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Musatova EV, Tveleneva AA, Martynov AV, Markova ZG, Shilova NV. Comparison of Amplification Methods of Single Trophoblast Cells for Their Subsequent Analysis Using Metaphase Comparative Genomic Hybridization. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418090107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Whole genome amplification (WGA) is a widely used molecular technique that is becoming increasingly necessary in genetic research on a range of sample types including individual cells, fossilized remains and entire ecosystems. Multiple methods of WGA have been developed, each with specific strengths and weaknesses, but with a common defect in that each method distorts the initial template DNA during the course of amplification. The type, extent, and circumstance of the bias vary with the WGA method and particulars of the template DNA. In this review, we endeavor to discuss the types of bias introduced, the susceptibility of common WGA techniques to these bias types, and the interdependence between bias and characteristics of the template DNA. Finally, we attempt to illustrate some of the criteria specific to the analytical platform and research application that should be considered to enable combination of the appropriate WGA method, template DNA, sequencing platform, and intended use for optimal results.
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Affiliation(s)
| | - John H Leamon
- CyVek Inc., 2 Barnes Industrial Road South, Wallingford, CT, 06492, USA.
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A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH. PLoS One 2013; 8:e67031. [PMID: 23825608 PMCID: PMC3692546 DOI: 10.1371/journal.pone.0067031] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/14/2013] [Indexed: 12/31/2022] Open
Abstract
Comprehensive genome wide analyses of single cells became increasingly important in cancer research, but remain to be a technically challenging task. Here, we provide a protocol for array comparative genomic hybridization (aCGH) of single cells. The protocol is based on an established adapter-linker PCR (WGAM) and allowed us to detect copy number alterations as small as 56 kb in single cells. In addition we report on factors influencing the success of single cell aCGH downstream of the amplification method, including the characteristics of the reference DNA, the labeling technique, the amount of input DNA, reamplification, the aCGH resolution, and data analysis. In comparison with two other commercially available non-linear single cell amplification methods, WGAM showed a very good performance in aCGH experiments. Finally, we demonstrate that cancer cells that were processed and identified by the CellSearch® System and that were subsequently isolated from the CellSearch® cartridge as single cells by fluorescence activated cell sorting (FACS) could be successfully analyzed using our WGAM-aCGH protocol. We believe that even in the era of next-generation sequencing, our single cell aCGH protocol will be a useful and (cost-) effective approach to study copy number alterations in single cells at resolution comparable to those reported currently for single cell digital karyotyping based on next generation sequencing data.
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Heffeter P, Pirker C, Kowol CR, Herrman G, Dornetshuber R, Miklos W, Jungwirth U, Koellensperger G, Keppler BK, Berger W. Impact of terminal dimethylation on the resistance profile of α-N-heterocyclic thiosemicarbazones. Biochem Pharmacol 2012; 83:1623-33. [PMID: 22426010 PMCID: PMC3342514 DOI: 10.1016/j.bcp.2012.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/05/2012] [Accepted: 03/06/2012] [Indexed: 12/24/2022]
Abstract
Triapine is an α-N-heterocyclic thiosemicarbazone with promising anticancer activity against hematologic malignancies but widely ineffective against solid tumor types in clinical trials. The anticancer activity of thiosemicarbazones can be dramatically increased by terminal dimethylation. KP1089 is a gallium compound containing two terminal dimethylated thiosemicarbazone ligands. To gain insights on the vulnerability of this highly active terminal dimethylated thiosemicarbazone to drug resistance mechanisms, a new cell model with acquired resistance against the lead compound KP1089 was established. Subsequent genomic analyses (arrayCGH and FISH) revealed amplification of the ABCC1 gene on double minute chromosomal DNA in KP1089-resistant cells as well as overexpression of ABCC1 and ABCG2 on the protein level. KP1089 was further confirmed as a substrate of ABCC1 and ABCG2 but not of ABCB1 using a panel of ABC transporter-overexpressing cell models as well as ABC transporter inhibitors. Moreover, glutathione depletion strongly enhanced KP1089 activity, although no glutathione conjugate formation by glutathione-S-transferase was observed. Thus, a co-transport of KP1089 together with glutathione is suggested. Finally, a panel of thiosemicarbazone derivatives was tested on the new KP1089-resistant cell line. Notably, KP1089-resistant cells were not cross-resistant against thiosemicarbazones lacking terminal dimethylation (e.g. Triapine) which are less active than KP1089. This suggests that terminal dimethylation of thiosemicarbazones – linked with distinctly enhanced anticancer activity – leads to altered resistance profiles compared to classical thiosemicarbazones making this compound class of interest for further (pre)clinical evaluation.
