51
|
Kaykov A, Nurse P. Analysis of Fission Yeast Single DNA Molecules on the Megabase Scale Using DNA Combing. Methods Mol Biol 2018; 1721:9-24. [PMID: 29423843 DOI: 10.1007/978-1-4939-7546-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
DNA combing enables the quantitative analysis of DNA replication, DNA recombination, DNA-protein interaction, and DNA methylation along genomic single DNA molecules at 1 kb resolution. However, DNA combing has been restricted to short 200-500 kb long DNA fragments, which introduces significant bias in data analysis. An improved DNA combing methodology that allows to routinely image Mb-scale single DNA molecules and occasionally up to full-length fission yeast chromosomes is presented in this chapter. DNA combing of Mb-scale single DNA molecules can be applied to accurately measure the dynamic properties of DNA replication such as the rate of origin firing, replication fork velocity, fork directionality and the frequency of fork blockage. In addition, Mb-scale single DNA molecules enable the quantitative analysis of complex genomic rearrangements including gross chromosomal translocations, repetitive DNA sequences, large deletions, and duplications, which are difficult to investigate with deep sequencing strategies.
Collapse
|
52
|
Abstract
Studies using Drosophila have played pivotal roles in advancing our understanding of molecular mechanisms of mitosis throughout the past decades, due to the short generation time and advanced genetic research of this organism. Drosophila is also an excellent model to study female meiosis in oocytes. Pathways such as the acentrosomal assembly of the meiotic spindle in oocytes are conserved from fly to humans. Collecting and manipulating large Drosophila oocytes for microscopy and biochemistry are both time and cost efficient, offering advantages over mouse or human oocytes. Therefore, Drosophila oocytes serve as an excellent platform for molecular studies of female meiosis using a combination of genetics, microscopy, and biochemistry. Here we describe key methods to observe the formation of the meiotic spindle either in fixed or in live oocytes. Moreover, biochemical methods are described to identify protein-protein interactions in vivo.
Collapse
Affiliation(s)
- Pierre Romé
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Hiroyuki Ohkura
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
| |
Collapse
|
53
|
Abstract
Cellular mRNA levels are determined by the rates of mRNA synthesis and mRNA decay. Typically, mRNA degradation kinetics are measured on a population of cells that are either chemically treated or genetically engineered to inhibit transcription. However, these manipulations can affect the mRNA decay process itself by inhibiting regulatory mechanisms that govern mRNA degradation, especially if they occur on short time-scales. Recently, single molecule fluorescent in situ hybridization (smFISH) approaches have been implemented to quantify mRNA decay rates in single, unperturbed cells. Here, we provide a step-by-step protocol that allows quantification of mRNA decay in single Saccharomyces cerevisiae using smFISH. Our approach relies on fluorescent labeling of single cytoplasmic mRNAs and nascent mRNAs found at active sites of transcription, coupled with mathematical modeling to derive mRNA half-lives. Commercially available, single-stranded smFISH DNA oligonucleotides (smFISH probes) are used to fluorescently label mRNAs followed by the quantification of cellular and nascent mRNAs using freely available spot detection algorithms. Our method enables quantification of mRNA decay of any mRNA in single, unperturbed yeast cells and can be implemented to quantify mRNA turnover in a variety of cell types as well as tissues.
Collapse
Affiliation(s)
- Tatjana Trcek
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY, USA.
| | - Samir Rahman
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| |
Collapse
|
54
|
Jetybayev IY, Bugrov AG, Buleu OG, Bogomolov AG, Rubtsov NB. Origin and Evolution of the Neo-Sex Chromosomes in Pamphagidae Grasshoppers through Chromosome Fusion and Following Heteromorphization. Genes (Basel) 2017; 8:genes8110323. [PMID: 29137168 PMCID: PMC5704236 DOI: 10.3390/genes8110323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/16/2022] Open
Abstract
In most phylogenetic lineages, the evolution of sex chromosomes is accompanied by their heteromorphization and degradation of one of them. The neo-sex chromosomes are useful model for studying early stages of these processes. Recently two lineages of the neo-sex chromosomes on different stages of heteromorphization was discovered in Pamphagidae family. The neo-sex chromosome heteromorphization was analyzed by generation of DNA probes derived from the neo-Xs and neo-Ys followed with chromosome painting in nineteen species of Pamphagidae family. The homologous regions of the neo-sex chromosomes were determined in closely related species with the painting procedure and image analysis with application of the Visualization of the Specific Signal in Silico software package. Results of these analyses and distribution of C-positive regions in the neo-sex chromosomes revealed details of the heteromorphization of the neo-sex chromosomes in species from both phylogenetic lineages of Pamphagidae grasshoppers. The hypothetical mechanism of the neo-Y degradation was suggested. It includes expansion of different repeats from the proximal neo-Y chromosome region by inversions, spreading them towards distal region. Amplification of these repeats leads to formation of C-positive regions and elimination of the C-negative regions located between them.
Collapse
Affiliation(s)
- Ilyas Yerkinovich Jetybayev
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
| | - Alexander Gennadievich Bugrov
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Olesya Georgievna Buleu
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Anton Gennadievich Bogomolov
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Nikolay Borisovich Rubtsov
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| |
Collapse
|
55
|
Guérit D, Lalonde M, Chartrand P. Telomerase RNA Imaging in Budding Yeast and Human Cells by Fluorescent In Situ Hybridization. Methods Mol Biol 2018; 1672:387-402. [PMID: 29043638 DOI: 10.1007/978-1-4939-7306-4_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Telomerase, the enzyme that elongates telomeres in most eukaryotes, is a ribonucleoprotein complex composed of a reverse transcriptase catalytic subunit (TERT in human, Est2 in the budding yeast S. cerevisiae), regulatory factors and a noncoding RNA called hTERC (in human) or TLC1 (in budding yeast). Telomerase trafficking is a major process in the biogenesis and regulation of telomerase action at telomeres. Due to its higher signal-to-noise ratio, imaging of the telomerase RNA moiety is frequently used to determine telomerase intracellular localization. Here we describe how to image telomerase RNA in human and yeast cells using fluorescence in situ hybridization.
Collapse
|
56
|
Hammons L, Brazauskas R, Pasquini M, Hamadani M, Hari P, D'Souza A. Presence of fluorescent in situ hybridization abnormalities is associated with plasma cell burden in light chain amyloidosis. Hematol Oncol Stem Cell Ther 2017; 11:105-111. [PMID: 28830801 DOI: 10.1016/j.hemonc.2017.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/06/2017] [Accepted: 07/23/2017] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE/BACKGROUND To assess abnormalities found on CD138-enriched fluorescent in situ hybridization (FISH) studies on pre-treatment bone marrow in systemic amyloid light-chain amyloidosis (AL) and correlate findings between these abnormalities with organ involvement and 1-year survival. METHODS We reviewed 107 patients with systemic AL to identify the impact of a diagnostic FISH study done on plasma cell-enriched bone marrow in our institution between January 2010 and January 2015; 77 had pre-treatment testing performed. RESULTS A total of 77 (61%) patients had abnormal FISH including: hyperdiploidy (29%), t(11;14), (20%), hypodiploidy (16%), t(4;14), (1%), del17p (5%), and+1q21 (5%). Abnormal FISH studies were more likely in those patients with plasma cell involvement≥10% (p=.002). FISH abnormalities were not shown to correlate with stage, cardiac involvement, or survival at 1year. One-year survival was significantly affected by stage at diagnosis and presence of cardiac and hepatic amyloid involvement. CONCLUSION We conclude that in AL, FISH abnormalities are associated with clonal burden. We found no impact of these markers on the type of organ involvement or 1-year survival.
Collapse
Affiliation(s)
- Lindsay Hammons
- Medical College of Wisconsin Graduate School, Milwaukee, WI, USA
| | - Ruta Brazauskas
- Division of Biostatistics, Institute of Health and Safety, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Marcelo Pasquini
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mehdi Hamadani
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Parameswaran Hari
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anita D'Souza
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
| |
Collapse
|
57
|
Bagheri G, Lehner JD, Zhong J. Enhanced detection of Rickettsia species in Ixodes pacificus using highly sensitive fluorescence in situ hybridization coupled with Tyramide Signal Amplification. Ticks Tick Borne Dis 2017; 8:915-921. [PMID: 28882513 DOI: 10.1016/j.ttbdis.2017.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 07/12/2017] [Accepted: 08/02/2017] [Indexed: 10/19/2022]
Abstract
Ixodes pacificus is a host of many bacteria including Rickettsia species phylotypes G021 and G022. As part of the overall goal of understanding interactions of phylotypes with their tick host, this study focused on molecular detection of rickettsiae in ovarian and midgut tissue of I. pacificus by fluorescent in situ hybridization (FISH), PCR, and ultrastructural analysis. Of three embedding media (Technovit 8100, Unicryl, and paraffin) tested for generating thin sections, tissues embedded in paraffin resulted in the visualization of bacteria with low autofluorescence in FISH. Digoxigenin-labeled probes were used in FISH to intensify bacterial hybridization signals using Tyramide Signal Amplification reaction. Using this technique, rickettsiae were detected in the cytoplasm of oocytes of I. pacificus. The presence of rickettsiae in the ovary and midgut was further confirmed by PCR and transmission electron microscopic analysis. Overall, the methods in this study can be used to identify locations of tick-borne bacteria in tick tissues and understand transmission routes of bacterial species in ticks.
Collapse
Affiliation(s)
- Ghazaleh Bagheri
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - Jeremy D Lehner
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - Jianmin Zhong
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA.
| |
Collapse
|
58
|
Abstract
Background Although Tellinidae is one of the largest and most diverse families of bivalves, its taxonomy is utterly chaotic. This is mainly due to the morphological diversity and homoplasy displayed by their shells and to the scarcity of the molecular phylogenetic studies performed on them. A molecular cytogenetic analysis of four tellin shell species, Bosemprella incarnata, Macomangulus tenuis, Moerella donacina and Serratina serrata, was performed. To molecularly characterize the analyzed specimens, the sequence of a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) was also studied. Results The karyotypes of the four species were composed of different amounts of bi-armed and telocentric chromosomes. The chromosomal mapping of 45S and 5S rDNA and H3 histone gene clusters by fluorescent in situ hybridization also revealed conspicuous differences on the distribution of these DNA sequences on their karyotypes. Vertebrate type telomeric sequences were located solely on both ends of each chromosome in all four tellin shells. Conclusion We present clear evidence of the valuable information provided by FISH signals in both analyzing chromosome evolution in Tellinidae and as a further tool in identifying tellin shell specimens for molecular phylogenies.
Collapse
Affiliation(s)
- Daniel García-Souto
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310, Vigo, Spain
| | - Gonzalo Ríos
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310, Vigo, Spain
| | - Juan J Pasantes
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310, Vigo, Spain.
| |
Collapse
|
59
|
Klufas MA, Richter E, Itty S, Moreno C, McCannel CA, McCannel TA. Comparison of Gene Expression Profiling and Chromosome 3 Analysis by Fluorescent in situ Hybridization and Multiplex Ligation Probe Amplification in Fine-Needle Aspiration Biopsy Specimens of Uveal Melanoma. Ocul Oncol Pathol 2017; 4:16-20. [PMID: 29344493 DOI: 10.1159/000468941] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/01/2017] [Indexed: 02/03/2023] Open
Abstract
Purpose The aim of this paper was to assess the concordance between results of DecisionDx-UM specific gene expression profiling (GEP) and fluorescence in situ hybridization (FISH) for chromosome 3 analysis, and between DecisionDx-UM GEP and multiplex ligation probe amplification (MLPA) in uveal melanoma undergoing intraoperative fine-needle aspiration biopsy (FNAB) for metastatic prognostication during brachytherapy. Methods We retrospectively reviewed consecutive patients diagnosed with posterior uveal melanoma who underwent intraoperative FNAB prior to placement of an iodine-125 radioactive plaque between 2012 and 2014. Two cohorts of patients were identified: Cohort 1 - tumors in which both GEP and FISH results were obtained, and Cohort 2 - tumors in which both GEP and MLPA results were obtained. Results Forty-four patients were identified for Cohort 1. FISH and GEP results were discordant in 7 tumors (15.9%). Forty-three patients were identified for Cohort 2. MLPA and GEP were discordant in 7 tumors (16.3%). Conclusions Discordance between GEP and chromosome 3 status by FISH and MLPA occurred in our series at a rate of 15.9 and 16.3%, respectively. Caution must be advised when counseling a patient with a good-prognosis GEP "Class 1" result that the uveal tumor may actually harbor monosomy 3, which is associated with a poor prognosis for metastasis in nearly 20% of the patients.
