1
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Fuller KA. Chromosomal assessment of haematological malignancies: Flow-FISHing for genetic abnormalities. Pathology 2024:S0031-3025(24)00130-2. [PMID: 38862379 DOI: 10.1016/j.pathol.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 05/19/2024] [Indexed: 06/13/2024]
Affiliation(s)
- Kathy A Fuller
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia.
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2
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Hanlon VC, Chan DD, Hamadeh Z, Wang Y, Mattsson CA, Spierings DC, Coope RJ, Lansdorp PM. Construction of Strand-seq libraries in open nanoliter arrays. CELL REPORTS METHODS 2022; 2:100150. [PMID: 35474869 PMCID: PMC9017222 DOI: 10.1016/j.crmeth.2021.100150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/22/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022]
Abstract
Single-cell Strand-seq generates directional genomic information to study DNA repair, assemble genomes, and map structural variation onto chromosome-length haplotypes. We report a nanoliter-volume, one-pot (OP) Strand-seq library preparation protocol in which reagents are added cumulatively, DNA purification steps are avoided, and enzymes are inactivated with a thermolabile protease. OP-Strand-seq libraries capture 10%-25% of the genome from a single-cell with reduced costs and increased throughput.
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Affiliation(s)
| | - Daniel D. Chan
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Zeid Hamadeh
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Yanni Wang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | | | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Robin J.N. Coope
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Peter M. Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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3
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Gao K, Zhou Y, Lu Q, Lu J, Su L, Su R, Zhang M, Tian Y, Wu L, Yan X. High-Throughput Human Telomere Length Analysis at the Single-Chromosome Level by FISH Coupled with Nano-Flow Cytometry. Anal Chem 2021; 93:9531-9540. [PMID: 34197088 DOI: 10.1021/acs.analchem.1c01544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Telomere length (TL) is a highly relevant biomarker for age-associated diseases and cancer, yet its clinical applications have been hindered by the inability of existing methods to rapidly measure the TL distribution and the percentage of chromosomes with critically short telomeres (CSTs, < 3 kb). Herein, we report the development of a high-throughput method to measure TL at the single-chromosome level. Metaphase chromosomes are isolated, hybridized with the Alexa Fluor 488-labeled telomeric peptide nucleic acid probe, and analyzed using a laboratory-built ultrasensitive nano-flow cytometer. The fluorescence intensity of individual chromosomes is converted to TL in kilobases upon external calibration. With an analysis rate of several thousand chromosomes per minute, a statistically robust TL distribution histogram is acquired in minutes, and the percentage of chromosomes with CSTs can be quickly assessed. By analyzing peripheral blood lymphocytes of 158 healthy donors, TL is found to shorten with age at a rate of 64 ± 3 bp/year and the percentage of chromosomes with CSTs increases with age at a rate of 0.32 ± 0.02%/year. Moreover, the data of 28 patients with chronic myeloid leukemia (CML) indicate that telomeres are significantly shorter at the time of diagnosis and the clinical phases of CML are closely associated with TL and the percentage of chromosomes with CSTs. This powerful tool could greatly deepen our understanding of telomere biology and improve the clinical utility of telomere biomarkers.
