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Greitens C, Leroux JC, Burger M. The intracellular visualization of exogenous DNA in fluorescence microscopy. Drug Deliv Transl Res 2024; 14:2242-2261. [PMID: 38526634 PMCID: PMC11208204 DOI: 10.1007/s13346-024-01563-4] [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] [Accepted: 02/28/2024] [Indexed: 03/27/2024]
Abstract
In the development of non-viral gene delivery vectors, it is essential to reliably localize and quantify transfected DNA inside the cell. To track DNA, fluorescence microscopy methods are commonly applied. These mostly rely on fluorescently labeled DNA, DNA binding proteins fused to a fluorescent protein, or fluorescence in situ hybridization (FISH). In addition, co-stainings are often used to determine the colocalization of the DNA in specific cellular compartments, such as the endolysosomes or the nucleus. We provide an overview of these DNA tracking methods, advice on how they should be combined, and indicate which co-stainings or additional methods are required to draw precise conclusions from a DNA tracking experiment. Some emphasis is given to the localization of exogenous DNA inside the nucleus, which is the last step of DNA delivery. We argue that suitable tools which allow for the nuclear detection of faint signals are still missing, hampering the rational development of more efficient non-viral transfection systems.
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Affiliation(s)
- Christina Greitens
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Jean-Christophe Leroux
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.
| | - Michael Burger
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.
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2
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Mikziński P, Kraus K, Widelski J, Paluch E. Modern Microbiological Methods to Detect Biofilm Formation in Orthopedy and Suggestions for Antibiotic Therapy, with Particular Emphasis on Prosthetic Joint Infection (PJI). Microorganisms 2024; 12:1198. [PMID: 38930580 PMCID: PMC11205407 DOI: 10.3390/microorganisms12061198] [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: 05/12/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Biofilm formation is a serious problem that relatively often causes complications in orthopedic surgery. Biofilm-forming pathogens invade implanted foreign bodies and surrounding tissues. Such a condition, if not limited at the appropriate time, often requires reoperation. This can be partially prevented by selecting an appropriate prosthesis material that prevents the development of biofilm. There are many modern techniques available to detect the formed biofilm. By applying them we can identify and visualize biofilm-forming microorganisms. The most common etiological factors associated with biofilms in orthopedics are: Staphylococcus aureus, coagulase-negative Staphylococci (CoNS), and Enterococcus spp., whereas Gram-negative bacilli and Candida spp. also deserve attention. It seems crucial, for therapeutic success, to eradicate the microorganisms able to form biofilm after the implantation of endoprostheses. Planning the effective targeted antimicrobial treatment of postoperative infections requires accurate identification of the microorganism responsible for the complications of the procedure. The modern microbiological testing techniques described in this article show the diagnostic options that can be followed to enable the implementation of effective treatment.
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Affiliation(s)
- Paweł Mikziński
- Faculty of Medicine, Wroclaw Medical University, Wyb. Pasteura 1, 50-376 Wroclaw, Poland; (P.M.); (K.K.)
| | - Karolina Kraus
- Faculty of Medicine, Wroclaw Medical University, Wyb. Pasteura 1, 50-376 Wroclaw, Poland; (P.M.); (K.K.)
| | - Jarosław Widelski
- Department of Pharmacognosy with Medicinal Plants Garden, Lublin Medical University, 20-093 Lublin, Poland;
| | - Emil Paluch
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, Tytusa Chalubinskiego 4, 50-376 Wroclaw, Poland
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3
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Tzeng HE, Lee YW, Lin CT, Chuang SS, Li CC, Chuang WH, Hsu CA, Wang YH, Tien HF, Wu SJ. Multicolour and lineage-specific interphase chromosome Flow-FISH: method development and clinical validation. Pathology 2024:S0031-3025(24)00129-6. [PMID: 38852040 DOI: 10.1016/j.pathol.2024.04.001] [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: 10/17/2023] [Revised: 03/01/2024] [Accepted: 04/14/2024] [Indexed: 06/10/2024]
Abstract
Flow cytometry can be applied in the detection of fluorescence in situ hybridisation (FISH) signals to efficiently analyse chromosomal aberrations. However, such interphase chromosome (IC) Flow-FISH protocols are currently limited to detecting a single colour. Furthermore, combining IC Flow-FISH with conventional multicolour flow cytometry is difficult because the DNA-denaturation step in FISH assay also disrupts cellular integrity and protein structures, precluding subsequent antigen-antibody binding and hindering concurrent labeling of surface antigens and FISH signals. We developed a working protocol for concurrent multicolour flow cytometry detection of nuclear IC FISH signals and cell surface markers. The protocol was validated by assaying sex chromosome content of blood cells, which was indicative of chimerism status in patients who had received sex-mismatched allogeneic haematopoietic stem cell transplants (allo-HSCT). The method was also adapted to detect trisomy 12 in chronic lymphocytic leukaemia (CLL) subjects. We first demonstrated the feasibility of this protocol in detecting multiple colours and concurrent nuclear and surface signals with high agreement. In clinical validation experiments, chimerism status was identified in clinical samples (n=56) using the optimised IC Flow-FISH method; the results tightly corresponded to those of conventional slide-based FISH (R2=0.9649 for XX cells and 0.9786 for XY cells). In samples from patients who received sex-mismatched allo-HSCT, individual chimeric statuses in different lineages could be clearly distinguished with high flexibility in gating strategies. Furthermore, in CLL samples with trisomy 12, this method could demonstrate that enriched trisomy 12 FISH signal was present in B cells rather than in T cells. Finally, by performing combined labelling of chromosome 12, X chromosome, and surface markers, we could detect rare residual recipient CLL cells with trisomy 12 after allo-HSCT. This adaptable protocol for multicolour and lineage-specific IC Flow-FISH advances the technique to allow for its potential application in various clinical contexts where conventional FISH assays are currently being utilised.
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Affiliation(s)
- Huey-En Tzeng
- Division of Hematology/Medical Oncology, Department of Medicine, Taichung Veterans General Hospital, Taichung City, Taiwan; Ph.D. Program for Cancer Molecular Biology and Drug Discovery, and Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Department of Post-Baccalaureate Medicine, College of Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Yi-Wei Lee
- Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Ting Lin
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Shih-Sung Chuang
- Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan; Center of Stem Cell and Precision Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Chi-Cheng Li
- Center of Stem Cell and Precision Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Wen-Hui Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Cheng-An Hsu
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Hua Wang
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hwei-Fang Tien
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, Far-East Memorial Hospital, New Taipei City, Taiwan
| | - Shang-Ju Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan.
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4
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Kairišs K, Sokolova N, Zilova L, Schlagheck C, Reinhardt R, Baumbach T, Faragó T, van de Kamp T, Wittbrodt J, Weinhardt V. Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach. Sci Rep 2024; 14:8543. [PMID: 38609416 PMCID: PMC11015006 DOI: 10.1038/s41598-024-58766-5] [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: 01/08/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.
