FISH and further promoting its short hybridization time and reduced reagent consumption.
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15
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Patabadige DEW, Mickleburgh T, Ferris L, Brummer G, Culbertson AH, Culbertson CT. High‐throughput microfluidic device for single cell analysis using multiple integrated soft lithographic pumps. Electrophoresis 2016; 37:1337-44. [DOI: 10.1002/elps.201500557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 01/07/2023]
Affiliation(s)
| | - Tom Mickleburgh
- Department of Chemistry Kansas State University Manhattan KS USA
| | - Lorin Ferris
- Department of Chemistry Kansas State University Manhattan KS USA
| | - Gage Brummer
- Department of Chemistry Kansas State University Manhattan KS USA
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16
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Konry T, Sarkar S, Sabhachandani P, Cohen N. Innovative Tools and Technology for Analysis of Single Cells and Cell-Cell Interaction. Annu Rev Biomed Eng 2016; 18:259-84. [PMID: 26928209 DOI: 10.1146/annurev-bioeng-090215-112735] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Heterogeneity in single-cell responses and intercellular interactions results from complex regulation of cell-intrinsic and environmental factors. Single-cell analysis allows not only detection of individual cellular characteristics but also correlation of genetic content with phenotypic traits in the same cell. Technological advances in micro- and nanofabrication have benefited single-cell analysis by allowing precise control of the localized microenvironment, cell manipulation, and sensitive detection capabilities. Additionally, microscale techniques permit rapid, high-throughput, multiparametric screening that has become essential for -omics research. This review highlights innovative applications of microscale platforms in genetic, proteomic, and metabolic detection in single cells; cell sorting strategies; and heterotypic cell-cell interaction. We discuss key design aspects of single-cell localization and isolation in microfluidic systems, dynamic and endpoint analyses, and approaches that integrate highly multiplexed detection of various intracellular species.
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Affiliation(s)
- Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Saheli Sarkar
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Pooja Sabhachandani
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Noa Cohen
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
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Derrick T, Last AR, Burr SE, Roberts CH, Nabicassa M, Cassama E, Bailey RL, Mabey DCW, Burton MJ, Holland MJ. Inverse relationship between microRNA-155 and -184 expression with increasing conjunctival inflammation during ocular Chlamydia trachomatis infection. BMC Infect Dis 2016; 16:60. [PMID: 26842862 PMCID: PMC4739388 DOI: 10.1186/s12879-016-1367-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 01/22/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Trachoma, a preventable blinding eye disease, is initiated by ocular infection with Chlamydia trachomatis (Ct). We previously showed that microRNAs (miR) -147b and miR-1285 were up-regulated in inflammatory trachomatous scarring. During the initial stage of disease, follicular trachoma with current Ct infection, the differential expression of miR has not yet been investigated. METHODS Conjunctival samples were collected from 163 children aged 1-9 years old living in a trachoma-endemic region of Guinea Bissau, West Africa. Small RNA sequencing (RNAseq) was carried out on samples from five children with follicular trachoma and current Ct infection and five children with healthy conjunctivae and no Ct infection. Small RNAseq was also carried out on human epithelial cell lines infected with ocular Ct strains A2497 and isogenic plasmid-free A2497 in vitro. Results were validated by quantitative PCR (qPCR) in 163 clinical samples. RESULTS Differential expression of RNAseq data identified 12 miR with changes in relative expression during follicular trachoma, of which 9 were confirmed as differentially expressed by qPCR (miR-155, miR-150, miR-142, miR-181b, miR-181a, miR-342, miR-132, miR-4728 and miR-184). MiR-155 and miR-184 expression had a direct relationship with the degree of clinical inflammation. MiR-155 was up-regulated (OR = 2.533 ((95 % CI = 1.291-4.971); P = 0.0069) and miR-184 was down-regulated (OR = 0.416 ((95 % CI = 0.300-0.578); P = 1.61*10(-7)) as the severity of clinical inflammation increased. Differential miR expression was not detected in HEp-2 or HCjE epithelial cells 48 h post infection with Ct in vitro. HCjE cells, a conjunctival epithelial cell line, had a markedly different miR background expression compared to HEp-2 cells. CONCLUSIONS In follicular trachoma, expression of miR-155 and miR-184 is correlated with the severity of inflammation. This likely reflects host regulation of the immune response and a prolonged period of wound healing following the clearance of Ct. Prolonged healing may be associated with subsequent development of scarring trachoma.
