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Cao D, Qin X, Wang W, Zhang Y, Peng S, Gong H, Luo Q, Yang J. Designing a Hybrid Chain Reaction Probe for Multiplex Transcripts Assay with High-Level Imaging. ACS Nano 2024; 18:618-629. [PMID: 38154106 DOI: 10.1021/acsnano.3c08720] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
The hybrid chain reaction (HCR), an isothermal and enzyme-free amplification strategy, has found extensive use in fluorescent in situ hybridization (FISH) assays. However, the existing HCRs are limited, being time-consuming processes and low-efficiency imaging due to weak signal, significantly restricting their application in transcriptomic assays. To address the limitations, we developed nine orthogonal HCR hairpin-pair (hp) probes in this study to enable efficient signal amplification for multiplex assays. To enhance the efficiency and imaging quality of multiplex assays using these HCR probes, we employed two strategies. First, we coupled fluorescent molecules to HCR hairpins via disulfide bonds, facilitating easy removal through chemical cleavage. As a result, the workflow was greatly simplified. Second, we combined HCR with in situ rolling circle amplification (ISRCA), creating ISRCA-HCR, which achieved a 17-fold signal amplification. ISRCA-HCR demonstrated a high-level imaging capability for spatial cell type assays. This study shows the application for cell typing based on the developed HCR probes, enabling accurate and high-level signal amplification for multiplex FISH imaging. This provides an effective research tool for transcriptome and spatial cell type analysis.
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Affiliation(s)
- Dongjian Cao
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xinxin Qin
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wenjing Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ying Zhang
- Class 202001, School of Engineering Science, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Sunxiang Peng
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Hui Gong
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qingming Luo
- School of Biomedical Engineering, Hainan University, Haikou 570228, China
| | - Jie Yang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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Ampatzidou M, Papadhimitriou SI, Paisiou A, Paterakis G, Tzanoudaki M, Papadakis V, Florentin L, Polychronopoulou S. The Prognostic Effect of CDKN2A/2B Gene Deletions in Pediatric Acute Lymphoblastic Leukemia (ALL): Independent Prognostic Significance in BFM-Based Protocols. Diagnostics (Basel) 2023; 13:diagnostics13091589. [PMID: 37174980 PMCID: PMC10178600 DOI: 10.3390/diagnostics13091589] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
One of the most frequent genes affected in pediatric ALL is the CDKN2A/2B gene, acting as a secondary cooperating event and playing an important role in cell-cycle regulation and chemosensitivity. Despite its inclusion in combined CNA (copy-number alterations) classifiers, like the IKZF1plus entity and the UKALL CNA profile, the prognostic impact of the individual gene deletions outside the context of a combined CNA evaluation remains controversial. Addressing the CDKN2A/2B deletions' additive prognostic effect in current risk-stratification algorithms, we present a retrospective study of a Greek pediatric ALL cohort comprising 247 patients studied over a 24-year period (2000-2023). Herein, we provide insight regarding the correlation with disease features, MRD clearance, and independent prognostic significance for this ALL cohort treated with contemporary BFM-based treatment protocols. Within an extended follow-up time of 135 months, the presence of the CDKN2A/2B deletions (biallelic or monoallelic) was associated with inferior EFS rates (65.1% compared to 91.8% for the gene non-deleted subgroup, p < 0.001), with the relapse rate accounting for 22.2% and 5.9%, respectively (p < 0.001). The presence of the biallelic deletion was associated with the worst outcomes (EFS 57.2% vs. 89.6% in the case of any other status, monoallelic or non-deleted, p < 0.001). Survival differences were demonstrated for B-ALL cases (EFS 65.3% vs. 93.6% for the non-deleted B-ALL subgroup, p < 0.001), but the prognostic effect was not statistically significant within the T-ALL cohort (EFS 64.3 vs. 69.2, p = 0.947). The presence of the CDKN2A/2B deletions clearly correlated with inferior outcomes within all protocol-defined risk groups (standard risk (SR): EFS 66.7% vs. 100%, p < 0.001, intermediate risk (IR): EFS 77.1% vs. 97.9%, p < 0.001, high risk (HR): EFS 42.1% vs. 70.5% p < 0.001 for deleted vs non-deleted cases in each patient risk group); additionally, in this study, the presence of the deletion differentiated prognosis within both MRD-positive and -negative subgroups on days 15 and 33 of induction. In multivariate analysis, the presence of the CDKN2A/2B deletions was the most important prognostic factor for relapse and overall survival, yielding a hazard ratio of 5.2 (95% confidence interval: 2.59-10.41, p < 0.001) and 5.96 (95% confidence interval: 2.97-11.95, p < 0.001), respectively, designating the alteration's independent prognostic significance in the context of modern risk stratification. The results of our study demonstrate that the presence of the CDKN2A/2B deletions can further stratify all existing risk groups, identifying patient subgroups with different outcomes. The above biallelic deletions could be incorporated into future risk-stratification algorithms, refining MRD-based stratification. In the era of targeted therapies, future prospective controlled clinical trials will further explore the possible use of cyclin-dependent kinase inhibitors (CDKIs) in CDKN2A/2B-affected ALL pediatric subgroups.