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Affiliation(s)
- Kristaps Kairišs
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Lucie Zilova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
| | - Christina Schlagheck
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Robert Reinhardt
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tomáš Faragó
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Thomas van de Kamp
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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Rossi S, Marinello A, Pagliaro A, Franceschini D, Navarria P, Finocchiaro G, Toschi L, Scorsetti M, Santoro A. Current treatment approaches for brain metastases in ALK/ ROS1/ NTRK-positive non-small-cell lung cancer. Expert Rev Anticancer Ther 2023; 23:29-41. [PMID: 36548111 DOI: 10.1080/14737140.2023.2162044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Oncogene-addicted non-small cell lung cancer (NSCLC) patients present a high incidence of CNS metastases either at diagnosis or during the course of the disease. In this case, patients present with worse prognosis and are often excluded from clinical trials unless brain metastases are pre-treated or clinically stable. AREAS COVERED As a result of the discovery of several oncogenic drivers in ALK/ROS1/NTRK-positive NSCLC, targeted agents have been tested in several trials. We evaluate and compare the intracranial efficacy of available targeted agents in ALK/ROS1/NTRK-positive NSCLC based on subgroup analysis from pivotal trials. EXPERT OPINION Last-generation ALK inhibitors have shown slightly superior intracranial activity but pivotal trials do not consider the same endpoints for intracranial efficacy, therefore data are not comparable. Local treatments for BM including surgical resection, stereotactic radiosurgery (SRS) and WBRT, should be integrated with systemic therapies basing on specific criteria like presence of oligoprogression or symptomatic progression.
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Affiliation(s)
- Sabrina Rossi
- Medical Oncology and Hematology Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Arianna Marinello
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Arianna Pagliaro
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Davide Franceschini
- Department of Radiotherapy and Radiosurgery, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Pierina Navarria
- Department of Radiotherapy and Radiosurgery, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Giovanna Finocchiaro
- Medical Oncology and Hematology Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Luca Toschi
- Medical Oncology and Hematology Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Marta Scorsetti
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Department of Radiotherapy and Radiosurgery, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Armando Santoro
- Medical Oncology and Hematology Unit, IRCCS Humanitas Research Hospital, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
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6
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Viushkov VS, Lomov NA, Rubtsov MA, Vassetzky YS. Visualizing the Genome: Experimental Approaches for Live-Cell Chromatin Imaging. Cells 2022; 11:cells11244086. [PMID: 36552850 PMCID: PMC9776900 DOI: 10.3390/cells11244086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Over the years, our vision of the genome has changed from a linear molecule to that of a complex 3D structure that follows specific patterns and possesses a hierarchical organization. Currently, genomics is becoming "four-dimensional": our attention is increasingly focused on the study of chromatin dynamics over time, in the fourth dimension. Recent methods for visualizing the movements of chromatin loci in living cells by targeting fluorescent proteins can be divided into two groups. The first group requires the insertion of a special sequence into the locus of interest, to which proteins that recognize the sequence are recruited (e.g., FROS and ParB-INT methods). In the methods of the second approach, "programmed" proteins are targeted to the locus of interest (i.e., systems based on CRISPR/Cas, TALE, and zinc finger proteins). In the present review, we discuss these approaches, examine their strengths and weaknesses, and identify the key scientific problems that can be studied using these methods.
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Affiliation(s)
- Vladimir S. Viushkov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nikolai A. Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail A. Rubtsov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Center for Industrial Technologies and Entrepreneurship, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Yegor S. Vassetzky
- CNRS UMR9018, Université Paris-Saclay, Gustave Roussy, 94805 Villejuif, France
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Correspondence:
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7
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Tirrò E, Massimino M, Broggi G, Romano C, Minasi S, Gianno F, Antonelli M, Motta G, Certo F, Altieri R, Manzella L, Caltabiano R, Barbagallo GMV, Buttarelli FR, Magro G, Giangaspero F, Vigneri P. A Custom DNA-Based NGS Panel for the Molecular Characterization of Patients With Diffuse Gliomas: Diagnostic and Therapeutic Applications. Front Oncol 2022; 12:861078. [PMID: 35372034 PMCID: PMC8969903 DOI: 10.3389/fonc.2022.861078] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
The management of patients with Central Nervous System (CNS) malignancies relies on the appropriate classification of these tumors. Recently, the World Health Organization (WHO) has published new criteria underlining the importance of an accurate molecular characterization of CNS malignancies, in order to integrate the information generated by histology. Next generation sequencing (NGS) allows single step sequencing of multiple genes, generating a comprehensive and specific mutational profile of the tumor tissue. We developed a custom NGS-based multi-gene panel (Glio-DNA panel) for the identification of the correct glioma oncotype and the detection of its essential molecular aberrations. Specifically, the Glio-DNA panel targets specific genetic and chromosomal alterations involving ATRX chromatin remodeler (ATRX), cyclin dependent kinase inhibitor 2A (CDKN2A), isocitrate dehydrogenase (NADP+) 1 (IDH1) and the telomerase reverse transcriptase (TERT) promoter while also recognizing the co-deletion of 1p/19q, loss of chromosome 10 and gain of chromosome 7. Furthermore, the Glio-DNA panel also evaluates the methylation level of the O-6-methylguanine-DNA methyltransferase (MGMT) gene promoter that predicts temozolomide efficacy. As knowledge of the mutational landscape of each glioma is mandatory to define a personalized therapeutic strategy, the Glio-DNA panel also identifies alterations involving “druggable” or “actionable” genes. To test the specificity of our panel, we used two reference mutated DNAs verifying that NGS allele frequency measurement was highly accurate and sensitive. Subsequently, we performed a comparative analysis between conventional techniques - such as immunohistochemistry or fluorescence in situ hybridization - and NGS on 60 diffuse glioma samples that had been previously characterized. The comparison between conventional testing and NGS showed high concordance, suggesting that the Glio-DNA panel may replace multiple time-consuming tests. Finally, the identification of alterations involving different actionable genes matches glioma patients with potential targeted therapies available through clinical trials. In conclusion, our analysis demonstrates NGS efficacy in simultaneously detecting different genetic alterations useful for the diagnosis, prognosis and treatment of adult patients with diffuse glioma.
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Affiliation(s)
- Elena Tirrò
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
- Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
- *Correspondence: Elena Tirrò,
| | - Michele Massimino
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giuseppe Broggi
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Anatomic Pathology, University of Catania, Catania, Italy
| | - Chiara Romano
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Simone Minasi
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, La Sapienza University, Rome, Italy
| | - Francesca Gianno
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, La Sapienza University, Rome, Italy
| | - Manila Antonelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, La Sapienza University, Rome, Italy
| | - Gianmarco Motta
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
| | - Francesco Certo
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Neurological Surgery, Policlinico “G. Rodolico - San Marco” University Hospital, University of Catania, Catania, Italy
| | - Roberto Altieri
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Neurological Surgery, Policlinico “G. Rodolico - San Marco” University Hospital, University of Catania, Catania, Italy
| | - Livia Manzella
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Anatomic Pathology, University of Catania, Catania, Italy
| | - Giuseppe Maria Vincenzo Barbagallo
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Neurological Surgery, Policlinico “G. Rodolico - San Marco” University Hospital, University of Catania, Catania, Italy
| | - Francesca Romana Buttarelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, La Sapienza University, Rome, Italy
| | - Gaetano Magro
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, Anatomic Pathology, University of Catania, Catania, Italy
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, La Sapienza University, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Paolo Vigneri
- Center of Experimental Oncology and Hematology Azienda Ospedaliero Universitaria (AOU) Policlinico “G. Rodolico - San Marco”, Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
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8
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Synthetic chemical ligands and cognate antibodies for biorthogonal drug targeting and cell engineering. Adv Drug Deliv Rev 2021; 170:281-293. [PMID: 33486005 DOI: 10.1016/j.addr.2021.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/08/2021] [Indexed: 12/27/2022]
Abstract
A vast range of biomedical applications relies on the specificity of interactions between an antigen and its cognate receptor or antibody. This specificity can be highest when said antigen is a non-natural (synthetic) molecule introduced into a biological setting as a bio-orthogonal ligand. This review aims to present the development of this methodology from the early discovery of haptens a century ago to the recent clinical trials. We discuss such methodologies as antibody recruitment, artificial internalizing receptors and chemically induced dimerization, present the use of chimeric receptors and/or bispecific antibodies to achieve drug targeting and transcytosis, and illustrate how these platforms most impressively found use in the engineering of therapeutic cells such as the chimeric antigen receptor cells. This review aims to be of interest to a broad scientific audience and to spur the development of synthetic artificial ligands for biomedical applications.