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Affiliation(s)
- Kaimin Gao
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Yingxing Zhou
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Quanyi Lu
- Department of Hematology, Affiliated Zhongshan Hospital of Xiamen University, Xiamen 361004, PR China
| | - Jingyuan Lu
- Department of Hematology, Affiliated Zhongshan Hospital of Xiamen University, Xiamen 361004, PR China
| | - Liyun Su
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Rui Su
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, PR China
| | - Miaomiao Zhang
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Ye Tian
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Lina Wu
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Xiaomei Yan
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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4
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Stanley J, Hui H, Erber W, Clynick B, Fuller K. Analysis of human chromosomes by imaging flow cytometry. CYTOMETRY PART B-CLINICAL CYTOMETRY 2021; 100:541-553. [PMID: 34033226 DOI: 10.1002/cyto.b.22023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/18/2021] [Accepted: 05/14/2021] [Indexed: 12/29/2022]
Abstract
Chromosomal analysis is traditionally performed by karyotyping on metaphase spreads, or by fluorescent in situ hybridization (FISH) on interphase cells or metaphase spreads. Flow cytometry was introduced as a new method to analyze chromosomes number (ploidy) and structure (telomere length) in the 1970s with data interpretation largely based on fluorescence intensity. This technology has had little uptake for human cytogenetic applications primarily due to analytical challenges. The introduction of imaging flow cytometry, with the addition of digital images to standard multi-parametric flow cytometry quantitative tools, has added a new dimension. The ability to visualize the chromosomes and FISH signals overcomes the inherent difficulties when the data is restricted to fluorescence intensity. This field is now moving forward with methods being developed to assess chromosome number and structure in whole cells (normal and malignant) in suspension. A recent advance has been the inclusion of immunophenotyping such that antigen expression can be used to identify specific cells of interest for specific chromosomes and their abnormalities. This capability has been illustrated in blood cancers, such as chronic lymphocytic leukemia and plasma cell myeloma. The high sensitivity and specificity achievable highlights the potential imaging flow cytometry has for cytogenomic applications (i.e., diagnosis and disease monitoring). This review introduces and describes the development, current status, and applications of imaging flow cytometry for chromosomal analysis of human chromosomes.
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Affiliation(s)
- Jason Stanley
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Henry Hui
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Wendy Erber
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia.,PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
| | - Britt Clynick
- Institute for Respiratory Health, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
| | - Kathy Fuller
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
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5
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Sun C, Wang K, Stock AJ, Gong Y, Demarest TG, Yang B, Giri N, Harrington L, Alter BP, Savage SA, Bohr VA, Liu Y. Re-equilibration of imbalanced NAD metabolism ameliorates the impact of telomere dysfunction. EMBO J 2020; 39:e103420. [PMID: 32935380 PMCID: PMC7604620 DOI: 10.15252/embj.2019103420] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 12/16/2022] Open
Abstract
Short telomeres are a principal defining feature of telomere biology disorders, such as dyskeratosis congenita (DC), for which there are no effective treatments. Here, we report that primary fibroblasts from DC patients and late generation telomerase knockout mice display lower nicotinamide adenine dinucleotide (NAD) levels, and an imbalance in the NAD metabolome that includes elevated CD38 NADase and reduced poly(ADP‐ribose) polymerase and SIRT1 activities, respectively, affecting many associated biological pathways. Supplementation with the NAD precursor, nicotinamide riboside, and CD38 inhibition improved NAD homeostasis, thereby alleviating telomere damage, defective mitochondrial biosynthesis and clearance, cell growth retardation, and cellular senescence of DC fibroblasts. These findings reveal a direct, underlying role of NAD dysregulation when telomeres are short and underscore its relevance to the pathophysiology and interventions of human telomere‐driven diseases.