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Affiliation(s)
- Mirella Ampatzidou
- Department of Pediatric Hematology-Oncology (TAO), "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Stefanos I Papadhimitriou
- Laboratory of Hematology, Unit of Molecular Cytogenetics, "G. Gennimatas" General Hospital, 11527 Athens, Greece
| | - Anna Paisiou
- Bone Marrow Transplantation Unit, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Georgios Paterakis
- Laboratory of Flow Cytometry, Department of Immunology, "G. Gennimatas" General Hospital, 11527 Athens, Greece
| | - Marianna Tzanoudaki
- Department of Immunology, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Vassilios Papadakis
- Department of Pediatric Hematology-Oncology (TAO), "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Lina Florentin
- Alfa Laboratory Diagnostic Center, YGEIA Hospital, 11524 Athens, Greece
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology-Oncology (TAO), "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
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Liu S, Morihiro K, Takeuchi F, Li Y, Okamoto A. Interstrand crosslinking oligonucleotides elucidate the effect of metal ions on the methylation status of repetitive DNA elements. Front Chem 2023; 11:1122474. [PMID: 36711237 PMCID: PMC9881727 DOI: 10.3389/fchem.2023.1122474] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
DNA methylation plays an important physiological function in cells, and environmental changes result in fluctuations in DNA methylation levels. Metal ions have become both environmental and health concerns, as they have the potential to disrupt the genomic DNA methylation status, even on specific sequences. In the current research, the methylation status of two typical repetitive DNA elements, i.e., long-interspersed nuclear element-1 (LINE-1) and alpha satellite (α-sat), was imaged and assessed using methylation-specific fluorescence in situ hybridization (MeFISH). This technique elucidated the effect of several metal ions on the methylation levels of repetitive DNA sequences. The upregulation and downregulation of the methylation levels of repetitive DNA elements by various metal ions were confirmed and depended on their concentration. This is the first example to investigate the effects of metal ions on DNA methylation in a sequence-specific manner.
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Affiliation(s)
- Shan Liu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kunihiko Morihiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Fumika Takeuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Yufeng Li
- The Key Laboratory of Molecular Oncology of Hebei Province, Tangshan People’s Hospital, Tangshan, Hebei, China
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan,*Correspondence: Akimitsu Okamoto,
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Krishnan N, Tanaka T, Fiorito G, Genta FA, Imperadore P. Editorial: Methods and applications in invertebrate physiology. Front Physiol 2023; 14:1158972. [PMID: 36875030 PMCID: PMC9982125 DOI: 10.3389/fphys.2023.1158972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Affiliation(s)
- Natraj Krishnan
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Fernando Ariel Genta
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
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Alexandrov OS, Romanov DV, Divashuk MG, Razumova OV, Ulyanov DS, Karlov GI. Study and Physical Mapping of the Species-Specific Tandem Repeat CS-237 Linked with 45S Ribosomal DNA Intergenic Spacer in Cannabis sativa L. Plants (Basel) 2022; 11:1396. [PMID: 35684169 PMCID: PMC9183113 DOI: 10.3390/plants11111396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Hemp (Cannabis sativa L.) is a valuable crop and model plant for studying sex chromosomes. The scientific interest in the plant has led to its whole genome sequencing and the determination of its cytogenetic characteristics. A range of cytogenetic markers (subtelomeric repeat CS-1, 5S rDNA, and 45S rDNA) has been mapped onto hemp's chromosomes by fluorescent in situ hybridization (FISH). In this study, another cytogenetic marker (the tandem repeat CS-237, with a 237 bp monomer) was found, studied, and localized on chromosomes by FISH. The signal distribution and karyotyping revealed that the CS-237 probe was localized in chromosome 6 with one hybridization site and in chromosome 8 with two hybridization sites, one of which colocalizes with the 45S rDNA probe (with which a nucleolus organizer region, NOR, was detected). A BLAST analysis of the genomic data and PCR experiments showed that the modified CS-237 monomers (delCS-237, 208 bp in size) were present in the intergenic spacers (IGSs) of hemp 45S rDNA monomers. Such a feature was firstly observed in Cannabaceae species. However, IGS-linked DNA repeats were found in several plant species of other families (Fabaceae, Solanaceae, and Asteraceae). This phenomenon is discussed in this article. The example of CS-237 may be useful for further studying the phenomenon as well as for the physical mapping of hemp chromosomes.