Collapse
Affiliation(s)
- Michael A Klufas
- Department of Ophthalmology at Stein Eye Institute, University of California, Los Angeles, CA, USA
| | - Elizabeth Richter
- Department of Ophthalmology at Stein Eye Institute, University of California, Los Angeles, CA, USA
| | - Sujit Itty
- Department of Ophthalmology at Stein Eye Institute, University of California, Los Angeles, CA, USA
| | - Christian Moreno
- Department of Ophthalmology at Stein Eye Institute, University of California, Los Angeles, CA, USA
| | - Colin A McCannel
- Department of Ophthalmology at Stein Eye Institute, University of California, Los Angeles, CA, USA.,Department of Ophthalmology at Doheny Eye Institute, University of California, Los Angeles, CA, USA
| | - Tara A McCannel
- Department of Ophthalmology at Stein Eye Institute, University of California, Los Angeles, CA, USA.,Department of Ophthalmology at Doheny Eye Institute, University of California, Los Angeles, CA, USA
| |
Collapse
|
60
|
Kim H, Cho JH, Sonn CH, Kim JW, Choi Y, Lee J, Kim J. Circulating Aneuploid Cells Detected in the Blood of Patients with Infectious Lung Diseases. Korean J Thorac Cardiovasc Surg 2017; 50:126-129. [PMID: 28382274 PMCID: PMC5380208 DOI: 10.5090/kjtcs.2017.50.2.126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/03/2016] [Accepted: 12/13/2016] [Indexed: 11/16/2022]
Abstract
The identification of circulating tumor cells (CTCs) is clinically important for diagnosing cancer. We have previously developed a size-based filtration platform followed by epithelial cell adhesion molecule immunofluorescence staining for detecting CTCs. To characterize CTCs independently of cell surface protein expression, we incorporated a chromosomal fluorescence in situ hybridization (FISH) assay to detect abnormal copy numbers of chromosomes in cells collected from peripheral blood samples by the size-based filtration platform. Aneuploid cells were detected in the peripheral blood of patients with lung cancer. Unexpectedly, aneuploid cells were also detected in the control group, which consisted of peripheral blood samples from patients with benign lung diseases, such as empyema necessitatis and non-tuberculous mycobacterial lung disease. These findings suggest that chromosomal abnormalities are observed not only in tumor cells, but also in benign infectious diseases. Thus, our findings present new considerations and bring into light the possibility of false positives when using FISH for cancer diagnosis.
Collapse
Affiliation(s)
- Hongsun Kim
- Department of Thoracic and Cardiovascular Surgery, Sungkyunkwan University School of Medicine
| | - Jong Ho Cho
- Department of Thoracic and Cardiovascular Surgery, Sungkyunkwan University School of Medicine
| | - Chung-Hee Sonn
- Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Jae-Won Kim
- Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Yul Choi
- Department of Thoracic and Cardiovascular Surgery, Sungkyunkwan University School of Medicine
| | - Jinseon Lee
- Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Jhingook Kim
- Department of Thoracic and Cardiovascular Surgery, Sungkyunkwan University School of Medicine; Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine
| |
Collapse
|
61
|
Hatirnaz S, Ozer A, Hatirnaz E, Atasever M, Başaranoglu S, Kanat-Pektas M, Api M. Pre-implantation genetic screening among women experiencing recurrent failure of in vitro fertilization. Int J Gynaecol Obstet 2017; 137:314-318. [PMID: 28258586 DOI: 10.1002/ijgo.12135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/12/2017] [Accepted: 02/27/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To determine the efficiency of pre-implantation genetic screening (PGS) among women scheduled to undergo intracytoplasmic sperm injection who had experienced recurrent in vitro fertilization (IVF) failure. METHODS The present retrospective cohort study reviewed the medical records of consecutive women who had experienced recurrent IVF failure and had presented at a private IVF facility in Trabzon Province, Turkey, to undergo intracytoplasmic sperm injection between May 1, 2012, and December 31, 2014. Patient data and perinatal outcomes were compared between patients who underwent PGS and those who did not. RESULTS There were 88 patients included in the study; 43 patients had undergone PGS and 45 had declined to do so. No differences were detected in the clinical pregnancy rate (P=0.846), spontaneous abortion rate (P=0.416), number of perinatal deaths (P=0.162), or the number of live deliveries (P=0.188) between the groups of patients. The pregnancies included in the study resulted in 25 neonates being delivered; 24 had normal karyotypes, and one neonate from the control group had a karyotype of 46, XX, 9ph. Among the 19 embryos that were not transferred, the most frequently encountered chromosomal anomalies were diploidy, monosomy X, and 2N/N/4N mosaicism, detected in 7 (37%), 2 (11%), and 2 (11%) embryos, respectively. CONCLUSION PGS had no effect on perinatal outcomes among women experiencing recurrent IVF failure.
Collapse
Affiliation(s)
| | - Alev Ozer
- Department of Obstetrics and Gynecology, Kahramanmaras Sutcu Imam University Hospital, Kahramanmaras, Turkey
| | - Ebru Hatirnaz
- Private Bilge Hospital, Kucukkoy, Gaziosmanpasa, Turkey
| | - Melahat Atasever
- Department of Obstetrics and Gynecology, Giresun University Hospital, Giresun, Turkey
| | | | - Mine Kanat-Pektas
- Department of Obstetrics and Gynecology, Kocatepe University Hospital, Afyon, Turkey
| | - Murat Api
- Department of Obstetrics and Gynecology, Aydin University Hospital, Istanbul, Turkey
| |
Collapse
|
62
|
Haisley KR, Dolan JP, Olson SB, Toledo-Valdovinos SA, Hart KD, Bakis G, Enestvedt BK, Hunter JG. Sponge Sampling with Fluorescent In Situ Hybridization as a Screening Tool for the Early Detection of Esophageal Cancer. J Gastrointest Surg 2017; 21:215-221. [PMID: 27561634 DOI: 10.1007/s11605-016-3239-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/03/2016] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Sponge cytology is a novel screening tool for esophageal cancer but has been unable to be validated for widespread use. Our aim was to apply fluorescent in situ hybridization to sponge cytology samples in order to evaluate the safety and efficacy of this modality in screening for esophageal cancer. MATERIALS AND METHODS At a single, multidisciplinary, NCI-designated cancer center, patients completed sponge cytology sampling prior to upper endoscopy. Samples were analyzed by p53 fluorescent in situ hybridization, and results were compared to the endoscopic diagnosis. RESULTS Fifty patients were enrolled (96 % Caucasian, 68 % male, median age of 67). All patients successfully swallowed the capsule. No complications (string breakage, bleeding, mucosal injury) occurred. Endoscopy revealed that 38 % had normal esophageal mucosa and 62 % had an esophageal mucosal abnormality. In total, six samples demonstrated p53 loss (94 % specificity for any abnormality). The sensitivity of the p53 fluorescent in situ hybridization probe was13.3 % for any abnormality, 10 % for intestinal metaplasia, and 0 % for dysplasia or esophageal cancer. DISCUSSION Esophageal sponge cytology is a promising, safe, and tolerable method for collecting esophageal cell samples. However, our data suggest that p53 fluorescent in situ hybridization does not improve the sensitivity for detecting cancer in these samples.
Collapse
Affiliation(s)
- Kelly R Haisley
- Division of Gastrointestinal and General Surgery, Department of Surgery, Oregon Health and Science University, 3181 SW Sam Jackson Pk Rd, L223A, Portland, OR, 97239, USA
| | - James P Dolan
- Division of Gastrointestinal and General Surgery, Department of Surgery, Oregon Health and Science University, 3181 SW Sam Jackson Pk Rd, L223A, Portland, OR, 97239, USA
| | - Susan B Olson
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Sergio A Toledo-Valdovinos
- Division of Gastrointestinal and General Surgery, Department of Surgery, Oregon Health and Science University, 3181 SW Sam Jackson Pk Rd, L223A, Portland, OR, 97239, USA
| | - Kyle D Hart
- Division of Gastrointestinal and General Surgery, Department of Surgery, Oregon Health and Science University, 3181 SW Sam Jackson Pk Rd, L223A, Portland, OR, 97239, USA
| | - Gene Bakis
- Department of Gastroenterology, Oregon Health and Science University, Portland, OR, USA
| | - Brintha K Enestvedt
- Department of Gastroenterology, Oregon Health and Science University, Portland, OR, USA
| | - John G Hunter
- Division of Gastrointestinal and General Surgery, Department of Surgery, Oregon Health and Science University, 3181 SW Sam Jackson Pk Rd, L223A, Portland, OR, 97239, USA.
| |
Collapse
|
63
|
Zahedipour F, Ranjbaran R, Behzad Behbahani A, Afshari KT, Okhovat MA, Tamadon G, Sharifzadeh S. Development of Flow Cytometry- Fluorescent In Situ Hybridization (Flow-FISH) Method for Detection of PML/RARa Chromosomal Translocation in Acute Promyelocytic Leukemia Cell Line. Avicenna J Med Biotechnol 2017; 9:104-108. [PMID: 28496950 PMCID: PMC5410127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND Acute Promyelocytic Leukemia (APL) is a subclass of acute myeloid leukemia. The chromosomal aberration in 95% of APL cases is t(15; 17) (q22; q21), which prevents cell differentiation. Characterization of the underlying molecular lesion is valuable in determining optimal treatment strategy. The goal of this study was to develop a new and powerful Flow- FISH technique to detect the long isoform (L) of PML-RARa fusion transcript in NB4 cell line. METHODS To achieve the best condition for fixation, two different fixatives including 2% paraformaldehyde and 75% ethanol were used. 0.2% Triton X-100 and 0.2% saponin were used for the permeabilization step .In hybridization, a wide range of times and temperatures were used and probe was designed in FRET system. Results were confirmed by fluorescent microscope assay and reverse transcription PCR. RESULTS In the present study, a novel technique was successfully optimized that combines in situ hybridization with flow cytometry to detect the presence of PML-RARa transcript. Using standard fixation and permeabilization protocol of 2% PFA and 0.2% saponin gave the best fluorescent results in flow cytometry. Also, results indicated that the optimum time and temperature for hybridization was 2 hr at 42°C. The results of reverse transcription PCR and fluorescent microscopy confirmed the presence of PML-RARa transcript. CONCLUSION The concordance between the results of Flow-FISH and those of two other techniques including reverse transcription PCR and FISH indicated that this method would be applicable as a diagnostic test for APL in clinical samples and MRD monitoring.