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Affiliation(s)
- Tamsyn Derrick
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Anna R Last
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Sarah E Burr
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia.
| | - Chrissy H Roberts
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Meno Nabicassa
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea Bissau.
| | - Eunice Cassama
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea Bissau.
| | - Robin L Bailey
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - David C W Mabey
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Matthew J Burton
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Martin J Holland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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19
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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20
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Liu Z, Lee Y, Jang JH, Li Y, Han X, Yokoi K, Ferrari M, Zhou L, Qin L. Microfluidic cytometric analysis of cancer cell transportability and invasiveness. Sci Rep 2015; 5:14272. [PMID: 26404901 PMCID: PMC4585905 DOI: 10.1038/srep14272] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 08/24/2015] [Indexed: 11/09/2022] Open
Abstract
The extensive phenotypic and functional heterogeneity of cancer cells plays an important role in tumor progression and therapeutic resistance. Characterizing this heterogeneity and identifying invasive phenotype may provide possibility to improve chemotherapy treatment. By mimicking cancer cell perfusion through circulatory system in metastasis, we develop a unique microfluidic cytometry (MC) platform to separate cancer cells at high throughput, and further derive a physical parameter ‘transportability’ to characterize the ability to pass through micro-constrictions. The transportability is determined by cell stiffness and cell-surface frictional property, and can be used to probe tumor heterogeneity, discriminate more invasive phenotypes and correlate with biomarker expressions in breast cancer cells. Decreased cell stiffness and cell-surface frictional force leads to an increase in transportability and may be a feature of invasive cancer cells by promoting cell perfusion through narrow spaces in circulatory system. The MC-Chip provides a promising microfluidic platform for studying cell mechanics and transportability could be used as a novel marker for probing tumor heterogeneity and determining invasive phenotypes.
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Affiliation(s)
- Zongbin Liu
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Yeonju Lee
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Joon hee Jang
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Ying Li
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Xin Han
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Kenji Yokoi
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Mauro Ferrari
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Ledu Zhou
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA.,Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA.,Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
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21
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X-FISH: Analysis of cellular RNA expression patterns using flow cytometry. J Immunol Methods 2015; 423:111-9. [PMID: 25997675 DOI: 10.1016/j.jim.2015.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/14/2015] [Accepted: 04/27/2015] [Indexed: 12/13/2022]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful technique for the detection of RNA or DNA within cells and tissues, which provides a unique link between molecular and cell biology. This technique is broadly applicable across a range of biological systems. While FISH has been previously adapted to flow-based platforms, their use remains limited because of procedural challenges and costs associated with commercial kits. Herein we present a protocol that modifies existing techniques to sensitively and specifically detect and examine RNA expression patterns in primary cells and cell lines using flow cytometry (expression-FISH; X-FISH). As relevant examples, we show how this technique can be used to monitor changes in mRNA expression following activation, how it can be combined with antibody staining to study RNA and protein in the same sample, and how it can help distinguish among subsets in a mixed cell population. X-FISH can integrate multiple probes and can be performed in conjunction with other assays, allowing for informative multiparametric analyses and increased statistical robustness. For non-classical comparative animal models this procedure provides a time saving alternative to de novo production of antibody-based markers. Finally, X-FISH provides an economical solution that is applicable to conventional as well as multi-spectral imaging flow cytometry platforms.
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22
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Abstract
Droplet microfluidics may soon change the paradigm of performing chemical analyses and related instrumentation.
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Affiliation(s)
- Evgenia Yu Basova
- Masaryk University
- CEITEC, Central European Institute Technology
- Brno
- Czech Republic
| | - Frantisek Foret
- Masaryk University
- CEITEC, Central European Institute Technology
- Brno
- Czech Republic
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic
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23
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Win Z, Vrla GD, Steucke KE, Sevcik EN, Hald ES, Alford PW. Smooth muscle architecture within cell-dense vascular tissues influences functional contractility. Integr Biol (Camb) 2014; 6:1201-10. [DOI: 10.1039/c4ib00193a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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24
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Wu M, Singh AK. Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and posttranslational modifications at single-cell resolution. ACTA ACUST UNITED AC 2014; 19:587-92. [PMID: 25027027 DOI: 10.1177/2211068214542247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cell signaling is a dynamic and complex process. A typical signaling pathway may begin with activation of cell surface receptors, leading to activation of a kinase cascade that culminates in induction of messenger RNA (mRNA) and noncoding microRNA (miRNA) production in the nucleus, followed by modulation of mRNA expression by miRNAs in the cytosol, and end with production of proteins in response to the signaling pathway. Signaling pathways involve proteins, miRNA, and mRNAs, along with various forms of transient posttranslational modifications, and detecting each type of signaling molecule requires categorically different sample preparation methods such as Western blotting for proteins, PCR for nucleic acids, and flow cytometry for posttranslational modifications. Since we know that cells in populations behave heterogeneously,(1) especially in the cases of stem cells, cancer, and hematopoiesis, there is need for a new technology that provides capability to detect and quantify multiple categories of signaling molecules in intact single cells to provide a comprehensive view of the cell's physiological state. In this Technology Brief, we describe our automated microfluidic platform with a portfolio of customized molecular assays that can detect nucleic acids, proteins, and posttranslational modifications in single intact cells with >95% reduction in reagent requirement in under 8 h.