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Okamoto A. Next-generation fluorescent nucleic acids probes for microscopic analysis of intracellular nucleic acids. Appl Microsc 2019; 49:14. [PMID: 33580316 PMCID: PMC7818349 DOI: 10.1186/s42649-019-0017-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/30/2019] [Indexed: 01/09/2023] Open
Abstract
Fluorescence imaging of nucleic acids is a very important technique necessary to understand gene expression and the resulting changes in cell function. This mini-review focuses on sequence-specific fluorescence imaging of intracellular RNA and methylated DNA using fluorescent nucleic acid probes. A couple of functional fluorescent nucleic acid probes developed by our laboratory are introduced and the examples of their application to fluorescence imaging of intracellular nucleic acids are described.
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Affiliation(s)
- Akimitsu Okamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
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10
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FANG HS, LANG MF, SUN J. New Methods for Cell Cycle Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61186-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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Rosas G, Ruiz R, Araujo JM, Pinto JA, Mas L. ALK rearrangements: Biology, detection and opportunities of therapy in non-small cell lung cancer. Crit Rev Oncol Hematol 2019; 136:48-55. [PMID: 30878128 DOI: 10.1016/j.critrevonc.2019.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/06/2019] [Accepted: 02/13/2019] [Indexed: 12/26/2022] Open
Abstract
The ALK receptor tyrosine kinase (ALK) gene encodes a transmembrane protein rearranged in 2-7% of non-small cell lung cancer (NSCLC) cases. This gene has become the second most studied therapeutic target after EGFR due to the implied therapeutic opportunities. While the diagnostic of ALK rearrangements is well established, small molecules targeting ALK are in constant evolution because tumor cells eventually will develop mechanisms of resistance. In this review we describe the biology of the ALK gene, alterations, epidemiology, diagnostic tests as well as strategies of treatment.
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Affiliation(s)
- Gina Rosas
- Departamento de Patología, Instituto Nacional de Enfermedades Neoplásicas, Av. Angamos Este, 2520, Surquillo, Lima 34, Peru
| | - Rossana Ruiz
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Av. Guardia Civil 571, San Borja, Lima 41-Peru; Departamento de Medicina Oncológica, Instituto Nacional de Enfermedades Neoplásicas, Av. Angamos Este, 2520, Surquillo, Lima 34-Peru
| | - Jhajaira M Araujo
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Av. Guardia Civil 571, San Borja, Lima 41-Peru
| | - Joseph A Pinto
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Av. Guardia Civil 571, San Borja, Lima 41-Peru
| | - Luis Mas
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Av. Guardia Civil 571, San Borja, Lima 41-Peru; Departamento de Medicina Oncológica, Instituto Nacional de Enfermedades Neoplásicas, Av. Angamos Este, 2520, Surquillo, Lima 34-Peru.
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12
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Nozeret K, Loll F, Cardoso GM, Escudé C, Boutorine AS. Interaction of fluorescently labeled pyrrole-imidazole polyamide probes with fixed and living murine and human cells. Biochimie 2018; 149:122-134. [DOI: 10.1016/j.biochi.2018.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 03/14/2018] [Indexed: 12/26/2022]
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13
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Brocken DJ, Tark-Dame M, Dame RT. The organization of bacterial genomes: Towards understanding the interplay between structure and function. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.coisb.2018.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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Du Y, Chen B. Detection approaches for multidrug resistance genes of leukemia. DRUG DESIGN DEVELOPMENT AND THERAPY 2017; 11:1255-1261. [PMID: 28458519 PMCID: PMC5402920 DOI: 10.2147/dddt.s134529] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Leukemia is a clonal malignant hematopoietic stem cell disease. It is the sixth most lethal cancer and accounts for 4% of all cancers. The main form of treatment for leukemia is chemotherapy. While some cancer types with a higher incidence than leukemia, such as lung and gastric cancer, have shown a sharp decline in mortality rates in recent years, leukemia has not followed this trend. Drug resistance is often regarded as the main clinical obstacle to effective chemotherapy in patients diagnosed with leukemia. Many resistance mechanisms have now been identified, and multidrug resistance (MDR) is considered the most important and prevalent mechanism involved in the failure of chemotherapy in leukemia. In order to reverse MDR and improve leukemia prognosis, effective detection methods are needed to identify drug resistance genes at initial diagnosis. This article provides a comprehensive overview of published approaches for the detection of MDR in leukemia. Identification of relevant MDR genes and methods for early detection of these genes will be needed in order to treat leukemia more effectively.
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Affiliation(s)
- Ying Du
- Department of Hematology and Oncology (Key Department of Jiangsu Medicine), School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu Province, People's Republic of China
| | - Baoan Chen
- Department of Hematology and Oncology (Key Department of Jiangsu Medicine), School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu Province, People's Republic of China
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15
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Jeangkhwoa P, Bandhaya A, Umpunjun P, Chuenboonngarm N, Panvisavas N. Identification of Cannabis sativa L. using the 1-kbTHCA synthase-fluorescence in situ hybridization probe. Sci Justice 2017; 57:101-106. [PMID: 28284435 DOI: 10.1016/j.scijus.2016.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 10/20/2022]
Abstract
This study reports a successful application of fluorescence in situ hybridization (FISH) technique in the identification of Cannabis sativa L. cells recovered from fresh and dried powdered plant materials. Two biotin-16-dUTP-labeled FISH probes were designed from the Cannabis-specific tetrahydrocannabinolic acid synthase (THCAS) gene and the ITS region of the 45S rRNA gene. Specificity of probe-target hybridization was tested against the target and 4 non-target plant species, i.e., Humulus lupulus, Mitragyna speciosa, Papaver sp., and Nicotiana tabacum. The 1-kb THCA synthase hybridization probe gave Cannabis-specific hybridization signals, unlike the 700-bp Cannabis-ITS hybridization probe. Probe-target hybridization was also confirmed against 20 individual Cannabis plant samples. The 1-kb THCA synthase and 700-bp Cannabis-ITS hybridization probes clearly showed 2 hybridization signals per cell with reproducibility. The 1-kb THCA synthase probe did not give any FISH signal when tested against H. lupulus, its closely related member of the Canabaceae family. It was also showed that 1-kb THCA synthase FISH probe can be applied to identify small amount of dried powdered Cannabis material with an addition of rehydration step prior to the experimental process. This study provided an alternative identification method for Cannabis trace.