Collapse
Affiliation(s)
- Fatemeh Zahedipour
- Diagnostic Laboratory Sciences and Technology Research Center, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran, Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Ranjbaran
- Diagnostic Laboratory Sciences and Technology Research Center, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Khalil Tavakol Afshari
- Buali Research Institute, Immunology Research Center, Immunogenetic and Cell Culture Lab, Mashhad University of Medical Science, Mashhad, Iran
| | - Mohammad Ali Okhovat
- Diagnostic Laboratory Sciences and Technology Research Center, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamhossein Tamadon
- Diagnostic Laboratory Sciences and Technology Research Center, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sedigheh Sharifzadeh
- Diagnostic Laboratory Sciences and Technology Research Center, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran,Corresponding author: Sedigheh Sharifzadeh, Ph.D., Diagnostic Laboratory Sciences and Technology Research Center, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran Tel: +98 711 2270301 Fax: +98 711 2270301 E-mail:
| |
Collapse
|
64
|
Arumugam B, Samuel CR, Thyagarajan SS. Balanced Autosomal Translocations in Two Women Reporting Recurrent Miscarriage. J Clin Diagn Res 2016; 10:GD01-GD03. [PMID: 28208880 DOI: 10.7860/jcdr/2016/23828.9075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/22/2016] [Indexed: 12/31/2022]
Abstract
Spontaneous abortion or loss of fetus prior to 20 weeks of gestation is observed in 15-20% of clinically recognized pregnancies. Recurrent Miscarriage (RM) is defined as three or more consecutive pregnancy losses and it affects 1-2% of women. Parental chromosomal rearrangements account for 2-5% of RM. This report describes two couples with a clinical history of RM who were subjected to conventional cytogenetic analysis to ascertain the chromosomal aetiology. Analysis of GTG-banded metaphases obtained from cultured lymphocytes at approximately 500-band resolution revealed balanced translocation in the female spouses as 46,XX,t(8;11)(p11.2;q23.3) in BR27W and 46,XX,t(5;7)(p15.1;q32) pat in BR49W. Both the male partners exhibited 46,XY karyotype. Fluorescent In Situ Hybridization (FISH) analysis was subsequently carried out to confirm the balanced translocation using suitable whole chromosome paint probes. These balanced chromosomal abnormalities in the parents could be responsible for the repeated fetal losses. Hence, karyotype analysis should be a mandatory etiological investigation for couples with RM towards genetic counselling. Disruption of critical genes through these rearrangements could also underlie the pregnancy outcome.
Collapse
Affiliation(s)
- Brindha Arumugam
- Research Scholar, Department of Genetics, Dr. ALM PG IBMS, University of Madras , Chennai, Tamilnadu, India
| | - Chandra R Samuel
- Associate Professor, Department of Genetics, Dr. ALM PG IBMS, University of Madras , Chennai, Tamilnadu, India
| | | |
Collapse
|
65
|
Nguyen YT, Kieu HT, West S, Dang YT, Horn H. Community structure of a sulfate-reducing consortium in lead-contaminated wastewater treatment process. World J Microbiol Biotechnol 2017; 33:10. [PMID: 27873195 DOI: 10.1007/s11274-016-2180-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
Abstract
This study evaluated the capacity to remove lead by an indigenous consortium of five sulfate-reducing bacteria (SRB): Desulfobacterium autotrophicum, Desulfomicrobium salsugmis, Desulfomicrobium escambiense, Desulfovibrio vulgaris, and Desulfovibrio carbinolicus, using continuous moving bed biofilm reactor systems. Four continuous moving bed biofilm reactors (referred as R1-R4) were run in parallel for 40 days at lead loading rates of 0, 20, 30 and 40 mg l-1 day-1, respectively. The impact of lead on community structure of the SRB consortium was investigated by dsrB gene-based denaturing gradient gel electrophoresis (dsrB-based DGGE), fluorescence in situ hybridization (FISH) and chemical analysis. These results indicated that D. escambiense and D. carbinolicus were dominant in all analyzed samples and played a key role in lead removal in R2 (20 mg l-1 day-1) and R3 (30 mg l-1 day-1). However, in R4 (40 mg l-1 day-1), these two strains were barely detected by FISH and dsrB-based DGGE. As a result, SRB activity was severely affected by lead toxicity. High lead removal efficiencies of lead (99-100%) were observed in R2 and R3 throughout the operation, whereas that in R4 was significantly decreased (91%) after 40 days of operation. This data strongly implied that the investigated SRB consortium might have potential application for lead removal. Moreover, to improve the efficiency of the lead treatment process, the lead loading rates below the inhibitory level to SRB activity should be selected.
Collapse
|
66
|
Tursellino MN, Silva DMZDA, Abad CQ, Blacio WAM, Romero ORS, Oliveira C. First cytogenetic analysis of Ichthyoelephas humeralis (Günther, 1860) by conventional and molecular methods with comments on the karyotypic evolution in Prochilodontidae. Comp Cytogenet 2016; 10:615-624. [PMID: 28123682 PMCID: PMC5240513 DOI: 10.3897/compcytogen.v10i4.9858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/08/2016] [Indexed: 06/06/2023]
Abstract
We used conventional cytogenetic techniques (Giemsa, C-banding, Ag-NOR), and fluorescent in situ hybridization (FISH) with 5S and 18S rDNA probes to investigate the karyotype and cytogenetic characteristics of Ichthyoelephas humeralis (Günther, 1860) from Ecuador. The specimens studied have a karyotype with 2n=54 biarmed chromosomes (32 M + 22 SM) and C-positive heterochromatin located on the centromeric, pericentromeric, interstitial, and terminal regions of some chromosomes. The nucleolus organizer regions occurred terminally on the long arm of chromosome pair 2. FISH confirmed the presence of only one 18S rDNA cluster with nonsyntenic localization with the 5S rDNA. Cytogenetic data allow us to refute the earlier morphological hypothesis of a sister relationship between Semaprochilodus Fowler, 1941 and Ichthyoelephas Posada Arango, 1909 and support the molecular proposal that Ichthyoelephas is a sister group to the monophyletic clade containing Prochilodus Agassiz, 1829 and Semaprochilodus.
Collapse
Affiliation(s)
- Mauro Nirchio Tursellino
- Universidad Técnica de Machala, Facultad de Ciencias Agropecuarias, Av. Panamericana Km 51/2, Vía Machala Pasaje, El Oro, Ecuador
- Universidad de Oriente, Escuela de Ciencias Aplicadas del Mar, Boca de Río, Península de Macanao, Estado Nueva Esparta, Venezuela
| | - Duílio Mazzoni Zerbinato de Andrade Silva
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista (UNESP), Departamento de Morfologia, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil. CEP: 18618-689
| | - César Quezada Abad
- Universidad Técnica de Machala, Facultad de Ciencias Agropecuarias, Av. Panamericana Km 51/2, Vía Machala Pasaje, El Oro, Ecuador
| | - Wilmer Arnoldo Moreira Blacio
- Universidad Técnica de Machala, Facultad de Ciencias Agropecuarias, Av. Panamericana Km 51/2, Vía Machala Pasaje, El Oro, Ecuador
| | - Omar Rogerio Sánchez Romero
- Universidad Técnica de Machala, Facultad de Ciencias Agropecuarias, Av. Panamericana Km 51/2, Vía Machala Pasaje, El Oro, Ecuador
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista (UNESP), Departamento de Morfologia, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil. CEP: 18618-689
| |
Collapse
|
67
|
Abstract
Tendons are important components of our musculoskeletal system. Injuries to these tissues are very common, resulting from occupational-related injuries, sports-related trauma, and age-related degeneration. Unfortunately, there are few treatment options, and current therapies rarely restore injured tendons to their original function. An improved understanding of the pathways regulating their development and repair would have significant impact in stimulating the formulation of regenerative-based approaches for tendon injury. The zebrafish provides an ideal system in which to perform genetic and chemical screens to identify new pathways involved in tendon biology. Until recently, there had been few descriptions of tendons and ligaments in the zebrafish and their similarity to mammalian tendon tissues. In this chapter, we describe the development of the zebrafish tendon and ligament tissues in the context of their gene expression, structure, and interactions with neighboring musculoskeletal tissues. We highlight the similarities with tendon development in higher vertebrates, showing that the craniofacial tendons and ligaments in zebrafish morphologically, molecularly, and structurally resemble mammalian tendons and ligaments from embryonic to adult stages. We detail methods for fluorescent in situ hybridization and immunohistochemistry as an assay to examine morphological changes in the zebrafish musculoskeleton. Staining assays such as these could provide the foundation for screen-based approaches to identify new regulators of tendon development, morphogenesis, and repair. These discoveries would provide new targets and pathways to study in the context of regenerative medicine-based approaches to improve tendon healing.
Collapse
Affiliation(s)
- J W Chen
- Massachusetts General Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - J L Galloway
- Massachusetts General Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| |
Collapse
|
68
|
Egan D, Radich J. Making the diagnosis, the tools, and risk stratification: More than just BCR-ABL. Best Pract Res Clin Haematol 2016; 29:252-263. [PMID: 27839566 DOI: 10.1016/j.beha.2016.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
The implementation of cytogenetic and molecular techniques into standard clinical practice has improved our ability to more accurately diagnose and monitor CML. Routine peripheral blood BCR-ABL transcript testing can help monitor response, predict outcome, and detect early resistance or poor adherence to TKI therapy. The widely-used Sokal, Hasford and EUTOS clinical risk stratification scores were developed in patients receiving chemotherapy, interferon and imatinib, respectively; their predictive ability in patients receiving next-generation tyrosine kinase inhibitors (TKIs) remains to be established. Newer more sensitive molecular techniques are being developed that may aid in the expanding emphasis on discontinuing therapy in patients with a deep and consistent molecular response.
Collapse
Affiliation(s)
- Daniel Egan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, United States.
| | - Jerald Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, United States.
| |
Collapse
|
69
|
Wu J, Lin Y, He X, Yang H, He P, Fu X, Li G, Gu X. Comparison of detection methods and follow-up study on the tyrosine kinase inhibitors therapy in non-small cell lung cancer patients with ROS1 fusion rearrangement. BMC Cancer 2016; 16:599. [PMID: 27488371 PMCID: PMC4973062 DOI: 10.1186/s12885-016-2582-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 07/19/2016] [Indexed: 01/15/2023] Open
Abstract
Background The screening of ROS proto-oncogene 1, receptor tyrosine kinase(ROS1) fusion rearrangement might be potentially beneficial for an effective therapy against non-small cell lung cancer (NSCLC). However, the three main ROS1 rearrangement detection methods have limitations, and no routine protocol for the detection of ROS1 rearrangement in NSCLC is available. In this study, our aims were to compare immunohistochemistry (IHC), fluorescent in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (qRT-PCR) in their ability to detect ROS1 rearrangement in NSCLC, and discuss the clinical characteristics and histopathology of the patients with ROS1 rearrangement. Moreover, the effects of tyrosine kinase inhibitors (TKIs) therapy on the patients with ROS1 rearrangement and advanced stage disease (III b–IV) were investigated. Methods Patients with a previously diagnosed NSCLC were recruited in this study from November 2013 to October 2015. IHC was performed using the D4D6 monoclonal antibody (mAb) in an automatic IHC instrument, while FISH and qRT-PCR were carried out to confirm the IHC results. FISH and qRT-PCR positive cases underwent direct sequencing. After detection, patients with advanced ROS1 rearranged NSCLC had received TKI therapy. Results Two hundred and thirty-eight patients were included in this study. ROS1 rearrangement was detected in 10 patients. The concordant rate of FISH and qRT-PCR results was 100 %, while in the FISH and IHC results high congruence was present when IHC showed a diffusely (≥60 % tumor cells) 2–3+ cytoplasmic reactivity pattern. Patients harboring ROS1 rearrangement were mostly young (8/10), females (7/10) and non-smokers (7/10) with adenocarcinoma (10/10) and acinar pattern. Most of their tumor were in intermediate grade (6/8). Among these 10 patients, three of them in stage IV with ROS1 rearrangement gained benefits from ROS1 TKI therapy. Conclusions IHC, FISH and qRT-PCR can reliably detect ROS1 rearrangement in NSCLC, while IHC can be used as a preliminary screening tool. These results supported the efficacy of ROS1 TKI therapy in treating advanced NSCLC patients with ROS1 rearrangement. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2582-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jieyu Wu
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Yunen Lin
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Xinming He
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Haihong Yang
- Department of Cardiothoracic Surgery, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ping He
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Xinge Fu
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Guangqiu Li
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Xia Gu
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China.
| |
Collapse
|
70
|
Ennouri H, Miladi B, Diaz SZ, Güelfo LAF, Solera R, Hamdi M, Bouallagui H. Effect of thermal pretreatment on the biogas production and microbial communities balance during anaerobic digestion of urban and industrial waste activated sludge. Bioresour Technol 2016; 214:184-191. [PMID: 27132226 DOI: 10.1016/j.biortech.2016.04.076] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/11/2016] [Accepted: 04/16/2016] [Indexed: 05/28/2023]
Abstract
The effect of thermal pre-treatment on the microbial populations balance and biogas production was studied during anaerobic digestion of waste activated sludge (WAS) coming from urban (US: urban sludge) and industrial (IS: industrial sludge) wastewater treatment plants (WWTP). The highest biogas yields of 0.42l/gvolatile solid (VS) removed and 0.37l/gVS removed were obtained with urban and industrial sludge pre-treated at 120°C, respectively. Fluorescent in situ hybridization (FISH) was used to quantify the major Bacteria and Archaea groups. Compared to control trails without pretreatment, Archaea content increased from 34% to 86% and from 46% to 83% for pretreated IS and US, respectively. In fact, the thermal pre-treatment of WAS enhanced the growth of hydrogen-using methanogens (HUMs), which consume rapidly the H2 generated to allow the acetogenesis. Therefore, the stable and better performance of digesters was observed involving the balance and syntrophic associations between the different microbial populations.