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Affiliation(s)
- Chongkui Sun
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, Baltimore, MD, USA
| | - Kun Wang
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, Baltimore, MD, USA
| | - Amanda J Stock
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, Baltimore, MD, USA
| | - Yi Gong
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, Baltimore, MD, USA
| | - Tyler G Demarest
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, Baltimore, MD, USA
| | - Beimeng Yang
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, Baltimore, MD, USA
| | - Neelam Giri
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lea Harrington
- Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montréal, QC, Canada
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vilhelm A Bohr
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, Baltimore, MD, USA
| | - Yie Liu
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, Baltimore, MD, USA
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6
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Smith LD, Liu Y, Zahid MU, Canady TD, Wang L, Kohli M, Cunningham BT, Smith AM. High-Fidelity Single Molecule Quantification in a Flow Cytometer Using Multiparametric Optical Analysis. ACS NANO 2020; 14:2324-2335. [PMID: 31971776 PMCID: PMC7295608 DOI: 10.1021/acsnano.9b09498] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Microfluidic techniques are widely used for high-throughput quantification and discrete analysis of micron-scale objects but are difficult to apply to molecular-scale targets. Instead, single-molecule methods primarily rely on low-throughput microscopic imaging of immobilized molecules. Here we report that commercial-grade flow cytometers can detect single nucleic acid targets following enzymatic extension and dense labeling with multiple distinct fluorophores. We focus on microRNAs, short nucleic acids that can be extended by rolling circle amplification (RCA). We labeled RCA-extended microRNAs with multicolor fluorophores to generate repetitive nucleic acid products with submicron sizes and tunable multispectral profiles. By cross-correlating the multiparametric optical features, signal-to-background ratios were amplified 1600-fold to allow single-molecule detection across 4 orders of magnitude of concentration. The limit of detection was measured to be 47 fM, which is 100-fold better than gold-standard methods based on polymerase chain reaction. Furthermore, multiparametric analysis allowed discrimination of different microRNA sequences in the same solution using distinguishable optical barcodes. Barcodes can apply both ratiometric and colorimetric signatures, which could facilitate high-dimensional multiplexing. Because of the wide availability of flow cytometers, we anticipate that this technology can provide immediate access to high-throughput multiparametric single-molecule measurements and can further be adapted to the diverse range of molecular amplification methods that are continually emerging.
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Affiliation(s)
- Lucas D Smith
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yang Liu
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Mohammad U Zahid
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Taylor D Canady
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Liang Wang
- Department of Tumor Biology , H. Lee Moffitt Cancer Center , Tampa , Florida 33612 , United States
| | - Manish Kohli
- Department of Genitourinary Oncology , H. Lee Moffitt Cancer Center , Tampa , Florida 33612 United States
| | - Brian T Cunningham
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Department of Electrical and Computer Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Cancer Center at Illinois , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Andrew M Smith
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Cancer Center at Illinois , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carle Illinois College of Medicine , Urbana , Illinois 61801 , United States
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7
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Figueroa RI, de Bustos A, Cuadrado Á. A novel FISH technique for labeling the chromosomes of dinoflagellates in suspension. PLoS One 2018; 13:e0204382. [PMID: 30356238 PMCID: PMC6200182 DOI: 10.1371/journal.pone.0204382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/11/2018] [Indexed: 11/19/2022] Open
Abstract
Dinoflagellates possess some of the largest known genomes. However, the study of their chromosomes is complicated by their similar size and their inability to be distinguished by traditional banding techniques. Dinoflagellate chromosomes lack nucleosomes and are present in a liquid crystalline state. In addition, approaches such as fluorescent in situ hybridization (FISH) are problematic because chromosomes are difficult to isolate from the nuclear membrane, which in dinoflagellates remains intact, also during mitosis. Here we describe a novel, reliable and effective technique to study dinoflagellate chromosomes by physical mapping of repetitive DNA sequences in chromosomes in suspension (FISH-IS), rather than on a microscope slide. A suspension of non-fixed chromosomes was achieved by lysing the cells and destabilizing the nuclear envelope. This treatment resulted in the release of the permanently condensed chromosomes in a high-quality chromosomal suspension. Nevertheless, slide preparations of the chromosomes were not suitable for conventional FISH because the nuclear integrity and chromosomal morphology was destroyed. Our newly developed, simple and efficient FISH-IS technique employs fluorescently labeled, synthetic short sequence repeats that are hybridized with suspended, acetic-acid-pretreated chromosomes for 1 h at room temperature. The method can be successfully used to discriminate single chromosomes or specific chromosomal regions, depending on the specificity of the repeat sequences used as probes. The combination of FISH-IS and flow sorting will improve genomic studies of dinoflagellates, overcoming the difficulties posed by their huge genomes, including long stretches of non-coding sequences in multiple copies and the presence of high-copy-number tandem gene arrays.