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Affiliation(s)
- Pattraporn Jeangkhwoa
- M.Sc. Program in Plant Science, Department of Plant Science, Faculty of Science and Department of Pharmaceutical Botany, Faculty of Pharmacy, Mahidol University, Thailand
| | - Achirapa Bandhaya
- Forensic Science Program, Faculty of Science, Mahidol University, Thailand
| | - Puangpaka Umpunjun
- Department of Plant Science, Faculty of Science, Mahidol University, Thailand
| | | | - Nathinee Panvisavas
- Forensic Science Program, Faculty of Science, Mahidol University, Thailand; Department of Plant Science, Faculty of Science, Mahidol University, Thailand.
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Nozeret K, Bonan M, Yarmoluk SM, Novopashina DS, Boutorine AS. Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA. Bioorg Med Chem 2015; 23:5932-45. [PMID: 26190459 DOI: 10.1016/j.bmc.2015.06.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 11/18/2022]
Abstract
Synthetic minor groove-binding pyrrole-imidazole polyamides labeled by fluorophores are promising candidates for fluorescence imaging of double-stranded DNA in isolated chromosomes or fixed and living cells. We synthesized nine hairpin and two head-to-head tandem polyamides targeting repeated sequences from mouse major satellites. Their interaction with synthetic target dsDNA has been studied by physico-chemical methods in vitro before and after coupling to various fluorophores. Great variability in affinities and fluorescence properties reveals a conclusion that these properties do not only rely on recognition rules, but also on other known and unknown structural factors. Individual testing of each probe is needed before cellular applications.
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Affiliation(s)
- Karine Nozeret
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France.
| | - Marc Bonan
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France; Université Paris René Descartes, 12 Rue de l'École de Médecine, 75006 Paris, France.
| | - Serguiy M Yarmoluk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, ul. Zabolotnogo, 150, P.O. 88, 03187 Kiev, Ukraine.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Lavrentyev prosp., 8, 630090 Novosibirsk, Russia.
| | - Alexandre S Boutorine
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France.
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17
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Kao KJ, Tai CH, Chang WH, Yeh TS, Chen TC, Lee GB. A fluorescence in situ hybridization (FISH) microfluidic platform for detection of HER2 amplification in cancer cells. Biosens Bioelectron 2015; 69:272-9. [DOI: 10.1016/j.bios.2015.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
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18
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Machado A, Castro J, Cereija T, Almeida C, Cerca N. Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method. PeerJ 2015; 3:e780. [PMID: 25737820 PMCID: PMC4338769 DOI: 10.7717/peerj.780] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/30/2015] [Indexed: 11/20/2022] Open
Abstract
Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situ Hybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.6-99.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis.
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Affiliation(s)
- António Machado
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Joana Castro
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Tatiana Cereija
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Carina Almeida
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Nuno Cerca
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
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Nozeret K, Loll F, Escudé C, Boutorine AS. Polyamide fluorescent probes for visualization of repeated DNA sequences in living cells. Chembiochem 2015; 16:549-54. [PMID: 25639955 DOI: 10.1002/cbic.201402676] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Indexed: 11/07/2022]
Abstract
DNA imaging in living cells usually requires transgenic approaches that modify the genome. Synthetic pyrrole-imidazole polyamides that bind specifically to the minor groove of double-stranded DNA (dsDNA) represent an attractive approach for in-cell imaging that does not necessitate changes to the genome. Nine hairpin polyamides that target mouse major satellite DNA were synthesized. Their interactions with synthetic target dsDNA fragments were studied by thermal denaturation, gel-shift electrophoresis, circular dichroism, and fluorescence spectroscopy. The polyamides had different affinities for the target DNA, and fluorescent labeling of the polyamides affected their affinity for their targets. We validated the specificity of the probes in fixed cells and provide evidence that two of the probes detect target sequences in mouse living cell lines. This study demonstrates for the first time that synthetic compounds can be used for the visualization of the nuclear substructures formed by repeated DNA sequences in living cells.
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Affiliation(s)
- Karine Nozeret
- Structure and Instability of Genomes, Sorbonne Universités, Muséum national d'Histoire naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris Cedex 05 (France)
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20
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21
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Bogomolov AG, Karamysheva TV, Rubtsov NB. Fluorescence in situ hybridization with DNA probes derived from individual chromosomes and chromosome regions. Mol Biol 2014. [DOI: 10.1134/s002689331406003x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Jensen E. Technical review: In situ hybridization. Anat Rec (Hoboken) 2014; 297:1349-53. [PMID: 24810158 DOI: 10.1002/ar.22944] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/19/2014] [Accepted: 04/02/2014] [Indexed: 01/26/2023]
Abstract
In situ hybridization is a technique that is used to detect nucleotide sequences in cells, tissue sections, and even whole tissue. This method is based on the complementary binding of a nucleotide probe to a specific target sequence of DNA or RNA. These probes can be labeled with either radio-, fluorescent-, or antigen-labeled bases. Depending on the probe used, autoradiography, fluorescence microscopy, or immunohistochemistry, respectively, are used for visualization. In situ hybridization is extensively used in research, as well as clinical applications, especially for diagnostic purposes. This review discusses the basic technique of in situ hybridization. The standard in situ hybridization process is reviewed, and different types of in situ hybridization, their applications, and advantages and disadvantages are discussed.
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Affiliation(s)
- Ellen Jensen
- 35Southern Cross Rd., Kohimarama, Auckland, New Zealand
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23
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McNamara LE, Dalby MJ, Tsimbouri MP. The use of microarrays and fluorescence in situ hybridization for the study of mechanotransduction from topography. Methods Cell Biol 2014; 119:293-309. [PMID: 24439291 DOI: 10.1016/b978-0-12-416742-1.00015-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The combination of transcriptomic analysis and fluorescence in situ hybridization (FISH) provides a robust methodology to study genomic changes in different biological conditions. Microarrays allow a global study of gene expression in response to the conditions of interest, with comparison between control(s) and one or more test condition(s). The messenger RNA amplification step permits detection of even low abundance transcripts, a critical advantage for applications such as biomaterials research, where the starting material may be limited. Different types of microarrays are commercially available that allow the investigation of specific features, such as exon arrays, microRNA arrays, and gene arrays. Microarrays are available for different model organisms, but we use Affymetrix ® HuGene ® ST (Sense Target) arrays, a type of gene array for analysis of human samples. FISH involves fluorescent detection of probe DNA hybridized to an in situ chromosomal target that can be either whole chromosomes or chromosomal segments. The overall hybridization is similar to labeling with radioactive probes but the incorporation of fluorescent detection of the probe sequences allows for high sensitivity in a simple and quick assay. FISH can be applied to a variety of specimen types depending on the study of interest. In this chapter, we describe the methodologies of these two techniques and provide technical tips that should help overcome challenges in carrying them out.