Collapse
Affiliation(s)
- Hajer Ennouri
- Université de Carthage, LR: LETMi, INSAT, B.P. 676, 1080 Tunis, Tunisia; Faculty of Marine and Environmental Sciences, University of Cádiz, Pol. Río San Pedro s/n, 11510 Puerto Real (Cádiz), Spain
| | - Baligh Miladi
- Université de Carthage, LR: LETMi, INSAT, B.P. 676, 1080 Tunis, Tunisia
| | - Soraya Zahedi Diaz
- Faculty of Marine and Environmental Sciences, University of Cádiz, Pol. Río San Pedro s/n, 11510 Puerto Real (Cádiz), Spain
| | | | - Rosario Solera
- Faculty of Marine and Environmental Sciences, University of Cádiz, Pol. Río San Pedro s/n, 11510 Puerto Real (Cádiz), Spain
| | - Moktar Hamdi
- Université de Carthage, LR: LETMi, INSAT, B.P. 676, 1080 Tunis, Tunisia
| | - Hassib Bouallagui
- Université de Carthage, LR: LETMi, INSAT, B.P. 676, 1080 Tunis, Tunisia.
| |
Collapse
|
71
|
Shoji T, Saito R, Kanamori M, Sonoda Y, Watanabe M, Tominaga T. Sarcoma-like tumor originating from oligodendroglioma. Brain Tumor Pathol 2016; 33:255-60. [PMID: 27333891 DOI: 10.1007/s10014-016-0268-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
We present a case of sarcoma occurring at a site of resected oligodendroglioma without preceding radiotherapy or chemotherapy. Oligosarcoma occurring at sites of resected oligodendroglioma or anaplastic oligodendroglioma with sarcomatous components are rare. Although meningioma or sarcoma-like lesions are sometimes reported after glioma-targeted radiotherapy, those without preceding radiotherapy are quite rare. Moreover, cases of sarcoma without oligodendroglial components occurring at a site of resected oligodendroglioma have never been reported. In this case, fluorescent in situ hybridization analysis revealed 1p/19q co-deletion in both the first tumor and second tumors. Additionally, immunohistochemistry revealed mutated isocitrate dehydrogenase 1 in both tumors. Taken together, these findings suggest a monoclonal tumor origin. Consequently, this case may indicate a new mechanism of development of sarcomatous lesions occurring at the site of a resected glioma.
Collapse
|
72
|
He M, Chen K, Li S, Zhang S, Zheng J, Hu X, Gao L, Chen J, Song X, Zhang W, Wang J, Yang J. Clinical Significance of "Double-hit" and "Double-protein" expression in Primary Gastric B-cell Lymphomas. J Cancer 2016; 7:1215-25. [PMID: 27390596 PMCID: PMC4934029 DOI: 10.7150/jca.15395] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/26/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND AND AIMS: Primary gastric B-cell lymphoma is the second most common malignancy of the stomach. There are many controversial issues about its diagnosis, treatment and clinical management. “Double-hit” and “double-protein” involving gene rearrangement and protein expression of c-Myc and bcl2/bcl6 are the most used terms to describe DLBCL poor prognostic factors in recent years. However, very little is known about the role of these prognostic factors in primary gastric B-cell lymphomas. This study aims to obtain a molecular pathology prognostic model of gastric B-cell lymphoma for clinical stratified management by evaluating how the “double-hit” and “double-protein” in tumor cells as well as microenvironmental reaction of tumor stromal tissue affect clinical outcome in primary gastric B-cell lymphomas. METHODS: Data and tissues of 188 cases diagnosed with gastric B-cell lymphomas were used in this study. Tumor tissue microarray (TMA) of formalin fixed and paraffin embedded (FFPE) tissues was constructed for fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) analysis with a serial of biomarkers containing MYC, BCL2, BCL6, CD31, SPARC, CD10, MUM1 and Ki-67. Modeled period analysis was used to estimate 3-year and 5-year overall survival (OS) and disease-free survival (DFS) distributions. RESULTS: There was no definite “double-hit” case though the gene rearrangement of c-Myc (5.9%), bcl2 (0.1%) and bcl6 (7.4%) was found in gastric B-cell lymphomas. The gene amplification or copy gains of c-Myc (10.1%), bcl-2 (17.0%) and bcl-6 (0.9%) were present in these lymphomas. There were 12 cases of the lymphomas with the “double-protein” expression of MYC and BCL2/BCL6. All patients with “double-protein” gastric B-cell lymphomas had poor outcome compared with those without. More importantly, “MYC-BCL2-BCL6” negative group of gastric B-cell lymphoma patients had favorable clinical outcome regardless clinical stage, pathological types and therapeutic modalities. And the similar better prognosis was found in the cases with low microvessel density (MVD) in tumor tissue and high expression of SPARC (SPARC≥5%) in stromal cells. CONCLUSIONS: “Double-hit” lymphoma was rare among primary gastric lymphoma, while patients with multiple gene amplification and/or copy gains of c-Myc, bcl2 and bcl6, and “double-protein” gastric B-cell lymphomas had a poor clinical outcome. In addition, patients with MYC, BCL2 and BCL6 expression negative or low MVD in tumor tissue with high expression of SPARC in stromal cells could have better prognosis than other gastric B-cell lymphomas regardless of their clinical stage and pathological types. These results would be of very importance for clinical stratified management and precision medicine of gastric B-cell lymphomas.
Collapse
Affiliation(s)
- Miaoxia He
- 1. Department of Pathology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, CHINA; 2. Molecular Pathology, Cellular & Molecular Pathology Branch, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Keting Chen
- 3. Department of Hematology, Changhai Hospital, The Second Military Medical University, University, Shanghai 200433, CHINA
| | - Suhong Li
- 4. Department of Pathology, Children Hospital and Women Health Center of Shanxi, Taiyuan 030013, CHINA
| | - Shimin Zhang
- 5. Division of Molecular Pathology, Joint Pathology Center, Washington, DC 20817, USA
| | - Jianming Zheng
- 1. Department of Pathology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, CHINA
| | - Xiaoxia Hu
- 3. Department of Hematology, Changhai Hospital, The Second Military Medical University, University, Shanghai 200433, CHINA
| | - Lei Gao
- 3. Department of Hematology, Changhai Hospital, The Second Military Medical University, University, Shanghai 200433, CHINA
| | - Jie Chen
- 3. Department of Hematology, Changhai Hospital, The Second Military Medical University, University, Shanghai 200433, CHINA
| | - Xianmin Song
- 3. Department of Hematology, Changhai Hospital, The Second Military Medical University, University, Shanghai 200433, CHINA
| | - Weiping Zhang
- 3. Department of Hematology, Changhai Hospital, The Second Military Medical University, University, Shanghai 200433, CHINA
| | - Jianmin Wang
- 3. Department of Hematology, Changhai Hospital, The Second Military Medical University, University, Shanghai 200433, CHINA
| | - Jianmin Yang
- 3. Department of Hematology, Changhai Hospital, The Second Military Medical University, University, Shanghai 200433, CHINA
| |
Collapse
|
73
|
Rosoux A, Pauwels P, Duplaquet F, D'Haene N, Weynand B, Delos M, Menon R, Heukamp LC, Thunnissen E, Ocak S. Effectiveness of crizotinib in a patient with ALK IHC-positive/FISH-negative metastatic lung adenocarcinoma. Lung Cancer 2016; 98:118-121. [PMID: 27393517 DOI: 10.1016/j.lungcan.2016.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/30/2016] [Accepted: 06/01/2016] [Indexed: 11/30/2022]
Abstract
We report a case of crizotinib effectiveness in a heavily pretreated patient with a metastatic NSCLC initially considered IHC-positive and FISH-negative for ALK rearrangement. After repeated analyses of tumor samples, borderline ALK FISH-positivity (18.5% positive cells) was demonstrated.
Collapse
Affiliation(s)
- A Rosoux
- Division of Pulmonology, Université catholique de Louvain (UCL), CHU UCL Namur, Yvoir, Belgium
| | - P Pauwels
- Center for Oncologic Research (CORE), Antwerp University, Antwerp, Belgium
| | - F Duplaquet
- Division of Pulmonology, Université catholique de Louvain (UCL), CHU UCL Namur, Yvoir, Belgium
| | - N D'Haene
- Department of Pathology, Université Libre de Bruxelles (ULB), Hôpital Erasme, Brussels, Belgium
| | - B Weynand
- Department of pathology, UZ Leuven, Leuven, Belgium
| | - M Delos
- Department of Pathology, UCL, CHU UCL Namur, Yvoir, Belgium
| | - R Menon
- Neo New Oncology GmbH, Cologne, Germany
| | | | - E Thunnissen
- Department of Pathology, VU University, Amsterdam, Netherlands
| | - S Ocak
- Division of Pulmonology, Université catholique de Louvain (UCL), CHU UCL Namur, Yvoir, Belgium.
| |
Collapse
|
74
|
Cao L, Yin G, Cao Z, Bing X, Ding W. Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian. Genetica 2016; 144:325-33. [PMID: 27178280 DOI: 10.1007/s10709-016-9901-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
Abstract
A Ty3/gypsy-retrotransposon-type transposon was found in the genome of the Jian carp (Cyprinus carpio var. Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon). The full-length JRE retrotransposon is 5126 bp, which includes two long terminal repeats of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames between them: 4203 bp encoding the group-specific antigen (GAG) and polyprotein (POL). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7, 40, and 32.8 %, to retrotransposons of Azumapecten farreri, Mizuhopecten yessoensis, and Xiphophorus maculatus, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE transposon in the genome of the Jian carp is 124, determined with real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues, the liver, kidney, blood, muscle, and gonad, and slightly higher in the kidney and liver than in the other tissues.
Collapse
|
75
|
Xu C, Han H, Jia S, Zhao Q. Influence of phenol on ammonia removal in an intermittent aeration bioreactor treating biologically pretreated coal gasification wastewater. J Environ Sci (China) 2016; 43:99-105. [PMID: 27155414 DOI: 10.1016/j.jes.2015.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/29/2015] [Accepted: 09/01/2015] [Indexed: 06/05/2023]
Abstract
A laboratory-scale intermittent aeration bioreactor was investigated to treat biologically pretreated coal gasification wastewater that was mainly composed of NH3-N and phenol. The results showed that increasing phenol loading had an adverse effect on NH3-N removal; the concentration in effluent at phenol loading of 40mgphenol/(L·day) was 7.3mg/L, 36.3% of that at 200mg phenol/(L·day). The enzyme ammonia monooxygenase showed more sensitivity than hydroxylamine oxidoreductase to the inhibitory effect of phenol, with 32.2% and 10.5% activity inhibition, respectively at 200mg phenol/(L·day). Owing to intermittent aeration conditions, nitritation-type nitrification and simultaneous nitrification and denitrification (SND) were observed, giving a maximum SND efficiency of 30.5%. Additionally, ammonia oxidizing bacteria (AOB) and denitrifying bacteria were the main group identified by fluorescent in situ hybridization. However, their relative abundance represented opposite variations as phenol loading increased, ranging from 30.1% to 17.5% and 7.6% to 18.2% for AOB and denitrifying bacteria, respectively.