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Affiliation(s)
- Rosa I Figueroa
- Instituto Español de Oceanografia (IEO), Subida a Radio Faro 50, Vigo, Spain
| | - Alfredo de Bustos
- Universidad de Alcala (UAH), Dpto Biomedicina y Biotecnología, Alcalá de Henares, Madrid, Spain
| | - Ángeles Cuadrado
- Universidad de Alcala (UAH), Dpto Biomedicina y Biotecnología, Alcalá de Henares, Madrid, Spain
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8
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Verona MD, Verdolino V, Palazzesi F, Corradini R. Focus on PNA Flexibility and RNA Binding using Molecular Dynamics and Metadynamics. Sci Rep 2017; 7:42799. [PMID: 28211525 PMCID: PMC5314342 DOI: 10.1038/srep42799] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/13/2017] [Indexed: 12/20/2022] Open
Abstract
Peptide Nucleic Acids (PNAs) can efficiently target DNA or RNA acting as chemical tools for gene regulation. Their backbone modification and functionalization is often used to increase the affinity for a particular sequence improving selectivity. The understanding of the trading forces that lead the single strand PNA to bind the DNA or RNA sequence is preparatory for any further rational design, but a clear and unique description of this process is still not complete. In this paper we report further insights into this subject, by a computational investigation aiming at the characterization of the conformations of a single strand PNA and how these can be correlated to its capability in binding DNA/RNA. Employing Metadynamics we were able to better define conformational pre-organizations of the single strand PNA and γ-modified PNA otherwise unrevealed through classical molecular dynamics. Our simulations driven on backbone modified PNAs lead to the conclusion that this γ-functionalization affects the single strand preorganization and targeting properties to the DNA/RNA, in agreement with circular dichroism (CD) spectra obtained for this class of compounds. MD simulations on PNA:RNA dissociation and association mechanisms allowed to reveal the critical role of central bases and preorganization in the binding process.
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Affiliation(s)
| | - Vincenzo Verdolino
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o Università della Svizzera Italiana Campus, 6900 Lugano, Switzerland
- Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Ferruccio Palazzesi
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o Università della Svizzera Italiana Campus, 6900 Lugano, Switzerland
- Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Roberto Corradini
- Dipartimento di Chimica, University of Parma, Italy, 43124, Italy
- National Institute for Biostructures and Biosystems (INBB)-Viale delle Medaglie d’Oro, 305, 00136 Roma, Italy
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9
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Fluorescence imaging of chromosomal DNA using click chemistry. Sci Rep 2016; 6:33217. [PMID: 27620982 PMCID: PMC5020420 DOI: 10.1038/srep33217] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/23/2016] [Indexed: 11/08/2022] Open
Abstract
Chromosome visualization is essential for chromosome analysis and genetic diagnostics. Here, we developed a click chemistry approach for multicolor imaging of chromosomal DNA instead of the traditional dye method. We first demonstrated that the commercially available reagents allow for the multicolor staining of chromosomes. We then prepared two pro-fluorophore moieties that served as light-up reporters to stain chromosomal DNA based on click reaction and visualized the clear chromosomes in multicolor. We applied this strategy in fluorescence in situ hybridization (FISH) and identified, with high sensitivity and specificity, telomere DNA at the end of the chromosome. We further extended this approach to observe several basic stages of cell division. We found that the click reaction enables direct visualization of the chromosome behavior in cell division. These results suggest that the technique can be broadly used for imaging chromosomes and may serve as a new approach for chromosome analysis and genetic diagnostics.
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10
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Foundations of identifying individual chromosomes by imaging flow cytometry with applications in radiation biodosimetry. Methods 2016; 112:18-24. [PMID: 27524557 DOI: 10.1016/j.ymeth.2016.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 07/24/2016] [Accepted: 08/08/2016] [Indexed: 11/23/2022] Open
Abstract
Biodosimetry is an important tool for triage in the case of large-scale radiological or nuclear emergencies, but traditional microscope-based methods can be tedious and prone to scorer fatigue. While the dicentric chromosome assay (DCA) has been adapted for use in triage situations, it is still time-consuming to create and score slides. Recent adaptations of traditional biodosimetry assays to imaging flow cytometry (IFC) methods have dramatically increased throughput. Additionally, recent improvements in image analysis algorithms in the IFC software have resulted in improved specificity for spot counting of small events. In the IFC method for the dicentric chromosome analysis (FDCA), lymphocytes isolated from whole blood samples are cultured with PHA and Colcemid. After incubation, lymphocytes are treated with a hypotonic solution and chromosomes are isolated in suspension, labelled with a centromere marker and stained for DNA content with DRAQ5. Stained individual chromosomes are analyzed on the ImageStream®X (EMD-Millipore, Billerica, MA) and mono- and dicentric chromosome populations are identified and enumerated using advanced image processing techniques. Both the preparation of the isolated chromosome suspensions as well as the image analysis methods were fine-tuned in order to optimize the FDCA. In this paper we describe the method to identify and score centromeres in individual chromosomes by IFC and show that the FDCA method may further improve throughput for triage biodosimetry in the case of large-scale radiological or nuclear emergencies.