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Thomas P, Franco CMM. Intracellular Bacteria in Plants: Elucidation of Abundant and Diverse Cytoplasmic Bacteria in Healthy Plant Cells Using In Vitro Cell and Callus Cultures. Microorganisms 2021; 9:269. [PMID: 33525492 PMCID: PMC7912260 DOI: 10.3390/microorganisms9020269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/31/2020] [Revised: 01/21/2021] [Accepted: 01/23/2021] [Indexed: 12/12/2022] Open
Abstract
This study was initiated to assess whether the supposedly axenic plant cell cultures harbored any cultivation-recalcitrant endophytic bacteria (CREB). Adopting live-cell imaging with bright-field, fluorescent and confocal microscopy and bacterial 16S-rRNA gene taxonomic profiling, we report the cytoplasmic association of abundant and diverse CREBs in long-term actively maintained callus and cell suspension cultures of different plant species. Preliminary bright-field live-cell imaging on grape cell cultures showed abundant intracellular motile micro-particles resembling bacteria, which proved uncultivable on enriched media. Bacterial probing employing DNA stains, transmission electron microscopy, and Eubacterial FISH indicated abundant and diverse cytoplasmic bacteria. Observations on long-term maintained/freshly established callus stocks of different plant species-grapevine, barley, tobacco, Arabidopsis, and medicinal species-indicated intracellular bacteria as a common phenomenon apparently originating from field shoot tissues.Cultivation-independent 16S rRNA gene V3/V3-V4 amplicon profiling on 40-year-old grape cell/callus tissues revealed a high bacterial diversity (>250 genera), predominantly Proteobacteria, succeeded by Firmicutes, Actinobacteria, Bacteriodetes, Planctomycetes, and 20 other phyla, including several candidate phyla. PICRUSt analysis revealed diverse functional roles for the bacterial microbiome, majorly metabolic pathways. Thus, we unearth the widespread association of cultivation-recalcitrant intracellular bacteria "Cytobacts" inhabiting healthy plant cells, sharing a dynamic mutualistic association with cell hosts.
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Affiliation(s)
- Pious Thomas
- Thomas Biotech & Cytobacts Centre for Biosciences, Amruthahalli, Bengaluru 560092, India
| | - Christopher M. M. Franco
- Department of Medical Biotechnology, College of Medicine & Public Health, Flinders University, Bedford Park, Adelaide, SA 5042, Australia
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Araújo NP, Bonvicino C, Svartman M. Comparative cytogenetics of four species of Thrichomys (Rodentia: Echimyidae). Genome 2018; 62:31-41. [PMID: 30481091 DOI: 10.1139/gen-2018-0147] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Thrichomys Trouessart, 1880 is a genus of echimyid rodents endemic to South America, distributed from northeastern Brazil to Paraguay and Bolivia. Although all the recognized species of this genus have already been karyotyped, detailed comparative cytogenetic analyses have not been performed yet. We karyologically analyzed four species of Thrichomys from different Brazilian states. Our analyses included GTG- and CBG-banding, silver-staining of the nucleolar organizer regions (Ag-NORs), and fluorescent in situ hybridization (FISH) with telomeric and 45S rDNA probes. Comparative GTG-banding suggested that the interspecific variation may result from Robertsonian rearrangements, pericentric and paracentric inversions, centromere repositioning, and heterochromatin variation. FISH with a telomeric probe showed interspecies variation in interstitial telomeric sequences (ITs) distribution. Our results represent the most complete data on the cytogenetics of Thrichomys reported to date and give an insight into the chromosome evolution of this genus.