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Affiliation(s)
- Petra Heffeter
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
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Luebke AM, Baudis M, Matthaei H, Vashist YK, Verde PE, Hosch SB, Erbersdobler A, Klein CA, Izbicki JR, Knoefel WT, Stoecklein NH. Losses at chromosome 4q are associated with poor survival in operable ductal pancreatic adenocarcinoma. Pancreatology 2011; 12:16-22. [PMID: 22487468 DOI: 10.1016/j.pan.2011.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Here we tested the prognostic impact of genomic alterations in operable localized pancreatic ductal adenocarcinoma (PDAC). Fifty-two formalin-fixed and paraffin-embedded primary PDAC were laser micro-dissected and were investigated by comparative genomic hybridization after whole genome amplification using an adapter-linker PCR. Chromosomal gains and losses were correlated to clinico-pathological parameters and clinical follow-up data. The most frequent aberration was loss on chromosome 17p (65%) while the most frequent gains were detected at 2q (41%) and 8q (41%), respectively. The concomitant occurrence of losses at 9p and 17p was found to be statistically significant. Higher rates of chromosomal losses were associated with a more advanced primary tumor stage and losses at 9p and 18q were significantly associated with presence of lymphatic metastasis (chi-square: p = 0.03, p = 0.05, respectively). Deletions on chromosome 4 were of prognostic significance for overall survival and tumor recurrence (Cox-multivariate analysis: p = 0.026 and p = 0.021, respectively). In conclusion our data suggest the common alterations at chromosome 8q, 9p, 17p and 18q as well as the prognostic relevant deletions on chromosome 4q as relevant for PDAC progression. Our comprehensive data from 52 PDAC should provide a basis for future studies with a higher resolution to discover the relevant genes located within the chromosomal aberrations identified.
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MESH Headings
- Adenocarcinoma/genetics
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/pathology
- Chromosome Aberrations
- Chromosome Deletion
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 18
- Chromosomes, Human, Pair 4
- Chromosomes, Human, Pair 8
- Chromosomes, Human, Pair 9
- Comparative Genomic Hybridization
- Female
- Humans
- Male
- Middle Aged
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/pathology
- Prognosis
- Survival Analysis
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Affiliation(s)
- A M Luebke
- Klinik und Poliklinik für Allgemein-, Visceral- und Thoraxchirurgie, Universitätsklinikum Hamburg-Eppendorf, Germany
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6
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Schmid K, Oehl N, Wrba F, Pirker R, Pirker C, Filipits M. EGFR/KRAS/BRAF mutations in primary lung adenocarcinomas and corresponding locoregional lymph node metastases. Clin Cancer Res 2009; 15:4554-60. [PMID: 19584155 DOI: 10.1158/1078-0432.ccr-09-0089] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The epidermal growth factor receptor (EGFR) and its downstream factors KRAS and BRAF are mutated with different frequencies in non-small cell lung cancer and mutations predict clinical response to EGFR inhibitors. The present study compared the mutational status of EGFR, KRAS, and BRAF in primary tumors with the one in corresponding lymph node metastases. EXPERIMENTAL DESIGN Direct bidirectional sequencing of EGFR gene exons 18 to 21, KRAS gene codons 12/13 and 61 to 68, and BRAF exon 15 was done on 96 paired samples of primary lung adenocarcinomas and corresponding locoregional lymph node metastases. In addition, comparative genomic hybridization analyses in two pairs of corresponding primary and metastatic tumor samples with discordant EGFR mutation status were done. RESULTS Mutations in EGFR, KRAS, and BRAF