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Affiliation(s)
- Meiye Wu
- Sandia National Laboratory, Livermore, CA, USA
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25
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Sperveslage J, Hoffmeister M, Henopp T, Klöppel G, Sipos B. Establishment of robust controls for the normalization of miRNA expression in neuroendocrine tumors of the ileum and pancreas. Endocrine 2014; 46:226-30. [PMID: 24535468 DOI: 10.1007/s12020-014-0202-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 02/03/2014] [Indexed: 01/16/2023]
Abstract
There is need to determine tissue-specific robust controls for normalization of microRNA expression to avoid false results and misinterpretation. The aim of this study was to evaluate the expression of different small RNAs in neuroendocrine tumors (NETs) and their suitability as normalizers in miRNA real-time PCR experiments. We investigated the expression of the nine small RNAs miR-93, miR-191, SNORD48, SNORD61, SNORD68, SNORD72, SNORD95, SNORD96a, and RNU6-2 in formalin-fixed, paraffin-embedded tissue samples of 25 ileal NETs by real-time PCR determining the most stable controls for expression normalization using four different algorithms. This analysis was expended to ten pancreatic NETs. Finally, five small RNAs were further tested as normalizers for miRNA-133a expression, which is known to be downregulated in metastases of ileal NETs, in ten matched pairs of ileal NETs and their metastases. Ranking of the expression results revealed the following order of stability from high to low: SNORD61 < SNORD95 < SNORD72 < SNORD96a < SNORD68 < miR-191 < miR-93 < RNU6-2 < SNORD48 for ileal NETs and SNORD95 < miR-93 < SNORD96a < SNORD61 < SNORD68 < SNORD72 < RNU6-2 < miR-191 < SNORD48 for pancreatic NETs. The determination of SNORD61 and SNORD95 for ileal NETs and SNORD95 and miR-93 for pancreatic NETs as good normalizers presents a useful tool for experiments involving the analysis of miRNA expression.
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Affiliation(s)
- J Sperveslage
- Institute of Pathology, University of Tübingen, Liebermeisterstr.8, 72076, Tübingen, Germany,
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26
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Palanichamy JK, Rao DS. miRNA dysregulation in cancer: towards a mechanistic understanding. Front Genet 2014; 5:54. [PMID: 24672539 PMCID: PMC3957189 DOI: 10.3389/fgene.2014.00054] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/02/2014] [Indexed: 12/17/2022] Open
Abstract
It is now well known that gene expression is intricately regulated inside each cell especially in mammals. There are multiple layers of gene regulation active inside a cell at a given point of time. Gene expression is regulated post-transcriptionally by microRNAs and other factors. Mechanistically, microRNAs are known to bind to the 3’ UTR of mRNAs and cause repression of gene expression and the number of known microRNAs continues to increase every day. Dysregulated microRNA signatures in different types of cancer are being uncovered consistently implying their importance in cellular homeostasis. However when studied in isolation in mouse models, clear-cut cellular and molecular mechanisms have been described only for a select few microRNAs. What is the reason behind this discrepancy? Are microRNAs small players in gene regulation helping only to fine tune gene expression? Or are their roles tissue and cell type-specific with single-cell level effects on mRNA expression and microRNA threshold levels? Or does it all come down to the technical limitations of high-throughput techniques, resulting in false positive results? In this review, we will assess the challenges facing the field and potential avenues for resolving the cellular and molecular mechanisms of these small but important regulators of gene expression.
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Affiliation(s)
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, CA, USA ; Jonsson Comprehensive Cancer Center, University of California Los Angeles, CA, USA ; Broad Stem Cell Research Center, University of California Los Angeles, CA, USA ; Division of Biology, California Institute of Technology Pasadena, CA, USA
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27
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Devonshire AS, Baradez MO, Morley G, Marshall D, Foy CA. Validation of high-throughput single cell analysis methodology. Anal Biochem 2014; 452:103-13. [PMID: 24631519 DOI: 10.1016/j.ab.2014.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 01/04/2023]
Abstract
High-throughput quantitative polymerase chain reaction (qPCR) approaches enable profiling of multiple genes in single cells, bringing new insights to complex biological processes and offering opportunities for single cell-based monitoring of cancer cells and stem cell-based therapies. However, workflows with well-defined sources of variation are required for clinical diagnostics and testing of tissue-engineered products. In a study of neural stem cell lines, we investigated the performance of lysis, reverse transcription (RT), preamplification (PA), and nanofluidic qPCR steps at the single cell level in terms of efficiency, precision, and limit of detection. We compared protocols using a separate lysis buffer with cell capture directly in RT-PA reagent. The two methods were found to have similar lysis efficiencies, whereas the direct RT-PA approach showed improved precision. Digital PCR was used to relate preamplified template copy numbers to Cq values and reveal where low-quality signals may affect the analysis. We investigated the impact of calibration and data normalization strategies as a means of minimizing the impact of inter-experimental variation on gene expression values and found that both approaches can improve data comparability. This study provides validation and guidance for the application of high-throughput qPCR workflows for gene expression profiling of single cells.