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Affiliation(s)
- Laura E McNamara
- Centre for Cell Engineering, Institute of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Matthew J Dalby
- Centre for Cell Engineering, Institute of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Monica P Tsimbouri
- Centre for Cell Engineering, Institute of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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24
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Shete A, Rao P, Pati D, Merchant F. Spatial quantitation of FISH signals in diploid versus aneuploid nuclei. Cytometry A 2013; 85:339-52. [PMID: 24347051 DOI: 10.1002/cyto.a.22426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 09/27/2013] [Accepted: 11/21/2013] [Indexed: 12/21/2022]
Abstract
Fluorescence in situ hybridization (FISH) is the most widely used molecular technique to visualize chromosomal abnormalities. Here, we describe a novel 3D modeling approach to allow precise shape estimation and localization of FISH signals in the nucleus of human embryonic stem cells (hES) undergoing progressive but defined aneuploidy. The hES cell line WA09 acquires an extra copy of chromosome 12 in culture with increasing passages. Both diploid and aneuploid nuclei were analyzed to quantitate the differences in the localization of centromeric FISH signals for chromosome 12 as it transitions from euploidy to aneuploidy. We employed superquadric modeling primitives coupled with principal component analysis to determine the 3D position of FISH signals within the nucleus. A novel aspect of our modeling approach is that it allows comparison of FISH signals across multiple cells by normalizing the position of the centromeric signals relative to a reference landmark in oriented nuclei. Using this model we present evidence of changes in the relative positioning of centromeres in trisomy-12 cells when compared with diploid cells from the same population. Our analysis also suggests a significant change in the spatial distribution of at least one of the FISH signals in the aneuploid chromosome complements implicating that an overall change in centromere position may occur in trisomy-12 due to the addition of an extra chromosome. These studies underscore the unique utility of our modeling algorithms in quantifying FISH signals in three dimensions.
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Affiliation(s)
- Amol Shete
- Department of Computer Science, University of Houston, Houston, Texas
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25
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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Machado A, Almeida C, Salgueiro D, Henriques A, Vaneechoutte M, Haesebrouck F, Vieira MJ, Rodrigues L, Azevedo NF, Cerca N. Fluorescence in situ Hybridization method using Peptide Nucleic Acid probes for rapid detection of Lactobacillus and Gardnerella spp. BMC Microbiol 2013; 13:82. [PMID: 23586331 PMCID: PMC3637831 DOI: 10.1186/1471-2180-13-82] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/27/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) is a common vaginal infection occurring in women of reproductive age. It is widely accepted that the microbial switch from normal microflora to BV is characterized by a decrease in vaginal colonization by Lactobacillus species together with an increase of Gardnerella vaginalis and other anaerobes. Our goal was to develop and optimize a novel Peptide Nucleic Acid (PNA) Fluorescence in situ Hybridization assay (PNA FISH) for the detection of Lactobacillus spp. and G. vaginalis in mixed samples. RESULTS Therefore, we evaluated and validated two specific PNA probes by using 36 representative Lactobacillus strains, 22 representative G. vaginalis strains and 27 other taxonomically related or pathogenic bacterial strains commonly found in vaginal samples. The probes were also tested at different concentrations of G. vaginalis and Lactobacillus species in vitro, in the presence of a HeLa cell line. Specificity and sensitivity of the PNA probes were found to be 98.0% (95% confidence interval (CI), from 87.8 to 99.9%) and 100% (95% CI, from 88.0 to 100.0%), for Lactobacillus spp.; and 100% (95% CI, from 92.8 to 100%) and 100% (95% CI, from 81.5 to 100.0%) for G. vaginalis. Moreover, the probes were evaluated in mixed samples mimicking women with BV or normal vaginal microflora, demonstrating efficiency and applicability of our PNA FISH. CONCLUSIONS This quick method accurately detects Lactobacillus spp. and G. vaginalis species in mixed samples, thus enabling efficient evaluation of the two bacterial groups, most frequently encountered in the vagina.
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Affiliation(s)
- António Machado
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
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Ram S, Rodríguez JJ, Bosco G. Segmentation and detection of fluorescent 3D spots. Cytometry A 2012; 81:198-212. [DOI: 10.1002/cyto.a.22017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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FISHprep: A Novel Integrated Device for Metaphase FISH Sample Preparation. MICROMACHINES 2011. [DOI: 10.3390/mi2020116] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Hirose T, Sugiyama S. A simple DNA Characterization method using fiber-fluorescence in situ hybridization performed without DNA fragmentation. Photochem Photobiol 2011; 87:470-3. [PMID: 21366598 DOI: 10.1111/j.1751-1097.2010.00854.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We performed high-resolution fluorescence imaging of lambda phage DNA molecules hybridized with fluorescent-labeled DNA and peptide nucleic acid probes. In this method, the target DNA and probe were mixed, rapidly denatured and then subjected to liquid hybridization conditions. The hybridized DNA sample was then spotted onto a nontreated glass substrate and subjected to molecular combing. The resultant continuous fluorescence signal of intact lambda DNA shows that the fluorescent-labeled probes bound to the predicted sites but in a pattern that was clearly different to the beads-on-a-string pattern typical for fiber-fluorescence in situ hybridization. The key changes to the conventional method are hybridization of the free target DNA in liquid and lowering the denaturation temperature. The method described here allows the rapid and direct visualization of the specific binding sites of intact DNA molecules without damaging the DNA fibers and causing fragmentation of the fluorescence signal. This technique should be a useful tool in studies of genetics and also large-scale DNA sequencing projects.
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Affiliation(s)
- Tamaki Hirose
- Nanobiotechnology Laboratory, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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Hovhannisyan GG. Fluorescence in situ hybridization in combination with the comet assay and micronucleus test in genetic toxicology. Mol Cytogenet 2010; 3:17. [PMID: 20840797 PMCID: PMC2949878 DOI: 10.1186/1755-8166-3-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/15/2010] [Indexed: 02/04/2023] Open
Abstract
Comet assay and micronucleus (MN) test are widely applied in genotoxicity testing and biomonitoring. While comet assay permits to measure direct DNA-strand breaking capacity of a tested agent MN test allows estimating the induced amount of chromosome and/or genome mutations. The potential of these two methods can be enhanced by the combination with fluorescence in situ hybridization (FISH) techniques. FISH plus comet assay allows the recognition of targets of DNA damage and repairing directly. FISH combined with MN test is able to characterize the occurrence of different chromosomes in MN and to identify potential chromosomal targets of mutagenic substances. Thus, combination of FISH with the comet assay or MN test proved to be promising techniques for evaluation of the distribution of DNA and chromosome damage in the entire genome of individual cells. FISH technique also permits to study comet and MN formation, necessary for correct application of these methods. This paper reviews the relevant literature on advantages and limitations of Comet-FISH and MN-FISH assays application in genetic toxicology.
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Affiliation(s)
- Galina G Hovhannisyan
- Department of Genetics and Cytology, State University, Biological Faculty, 1 Alex Manoukian Street, Yerevan 375025, Armenia.