were observed in 7 (7%), 36 (38%), and 2 (2%) patients, respectively. Interestingly, KRAS mutations were observed in two patients with an EGFR mutation. Mutations in primary tumors and lymph node metastases were identical in 1 of 7 (14%) patients in case of EGFR and 11 of 36 (31%) patients in case of KRAS. One patient harbored different KRAS mutations in primary and corresponding metastatic tumors. Comparative genomic hybridization analysis revealed similar patterns of chromosomal changes, strongly supporting a common clonal origin of primary tumors and metastases. CONCLUSIONS The possibility of differences in the mutational status of EGFR, KRAS, BRAF between primary tumors and corresponding lymph node metastases should be considered whenever these mutations are used for the selection of patients for EGFR-directed tyrosine kinase inhibitor therapy.
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Affiliation(s)
- Katharina Schmid
- Clinical Institute of Pathology and Department of Medicine I, Medical University of Vienna, Waehringer Guertel 18-20, Vienna A-1090, Austria.
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Simultaneous blockade of the epidermal growth factor receptor/mammalian target of rapamycin pathway by epidermal growth factor receptor inhibitors and rapamycin results in reduced cell growth and survival in biliary tract cancer cells. Mol Cancer Ther 2009; 8:1547-56. [DOI: 10.1158/1535-7163.mct-09-0003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Preimplantation genetic diagnosis (PGD) for monogenic diseases has known a considerable evolution since its first application in the early 1990s. Especially the technical aspects of the genetic diagnosis itself, the single-cell genetic analysis, has constantly evolved to reach levels of accuracy and efficiency nearing those of genetic diagnosis on regular DNA samples. In this review, we will focus on the molecular biological techniques that are currently in use in the most advanced centers for PGD for monogenic disorders, including multiplex polymerase chain reaction (PCR) and post-PCR diagnostic methods, whole genome amplification (WGA) and multiple displacement amplification (MDA). As it becomes more and more clear that when it comes to ethically difficult indications, PGD goes further than prenatal diagnosis (PND), we will also briefly discuss ethical issues.
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Affiliation(s)
- Claudia Spits
- Department of Embryology and Genetics of the Vrije Universiteit Brussel and the Centre for Medical Genetics of the UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium.
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Paris PL. A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue. Methods Mol Biol 2009; 556:89-98. [PMID: 19488873 DOI: 10.1007/978-1-60327-192-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
High-resolution genomic arrays and next-generation sequencers are some of the genome-based technologies poised to make significant contributions in the near future to basic and clinical science. The success of these technologies, and most certainly their translation into the clinic, will require that they produce high quality, reproducible data from small archived tumor specimens, including biopsies. DNA from patient samples, especially archival tissue, can be a limiting factor and lead to the need for amplification of the starting material. A variety of whole-genome amplification techniques are available, but choosing the most reliable, reproducible amplification technology that will be suitable for use across a wide spectrum of clinical specimens is essential. Sigma's whole-genome amplification kit provides a robust, highly reliable, and versatile amplification system across a variety of DNA sources. This chapter will detail Sigma's amplification protocol along with an optimized DNA extraction protocol for formalin-fixed and paraffin-embedded tissue.