Collapse
Affiliation(s)
- Chunyan Xu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hongjun Han
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Shengyong Jia
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qian Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| |
Collapse
|
76
|
Lim SM, Yoo JE, Lim KH, Meng Tai DW, Cho BC, Park YN. Rare Incidence of ROS1 Rearrangement in Cholangiocarcinoma. Cancer Res Treat 2016; 49:185-192. [PMID: 27121721 PMCID: PMC5266400 DOI: 10.4143/crt.2015.497] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/02/2016] [Indexed: 12/23/2022] Open
Abstract
Purpose The recent discovery and characterization of an oncogenic ROS1 gene rearrangement has raised significant interest because small molecule inhibitors are effective in these tumors. The aim of this study was to determine frequency and clinicopathological features associated with ROS1 rearrangement in patients with cholangiocarcinoma (CCA). Materials and Methods A total of 261 patients who underwent surgery for CCA between October 1997 and August 2013 were identified from an international, multi-institutional database. ROS1 rearrangement was evaluated by break-apart fluorescence in situ hybridization using tissue microarrays of these patients. Results Of 261 CCA evaluated, three cases (1.1%) showed ROS1 rearrangement by fluorescence in situ hybridization (FISH), all of which were derived from intrahepatic origin. ROS1 protein expression was observed in 38 samples (19.1%). Significantly larger tumor size was observed in ROS1 immunohistochemistry (IHC)–negative patients compared with ROS1 IHC–positive patients. ROS1 FISH–positive patients had a single tumor with a median size of 4 cm and well-to-moderate differentiation. Overall, there was no difference in terms of baseline characteristics, overall survival, and recurrence-free survival between ROS1-positive and -negative patients. Conclusion ROS1 rearrangement was detected in 1.1% of CCA patients. Although rare, conduct of clinical trials using ROS1 inhibitors in these genetically unique patients is warranted.
Collapse
Affiliation(s)
- Sun Min Lim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,Division of Medical Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Jeong Eun Yoo
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore
| | - David Wai Meng Tai
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Byoung Chul Cho
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Young Nyun Park
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea.,BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.,Integrated Genomic Research Center for Metabolic Regulation, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
77
|
Shao R, Lao IW, Wang L, Yu L, Wang J, Fan Q. Clinicopathologic and radiologic features of extraskeletal myxoid chondrosarcoma: a retrospective study of 40 Chinese cases with literature review. Ann Diagn Pathol 2016; 23:14-20. [PMID: 27402218 DOI: 10.1016/j.anndiagpath.2016.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/21/2016] [Accepted: 04/04/2016] [Indexed: 01/20/2023]
Abstract
The aim of this study is to describe the clinicopathologic and radiologic features of 40 cases of extraskeletal myxoid chondrosarcoma (EMC) from China. There were 25 males and 15 females (sex ratio, 1.7:1). Apart from an adolescent, all patients were adults with a median age of 49years. Twenty-four tumors (60%) occurred in the lower limb and limb girdles, especially the thigh, followed by the upper limb and limb girdles (20%) and trunk (10%). Other less commonly involved locations included the head and neck, sacrococcygeal region, and perineum. Tumors ranged in size from 1.5 to 19cm (mean, 7cm). By radiology, they appeared as hypoattenuated or isoattenuated masses on computed tomography with hyperintense signal on T2-weighted magnetic resonance imaging. Intralesional hypointense septa were present in most cases. Of the 40 tumors, 30 belonged to the classic subtype, whereas 9 cases were cellular, and 1 case had a rhabdoid phenotype. Tumor cells showed variable expression of synaptophysin (36%), S-100 protein (29%), epithelial membrane antigen (11%), and neuron-specific enolase (7%). Ki-67 index was remarkably higher in the cellular variant (mean, 30%). EWSR1-related rearrangement was detected in 12 of 14 cases tested by fluorescence in situ hybridization using break-apart probes. The overall 5- and 7-year survival was 71% and 60%, respectively. Awareness of the imaging features may help pathologists in the diagnosis of EMC. Fluorescence in situ hybridization also serves as a useful diagnostic tool for EMC, especially in the distinction from its mimics.
Collapse
Affiliation(s)
- Rui Shao
- Department of Pathology, Zhenjiang First People's Hospital, Jiangsu University, Zhenjiang 212001, China
| | - I Weng Lao
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lei Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lin Yu
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jian Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Qinhe Fan
- Department of Pathology, Jiangsu Province Hospital, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210000, China
| |
Collapse
|
78
|
Kliot A, Ghanim M. Fluorescent in situ hybridization for the localization of viruses, bacteria and other microorganisms in insect and plant tissues. Methods 2016; 98:74-81. [PMID: 26678796 DOI: 10.1016/j.ymeth.2015.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/03/2015] [Accepted: 12/06/2015] [Indexed: 12/21/2022] Open
Abstract
Methods for the localization of cellular components such as nucleic acids, proteins, cellular vesicles and more, and the localization of microorganisms including viruses, bacteria and fungi have become an important part of any research program in biological sciences that enable the visualization of these components in fixed and live tissues without the need for complex processing steps. The rapid development of microscopy tools and technologies as well as related fluorescent markers and fluorophores for many cellular components, and the ability to design DNA and RNA sequence-based molecular probes and antibodies which can be visualized fluorescently, have rapidly advanced this field. This review will focus on some of the localizations methods which have been used in plants and insect pests in agriculture, and other microorganisms, which are rapidly advancing the research in agriculture-related fields.
Collapse
Affiliation(s)
- Adi Kliot
- Department of Entomology, The Volcani Center, Bet Dagan 50250, Israel
| | - Murad Ghanim
- Department of Entomology, The Volcani Center, Bet Dagan 50250, Israel.
| |
Collapse
|
79
|
Bridi LC, Rafael MS. GNBP domain of Anopheles darlingi: are polymorphic inversions and gene variation related to adaptive evolution? Genetica 2016; 144:99-106. [PMID: 26767379 DOI: 10.1007/s10709-016-9881-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 01/09/2016] [Indexed: 10/22/2022]
Abstract
Anopheles darlingi is the main malaria vector in humans in South America. In the Amazon basin, it lives along the banks of rivers and lakes, which responds to the annual hydrological cycle (dry season and rainy season). In these breeding sites, the larvae of this mosquito feed on decomposing organic and microorganisms, which can be pathogenic and trigger the activation of innate immune system pathways, such as proteins Gram-negative binding protein (GNBP). Such environmental changes affect the occurrence of polymorphic inversions especially at the heterozygote frequency, which confer adaptative advantage compared to homozygous inversions. We mapped the GNBP probe to the An. darlingi 2Rd inversion by fluorescent in situ hybridization (FISH), which was a good indicator of the GNBP immune response related to the chromosomal polymorphic inversions and adaptative evolution. To better understand the evolutionary relations and time of divergence of the GNBP of An. darlingi, we compared it with nine other mosquito GNBPs. The results of the phylogenetic analysis of the GNBP sequence between the species of mosquitoes demonstrated three clades. Clade I and II included the GNBPB5 sequence, and clade III the sequence of GNBPB1. Most of these sequences of GNBP analyzed were homologous with that of subfamily B, including that of An. gambiae (87 %), therefore suggesting that GNBP of An. darling belongs to subfamily B. This work helps us understand the role of inversion polymorphism in evolution of An. darlingi.
Collapse
|
80
|
Abstract
The study of the so-called unculturable bacteria is still considered a challenging task. However, given recent improvements in the sensitivity of culture-free approaches, the identification and characterization of such microbes in complex biological samples is now possible. In this chapter we report how endobacteria thriving inside arbuscular mycorrhizal fungi (AMF), which are themselves obligate biotrophs of plants, can be studied using a combination of in vitro culture, molecular biology, and microscopy techniques.
Collapse
Affiliation(s)
- Alessandro Desirò
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, Turin, 48824, Italy.
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 10125, USA.
| | - Alessandra Salvioli
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, Turin, 48824, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, Turin, 48824, Italy
| |
Collapse
|
81
|
Abstract
Fluorescent in situ hybridization (FISH) is a powerful cytogenetic technique for identifying chromosomes and mapping specific genes and DNA sequences on individual chromosomes. Genomic in situ hybridization (GISH) and multicolor FISH (mc-FISH) represent two special types of FISH techniques. Both GISH and mc-FISH experiments have general steps and features of FISH, including chromosome preparation, probe labeling, blocking DNA preparation, target-probe DNA hybridization, post-hybridization washes, and hybridization signal detection. Specifically, GISH uses total genomic DNA from two species as probe and blocking DNA, respectively, and it can differentiate chromosomes from different genomes. The mc-FISH takes advantage of simultaneous hybridization of several DNA probes labeled by different fluorochromes to different targets on the same chromosome sample. Hybridization signals from different probes are detected using different fluorescence filter sets. Multicolor FISH can provide more structural details for target chromosomes than single-color FISH. In this chapter, we present the general experimental procedures for these two techniques with specific details in the critical steps we have modified in our laboratories.
Collapse
Affiliation(s)
- Steven S Xu
- USDA-ARS, Cereal Crops Research Unit, Northern Crop Science Laboratory, 1605 Albrecht Blvd. North, Fargo, ND, 58102, USA.
| | - Zhao Liu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Qijun Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Zhixia Niu
- USDA-ARS, Cereal Crops Research Unit, Northern Crop Science Laboratory, 1605 Albrecht Blvd. North, Fargo, ND, 58102, USA
| | - Chao-Chien Jan
- USDA-ARS, Sunflower and Plant Biology Research Unit, Northern Crop Science Laboratory, Fargo, ND, 58102, USA
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| |
Collapse
|
82
|
Abstract
Antimicrobial susceptibility testing is needed to adapt Helicobacter pylori treatment to obtain the best results. Beside the standard phenotypic methods, molecular methods are increasingly used. The value of these molecular tests is that they are quick, independent of the transport conditions, easy to standardize, and commercial kits are available. In this article, these methods are reviewed, focusing on the determination of H pylori resistance to macrolides and fluoroquinolones, and mentioning also the methods used for tetracycline and rifampin.
Collapse
Affiliation(s)
- Francis Mégraud
- Bacteriology Laboratory, INSERM U853, University of Bordeaux, Bordeaux F-33000, France.
| | - Lucie Bénéjat
- Bacteriology Laboratory, INSERM U853, University of Bordeaux, Bordeaux F-33000, France
| | | | - Philippe Lehours
- Bacteriology Laboratory, INSERM U853, University of Bordeaux, Bordeaux F-33000, France
| |
Collapse
|
83
|
Wu S, Wang J, Zhou L, Su D, Liu Y, Liang X, Zhang S, Zeng X. Clinicopathological characteristics and outcomes of ROS1-rearranged patients with lung adenocarcinoma without EGFR, KRAS mutations and ALK rearrangements. Thorac Cancer 2015; 6:413-20. [PMID: 26273395 PMCID: PMC4511318 DOI: 10.1111/1759-7714.12191] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/08/2014] [Indexed: 11/28/2022] Open
Abstract
Background c-ros oncogene 1 (ROS1) rearrangement presents one of the newest molecular targets in non-small cell lung cancer (NSCLC). ROS1 rearrangement is predominantly found in adenocarcinoma cases and is exclusive to other oncogenes, such as epidermal growth factor receptor (EGFR), Kirsten rat sarcoma viral oncogene homolog (KRAS), and anaplastic lymphoma kinase (ALK). The aim of this study was to investigate the clinicopathological characteristics and outcomes of ROS1-rearranged patients with lung adenocarcinoma without EGFR and KRAS mutations and ALK rearrangements. Methods Wild-type EGFR/KRAS/ALK patients with lung adenocarcinoma were selected from Beijing Chest Hospital. Specimens were conducted in tissue microarrays. ROS1 rearrangement was screened using fluorescence in situ hybridization. Results Our study included 127 patients with lung adenocarcinoma without EGFR and KRAS mutations and ALK rearrangements. ROS1 rearrangement was detected in five (3.9%) of the 127 patients. Compared with ROS1-negative patients, the positive rate of ROS1 in female patients was significantly higher than in male patients (9.8% vs. 0.0%, P = 0.009). There were no differences in age, smoking status, stage or histological subtype between ROS1-positive and ROS1-negative patients. No significant difference in survival was detected between the ROS1-positive and ROS1-negative patients. Conclusions ROS1 rearrangement is a rare subset of lung adenocarcinoma. In 127 patients with lung adenocarcinoma, 3.9% of ROS1-positive patients with wild-type EGFR/KRAS/ALK were found.