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Affiliation(s)
- Naiara Pereira Araújo
- a Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627 - Pampulha, 31270-901, Belo Horizonte, MG, Brazil
| | - Cibele Bonvicino
- b Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fiocruz, e Divisão de Genética, INCA, Rio de Janeiro, RJ, Brazil
| | - Marta Svartman
- a Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627 - Pampulha, 31270-901, Belo Horizonte, MG, Brazil
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Barby FF, Ráb P, Lavoué S, Ezaz T, Bertollo LAC, Kilian A, Maruyama SR, Aguiar de Oliveira E, Artoni RF, Santos MH, Ilesanmi Jegede O, Hatanaka T, Tanomtong A, Liehr T, Cioffi MDB. From Chromosomes to Genome: Insights into the Evolutionary Relationships and Biogeography of Old World Knifefishes (Notopteridae; Osteoglossiformes). Genes (Basel) 2018; 9:E306. [PMID: 29921830 PMCID: PMC6027293 DOI: 10.3390/genes9060306] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 05/23/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 01/13/2023] Open
Abstract
In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the diversity present in this group. However, cytogenetic and genomic data are still scarce, making it difficult to track evolutionary trajectories within this order. In addition, their wide distribution, with groups endemic to different continents, hinders an integrative study that allows a globalized view of its evolutionary process. Here, we performed a detailed chromosomal analysis in Notopteridae fishes, using conventional and advanced molecular cytogenetic methods. Moreover, the genetic distances of examined species were assessed by genotyping using diversity arrays technology sequencing (DArTseq). These data provided a clear picture of the genetic diversity between African and Asian Notopteridae species, and were highly consistent with the chromosomal, geographical, and historical data, enlightening their evolutionary diversification. Here, we discuss the impact of continental drift and split of Pangea on their recent diversity, as well as the contribution to biogeographical models that explain their distribution, highlighting the role of the Indian subcontinent in the evolutionary process within the family.
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Affiliation(s)
- Felipe Faix Barby
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic.
| | - Sébastien Lavoué
- Institute of Oceanography, National Taiwan University, Roosevelt Road, Taipei 10617, Taiwan.
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory, Canberra, ACT 2617, Australia.
| | - Sandra Regina Maruyama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84030-900 Brazil.
| | - Mateus Henrique Santos
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84030-900 Brazil.
| | - Oladele Ilesanmi Jegede
- Department of Fisheries and Aquaculture, Adamawa State University, P.M.B. 25 Mubi. Adamawa State, Nigeria.
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen 40002, Thailand.
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany.
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
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Proskuryakova AA, Kulemzina AI, Perelman PL, Makunin AI, Larkin DM, Farré M, Kukekova AV, Lynn Johnson J, Lemskaya NA, Beklemisheva VR, Roelke-Parker ME, Bellizzi J, Ryder OA, O'Brien SJ, Graphodatsky AS. X Chromosome Evolution in Cetartiodactyla. Genes (Basel) 2017; 8:genes8090216. [PMID: 28858207 PMCID: PMC5615350 DOI: 10.3390/genes8090216] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 08/01/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 02/05/2023] Open
Abstract
The phenomenon of a remarkable conservation of the X chromosome in eutherian mammals has been first described by Susumu Ohno in 1964. A notable exception is the cetartiodactyl X chromosome, which varies widely in morphology and G-banding pattern between species. It is hypothesized that this sex chromosome has undergone multiple rearrangements that changed the centromere position and the order of syntenic segments over the last 80 million years of Cetartiodactyla speciation. To investigate its evolution we have selected 26 evolutionarily conserved bacterial artificial chromosome (BAC) clones from the cattle CHORI-240 library evenly distributed along the cattle X chromosome. High-resolution BAC maps of the X chromosome on a representative range of cetartiodactyl species from different branches: pig (Suidae), alpaca (Camelidae), gray whale (Cetacea), hippopotamus (Hippopotamidae), Java mouse-deer (Tragulidae), pronghorn (Antilocapridae), Siberian musk deer (Moschidae), and giraffe (Giraffidae) were obtained by fluorescent in situ hybridization. To trace the X chromosome evolution during fast radiation in specious families, we performed mapping in several cervids (moose, Siberian roe deer, fallow deer, and Pere David's deer) and bovid (muskox, goat, sheep, sable antelope, and cattle) species. We have identified three major conserved synteny blocks and rearrangements in different cetartiodactyl lineages and found that the recently described phenomenon of the evolutionary new centromere emergence has taken place in the X chromosome evolution of Cetartiodactyla at least five times. We propose the structure of the putative ancestral cetartiodactyl X chromosome by reconstructing the order of syntenic segments and centromere position for key groups.
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Affiliation(s)
- Anastasia A Proskuryakova
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave. 8/2, Novosibirsk 630090, Russia.
- Synthetic Biology Unit, Novosibirsk State University, Pirogova Str. 1, Novosibirsk 630090, Russia.
| | - Anastasia I Kulemzina
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave. 8/2, Novosibirsk 630090, Russia.