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Affiliation(s)
- Pamela L Paris
- Department of Urology, University of California at San Francisco, San Francisco, CA, USA
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Berthet N, Reinhardt AK, Leclercq I, van Ooyen S, Batéjat C, Dickinson P, Stamboliyska R, Old IG, Kong KA, Dacheux L, Bourhy H, Kennedy GC, Korfhage C, Cole ST, Manuguerra JC. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Mol Biol 2008; 9:77. [PMID: 18771595 PMCID: PMC2535778 DOI: 10.1186/1471-2199-9-77] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Accepted: 09/04/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phi29 polymerase based amplification methods provides amplified DNA with minimal changes in sequence and relative abundance for many biomedical applications. RNA virus detection using microarrays, however, can present a challenge because phi29 DNA polymerase cannot amplify RNA nor small cDNA fragments (<2000 bases) obtained by reverse transcription of certain viral RNA genomes. Therefore, ligation of cDNA fragments is necessary prior phi29 polymerase based amplification. We adapted the QuantiTect Whole Transcriptome Kit (Qiagen) to our purposes and designated the method as Whole Transcriptome Amplification (WTA). RESULTS WTA successfully amplified cDNA from a panel of RNA viruses representing the diversity of ribovirus genome sizes. We amplified a range of genome copy numbers from 15 to 4 x 10(7) using WTA, which yielded quantities of amplified DNA as high as 1.2 microg/microl or 10(10) target copies. The amplification factor varied between 10(9) and 10(6). We also demonstrated that co-amplification occurred when viral RNA was mixed with bacterial DNA. CONCLUSION This is the first report in the scientific literature showing that a modified WGA (WTA) approach can be successfully applied to viral genomic RNA of all sizes. Amplifying viral RNA by WTA provides considerably better sensitivity and accuracy of detection compared to random RT-PCR.
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Affiliation(s)
- Nicolas Berthet
- Genotyping of Pathogens and Public Health Technological Platform, Institut Pasteur, Paris, France
- Oncogenic Virus Epidemiology and Pathophysiology Unit, Institut Pasteur, Paris, France
| | - Anita K Reinhardt
- Genotyping of Pathogens and Public Health Technological Platform, Institut Pasteur, Paris, France
| | - India Leclercq
- Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur, Paris, France
- Université Paris 7 Denis Diderot, Paris, France
| | | | - Christophe Batéjat
- Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur, Paris, France
| | | | - Rayna Stamboliyska
- Genotyping of Pathogens and Public Health Technological Platform, Institut Pasteur, Paris, France
| | - Iain G Old
- European Office, Institut Pasteur, Paris, France
| | | | - Laurent Dacheux
- Lyssavirus dynamics and host adaptation Unit, Institut Pasteur, Paris, France
| | - Hervé Bourhy
- Lyssavirus dynamics and host adaptation Unit, Institut Pasteur, Paris, France
| | | | | | - Stewart T Cole
- Bacterial Molecular Genetics Unit, Institut Pasteur, Paris, France
| | - Jean-Claude Manuguerra
- Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur, Paris, France
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Evaluation of whole genome amplification protocols for array and oligonucleotide CGH. ACTA ACUST UNITED AC 2008; 16:198-206. [PMID: 18043282 DOI: 10.1097/pdm.0b013e3180f62ad5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Genome-based technologies such as genomic arrays and next generation sequencing are poised to make significant contributions to clinical oncology. However, translation of these technologies to the clinic will require that they produce high-quality reproducible data from small archived tumor specimens and biopsies. Herein, we report on a systematic and comprehensive microarray analysis comparing multiple whole genome amplification methods using a variety of difficult clinical specimens, including formalin-fixed and paraffin-embedded tissues. Quantitative analysis and clustering suggest that Sigma's whole genome amplification protocol performed best on all specimens and, moreover, worked well with a formalin-fixed, paraffin-embedded biopsy.