Collapse
Affiliation(s)
- Shafei Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Jinghui Wang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute Beijing, China
| | - Lijuan Zhou
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute Beijing, China
| | - Dan Su
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute Beijing, China
| | - Yuanyuan Liu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Xiaolong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| | - Shucai Zhang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute Beijing, China
| | - Xuan Zeng
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing, China
| |
Collapse
|
84
|
McCroskey Z, Bahar B, Hu Z, Wojcik EM, Barkan GA. Subclassifying atypia in urine cytology: what are the helpful features? J Am Soc Cytopathol 2015; 4:183-189. [PMID: 31051752 DOI: 10.1016/j.jasc.2014.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 11/03/2014] [Accepted: 11/03/2014] [Indexed: 06/09/2023]
Abstract
INTRODUCTION The diagnosis "atypical urothelial cells (AUC)" remains an unresolved problem, making many urologists dissatisfied and confused about the management strategy on these cases. To date, a few inspiring attempts were made to subclassify AUC into "atypical urothelial cells of undetermined significance" (AUC-US) and "atypical urothelial cells cannot exclude high grade" (AUC-H). The aim of our study was to investigate the most predictive for high-grade urothelial carcinoma (HGUC) cytomorphologic parameters and whether the proposed classification can be implemented in our institution. MATERIAL AND METHODS The electronic medical record system was searched for cytology specimens that were diagnosed as AUC from January 1, 2005 to March 1, 2013 and their relative clinical-pathological follow-up. All specimens were reviewed by an experienced cytopathologist by using 20 published "most predictive" for HGUC criteria. RESULTS A total of 162 AUC specimens were reclassified into 3 groups: AUC-H (n = 45), AUC-US (n = 51), and "negative for malignancy" (n = 66). The reclassification of AUC-H and "negative for malignancy" had 79% sensitivity, 77% specificity, 60% positive predictive value, and 89% negative predictive value to histologically proven HGUC diagnosis. CONCLUSIONS Our study demonstrated a good correlation between the presence of "HGUC-predictive" cytologic criteria and the final biopsy-proven HGUC in cytologic cases originally diagnosed as "atypical urothelial cells present." We identified 2 of the most predictive for HGUC on follow-up cytomorphologic parameters such as increased nuclear-cytoplasmic ratio >0.7 and coarse chromatin (16 abnormal cells per slide in average). These parameters, along with positive fluorescent in situ hybridization results can help during cytologic evaluation of urine specimens.
Collapse
Affiliation(s)
- Zulfia McCroskey
- Department of Pathology, Loyola University Medical Center, 2160 South First Avenue, Maywood, Illinois.
| | - Burak Bahar
- Department of Pathology, Loyola University Medical Center, 2160 South First Avenue, Maywood, Illinois
| | - Zhihong Hu
- Department of Pathology, Loyola University Medical Center, 2160 South First Avenue, Maywood, Illinois
| | - Eva M Wojcik
- Department of Pathology, Loyola University Medical Center, 2160 South First Avenue, Maywood, Illinois
| | - Güliz A Barkan
- Department of Pathology, Loyola University Medical Center, 2160 South First Avenue, Maywood, Illinois
| |
Collapse
|
85
|
Ma J, Cram DS, Zhang J, Shang L, Yang H, Pan H. Birth of a child with trisomy 9 mosaicism syndrome associated with paternal isodisomy 9: case of a positive noninvasive prenatal test result unconfirmed by invasive prenatal diagnosis. Mol Cytogenet 2015; 8:44. [PMID: 26120364 DOI: 10.1186/s13039-015-0145-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/25/2015] [Indexed: 12/31/2022] Open
Abstract
Background Non-invasive prenatal testing (NIPT) is currently used as a frontline screening test to identify fetuses with common aneuploidies. Occasionally, incidental NIPT results are conveyed to the clinician suggestive of fetuses with rare chromosome disease syndromes. We describe a child with trisomy 9 (T9) mosaicism where the prenatal history reported a positive NIPT result for T9 that was unconfirmed by conventional prenatal diagnosis. Methods NIPT was performed by low coverage whole genome plasma DNA sequencing. Karyotyping and fluorescent in situ hybridization (FISH) analysis with chromosome 9p-ter and 9q-ter probes was used to determine the somatic cell level of T9 mosaicism in the fetus and child. Quantitative fluorescent PCR (Q-PCR) of highly polymorphic short tandem repeat (STR) chromosome 9 markers was also performed to investigate the nature of the T9 mosaicism and the parental origin. Results A 22 month old girl presented with severe developmental delay, congenital cerebral dysplasia and congenital heart disease consistent with phenotypes associated with T9 mosaicism syndrome. Review of the prenatal testing history revealed a positive NIPT result for chromosome T9. However, follow up confirmatory karyotyping and FISH analysis of fetal cells returned a normal karyotype. Post-natal studies of somatic cell T9 mosaicism by FISH detected levels of approximately 20 % in blood and buccal cells. Q-PCR STR analysis of family DNA samples suggested that the T9 mosaicism originated by post-zygotic trisomic rescue of a paternal meiotic II chromosome 9 non-disjunction error resulting in the formation of two distinct somatic cell lines in the proband, one with paternal isodisomy 9 and one with T9. Conclusion This study shows that NIPT may also be a useful screening technology to increase prenatal detection rates of rare fetal chromosome disease syndromes.
Collapse
|
86
|
García-Souto D, Pérez-García C, Morán P, Pasantes JJ. Divergent evolutionary behavior of H3 histone gene and rDNA clusters in venerid clams. Mol Cytogenet 2015; 8:40. [PMID: 26106449 PMCID: PMC4477615 DOI: 10.1186/s13039-015-0150-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/09/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Histone H3 gene clusters have been described as highly conserved chromosomal markers in invertebrates. Surprisingly, in bivalves remarkable interspecific differences were found among the eight mussels and between the two clams in which histone H3 gene clusters have already been located. Although the family Veneridae comprises 10 % of the species of marine bivalves, their chromosomes are poorly studied. The clams belonging to this family present 2n = 38 chromosomes and similar karyotypes showing chromosome pairs gradually decreasing in length. In order to assess the evolutionary behavior of histone and rRNA multigene families in bivalves, we mapped histone H3 and ribosomal RNA probes to chromosomes of ten species of venerid clams. RESULTS In contrast with the reported conservation of histone H3 gene clusters and their intercalary location in invertebrates, these loci varied in number and were mostly subterminal in venerid clams. On the other hand, while a single 45S rDNA cluster, highly variable in location, was found in these organisms, 5S rDNA clusters showed interspecific differences in both number and location. The distribution patterns of these sequences were species-specific and mapped to different chromosomal positions in all clams but Ruditapes decussatus, in which one of the minor rDNA clusters and the major rDNA cluster co-located. CONCLUSION The diversity in the distribution patterns of histone H3 gene, 5S rDNA and 28S rDNA clusters found in venerid clams, together with their different evolutionary behaviors in other invertebrate taxa, strongly suggest that the control of the spreading of these multigene families in a group of organisms relies upon a combination of evolutionary forces that operate differently depending not only on the specific multigene family but also on the particular taxa. Our data also showed that H3 histone gene and rDNA clusters are useful landmarks to integrate nex-generation sequencing (NGS) and evolutionary genomic data in non-model species.
Collapse
Affiliation(s)
- Daniel García-Souto
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain
| | | | - Paloma Morán
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain
| | - Juan J Pasantes
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain
| |
Collapse
|
87
|
Vranic S, Marchiò C, Castellano I, Botta C, Scalzo MS, Bender RP, Payan-Gomez C, di Cantogno LV, Gugliotta P, Tondat F, di Celle PF, Mariani S, Gatalica Z, Sapino A. Immunohistochemical and molecular profiling of histologically defined apocrine carcinomas of the breast. Hum Pathol 2015. [PMID: 26208846 DOI: 10.1016/j.humpath.2015.05.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite the marked improvement in the understanding of molecular mechanisms and classification of apocrine carcinoma, little is known about its specific molecular genetic alterations and potentially targetable biomarkers. In this study, we explored immunohistochemical and molecular genetic characteristics of 37 invasive apocrine carcinomas using immunohistochemistry (IHC), fluorescent in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA), and next-generation sequencing (NGS) assays. IHC revealed frequent E-cadherin expression (89%), moderate (16%) proliferation activity [Ki-67, phosphohistone H3], infrequent (~10%) expression of basal cell markers [CK5/6, CK14, p63, caveolin-1], loss of PTEN (83%), and overexpression of HER2 (32%), EGFR (41%), cyclin D1 (50%), and MUC-1 (88%). MLPA assay revealed gene copy gains of MYC, CCND1, ZNF703, CDH1, and TRAF4 in 50% or greater of the apocrine carcinomas, whereas gene copy losses frequently affected BRCA2 (75%), ADAM9 (54%), and BRCA1 (46%). HER2 gain, detected by MLPA in 38% of the cases, was in excellent concordance with HER2 results obtained by IHC/FISH (κ = 0.915, P < .001). TOP2A gain was observed in one case, while five cases (21%) exhibited TOP2A loss. Unsupervised hierarchical cluster analysis revealed two distinct clusters: HER2-positive and HER2-negative (P = .03 and .04, respectively). NGS assay revealed mutations of the TP53 (2 of 7, 29%), BRAF/KRAS (2 of 7, 29%), and PI3KCA/PTEN genes (7 of 7, 100%). We conclude that morphologically defined apocrine carcinomas exhibit complex molecular genetic alterations that are consistent with the "luminal-complex" phenotype. Some of the identified molecular targets are promising biomarkers; however, functional studies are needed to prove these observations.
Collapse
Affiliation(s)
- Semir Vranic
- Department of Medical Sciences, University of Turin, Turin 10126, Italy; Department of Pathology, Clinical Center, University of Sarajevo, Sarajevo 71000, Bosnia and Herzegovina.
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin 10126, Italy
| | | | - Cristina Botta
- Department of Medical Sciences, University of Turin, Turin 10126, Italy
| | | | | | - Cesar Payan-Gomez
- Medical Genetics Center, Department of Cell Biology and Genetics, Center of Biomedical Genetics, Erasmus MC, Rotterdam 3015, the Netherlands; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá 110010, Colombia
| | | | | | - Fabrizio Tondat
- Center for Experimental Research and Medical Studies, San Giovanni Battista Hospital, Turin 10100, Italy
| | - Paola Francia di Celle
- Center for Experimental Research and Medical Studies, San Giovanni Battista Hospital, Turin 10100, Italy
| | - Sara Mariani
- Center for Experimental Research and Medical Studies, San Giovanni Battista Hospital, Turin 10100, Italy
| | | | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin 10126, Italy.
| |
Collapse
|
88
|
Rieger AM, Havixbeck JJ, Barreda DR. X-FISH: Analysis of cellular RNA expression patterns using flow cytometry. J Immunol Methods 2015; 423:111-9. [PMID: 25997675 DOI: 10.1016/j.jim.2015.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/14/2015] [Accepted: 04/27/2015] [Indexed: 12/13/2022]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful technique for the detection of RNA or DNA within cells and tissues, which provides a unique link between molecular and cell biology. This technique is broadly applicable across a range of biological systems. While FISH has been previously adapted to flow-based platforms, their use remains limited because of procedural challenges and costs associated with commercial kits. Herein we present a protocol that modifies existing techniques to sensitively and specifically detect and examine RNA expression patterns in primary cells and cell lines using flow cytometry (expression-FISH; X-FISH). As relevant examples, we show how this technique can be used to monitor changes in mRNA expression following activation, how it can be combined with antibody staining to study RNA and protein in the same sample, and how it can help distinguish among subsets in a mixed cell population. X-FISH can integrate multiple probes and can be performed in conjunction with other assays, allowing for informative multiparametric analyses and increased statistical robustness. For non-classical comparative animal models this procedure provides a time saving alternative to de novo production of antibody-based markers. Finally, X-FISH provides an economical solution that is applicable to conventional as well as multi-spectral imaging flow cytometry platforms.