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave. 8/2, Novosibirsk 630090, Russia.
- Synthetic Biology Unit, Novosibirsk State University, Pirogova Str. 1, Novosibirsk 630090, Russia.
| | - Alexey I Makunin
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave. 8/2, Novosibirsk 630090, Russia.
| | - Denis M Larkin
- The Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK.
| | - Marta Farré
- The Royal Veterinary College, University of London, Royal College Street, London NW1 0TU, UK.
| | - Anna V Kukekova
- Animal Sciences Department, College of ACES, University of Illinois at Urbana-Champaign, IL 61801, USA.
| | - Jennifer Lynn Johnson
- Animal Sciences Department, College of ACES, University of Illinois at Urbana-Champaign, IL 61801, USA.
| | - Natalya A Lemskaya
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave. 8/2, Novosibirsk 630090, Russia.
| | - Violetta R Beklemisheva
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave. 8/2, Novosibirsk 630090, Russia.
| | - Melody E Roelke-Parker
- Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA.
| | - June Bellizzi
- Catoctin Zoo and Wildlife Preserve, Thurmont, MD 21788, USA.
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA.
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint-Petersburg State University, Sredniy Av. 41A, Saint-Petersburg 199034, Russia.
- Oceanographic Center, Nova Southeastern University, Fort Lauderdale 3301 College Ave, Fort Lauderdale, FL 33314, USA.
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave. 8/2, Novosibirsk 630090, Russia.
- Synthetic Biology Unit, Novosibirsk State University, Pirogova Str. 1, Novosibirsk 630090, Russia.
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Borazanci E, Millis SZ, Kimbrough J, Doll N, Von Hoff D, Ramanathan RK. Potential actionable targets in appendiceal cancer detected by immunohistochemistry, fluorescent in situ hybridization, and mutational analysis. J Gastrointest Oncol 2017; 8:164-172. [PMID: 28280620 DOI: 10.21037/jgo.2017.01.14] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Appendiceal cancers are rare and consist of carcinoid, mucocele, pseudomyxoma peritonei (PMP), goblet cell carcinoma, lymphoma, and adenocarcinoma histologies. Current treatment involves surgical resection or debulking, but no standard exists for adjuvant chemotherapy or treatment for metastatic disease. METHODS Samples were identified from approximately 60,000 global tumors analyzed at a referral molecular profiling CLIA-certified laboratory. A total of 588 samples with appendix primary tumor sites were identified (male/female ratio of 2:3; mean age =55). Sixty-two percent of samples were adenocarcinomas (used for analysis); the rest consisted of 9% goblet cell, 15% mucinous; 6% pseudomyxoma, and less than 5% carcinoids and 2% neuroendocrine. Tests included sequencing [Sanger, next generation sequencing (NGS)], protein expression/immunohistochemistry (IHC), and gene amplification [fluorescent in situ hybridization (FISH) or CISH]. RESULTS Profiling across all appendiceal cancer histological subtypes for IHC revealed: 97% BRCP, 81% MRP1, 81% COX-2, 71% MGMT, 56% TOPO1, 5% PTEN, 52% EGFR, 40% ERCC1, 38% SPARC, 35% PDGFR, 35% TOPO2A, 25% RRM1, 21% TS, 16% cKIT, and 12% for TLE3. NGS revealed mutations in the following genes: 50.4% KRAS, 21.9% P53, 17.6% GNAS, 16.5% SMAD4, 10% APC, 7.5% ATM, 5.5% PIK3CA, 5.0% FBXW7, and 1.8% BRAF. CONCLUSIONS Appendiceal cancers show considerable heterogeneity with high levels of drug resistance proteins (BCRP and MRP1), which highlight the difficulty in treating these tumors and suggest an individualized approach to treatment. The incidence of low TS (79%) could be used as a backbone of therapy (using inhibitors such as 5FU/capecitabine or newer agents). Therapeutic options includeTOPO1 inhibitors (irinotecan/topotecan), EGFR inhibitors (erlotinib, cetuximab), PDGFR antagonists (regorafenib, axitinib), MGMT (temozolomide). Clinical trials targeting pathways involving KRAS, p53, GNAS, SMAD4, APC, ATM, PIK3CA, FBXW7, and BRAF may be also considered. Overall, appendiceal cancers have similar patterns in their molecular profile to pancreatic cancers (can we say this, any statistical analysis done?) and have differential expression from colorectal cancers. These findings indicate the need to evaluate patient samples for patterns in marker expression and alteration, in order to better understand the molecular biology and formulate a personalized therapy approach in these difficult to treat cancers (supported by a grant from Caris Life Sciences).