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31
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Xia S, Li J, Wang R, Li J, Zhang Z. Tracking composition and dynamics of nitrification and denitrification microbial community in a biofilm reactor by PCR-DGGE and combining FISH with flow cytometry. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2010.01.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Teo YN, Wilson JN, Kool ET. Polyfluorophores on a DNA backbone: a multicolor set of labels excited at one wavelength. J Am Chem Soc 2009; 131:3923-33. [PMID: 19254023 DOI: 10.1021/ja805502k] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We recently described the assembly of fluorescent deoxyriboside monomers ("fluorosides") into DNA-like phosphodiester oligomers (oligodeoxyfluorosides or ODFs) in which hydrocarbon and heterocyclic aromatic fluorophores interact both physically and electronically. Here we report the identification of a multicolor set of water-soluble ODF dyes that display emission colors across the visible spectrum, and all of which can be simultaneously excited by long-wavelength UV light at 340-380 nm. Multispectral dye candidates were chosen from a library of 4096 tetramer ODFs constructed on PEG-polystyrene beads using a simple long-pass filter to observe all visible colors at the same time. We resynthesized and characterized a set of 23 ODFs containing one to four individual chromophores and included 2-3 spacer monomers to increase aqueous solubility and minimize aggregation. Emission maxima of this set range from 376 to 633 nm, yielding apparent colors from violet to red, all of which can be visualized directly. The spectra of virtually all ODFs in this set varied considerably from the simple combination of monomer components, revealing extensive electronic interactions between the presumably stacked monomers. In addition, comparisons of anagrams in the set (isomers having the same components in a different sequence) reveal the importance of nearest-neighbor interactions in the emissive behavior. Preliminary experiments with human tumor (HeLa) cells, observing two ODFs by laser confocal microscopy, showed that they can penetrate the outer cellular membrane, yielding cytoplasmic localization. In addition, a set of four distinctly colored ODFs was incubated with live zebrafish embryos, showing tissue penetration, apparent biostability, and no apparent toxicity. The results suggest that ODF dyes may be broadly useful as labels in biological systems, allowing the simultaneous tracking of multiple species by color, and allowing visualization in moving systems where classical fluorophores fail.
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Abstract
During the past two decades fluorescent in-situ hybridization (FISH) has become a standard technique to directly localize, orient, and order genes in the genomes of a wide range of species. Despite the availability of a variety of probes, probe labeling and signal-detection systems, and advanced image analysis software, the core procedures used to carry out FISH remain the same. A detailed overview of these procedures, including target preparation (metaphase/interphase chromosomes and DNA fibers), probe labeling, in-situ hybridization, signal detection, and imaging, is here provided in a stepwise manner.
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Affiliation(s)
- Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
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Lerner B, Koushnir L, Yeshaya J. Segmentation and Classification of Dot and Non-Dot-Like Fluorescence in situ Hybridization Signals for Automated Detection of Cytogenetic Abnormalities. ACTA ACUST UNITED AC 2007; 11:443-9. [PMID: 17674627 DOI: 10.1109/titb.2007.894335] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Signal segmentation and classification of fluorescence in situ hybridization (FISH) images are essential for the detection of cytogenetic abnormalities. Since current methods are limited to dot-like signal analysis, we propose a methodology for segmentation and classification of dot and non-dot-like signals. First, nuclei are segmented from their background and from each other in order to associate signals with specific isolated nuclei. Second, subsignals composing non-dot-like signals are detected and clustered to signals. Features are measured to the signals and a subset of these features is selected representing the signals to a multiclass classifier. Classification using a naive Bayesian classifier (NBC) or a multilayer perceptron is accomplished. When applied to a FISH image database, dot and non-dot-like signals were segmented almost perfectly and then classified with accuracy of approximately 80% by either of the classifiers.
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Affiliation(s)
- Boaz Lerner
- Department of Electrical and Computer Engineering, Ben-Gurion University, Beer Sheva 84105, Israel.
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Cai W, Hsu AR, Li ZB, Chen X. Are quantum dots ready for in vivo imaging in human subjects? NANOSCALE RESEARCH LETTERS 2007; 2:265-281. [PMID: 21394238 PMCID: PMC3050636 DOI: 10.1007/s11671-007-9061-9] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2007] [Accepted: 04/24/2007] [Indexed: 04/14/2023]
Abstract
Nanotechnology has the potential to profoundly transform the nature of cancer diagnosis and cancer patient management in the future. Over the past decade, quantum dots (QDs) have become one of the fastest growing areas of research in nanotechnology. QDs are fluorescent semiconductor nanoparticles suitable for multiplexed in vitro and in vivo imaging. Numerous studies on QDs have resulted in major advancements in QD surface modification, coating, biocompatibility, sensitivity, multiplexing, targeting specificity, as well as important findings regarding toxicity and applicability. For in vitro applications, QDs can be used in place of traditional organic fluorescent dyes in virtually any system, outperforming organic dyes in the majority of cases. In vivo targeted tumor imaging with biocompatible QDs has recently become possible in mouse models. With new advances in QD technology such as bioluminescence resonance energy transfer, synthesis of smaller size non-Cd based QDs, improved surface coating and conjugation, and multifunctional probes for multimodality imaging, it is likely that human applications of QDs will soon be possible in a clinical setting.
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Affiliation(s)
- Weibo Cai
- The Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Stanford University School of Medicine, 1201 Welch Rd, P095, Stanford, CA, 94305-5484, USA
| | - Andrew R Hsu
- The Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Stanford University School of Medicine, 1201 Welch Rd, P095, Stanford, CA, 94305-5484, USA
| | - Zi-Bo Li
- The Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Stanford University School of Medicine, 1201 Welch Rd, P095, Stanford, CA, 94305-5484, USA
| | - Xiaoyuan Chen
- The Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Stanford University School of Medicine, 1201 Welch Rd, P095, Stanford, CA, 94305-5484, USA
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Lerner B, Yeshaya J, Koushnir L. On the classification of a small imbalanced cytogenetic image database. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2007; 4:204-15. [PMID: 17473314 DOI: 10.1109/tcbb.2007.070207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Solving a multiclass classification task using a small imbalanced database of patterns of high dimension is difficult due to the curse-of-dimensionality and the bias of the training toward the majority classes. Such a problem has arisen while diagnosing genetic abnormalities by classifying a small database of fluorescence in situ hybridization signals of types having different frequencies of occurrence. We propose and experimentally study using the cytogenetic domain two solutions to the problem. The first is hierarchical decomposition of the classification task, where each hierarchy level is designed to tackle a simpler problem which is represented by classes that are approximately balanced. The second solution is balancing the data by up-sampling the minority classes accompanied by dimensionality reduction. Implemented by the naive Bayesian classifier or the multilayer perceptron neural network, both solutions have diminished the problem and contributed to accuracy improvement. In addition, the experiments suggest that coping with the smallness of the data is more beneficial than dealing with its imbalance.
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Affiliation(s)
- Boaz Lerner
- Depsrtment of Elctrical and Computer Engineering, Ben-Gurion University, Beer-Sheva, Israel.