Collapse
|
89
|
Zhang X, Li K, Wu S, Shuai J, Fang W. Peptide nucleic acid fluorescence in-situ hybridization for identification of Vibrio spp. in aquatic products and environments. Int J Food Microbiol 2015; 206:39-44. [PMID: 25955286 DOI: 10.1016/j.ijfoodmicro.2015.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 04/02/2015] [Accepted: 04/11/2015] [Indexed: 11/26/2022]
Abstract
A peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method was developed for specific detection of the Vibrio genus. In silico analysis by BLAST and ProbeCheck showed that the designed PNA probe targeting the 16S rRNAs was suitable for specific identification of Vibrio. Specificity and sensitivity of the probe Vib-16S-1 were experimentally verified by its reactivity against 18 strains of 9 Vibrio species and 14 non-Vibrio strains of 14 representative species. The PNA-FISH assay was able to identify 47 Vibrio positive samples from selectively enriched cultures of 510 samples of aquatic products and environments, comparable with the results obtained by biochemical identification and real-time PCR. We conclude that PNA-FISH can be an alternative method for rapid identification of Vibrio species in a broad spectrum of seafood or related samples.
Collapse
Affiliation(s)
- Xiaofeng Zhang
- Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, People's Republic of China; Food Safety Key Laboratory of Zhejiang Province, Zhejiang Entry-Exit Inspection and Quarantine Bureau, 126 Fuchun Road, Hangzhou 310012, People's Republic of China
| | - Ke Li
- Food Safety Key Laboratory of Zhejiang Province, Zhejiang Entry-Exit Inspection and Quarantine Bureau, 126 Fuchun Road, Hangzhou 310012, People's Republic of China
| | - Shan Wu
- Food Safety Key Laboratory of Zhejiang Province, Zhejiang Entry-Exit Inspection and Quarantine Bureau, 126 Fuchun Road, Hangzhou 310012, People's Republic of China
| | - Jiangbing Shuai
- Food Safety Key Laboratory of Zhejiang Province, Zhejiang Entry-Exit Inspection and Quarantine Bureau, 126 Fuchun Road, Hangzhou 310012, People's Republic of China
| | - Weihuan Fang
- Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, People's Republic of China.
| |
Collapse
|
90
|
Yang X, Yue H, Ye H, Li C, Wei Q. Identification of a germ cell marker gene, the dead end homologue, in Chinese sturgeon Acipenser sinensis. Gene 2014; 558:118-25. [PMID: 25550043 DOI: 10.1016/j.gene.2014.12.059] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/18/2014] [Accepted: 12/24/2014] [Indexed: 12/19/2022]
Abstract
Dead end (dnd) encodes an RNA-binding protein that is essential for primordial germ cell (PGC) migration and gametogenesis in vertebrates. In this study, a Chinese sturgeon Acipenser sinensis dead end homologue, designated Asdnd, was identified and characterized. The full-length cDNA of Asdnd was 1630base pairs (bp) and encoded a peptide of 396 amino acid residues. Multiple sequence alignment showed that AsDnd shared six conserved regions of Dnd orthologs, including the RNA recognition motif. Phylogenetic analysis revealed that AsDnd was grouped with teleosts. By quantitative real-time PCR analysis, the Asdnd transcripts were found to originate from the maternal parent and be specifically expressed in gonads of immature Chinese sturgeons of both sexes. Fluorescent in situ hybridization indicated that Asdnd transcripts were restricted to germ cells. In the testis, Asdnd was abundant in spermatogonia and tended to gradually diminish in late spermatogenic stages, while strong signals were found in primary oocytes, as opposed to oogonia, in the ovary. Zebrafish PGCs were clearly visualized at 24h post-fertilization by co-injecting RFP-Asdnd 3' UTR and GFP-nos3 3' UTR mRNA, indicating that dnd 3' UTR has a conserved function among teleosts. Therefore, dnd could serve as a germ cell marker in Chinese sturgeon.
Collapse
Affiliation(s)
- Xiaoge Yang
- Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Huamei Yue
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China
| | - Huan Ye
- Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Chuangju Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.
| | - Qiwei Wei
- Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China; Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.
| |
Collapse
|
91
|
Van Bogaert N, De Jonghe K, Van Damme EJM, Maes M, Smagghe G. Quantitation and localization of pospiviroids in aphids. J Virol Methods 2014; 211:51-4. [PMID: 25455904 DOI: 10.1016/j.jviromet.2014.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/06/2014] [Accepted: 10/10/2014] [Indexed: 11/28/2022]
Abstract
In this paper, the potential role of aphids in viroid transmission was explored. Apterous aphids were fed on pospiviroid-infected plants and viroid targets in the aphids were consequently quantified through RT-qPCR and localized within the aphid body using fluorescence in situ hybridization (FISH). Based on the analytical sensitivity test, the limit of detection (LOD) was estimated at 1.69×10(6) viroid copies per individual aphid body. To localize the viroids in the aphids, a pospiviroid-generic Cy5-labelled probe was used and the fluorescent signal was determined by confocal microscopy. Viroids were clearly observed in the aphid's stylet and stomach, but not in the embryos. Viroids were detected in 29% of the aphids after a 24h feeding period, which suggests only a partial and low concentration viroid uptake by the aphid population including viroid concentrations under the LOD. However, these results show that viroids can be ingested by aphids while feeding on infected plants, thus potentially increasing the transmission risk. The combination of FISH and RT-qPCR provides reliable and fast localization and quantitation of viroid targets in individual aphids and thus constitutes a valuable tool in future epidemiological research.
Collapse
Affiliation(s)
- N Van Bogaert
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burgemeester Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - K De Jonghe
- Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burgemeester Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - E J M Van Damme
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - M Maes
- Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burgemeester Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - G Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| |
Collapse
|
92
|
Lee MY, Won HS, Baek JW, Cho JH, Shim JY, Lee PR, Kim A. Variety of prenatally diagnosed congenital heart disease in 22q11.2 deletion syndrome. Obstet Gynecol Sci 2014; 57:11-6. [PMID: 24596813 DOI: 10.5468/ogs.2014.57.1.11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/30/2013] [Accepted: 06/24/2013] [Indexed: 11/29/2022] Open
Abstract
Objective To analyze the spectrum of prenatally diagnosed congenital heart disease in a Korean population with 22q11.2 deletion syndrome, and to provide guidelines for screening 22q11.2 deletion prenatally. Methods This retrospective study evaluated 1,137 consecutive fetuses that had prenatal genetic testing for 22q11.2 deletion because of suspected congenital heart disease between September 2002 and December 2012, at Asan Medical Center, Seoul, Korea. Results Main cardiovascular diseases in the 53 fetuses with confirmed 22q11.2 deletions were tetralogy of Fallot (n = 24, 45%), interrupted aortic arch (n = 10, 19%), ventricular septal defect (n = 5, 9%), double outlet right ventricle (n = 4, 8%), and coarctation of the aorta (n = 4, 8%). Other cardiac defects were rarely associated with 22q11.2 deletion. One fetus had persistent truncus arteriosus, one had aortic stenosis, and one had hypoplastic right heart syndrome. Two fetuses had normal intracardiac anatomy with an isolated right aortic arch, and one had an isolated bilateral superior vena cava. Conclusion A variety of congenital heart diseases were seen during the prenatal period. Conotruncal cardiac defects except transposition of great arteries were strongly associated with 22q11.2 deletion. When such anomalies are diagnosed by fetal echocardiography, genetic testing for 22q11.2 deletion should be offered. Even if less frequent deletion-related cardiac defects are detected, other related anomalies, such as thymic hypoplasia or aplasia, should be evaluated to rule out a 22q11.2 deletion.
Collapse
|
93
|
Carvalho KC, Maia BM, Omae SV, Rocha AA, Covizzi LP, Vassallo J, Rocha RM, Soares FA. Best practice for PTEN gene and protein assessment in anatomic pathology. Acta Histochem 2014; 116:25-31. [PMID: 23746542 DOI: 10.1016/j.acthis.2013.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/18/2013] [Accepted: 04/25/2013] [Indexed: 12/14/2022]
Abstract
There is a lack of standardization of a best practice protocol for Phosphatase and Tensin Homolog (PTEN) assessment by immunohistochemistry in anatomic pathology routine practice. We performed immunohistochemistry for 19 antibodies against PTEN, eleven of which were excluded during the standardization step. Immunohistochemistry of the remaining eight antibodies was performed on a Tissue Microarray containing 55 prostate and 40 renal carcinoma samples. Fluorescent in situ hybridization (FISH) was used as reference standard for immunohistochemistry specificity evaluation. Concerning nuclear staining, polyclonal (Cat#22034-1-AP); 6H2.1 mMAb (Cat#ABM-2052), Y184 RabMAb (Cat#NB110-57441) and 217702 mMAb antibodies presented the highest agreement with fluorescent in situ hybridization (p<0.001 for all) and with regard to cytoplasmic staining, Y184 RabMAb (Cat#NB110-57441); polyclonal (Cat#22034-1-AP) and 217702 mMAb presented the highest agreement (p<0.001 for all). Our results indicate that several commercially available antibodies do not show reliability of sensitivity and specificity for PTEN evaluation and we propose 6H2.1 mMAb (Cat#ABM-2052) as the antibody of choice for laboratory standardization and best practice in clinical routine, which demonstrated excellent sensitivity for both nuclear and cytoplasmic staining, specificity for PTEN by Western blot and good correlation with PTEN status by FISH with regard to nuclear staining.