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12
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Tan DSP, Lambros MBK, Natrajan R, Reis-Filho JS. Getting it right: designing microarray (and not 'microawry') comparative genomic hybridization studies for cancer research. J Transl Med 2007; 87:737-54. [PMID: 17558419 DOI: 10.1038/labinvest.3700593] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The development of high-resolution microarray-based comparative genomic hybridization (aCGH), using cDNA, bacterial artificial chromosome (BAC) and oligonucleotide probes, is providing tremendous opportunities for translational research by facilitating detailed analysis of entire cancer genomes in a single experiment. However, this technology will only fulfil its promise if studies incorporating aCGH are designed with a full understanding of its current limitations and the strategies available to circumvent them. While there have been several excellent reviews on the current status of this technology, there is currently very little guidance available regarding the appropriate design of experiments incorporating aCGH (including the strengths and weaknesses of each platform), and how best to combine the results obtained from aCGH with other 'omic' technologies, including gene expression. In this review, we present the key design issues that need to be considered in order to optimize aCGH studies, including sample selection, the definition of appropriate experimental objectives, arguments for and against the various microarray platforms that are currently available, and methods for data validation and integration. It is envisaged that future well-designed aCGH studies will enhance our understanding of the genetic basis of cancer, and lead to the identification of novel predictive and prognostic cancer biomarkers, as well as molecular therapeutic targets in cancer.
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Affiliation(s)
- David S P Tan
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
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Haberler C, Slavc I, Czech T, Prayer D, Pirker C, Budka H, Hainfellner JA. Malignant predominantly minigemistocytic glioma in two infants: a distinctive glioma variant? Neuropathol Appl Neurobiol 2007; 33:169-78. [PMID: 17359358 DOI: 10.1111/j.1365-2990.2006.00823.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report unusual distinctive histopathological features in malignant supratentorial tumours of two infants (patient 1: congenital, patient 2: 30 months). Both patients had paraventricularly located well-delineated tumours. Gross total resection could be performed and postoperative chemotherapy was administered. At the last follow-up, 18 (patient 1) and 10 months (patient 2) postoperatively, both patients were in continuous complete remission. Histologically, both tumours were characterized by high cellular density and monomorphic appearance. Tumour cells were small to medium-sized and the majority of cells showed a distinctive minigemistocytic shape. A small fraction of cells lacked a distinct cytoplasm. Mitotic figures were abundant, tumour necrosis and hypertrophic vascular proliferations were absent. Immunohistochemically, the tumour cells expressed glial (GFAP, S100) and focally neuronal (NFP) proteins. Comparative genomic hybridization showed few, dissimilar chromosomal aberrations in the two tumours. Although sharp demarcation and monomorphic architecture of both tumours are reminiscent of a primitive neuroectodermal tumour, cytological and immunohistochemical glial differentiation refer to a glial tumour origin. To our knowledge the histopathological features of the described tumours do not correspond unequivocally to any established glioma variant and could represent a distinctive new glioma subtype.
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Affiliation(s)
- C Haberler
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
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Spiegl-Kreinecker S, Pirker C, Marosi C, Buchroithner J, Pichler J, Silye R, Fischer J, Micksche M, Berger W. Dynamics of chemosensitivity and chromosomal instability in recurrent glioblastoma. Br J Cancer 2007; 96:960-9. [PMID: 17342095 PMCID: PMC2360110 DOI: 10.1038/sj.bjc.6603652] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Glioblastoma multiforme is characterised by invasive growth and frequent recurrence. Here, we have analysed chromosomal changes in comparison to tumour cell aggressiveness and chemosensitivity of three cell lines established from a primary tumour and consecutive recurrences (BTL1 to BTL3) of a long-term surviving glioblastoma patient together with paraffin-embedded materials of five further cases with recurrent disease. Following surgery, the BTL patient progressed under irradiation/ lomustine but responded to temozolomide after re-operation to temozolomide. The primary tumour -derived BTL1 cells showed chromosomal imbalances typical of highly aggressive glioblastomas. Interestingly, BTL2 cells established from the first recurrence developed under therapy showed signs of enhanced chromosomal instability. In contrast, BTL3 cells from the second recurrence resembled a less aggressive subclone of the primary tumour. Although BTL2 cells exhibited a highly aggressive phenotype, BTL3 cells were characterised by reduced proliferative and migratory potential. Despite persistent methylation of the O6-methylguanine-DNA methyltransferase promoter, BTL3 cells exhibited the highest temozolomide sensitivity. A comparable situation was found in two out of five glioblastoma patients, both characterised by enhanced survival time, who also relapsed after surgery/chemotherapy with less aggressive recurrences. Taken together, our data suggest that pretreated glioblastoma patients may relapse with highly chemosensitive tumours confirming the feasibility of temozolomide treatment even in case of repeated recurrence.