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Tseng P, Weaver WM, Masaeli M, Owsley K, Di Carlo D. Research highlights: microfluidics meets big data. LAB ON A CHIP 2014; 14:828-832. [PMID: 24473594 DOI: 10.1039/c4lc90001d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this issue we highlight a collection of recent work in which microfluidic parallelization and automation have been employed to address the increasing need for large amounts of quantitative data concerning cellular function--from correlating microRNA levels to protein expression, increasing the throughput and reducing the noise when studying protein dynamics in single-cells, and understanding how signal dynamics encodes information. The painstaking dissection of cellular pathways one protein at a time appears to be coming to an end, leading to more rapid discoveries which will inevitably translate to better cellular control--in producing useful gene products and treating disease at the individual cell level. From these studies it is also clear that development of large scale mutant or fusion libraries, automation of microscopy, image analysis, and data extraction will be key components as microfluidics contributes its strengths to aid systems biology moving forward.
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Affiliation(s)
- Peter Tseng
- Department of Bioengineering, California NanoSystems Institute, Jonsson Comprehensive Cancer Center, University of California Los Angeles, 420 Westwood Plaza, 5121 Engineering V, Box 951600, Los Angeles, California 90095, USA.
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Wu M, Piccini ME, Singh AK. MiRNA detection at single-cell resolution using microfluidic LNA flow-FISH. Methods Mol Biol 2014; 1211:245-260. [PMID: 25218391 DOI: 10.1007/978-1-4939-1459-3_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Flow cytometry in combination with fluorescent in situ hybridization (flow-FISH) is a powerful technique that can be utilized to rapidly detect nucleic acids at single-cell resolution without the need for homogenization or nucleic acid extraction. Here, we describe a microfluidic-based method which enables the detection of microRNAs or miRNAs in single intact cells by flow-FISH using locked nucleic acid (LNA)-containing probes. Our method can be applied to all RNA species including mRNA and small noncoding RNA and is suitable for multiplexing with protein immunostaining in the same cell. For demonstration of our method, this chapter details the detection of miR155 and CD69 protein in PMA and ionomycin-stimulated Jurkat cells. We also include instructions on how to set up a microfluidic chip sample preparation station to prepare cells for imaging and analysis on a commercial flow cytometer or a custom-built micro-flow cytometer.
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Affiliation(s)
- Meiye Wu
- Biological Science and Technology, Sandia National Laboratories, MS 9292, 969, Livermore, CA, 94551-0969, USA
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30
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Ali MM, Li F, Zhang Z, Zhang K, Kang DK, Ankrum JA, Le XC, Zhao W. Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. Chem Soc Rev 2014; 43:3324-41. [DOI: 10.1039/c3cs60439j] [Citation(s) in RCA: 650] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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White AK, Heyries KA, Doolin C, Vaninsberghe M, Hansen CL. High-throughput microfluidic single-cell digital polymerase chain reaction. Anal Chem 2013; 85:7182-90. [PMID: 23819473 DOI: 10.1021/ac400896j] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Here we present an integrated microfluidic device for the high-throughput digital polymerase chain reaction (dPCR) analysis of single cells. This device allows for the parallel processing of single cells and executes all steps of analysis, including cell capture, washing, lysis, reverse transcription, and dPCR analysis. The cDNA from each single cell is distributed into a dedicated dPCR array consisting of 1020 chambers, each having a volume of 25 pL, using surface-tension-based sample partitioning. The high density of this dPCR format (118,900 chambers/cm(2)) allows the analysis of 200 single cells per run, for a total of 204,000 PCR reactions using a device footprint of 10 cm(2). Experiments using RNA dilutions show this device achieves shot-noise-limited performance in quantifying single molecules, with a dynamic range of 10(4). We performed over 1200 single-cell measurements, demonstrating the use of this platform in the absolute quantification of both high- and low-abundance mRNA transcripts, as well as micro-RNAs that are not easily measured using alternative hybridization methods. We further apply the specificity and sensitivity of single-cell dPCR to performing measurements of RNA editing events in single cells. High-throughput dPCR provides a new tool in the arsenal of single-cell analysis methods, with a unique combination of speed, precision, sensitivity, and specificity. We anticipate this approach will enable new studies where high-performance single-cell measurements are essential, including the analysis of transcriptional noise, allelic imbalance, and RNA processing.
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Affiliation(s)
- A K White
- Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
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