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Doshi S, Ray D, Stein K, Zhang J, Koduru P, Fogt F, Wellman A, Wat R, Mathews C. Economic Analysis of Alternative Strategies for Detection of ALK Rearrangements in Non Small Cell Lung Cancer. Diagnostics (Basel) 2016; 6:E4. [PMID: 26838801 DOI: 10.3390/diagnostics6010004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 11/24/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 11/17/2022] Open
Abstract
Identification of alterations in ALK gene and development of ALK-directed therapies have increased the need for accurate and efficient detection methodologies. To date, research has focused on the concordance between the two most commonly used technologies, fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC). However, inter-test concordance reflects only one, albeit important, aspect of the diagnostic process; laboratories, hospitals, and payors must understand the cost and workflow of ALK rearrangement detection strategies. Through literature review combined with interviews of pathologists and laboratory directors in the U.S. and Europe, a cost-impact model was developed that compared four alternative testing strategies—IHC only, FISH only, IHC pre-screen followed by FISH confirmation, and parallel testing by both IHC and FISH. Interviews were focused on costs of reagents, consumables, equipment, and personnel. The resulting model showed that testing by IHC alone cost less ($90.07 in the U.S., $68.69 in Europe) than either independent or parallel testing by both FISH and IHC ($441.85 in the U.S. and $279.46 in Europe). The strategies differed in cost of execution, turnaround time, reimbursement, and number of positive results detected, suggesting that laboratories must weigh the costs and the clinical benefit of available ALK testing strategies.
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Murgha Y, Beliveau B, Semrau K, Schwartz D, Wu CT, Gulari E, Rouillard JM. Combined in vitro transcription and reverse transcription to amplify and label complex synthetic oligonucleotide probe libraries. Biotechniques 2015; 58:301-7. [PMID: 26054766 DOI: 10.2144/000114298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/26/2015] [Indexed: 12/29/2022] Open
Abstract
Oligonucleotide microarrays allow the production of complex custom oligonucleotide libraries for nucleic acid detection-based applications such as fluorescence in situ hybridization (FISH). We have developed a PCR-free method to make single-stranded DNA (ssDNA) fluorescent probes through an intermediate RNA library. A double-stranded oligonucleotide library is amplified by transcription to create an RNA library. Next, dye- or hapten-conjugate primers are used to reverse transcribe the RNA to produce a dye-labeled cDNA library. Finally the RNA is hydrolyzed under alkaline conditions to obtain the single-stranded fluorescent probes library. Starting from unique oligonucleotide library constructs, we present two methods to produce single-stranded probe libraries. The two methods differ in the type of reverse transcription (RT) primer, the incorporation of fluorescent dye, and the purification of fluorescent probes. The first method employs dye-labeled reverse transcription primers to produce multiple differentially single-labeled probe subsets from one microarray library. The fluorescent probes are purified from excess primers by oligonucleotide-bead capture. The second method uses an RNA:DNA chimeric primer and amino-modified nucleotides to produce amino-allyl probes. The excess primers and RNA are hydrolyzed under alkaline conditions, followed by probe purification and labeling with amino-reactive dyes. The fluorescent probes created by the combination of transcription and reverse transcription can be used for FISH and to detect any RNA and DNA targets via hybridization.
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Affiliation(s)
| | - Brian Beliveau
- Department of Genetics, Harvard Medical School, Boston, MA
| | | | | | - Chao-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Erdogan Gulari
- MYcroarray, Ann Arbor, MI.,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI
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Kim H, Chung JH. Overview of clinicopathologic features of ALK-rearranged lung adenocarcinoma and current diagnostic testing for ALK rearrangement. Transl Lung Cancer Res 2015; 4:149-55. [PMID: 25870797 DOI: 10.3978/j.issn.2218-6751.2014.12.02] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/05/2014] [Indexed: 01/12/2023]
Abstract
Patients with non-small cell lung cancer (NSCLC) who harbor anaplastic lymphoma kinase (ALK) gene rearrangements can derive significant clinical benefit from ALK tyrosine kinase inhibitor. Accurate patient identification is absolutely crucial for successful using ALK inhibitor treatment. However, lung cancer patients with ALK gene rearrangement after ALK inhibitor therapy eventually develop acquired resistance to treatment. In this review, the authors summarize the clinicopathologic features of ALK-rearranged NSCLC and the pros and cons of current diagnostic testing. In addition, we discuss the current diagnostic flow of ALK testing and consideration of rebiopsy sample during disease progression in patients treated by ALK inhibitors.