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Affiliation(s)
| | - C Pirker
- Departments of Neurosurgery, Wagner Jauregg Hospital, Linz, Austria
| | - C Marosi
- Clinical Division of Oncology, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - J Buchroithner
- Departments of Neurosurgery, Wagner Jauregg Hospital, Linz, Austria
| | - J Pichler
- Department of Internal Medicine, Wagner Jauregg Hospital, Linz, Austria
| | - R Silye
- Institute of Pathology, Wagner Jauregg Hospital, Linz, Austria
| | - J Fischer
- Departments of Neurosurgery, Wagner Jauregg Hospital, Linz, Austria
| | - M Micksche
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - W Berger
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
- E-mail:
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Abstract
A recent progress in plant molecular biology has led to enormous available data of DNA sequences, including complete nuclear genomes of Arabidopsis, rice, and poplar. On the other hand, in plant species with more complex genomes, containing widespread repetitive sequences, it is important to establish genomic resources that help us to focus on particular part of genomes. Laser technology enables to handle with specific subcellular structures or even individual chromosomes. Here we present a comprehensive protocol to isolate and characterize DNA sequences derived from the sex chromosomes of white campion (Silene latifolia). This dioecious plant has become the most favorite model to study the structure, function, and evolution of plant sex chromosomes due to a large and distinguishable size of both the X and Y chromosomes. The protocol includes a versatile technique to prepare metaphase chromosomes from either germinating seeds or in vitro cultured hairy roots. Such slides can be used for laser chromosome microdissection, fluorescence in situ-hybridization mapping, and immunostaining. Here we also demonstrate some applications of the laser-dissected chromosome template, especially a modified FAST-FISH technique to paint individual chromosomes, and construction and screening of chromosome-specific DNA libraries.
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Affiliation(s)
- Roman Hobza
- Laboratory of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-612 65 Brno, Czech Republic
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Knijnenburg J, van der Burg M, Tanke HJ, Szuhai K. Optimized amplification and fluorescent labeling of small cell samples for genomic array-CGH. Cytometry A 2007; 71:585-91. [PMID: 17458882 DOI: 10.1002/cyto.a.20412] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Whole genome amplification (WGA) is usually needed in the genetic analysis of samples containing a low number of cells. In genome-wide analysis of DNA copy numbers by array comparative genomic hybridization (array-CGH) it is very important that the genome is evenly represented throughout the amplified product. All currently available WGA techniques are generating some degree of bias. METHODS A way to compensate for this is using a reference sample which is similarly amplified, as the introduced amplification bias will be leveled out. Additionally, direct labeling of the amplified DNA is performed to bypass the currently widely applied random primed labeling, which involves an additional amplification of the product and is introducing extra bias. RESULTS In this article it is shown that equal processing of the test and reference sample is indeed crucial to generate an optimal array-CGH profile of amplified DNA samples. Also presented here is that the labeling method may significantly effect the array-CGH result, it is shown that with direct chemical labeling using platinum derivates (ULS labeling) optimal array-CGH results are obtained. CONCLUSIONS We show that an optimized WGA strategy for both test and reference sample in combination with direct chemical labeling results in a reliable array-CGH profile of samples as low as a 30 cell equivalent.
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Affiliation(s)
- Jeroen Knijnenburg
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
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