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11
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Abstract
Biodosimetry is a method for measuring the dose of radiation to individuals using biological markers such as chromosome damage. Following mass casualty events, it is important to provide this information rapidly in order to assist with the medical management of potentially exposed casualties. Currently, the gold standard for biodosimetry is the dicentric chromosome assay, which accurately estimates the dose from the number of dicentric chromosomes in lymphocytes. To increase throughput of analysis following a large-scale mass casualty event, this assay has been adapted for use on the imaging flow cytometer. This chapter describes the methods for the identification and quantification of mono- and multicentric chromosomes using the imaging flow cytometer.
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Affiliation(s)
- Lindsay A Beaton-Green
- Radiobiology, Consumer and Clinical Radiation Protection Bureau, Health Canada, 775 Brookfield Rd., Ottawa, ON, Canada.
| | - Ruth C Wilkins
- Radiobiology, Consumer and Clinical Radiation Protection Bureau, Health Canada, 775 Brookfield Rd., Ottawa, ON, Canada
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12
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Hwang G, Lee H, Lee J. Direct fluorescence in situ hybridization on human metaphase chromosomes using quantum dot-platinum labeled DNA probes. Biochem Biophys Res Commun 2015; 467:328-33. [PMID: 26449454 DOI: 10.1016/j.bbrc.2015.09.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
Abstract
The telomere shortening in chromosomes implies the senescence, apoptosis, or oncogenic transformation of cells. Since detecting telomeres in aging and diseases like cancer, is important, the direct detection of telomeres has been a very useful biomarker. We propose a telomere detection method using a newly synthesized quantum dot (QD) based probe with oligonucleotide conjugation and direct fluorescence in situ hybridization (FISH). QD-oligonucleotides were prepared with metal coordination bonding based on platinum-guanine binding reported in our previous work. The QD-oligonucleotide conjugation method has an advantage where any sequence containing guanine at the end can be easily bound to the starting QD-Pt conjugate. A synthesized telomeric oligonucleotide was bound to the QD-Pt conjugate successfully and this probe hybridized specifically on the telomere of fabricated MV-4-11 and MOLT-4 chromosomes. Additionally, the QD-telomeric oligonucleotide probe successfully detected the telomeres on the CGH metaphase slide. Due to the excellent photostability and high quantum yield of QDs, the QD-oligonucleotide probe has high fluorescence intensity when compared to the organic dye-oligonucleotide probe. Our QD-oligonucleotide probe, conjugation method of this QD probe, and hybridization protocol with the chromosomes can be a useful tool for chromosome painting and FISH.
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Affiliation(s)
- Gyoyeon Hwang
- Chemical Kinomics Research Center, Future Convergence Research Division, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Biological Chemistry, Korea University of Science and Technology, 217, Gajeong-ro, Yuseong-gu, Deajeon, Republic of Korea
| | - Hansol Lee
- Chemical Kinomics Research Center, Future Convergence Research Division, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Jiyeon Lee
- Chemical Kinomics Research Center, Future Convergence Research Division, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Biological Chemistry, Korea University of Science and Technology, 217, Gajeong-ro, Yuseong-gu, Deajeon, Republic of Korea.