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Affiliation(s)
- Hyojin Kim
- 1 Department of Pathology, Seoul National University Hospital, College of Medicine, Seoul, Korea ; 2 Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jin-Haeng Chung
- 1 Department of Pathology, Seoul National University Hospital, College of Medicine, Seoul, Korea ; 2 Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
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Udager AM, Shi Y, Tomlins SA, Alva A, Siddiqui J, Cao X, Pienta KJ, Jiang H, Chinnaiyan AM, Mehra R. Frequent discordance between ERG gene rearrangement and ERG protein expression in a rapid autopsy cohort of patients with lethal, metastatic, castration-resistant prostate cancer. Prostate 2014; 74:1199-208. [PMID: 25043157 PMCID: PMC4156519 DOI: 10.1002/pros.22836] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 05/21/2014] [Indexed: 11/06/2022]
Abstract
BACKGROUND ERG rearrangements in localized prostate cancer can be detected with high sensitivity and specificity by immunohistochemistry (IHC). However, recent data suggest that ERG IHC may be less sensitive for ERG rearrangements in castration-resistant prostate cancer (CRPC). Thus, we sought to examine ERG protein expression in a cohort of rapid autopsy patients with lethal metastatic CRPC (mCRPC). METHODS A tissue microarray (TMA) of tumor sites from these patients was evaluated for ERG, prostate-specific antigen (PSA), and androgen receptor (AR) expression by IHC and correlated with ERG rearrangement status by fluorescent in situ hybridization (FISH). IHC was scored as the product of tumor cell staining intensity (0-3) and percentage of cells positive (0-100) (overall product score range = 0-300). RESULTS All 16 (100%) ERG rearrangement negative (ERG(neg) ) patients were also negative for ERG tumor cell expression (i.e., IHC product score = 0). Of the 10 ERG rearrangement positive (ERG(pos) ) patients, two (20%) were completely negative for ERG tumor cell expression, while eight (80%) had weak ERG expression (median IHC product score = 5-110). Of these eight ERG(pos) patients, five (63%) had at least one tumor site without any detectable ERG expression. For a given ERG(pos) patient, ERG expression varied both between and within tumor sites; AR and PSA expression also varied between tumor sites, and there was no significant correlation between ERG and AR or PSA expression. CONCLUSIONS These data reveal frequent discordance between ERG IHC and ERG FISH in ERG(pos) patients from this unique cohort of heavily treated lethal mCRPC.
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Affiliation(s)
- Aaron M. Udager
- Department of Pathology, University of Michigan Health System, Ann Arbor, MI 48109
| | - Yang Shi
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109
| | - Scott A. Tomlins
- Department of Pathology, University of Michigan Health System, Ann Arbor, MI 48109
- Department of Urology, University of Michigan Health System, Ann Arbor, MI 48109
- Comprehensive Cancer Center, University of Michigan Health System, Ann Arbor, MI 48109
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109
| | - Ajjai Alva
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Health System, Ann Arbor, MI 48109
- Comprehensive Cancer Center, University of Michigan Health System, Ann Arbor, MI 48109
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109
| | - Xuhong Cao
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109
| | - Kenneth J. Pienta
- The James Buchanan Brady Urological Institute, The Johns Hopkins Hospital, Baltimore, MD 21287
| | - Hui Jiang
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109
| | - Arul M. Chinnaiyan
- Department of Pathology, University of Michigan Health System, Ann Arbor, MI 48109
- Department of Urology, University of Michigan Health System, Ann Arbor, MI 48109
- Comprehensive Cancer Center, University of Michigan Health System, Ann Arbor, MI 48109
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109
- Howard Hughes Medical Institute, Ann Arbor, MI 48109
| | - Rohit Mehra
- Department of Pathology, University of Michigan Health System, Ann Arbor, MI 48109
- Comprehensive Cancer Center, University of Michigan Health System, Ann Arbor, MI 48109
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109
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Ji Y, Sheng L, Du X, Qiu G, Chen B, Wang X. Clinicopathological variables predicting HER-2 gene status in immunohistochemistry-equivocal (2+) invasive breast cancer. J Thorac Dis 2014; 6:896-904. [PMID: 25093085 DOI: 10.3978/j.issn.2072-1439.2014.07.27] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 07/03/2014] [Indexed: 01/21/2023]
Abstract