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Vigdor B, Lerner B. Accurate and Fast Off and Online Fuzzy ARTMAP-Based Image Classification With Application to Genetic Abnormality Diagnosis. ACTA ACUST UNITED AC 2006; 17:1288-300. [PMID: 17001988 DOI: 10.1109/tnn.2006.877532] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We propose and investigate the fuzzy ARTMAP neural network in off and online classification of fluorescence in situ hybridization image signals enabling clinical diagnosis of numerical genetic abnormalities. We evaluate the classification task (detecting a several abnormalities separately or simultaneously), classifier paradigm (monolithic or hierarchical), ordering strategy for the training patterns (averaging or voting), training mode (for one epoch, with validation or until completion) and model sensitivity to parameters. We find the fuzzy ARTMAP accurate in accomplishing both tasks requiring only very few training epochs. Also, selecting a training ordering by voting is more precise than if averaging over orderings. If trained for only one epoch, the fuzzy ARTMAP provides fast, yet stable and accurate learning as well as insensitivity to model complexity. Early stop of training using a validation set reduces the fuzzy ARTMAP complexity as for other machine learning models but cannot improve accuracy beyond that achieved when training is completed. Compared to other machine learning models, the fuzzy ARTMAP does not loose but gain accuracy when overtrained, although increasing its number of categories. Learned incrementally, the fuzzy ARTMAP reaches its ultimate accuracy very fast obtaining most of its data representation capability and accuracy by using only a few examples. Finally, the fuzzy ARTMAP accuracy for this domain is comparable with those of the multilayer perceptron and support vector machine and superior to those of the naive Bayesian and linear classifiers.
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Affiliation(s)
- Boaz Vigdor
- Pattern Analysis and Machine Learning Laboratory, Department of Electrical and Computer Engineering, Ben-Gurion University, Beer-Sheva 84105, Israel.
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Coffee R, Lazarchick J, Chévez-Barrios P, Howard G. Rapid diagnosis of orbital mantle cell lymphoma utilizing fluorescent in situ hybridization technology. Am J Ophthalmol 2005; 140:554-6. [PMID: 16139018 DOI: 10.1016/j.ajo.2005.03.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Revised: 03/11/2005] [Accepted: 03/12/2005] [Indexed: 10/25/2022]
Abstract
PURPOSE We describe a patient with an orbital lymphoma in which genetic analysis utilizing fluorescent in situ hybridization (FISH) on a touch preparation of the tumor identified the classic 11:14 translocation associated with a mantle cell lymphoma. DESIGN Clinicopathologic case report. METHODS A 76-year-old woman presented complaining of ptosis and was found to have an orbital lesion suspected of being a lymphoproliferative malignancy. A biopsy of the lesion was performed in the office, and the sample was processed using a touch preparation technique. RESULTS Genetic analysis utilizing FISH on a touch preparation of the tumor identified the classic 11:14 translocation associated with a mantle cell lymphoma. CONCLUSIONS FISH has become useful in the differential diagnosis of lymphoproliferative lesions. The touch preparation method requires smaller amounts of tissue than standard methods, and samples may be obtained in an office setting.
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Affiliation(s)
- Robert Coffee
- Department of Ophthalmology, Cullen Eye Institute, Baylor College of Medicine, One Baylor Plaza, MS 220, Houston, TX 77030, USA.
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Wang Y, Xu Z, Pierce JC, Guo X. Characterization of eastern oyster (Crassostrea virginica Gmelin) chromosomes by fluorescence in situ hybridization with bacteriophage P1 clones. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2005; 7:207-14. [PMID: 15933900 DOI: 10.1007/s10126-004-0051-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2004] [Accepted: 07/17/2004] [Indexed: 05/02/2023]
Abstract
Chromosome identification is an essential step in genomic research, which so far has not been possible in oysters. We tested bacteriophage P1 clones for chromosomal identification in the eastern oyster Crassostrea virginica, using fluorescence in situ hybridization (FISH). P1 clones were labeled with digoxigenin-11-dUTP using nick translation. Hybridization was detected with fluorescein-isothiocyanate-labeled anti-digoxigenin antibodies and amplified with 2 layers of antibodies. Nine of the 21 P1 clones tested produced clear and consistent FISH signals when Cot-1 DNA was used as a blocking agent against repetitive sequences. Karyotypic analysis and cohybridization positively assigned the 9 P1 clones to 7 chromosomes. The remaining 3 chromosomes can be separated by size and arm ratio. Five of the 9 P1 clones were sequenced at both ends, providing sequence-tagged sites that can be used to integrate linkage and cytogenetic maps. One sequence is part of the bone morphogenetic protein type 1b receptor, a member of the transforming growth factor superfamily, and mapped to the telomeric region of the long arm of chromosome 2. This study shows that large-insert clones such as P1 are useful as chromosome-specific FISH probes and for gene mapping in oysters.
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Affiliation(s)
- Yongping Wang
- Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
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Valárik M, Bartos J, Kovárová P, Kubaláková M, de Jong JH, Dolezel J. High-resolution FISH on super-stretched flow-sorted plant chromosomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 37:940-50. [PMID: 14996224 DOI: 10.1111/j.1365-313x.2003.02010.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A novel high-resolution fluorescence in situ hybridisation (FISH) strategy, using super-stretched flow-sorted plant chromosomes as targets, is described. The technique that allows longitudinal extension of chromosomes of more than 100 times their original metaphase size is especially attractive for plant species with large chromosomes, whose pachytene chromosomes are generally too long and heterochromatin patterns too complex for FISH analysis. The protocol involves flow cytometric sorting of metaphase chromosomes, mild proteinase-K digestion of air-dried chromosomes on microscopic slides, followed by stretching with ethanol:acetic acid (3 : 1). Stretching ratios were assessed in a number of FISH experiments with super-stretched chromosomes from barley, wheat, rye and chickpea, hybridised with 45S and 5S ribosomal DNAs and the [GAA]n microsatellite, the [TTTAGGG]n telomeric repeat and a bacterial artificial chromosome (BAC) clone as probes. FISH signals on stretched chromosomes were brighter than those on the untreated control, resulting from better accessibility of the stretched chromatin and maximum observed sensitivity of 1 kbp. Spatial resolution of neighbouring loci was improved down to 70 kbp as compared to 5-10 Mbp after FISH on mitotic chromosomes, revealing details of adjacent DNA sequences hitherto not obtained with any other method. Stretched chromosomes are advantageous over extended DNA fibres from interphase nuclei as targets for FISH studies because they still retain chromosomal integrity. Although the method is confined to species for which chromosome flow sorting has been developed, it provides a unique system for controlling stretching degree of mitotic chromosomes and high-resolution bar-code FISH.
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Affiliation(s)
- M Valárik
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Olomouc, Czech Republic
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Wang Y, Xu Z, Guo X. Differences in the rDNA-bearing chromosome divide the Asian-Pacific and Atlantic species of Crassostrea (Bivalvia, Mollusca). THE BIOLOGICAL BULLETIN 2004; 206:46-54. [PMID: 14977729 DOI: 10.2307/1543197] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Karyotype and chromosomal location of the major ribosomal RNA genes (rDNA) were studied using fluorescence in situ hybridization (FISH) in five species of CRASSOSTREA: three Asian-Pacific species (C. gigas, C. plicatula, and C. ariakensis) and two Atlantic species (C. virginica and C. rhizophorae). FISH probes were made by PCR amplification of the intergenic transcribed spacer between the 18S and 5.8S rRNA genes, and labeled with digoxigenin-11-dUTP. All five species had a haploid number of 10 chromosomes. The Atlantic species had 1-2 submetacentric chromosomes, while the three Pacific species had none. FISH with metaphase chromosomes detected a single telomeric locus for rDNA in all five species without any variation. In all three Pacific species, rDNA was located on the long arm of Chromosome 10 (10q)--the smallest chromosome. In the two Atlantic species, rDNA was located on the short arm of Chromosome 2 (2p)--the second longest chromosome. A review of other studies reveals the same distribution of NOR sites (putative rDNA loci) in three other species: on 10q in C. sikamea and C. angulata from the Pacific Ocean and on 2p in C. gasar from the western Atlantic. All data support the conclusion that differences in size and shape of the rDNA-bearing chromosome represent a major divide between Asian-Pacific and Atlantic species of CRASSOSTREA: This finding suggests that chromosomal divergence can occur under seemingly conserved karyotypes and may play a role in reproductive isolation and speciation.