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13
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Konry T, Lerner A, Yarmush ML, Smolina IV. Target DNA detection and quantitation on a single cell with single base resolution. TECHNOLOGY 2013; 1:88. [PMID: 24977169 PMCID: PMC4073798 DOI: 10.1142/s2339547813500088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In this report, we present a new method for sensitive detection of short DNA sites in single cells with single base resolution. The method combines peptide nucleic acid (PNA) openers as the tagging probes, together with isothermal rolling circle amplification (RCA) and fluorescence-based detection, all performed in a cells-in-flow format. Bis-PNAs provide single base resolution, while RCA ensures linear signal amplification. We applied this method to detect the oncoviral DNA inserts in cancer cell lines using a flow-cytometry system. We also demonstrated quantitative detection of the selected signature sites within single cells in microfluidic nano-liter droplets. Our results show single-nucleotide polymorphism (SNP) discrimination and detection of copy-number variations (CNV) under isothermal non-denaturing conditions. This new method is ideal for many applications in which ultra-sensitive DNA characterization with single base resolution is desired on the level of single cells.
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14
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Analysis of chromosome damage for biodosimetry using imaging flow cytometry. Mutat Res 2013; 756:192-5. [PMID: 23618924 DOI: 10.1016/j.mrgentox.2013.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 04/13/2013] [Indexed: 11/20/2022]
Abstract
The dicentric chromosome assay (DCA), which involves counting the frequency of dicentric chromosomes in mitotic lymphocytes and converting it to a dose-estimation for ionizing radiation exposure, is considered to be the gold standard for radiation biodosimetry. Furthermore, for emergency response, the DCA has been adapted for triage by simplifying the scoring method [1]. With the development of new technologies such as the imaging flow cytometer, it may now be possible to adapt this microscope-based method to an automated cytometry method. This technology allows the sensitivity of microscopy to be maintained while adding the increased throughput of flow cytometry. A new protocol is being developed to adapt the DCA to the imaging cytometer in order to further increase the rapid determination of a biological dose. Peripheral blood mononuclear cells (PBMC) were isolated from ex vivo irradiated whole blood samples using a density gradient separation method and cultured with PHA and Colcemid. After 48h incubation, the chromosomes were isolated, stained for DNA content with propidium iodide (PI) and labelled with a centromere marker. Stained chromosomes were then analyzed on the ImageStream(×) (EMD-Millipore, Billerica, MA). Preliminary results indicate that individual chromosomes can be identified and mono- and dicentric chromosomes can be differentiated by imaging cytometry. A dose response curve was generated using this technology. The details of the method and the dose response curve are presented and compared to traditional microscope scoring. Imaging cytometry is a new technology which enables the rapid, automated analysis of fluorescently labelled chromosomes. Adapting the dicentric assay to this technology has the potential for high throughput analysis for mass casualty events.
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Giorgi D, Farina A, Grosso V, Gennaro A, Ceoloni C, Lucretti S. FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy. PLoS One 2013; 8:e57994. [PMID: 23469124 PMCID: PMC3585268 DOI: 10.1371/journal.pone.0057994] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/29/2013] [Indexed: 11/23/2022] Open
Abstract
The large size and complex polyploid nature of many genomes has often hampered genomics development, as is the case for several plants of high agronomic value. Isolating single chromosomes or chromosome arms via flow sorting offers a clue to resolve such complexity by focusing sequencing to a discrete and self-consistent part of the whole genome. The occurrence of sufficient differences in the size and or base-pair composition of the individual chromosomes, which is uncommon in plants, is critical for the success of flow sorting. We overcome this limitation by developing a robust method for labeling isolated chromosomes, named Fluorescent In situ Hybridization In suspension (FISHIS). FISHIS employs fluorescently labeled synthetic repetitive DNA probes, which are hybridized, in a wash-less procedure, to chromosomes in suspension following DNA alkaline denaturation. All typical A, B and D genomes of wheat, as well as individual chromosomes from pasta (T. durum L.) and bread (T. aestivum L.) wheat, were flow-sorted, after FISHIS, at high purity. For the first time in eukaryotes, each individual chromosome of a diploid organism, Dasypyrum villosum (L.) Candargy, was flow-sorted regardless of its size or base-pair related content. FISHIS-based chromosome sorting is a powerful and innovative flow cytogenetic tool which can develop new genomic resources from each plant species, where microsatellite DNA probes are available and high quality chromosome suspensions could be produced. The joining of FISHIS labeling and flow sorting with the Next Generation Sequencing methodology will enforce genomics for more species, and by this mightier chromosome approach it will be possible to increase our knowledge about structure, evolution and function of plant genome to be used for crop improvement. It is also anticipated that this technique could contribute to analyze and sort animal chromosomes with peculiar cytogenetic abnormalities, such as copy number variations or cytogenetic aberrations.