BACKGROUND AND OBJECTIVE Human epidermal growth factor receptor-2 (HER-2) gene status is crucial to guide treatment decisions regarding the use of HER-2-targeted therapies in breast cancer. An invasive breast cancer with HER-2 2+ score is regarded as HER-2 status equivocal and should further determine by fluorescent in situ hybridization (FISH), which is considered the standard test for HER-2 status. Here, we aimed to establish a risk score to allow for prediction of the presence of HER-2 gene status. METHODS A total of 182 HER-2 2+ by immunohistochemistry (IHC) invasive breast cancer cases were enrolled in this study. The association between clinicopathological variables like age, sex, tumor grade, hormone receptor (HR) status, P53 and proliferation index (Ki67), and FISH result using US Food and Drug Administration (FDA) criteria was evaluated. Also, we compared the HER-2 FISH results using FDA criteria and 2013 American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) guideline. RESULTS The study population had a median age of 48 years (range, 29-78 years). Estrogen receptor (ER) was expressed in 131 (72.0%) patients. 73.1% of patients (133/182) were progesterone receptor (PR) positive. The median Ki67 value was 20% (range, 3-90%). There was good agreement between the FDA and 2013 ASCO/CAP guideline. Sixty-three of all patients were HER-2 FISH amplified (positive) based on FDA criteria. Tumors with HER-2 amplified were more likely to harbor ER negative (58.8% vs. 25.2%, P<0.001) or PR negative (57.1% vs. 26.3%, P<0.001) or P53 negative (44.8% vs. 29.8%, P=0.048). A significant high level of Ki67 was detected in HER-2 amplified groups (P=0.006). We created a risk score that comprised HR, P53 and Ki67. A significant association between risk score and HER-2 FISH amplification was observed (χ(2)=30.41, P<0.001). CONCLUSIONS This novel immunohistochemical risk score could be highly useful to predict the presence of HER-2 gene status in invasive breast cancer.
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Affiliation(s)
- Yongling Ji
- 1 Department of Radiation Therapy, 2 Department of Pathology, 3 Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Liming Sheng
- 1 Department of Radiation Therapy, 2 Department of Pathology, 3 Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Xianghui Du
- 1 Department of Radiation Therapy, 2 Department of Pathology, 3 Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Guoqin Qiu
- 1 Department of Radiation Therapy, 2 Department of Pathology, 3 Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Bo Chen
- 1 Department of Radiation Therapy, 2 Department of Pathology, 3 Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Xiaojia Wang
- 1 Department of Radiation Therapy, 2 Department of Pathology, 3 Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
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Ismail MF, Aly MS, Khaled HM, Mohamed HM. Detection of HER-2/neu, c-myc amplification and p53 inactivation by FISH in Egyptian patients with breast cancer. Ger Med Sci 2009; 7:Doc03. [PMID: 19675743 PMCID: PMC2716551 DOI: 10.3205/000062] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 04/27/2009] [Indexed: 01/22/2023]
Abstract
Breast cancer is a leading cause of cancer-related deaths in women worldwide. The clinical course of this disease is highly variable and clinicians continuously search for prognostic parameters that can accurately predict prognosis, and indicate a suitable adjuvant therapy for each patient. Amplification of the two oncogenes HER-2/neu and c-myc and inactivation of the tumor suppressor gene p53 are frequently encountered in breast carcinomas. The purpose of this study was to use the fluorescence in situ hybridization (FISH) for the assessment of HER-2/neu and c-myc amplification and p53 inactivation and to relate these molecular markers with the commonly used clinical and pathological factors. The study was conducted on 34 tissue samples obtained from 33 females and 1 male with breast carcinomas and 17 samples obtained from 16 females and 1 male with benign breast lesions. Results revealed that the level of HER-2/neu, c-myc and p53 in the malignant group was significantly increased as compared to the benign group. On relating the level of the molecular markers to clinicopathological factors, p53 was significantly associated with increased patient’s age. The sensitivity of the investigated markers significantly increased with larger tumor size. Concerning tumor grade, HER-2/neu and p53 showed a significant increase in low-grade tumors whereas c-myc showed a highly significant increase in high-grade tumors. With regard to disease staging, HER-2/neu and c-myc were the only markers that showed significant increase at late stages of disease. p53 and HER-2/neu were significantly associated with positive lymph nodal status. A significant correlation was obtained between the levels of the three biomarkers to each other. Conclusively, the combination of HER-2/neu, c-myc and p53 can stratify patients into different risk groups.
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Affiliation(s)
- Manal F Ismail
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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