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Affiliation(s)
- Yongping Wang
- Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, New Jersey 08349, USA
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Martins RR, Ramos HI, Llerena Jr. JC, Almeida JC. Investigação clínica e genética em meninas com baixa estatura idiopática. ACTA ACUST UNITED AC 2003. [DOI: 10.1590/s0004-27302003000600010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Em 10 meninas com diagnóstico de baixa estatura idiopática (BEI), realizamos avaliação citogenética após revisão clínica. Dois cariótipos foram anormais: mos 45,X/46,XX; mos 45,X/46,X,der(Xp)/46,X,r(X), e para sua elucidação foram aplicadas técnicas de citogenética molecular e análise de microssatélites, incluindo SHOX CA repeat. Os resultados confirmaram a origem dos cromossomos anômalos e a identificação da haploinsuficiência do gene SHOX. Nos oito casos com cariótipo normal, a pesquisa de mosaicismos crípticos pela técnica FISH através da sonda centromérica (DXZ1) em células de mucosa oral (nuc ish) evidenciou a presença de dois mosaicos verdadeiros (DXZ1x2/DXZ1x1). A revisão clínica da paciente com anomalia estrutural de X e das 2 meninas com mosaicismo detectados pelo nuc ish, mostrou a presença de 3 ou mais sinais clínicos observados na síndrome de Turner (ST). Estes resultados reafirmam a importância da análise citogenética em meninas com diagnóstico de BEI e sinais clínicos da ST. Os resultados do estudo molecular para o gene SHOX confirmam sua relação com estigmas da ST. Sendo normal o cariótipo, a pesquisa de mosaicismos crípticos em outros tecidos deve ser considerada. O diagnóstico mais preciso poderá modificar a conduta terapêutica, como indicação do GH nessas meninas.
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Affiliation(s)
- Rosa R.S. Martins
- Instituto Estadual de Diabetes e Endocrinologia; Universidade Federal do Rio de Janeiro
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Connally R, Veal D, Piper J. High resolution detection of fluorescently labeled microorganisms in environmental samples using time-resolved fluorescence microscopy. FEMS Microbiol Ecol 2002; 41:239-45. [DOI: 10.1111/j.1574-6941.2002.tb00985.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Abstract
A área de endocrinologia genética e oncológica tem sido alvo de enorme avanço nos anos recentes. A descoberta de genes responsáveis por neoplasias hereditárias nas últimas décadas representou uma fonte importante de informações concernentes à avaliação de risco, prevenção e aconselhamento genético. Neste particular, a caracterização do gene responsável pela neoplasia endócrina múltipla tipo 2 (MEN 2) representou a "pedra angular" para o desenvolvimento do campo de oncogenética clínica. Portanto, estima-se que o estudo genético e funcional das neoplasias hereditárias será igualmente capaz de liderar o avanço para um melhor manuseio clínico e terapêutico destas doenças. Um dos grandes desafios do futuro reside em se entender o intrincado mecanismo de interação entre genes e proteínas no controle do desenvolvimento e regulação dos diferentes sistemas biológicos. Uma das conseqüências mais antecipadas deste avanço é a sua aplicação para o tratamento específico e "individualizado" de todas as doenças humanas. Esta breve revisão tratará de aspectos gerais que envolvem o processo de identificação de novos genes e sua associação com condições clínicas específicas. As técnicas clássicas de clonagem serão apresentadas ao lado de estratégias modernas de identificação e análise de genes. O papel da bioinformática no Projeto Genoma Humano e o imenso potencial que esta informação traz para acelerar o processo de caracterização de novos grupos de genes serão brevemente discutidos.
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Weimer J, Koehler MR, Wiedemann U, Attermeyer P, Jacobsen A, Karow D, Kiechl M, Jonat W, Arnold N. Highly comprehensive karyotype analysis by a combination of spectral karyotyping (SKY), microdissection, and reverse painting (SKY-MD). Chromosome Res 2002; 9:395-402. [PMID: 11448041 DOI: 10.1023/a:1016735618513] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A technique disclosing most information about chromosome modifications is the technique of choice for the analysis of chromosome alterations. The newly developed method for microdissection of fluorescence-labeled chromosomes (FISH-MD) can improve upon this expectation in combination with 24-color spectral karyotyping (SKY). The highly efficient way to detect chromosome modifications by SKY and the detailed specification of aberrant chromosomes by FISH-MD prompted us to use both techniques in a combined approach called SKY-MD. First, an overview of chromosomal aberrations is obtained by spectral karyotyping and subsequently the derivative chromosomes recognized are characterized in a highly specific manner by microdissection and reverse painting. A small quantity of isolated material dissected directly from a 24-color metaphase is sufficient to obtain very detailed information about the chromosome regions and the breakpoints involved in the derivative chromosomes. Therefore, the combination of spectral karyotyping and microdissection in one procedure, and reverse painting can characterize chromosomal aberrations with a degree of specificity hitherto unknown from individual karyotyping experiments. In this article we compare the efficiency of both the SKY technique and that of classical microdissection with the efficiency obtained by SKY-MD.
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Affiliation(s)
- J Weimer
- Oncology Laboratory, Gynecology and Obstetrics Clinic, Christian-Albrechts University Kiel, Germany.
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Zhong XB, Lizardi PM, Huang XH, Bray-Ward PL, Ward DC. Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification. Proc Natl Acad Sci U S A 2001; 98:3940-5. [PMID: 11274414 PMCID: PMC31158 DOI: 10.1073/pnas.061026198] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rolling circle amplification (RCA) is a surface-anchored DNA replication reaction that can be exploited to visualize single molecular recognition events. Here we report the use of RCA to visualize target DNA sequences as small as 50 nts in peripheral blood lymphocytes or in stretched DNA fibers. Three unique target sequences within the cystic fibrosis transmembrane conductance regulator gene could be detected simultaneously in interphase nuclei, and could be ordered in a linear map in stretched DNA. Allele-discriminating oligonucleotide probes in conjunction with RCA also were used to discriminate wild-type and mutant alleles in the cystic fibrosis transmembrane conductance regulator, p53, BRCA-1, and Gorlin syndrome genes in the nuclei of cultured cells or in DNA fibers. These observations demonstrate that signal amplification by RCA can be coupled to nucleic acid hybridization and multicolor fluorescence imaging to detect single nucleotide changes in DNA within a cytological context or in single DNA molecules. This provides a means for direct physical haplotyping and the analysis of somatic mutations on a cell-by-cell basis.
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Affiliation(s)
- X B Zhong
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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