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Affiliation(s)
- Debora Giorgi
- ENEA – Italian National Agency for New Technologies, Energy and Sustainable Economic Development, CASACCIA Research Center, Rome, Italy
| | - Anna Farina
- ENEA – Italian National Agency for New Technologies, Energy and Sustainable Economic Development, CASACCIA Research Center, Rome, Italy
| | - Valentina Grosso
- ENEA – Italian National Agency for New Technologies, Energy and Sustainable Economic Development, CASACCIA Research Center, Rome, Italy
| | - Andrea Gennaro
- DAFNE – Department of Agriculture, Forestry, Nature and Energy, University of Tuscia, Viterbo, Italy
| | - Carla Ceoloni
- DAFNE – Department of Agriculture, Forestry, Nature and Energy, University of Tuscia, Viterbo, Italy
| | - Sergio Lucretti
- ENEA – Italian National Agency for New Technologies, Energy and Sustainable Economic Development, CASACCIA Research Center, Rome, Italy
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Abstract
A 2-day method using flow cytometry and FISH for interphase cells was developed to detect monosomy 7 cells in myelodysplastic syndrome patients. The method, Interphase Chromosome Flow-FISH (IC Flow-FISH), involves fixation of leukocytes from blood, membrane permeabilization, hybridization of cellular DNA with peptide nucleic acid probes with cells intact, and analysis by flow cytometry. Hundreds to thousands of monosomy 7 cells were consistently detected from 10-20 mL of blood in patients with monosomy 7. Proportions of monosomy 7 cells detected in IC Flow-FISH were compared with results from conventional cytogenetics; identification of monosomy 7 populations was verified with FACS; and patient and donor cells were mixed to test for sensitivity. IC Flow-FISH allows for detecting monosomy 7 without requiring bone marrow procurement or the necessity of metaphase spreads, and wider applications to other chromosomal abnormalities are in development.
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Doležel J, Vrána J, Safář J, Bartoš J, Kubaláková M, Simková H. Chromosomes in the flow to simplify genome analysis. Funct Integr Genomics 2012; 12:397-416. [PMID: 22895700 PMCID: PMC3431466 DOI: 10.1007/s10142-012-0293-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 07/30/2012] [Indexed: 11/25/2022]
Abstract
Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 10(2)-10(4) chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.
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Affiliation(s)
- Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, Czech Republic.
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Cecic IK, Li G, MacAulay C. Technologies supporting analytical cytology: clinical, research and drug discovery applications. JOURNAL OF BIOPHOTONICS 2012; 5:313-326. [PMID: 22271675 DOI: 10.1002/jbio.201100093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/08/2011] [Accepted: 12/30/2011] [Indexed: 05/31/2023]
Abstract
The tools and techniques developed for analytical cytology have become invaluable in expanding the development of cancer screening programs and biomarker discovery for personalized medicine. Detecting cellular, molecular, and functional changes of diseased tissue as defined by quantitative analytical methodologies has enhanced the field of medical diagnostics and prognostics. The focus of this review is to outline applications and recent technical advances in flow cytometry, laser scanning cytometry, image cytometry, and quantitative image analysis, as they pertain to clinical, research, and drug discovery applications.
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Affiliation(s)
- Ivana K Cecic
- Integrative Oncology Department, BC Cancer Research Centre, Vancouver, BC, Canada
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