Collapse
Affiliation(s)
- Kátia C Carvalho
- Department of Obstetrics and Gynecology, School of Medicine of Sao Paulo University, Sao Paulo, SP, Brazil
| | - Beatriz M Maia
- Research Center, Antonio Prudente Foundation, Hospital A.C. Camargo, Sao Paulo, SP, Brazil
| | - Samantha V Omae
- Research Center, Antonio Prudente Foundation, Hospital A.C. Camargo, Sao Paulo, SP, Brazil
| | - Antonio A Rocha
- Department of Microbiology, Immunology and Parasitology, UNIFESP, Sao Paulo, Brazil
| | - Luiz P Covizzi
- Department of Anatomic Pathology, Hospital A.C. Camargo, Sao Paulo, SP, Brazil
| | - José Vassallo
- Department of Anatomic Pathology, Hospital A.C. Camargo, Sao Paulo, SP, Brazil
| | - Rafael M Rocha
- Research Center, Antonio Prudente Foundation, Hospital A.C. Camargo, Sao Paulo, SP, Brazil; Department of Anatomic Pathology, Hospital A.C. Camargo, Sao Paulo, SP, Brazil.
| | - Fernando A Soares
- Research Center, Antonio Prudente Foundation, Hospital A.C. Camargo, Sao Paulo, SP, Brazil; Department of Anatomic Pathology, Hospital A.C. Camargo, Sao Paulo, SP, Brazil
| |
Collapse
|
94
|
Preusser M, Berghoff AS, Berger W, Ilhan-Mutlu A, Dinhof C, Widhalm G, Dieckmann K, Wöhrer A, Hackl M, von Deimling A, Streubel B, Birner P. High rate of FGFR1 amplifications in brain metastases of squamous and non-squamous lung cancer. Lung Cancer 2014; 83:83-9. [PMID: 24183471 DOI: 10.1016/j.lungcan.2013.10.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/09/2013] [Accepted: 10/05/2013] [Indexed: 11/20/2022]
Abstract
OBJECTIVES FGFR1 amplifications are common in squamous cell carcinoma and rare in adenocarcinoma of the lung, but have not been investigated in brain metastases of non-small cell lung cancer (NSCLC). MATERIALS AND METHODS We performed fluorescent in situ hybridization (FISH) for FGFR1 and immunohistochemistry for pAKT, PI3K, HIF1a and Ki67 in 175 NSCLC brain metastases and 11 matched primary tumors. ALK gene rearrangement status was available from a previous study. We performed statistical correlations of clinical, histopathological and molecular data. RESULTS FGFR1 amplifications were found in a total of 30/175 (17%) brain metastases: 4/21 (19%) squamous cell carcinomas, 20/130 (15.3%) adenocarcinomas, 2/12 (16.6%) adenosquamous carcinomas, 4/9 (44.4%) large cell carcinomas and 0/3 neuroendocrine large cell carcinoma. FGFR1 gene status was identical between primary tumors and brain metastases in 9/11 evaluable cases. In 2/11 cases (1 adenosquamous and 1 large cell carcinoma), FGFR1 amplifications were present only in the brain metastasis and not in the primary tumor. Furthermore, we found a significant positive correlation of ALK and FGFR1 gene amplification status in brain metastases (p<0.001, Chi square test). Patients with high-level FGFR1 amplifications had significantly higher number of visceral metastases (p<0.001, Chi square test). CONCLUSION Our findings argue for an enrichment of FGFR1 amplifications in brain metastases of adenocarcinomas (where they were 5-fold more frequent than reported for primary tumors) and possibly also of other non-squamous carcinomas, but not in squamous cell carcinomas of the lung. These results may be relevant for targeted therapy and prophylaxis of NSCLC brain metastases.
Collapse
|
95
|
Atieh T, Audoly G, Hraiech S, Lepidi H, Roch A, Rolain JM, Raoult D, Papazian L, Brégeon F. Evaluation of the diagnostic value of fluorescent in situ hybridization in a rat model of bacterial pneumonia. Diagn Microbiol Infect Dis 2013; 76:425-31. [PMID: 23747031 DOI: 10.1016/j.diagmicrobio.2013.04.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/12/2013] [Accepted: 04/26/2013] [Indexed: 10/26/2022]
Abstract
In severe nosocomial pneumonia, the pathogenic responsibility of bacteria isolated from airways is far from certain, and a lung biopsy is sometimes performed. However, detection and identification of pathogens are frequently unachieved. Here, we developed a protocol for direct visualization of bacteria within the lung tissue using fluorescent in situ hybridization (FISH) in a rat model of Acinetobacter baumannii pneumonia. The reference positive diagnosis of bacterial pneumonia was the presence of pathological signs of pneumonia associated with the proof of bacteria or bacterial PCR products into the parenchyma. By analysis of 122 sets of slices from 26 rats and using the eubacterial probe EUB-338, our results show that FISH reached a sensitivity and a diagnostic accuracy higher than that of optic microscopy (sensitivity: 96% versus 55.4% and diagnostic accuracy: 96.7% versus 66.4%), whereas both approaches had 100% specificity. FISH could be useful especially on negative biopsies from patients with suspected infectious pneumonia.
Collapse
Affiliation(s)
- Thérèse Atieh
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | | | | | | | | | | | | | | | | |
Collapse
|
96
|
Alì G, Proietti A, Niccoli C, Pelliccioni S, Borrelli N, Giannini R, Lupi C, Valetto A, Bertini V, Lucchi M, Mussi A, Fontanini G. EML4-ALK translocation in both metachronous second primary lung sarcomatoid carcinoma and lung adenocarcinoma: a case report. Lung Cancer 2013; 81:297-301. [PMID: 23664446 DOI: 10.1016/j.lungcan.2013.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/14/2013] [Accepted: 03/16/2013] [Indexed: 12/16/2022]
Abstract
The EML4-ALK gene translocation was described in a non small cell lung cancer (NSCLC) subset, with a potent oncogenic activity. It represents one of the newest molecular targets in NSCLC. We report on the case of a metachronous second primary lung sarcomatoid carcinoma after resection of lung adenocarcinoma both with ALK translocation, in a non-smoking patient. EML4-ALK rearrangement was detected with immunohistochemistry and confirmed with fluorescent in situ hybridization (FISH). To assess the clonal relationship between the two tumors, both adenocarcinoma and sarcomatoid carcinoma were analyzed by array comparative genomic hybridization (aCGH). We observed different genomic profiles suggesting that the tumors arose independently and were thus multiple primaries. To the best of our knowledge, this is the first report concerning the presence of the EML4-ALK fusion gene in a sarcomatoid carcinoma of the lung. Crizotinib, the ALK tyrosine kinase inhibitor, is highly effective in ALK-rearranged NSCLC; therefore, it may be imperative to identify all NSCLC that harbor ALK translocations in the near future. Starting from our evidence, tumors with sarcomatoid histology may need to be screened for the presence of EML4-ALK rearrangement.
Collapse
Affiliation(s)
- Greta Alì
- Unit of Pathological Anatomy, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
97
|
Kang MJ, Han SS, Jang JY, Park JW, Kwon W, Chang YR, Kim SW. Cancer cells with p53 deletion detected by fluorescent in situ hybridization in peritoneal drainage fluid is correlated with early peritoneal seeding in resectable pancreatic cancer. J Korean Surg Soc 2013; 84:209-15. [PMID: 23577315 PMCID: PMC3616274 DOI: 10.4174/jkss.2013.84.4.209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 01/08/2013] [Accepted: 02/20/2013] [Indexed: 01/26/2023]
Abstract
Purpose Free tumor cells in peritoneal fluid in patients with pancreatic cancer may have prognostic significance but there are few reports on methods for the effective detection of free tumor cells. The aims of this study were to identify free cancer cells in peritoneal fluid with fluorescent in situ hybridization (FISH) technique and to investigate its prognostic significance. Methods Twenty-eight patients with resectable pancreatic cancer who underwent surgical resection were included. Peritoneal washing and peritoneal drainage fluid were examined by FISH for p53 deletion. Results Among the study subjects, the R0 resection rate was 75%. None of the patients had positive cytology with Papanicolaou's method. p53 deletion was detected in 9 peritoneal washings (32.1%) and in 5 peritoneal drainage fluids (17.9%). After a median of 18 months of follow-up, 25 patients (89.3%) experienced recurrence and 14 patients (50.0%) had peritoneal seeding. Patients with p53 deletion detected in the peritoneal drainage fluid had positive radial margin (60.0% vs. 17.4%, P = 0.046) more frequently and a lower peritoneal metastasis free survival (median, 11.1 months vs. 30.3 months; P = 0.030). Curative resection (P < 0.001) and p53 deletion in peritoneal drainage fluid (P = 0.030) were independent risk factors of peritoneal metastasis free survival after multivariate analysis. Conclusion FISH technique detects free cancer cells with higher sensitivity compared to Papanicolaou's method. p53 deletion detected in peritoneal drainage fluid is correlated with positive radial resection margin and results in early peritoneal seeding. Patients with p53 deletion in peritoneal drainage fluid need more aggressive adjuvant treatment.
Collapse
Affiliation(s)
- Mee Joo Kang
- Department of Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | | | | | | | | | | | | |
Collapse
|
98
|
Venkateshwari A, Srimanjari K, Srilekha A, Begum A, Sujatha M, Sunitha T, Nallari P, Jyothy A. Mosaic triple X syndrome in a female with primary amenorrhea. Indian J Hum Genet 2012; 18:246-9. [PMID: 23162306 PMCID: PMC3491304 DOI: 10.4103/0971-6866.100790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND: Turner's syndrome is the most common chromosomal abnormality in females, affecting 1 in 2,500 live female births. It is a result of absence of an X chromosome or the presence of a structurally abnormal X chromosome. Its most consistent clinical features are short stature and ovarian failure. AIM: The aim of the study was to report a rare case of mosaic triple X syndrome in a female with primary amenorrhea. MATERIALS AND METHODS: The chromosomal analysis using GTG banding was carried out, which revealed a mosaicism with 45,XO/47,XXX chromosomal constitution. Fluorescent in situ hybridization was also carried out to further confirm the observation made in the study. CONCLUSION: The physical features presented by the female could be due to the 45,XO/47,XXX mosaicism and the karyotype analysis was consistent with the diagnosis and clinical symptoms. Triple X mosaicism was confirmed with conventional and molecular cytogenetic analysis.
Collapse
Affiliation(s)
- A Venkateshwari
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Begumpet, India
| | | | | | | | | | | | | | | |
Collapse
|
99
|
Abstract
AIM: To compare the differences in the numbers of Bifidobacterium, Bacteroides, Eubacterium rectale-Clostridium, Escherichia coli, Enterococcus, Clostridium difficile in stool samples between patients with hepatic cirrhosis and controls to understand the changes in intestinal flora in patients with hepatic cirrhosis.
METHODS: Stool samples collected from 29 patients with hepatic cirrhosis who were treated at the First People's Hospital of Zunyi during the period between March to December 2010 and 13 healthy volunteers were used in this study. The samples were fixed, smeared on slides, and analyzed by fluorescent in situ hybridization (FISH) and laser scanning confocal microscopy (LSCM). The t-test and rank correlation test were used for statistical analysis.
RESULTS: The numbers of Bifidobacterium, Bacteroides, Eubacterium rectale-Clostridium, Escherichia coli, Enterococcus, and Clostridium difficile were significantly lower in patients with hepatic cirrhosis than in controls (Z = -4.006, -4.34, -4.399, -4.174, -3.558, -3.95; all P < 0.01). The proportions of all 6 kinds of bacteria were changed. The numbers of obligate anaerobes such as Bifidobacteria and Bacteroides were reduced, while those of E. coli, Eubacterium rectale-Clostridium, Enterococcus, and ClostriDium difficile were increased (all P < 0.05). The numbers and portions of bacteria had no significant correlation with etiology and severity of hepatic cirrhosis (Child-Pugh classification).
CONCLUSION: The numbers and proportions of six kinds of bacteria changed in patients with hepatic cirrhosis. Changes in intestinal microflora have no significant correlation with etiology and Child-Pugh classification.
Collapse
|
100
|
Okumura K, Ikebe M, Shimokama T, Takeshita M, Kinjo N, Sugimachi K, Higashi H. An unusual enteropathy-associated T-cell lymphoma with MYC translocation arising in a Japanese patient: A case report. World J Gastroenterol 2012; 18:2434-7. [PMID: 22654438 PMCID: PMC3353381 DOI: 10.3748/wjg.v18.i19.2434] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 06/15/2011] [Accepted: 04/12/2012] [Indexed: 02/06/2023] Open
Abstract
Enteropathy-associated T-cell lymphoma (EATL) is a rare peripheral T-cell lymphoma classified into 2 types, with or without celiac disease, based on histology. Type 2 EATL is less commonly associated with celiac disease, in which cells are characterized by being monomorphic and small- to medium-sized. Cells are characterized by CD8 and CD56 expression and c-MYC oncogene locus gain. We present an atypical case of type 2 EATL in the jejunum, with human T-lymphotropic virus-1 that was CD4- CD8+ CD56- CD30- CD25- TIA-1+ and granzyme B+ on immunohistological staining. It also displayed translocation of chromosome 8p24 (c-MYC), as determined by fluorescent in situ hybridization. Mucosal spreading and intraepithelial invasion by lymphoma with villous atrophy were detected adjacent to the mucosal layer. The lymphoma may be derived from intraepithelial CD8+ T cells, similar to celiac disease.
Collapse
|