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Supremacy of modern morphometry in typing renal oncocytoma and malignant look-alikes. Histochem Cell Biol 2015; 144:147-56. [PMID: 25929744 DOI: 10.1007/s00418-015-1324-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2015] [Indexed: 12/31/2022]
Abstract
In the era of tumour type-specific therapies, the correct typing of renal tumours is of prime importance. As immunotyping and genotyping approaches are laborious and fall short of standardization, we used whole-scale computer-assisted morphometry instead. Three different types of renal tumours with different prognoses and therapies, notoriously prone to mistyping, were analysed . The sample of 335 tumours included clear cell renal cell carcinoma, chromophobe renal cell carcinoma and renal oncocytoma. The sample was analysed using H&E stains of tissue microarrrays in combination with an image-scanning software. Nuclear and cytoplasmic features were registered with the aid of computer-assisted morphometry. Features included shape, texture, colour and colour intensity for different cell compartments, e.g. nuclei and cytoplasm. The software passed several training steps for final validation. Using morphometry, we were able to classify the three renal tumour types correctly, with a 100 % specificity compared to the WHO typing. Nuclear features dominated the typing of chromophobe renal cell carcinoma, whereas cytoplasmic features were the leading classificators for renal oncocytoma. The grading of clear cell renal cell carcinoma attained a specificity of 80 %. In conclusion, modern morphometry may serve as a tool for typing renal epithelial tumours and additionally draws the attention to future nuclear research in chromophobe renal cell carcinoma.
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Zeng H, Weier JF, Wang M, Kassabian HJ, Polyzos AA, Baumgartner A, O'Brien B, Weier HUG. Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues. Curr Genomics 2013; 13:438-45. [PMID: 23450259 PMCID: PMC3426778 DOI: 10.2174/138920212802510510] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 02/03/2023] Open
Abstract
Despite their non-diseased nature, healthy human tissues may show a surprisingly large fraction of aneusomic or aneuploid cells. We have shown previously that hybridization of three to six non-isotopically labeled, chromosome-specific DNA probes reveals different proportions of aneuploid cells in individual compartments of the human placenta and the uterine wall. Using fluorescence in situ hybridization, we found that human invasive cytotrophoblasts isolated from anchoring villi or the uterine wall had gained individual chromosomes. Chromosome losses in placental or uterine tissues, on the other hand, were detected infrequently. A more thorough numerical analysis of all possible aneusomies occurring in these tissues and the investigation of their spatial as well as temporal distribution would further our understanding of the underlying biology, but it is hampered by the high cost of and limited access to DNA probes. Furthermore, multiplexing assays are difficult to set up with commercially available probes due to limited choices of probe labels. Many laboratories therefore attempt to develop their own DNA probe sets, often duplicating cloning and screening efforts underway elsewhere. In this review, we discuss the conventional approaches to the preparation of chromosome-specific DNA probes followed by a description of our approach using state-of-the-art bioinformatics and molecular biology tools for probe identification and manufacture. Novel probes that target gonosomes as well as two autosomes are presented as examples of rapid and inexpensive preparation of highly specific DNA probes for applications in placenta research and perinatal diagnostics.
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Affiliation(s)
- Hui Zeng
- Department of Cancer & DNA Damage Responses, Life Sciences Division, University of California, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Chromosome-specific DNA repeats: rapid identification in silico and validation using fluorescence in situ hybridization. Int J Mol Sci 2012; 14:57-71. [PMID: 23344021 PMCID: PMC3565251 DOI: 10.3390/ijms14010057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 12/09/2012] [Accepted: 12/10/2012] [Indexed: 12/12/2022] Open
Abstract
Chromosome enumeration in interphase and metaphase cells using fluorescence in situ hybridization (FISH) is an established procedure for the rapid and accurate cytogenetic analysis of cell nuclei and polar bodies, the unambiguous gender determination, as well as the definition of tumor-specific signatures. Present bottlenecks in the procedure are a limited number of commercial, non-isotopically labeled probes that can be combined in multiplex FISH assays and the relatively high price and effort to develop additional probes. We describe a streamlined approach for rapid probe definition, synthesis and validation, which is based on the analysis of publicly available DNA sequence information, also known as “database mining”. Examples of probe preparation for the human gonosomes and chromosome 16 as a selected autosome outline the probe selection strategy, define a timeline for expedited probe production and compare this novel selection strategy to more conventional probe cloning protocols.
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O'Brien B, Zeng H, Polyzos AA, Lemke KH, Weier JF, Wang M, Zitzelsberger HF, Weier HUG. Bioinformatics tools allow targeted selection of chromosome enumeration probes and aneuploidy detection. J Histochem Cytochem 2012. [PMID: 23204113 PMCID: PMC3636690 DOI: 10.1369/0022155412470955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Accurate determination of cellular chromosome complements is a highly relevant issue beyond prenatal/pre-implantation genetic analyses or stem cell research, because aneusomy may be an important mechanism by which organisms control the rate of fetal cellular proliferation and the fate of regenerating tissues. Typically, small amounts of individual cells or nuclei are assayed by in situ hybridization using chromosome-specific DNA probes. Careful probe selection is fundamental to successful hybridization experiments. Numerous DNA probes for chromosome enumeration studies are commercially available, but their use in multiplexed hybridization assays is hampered due to differing probe-specific hybridization conditions or a lack of a sufficiently large number of different reporter molecules. Progress in the International Human Genome Project has equipped the scientific community with a wealth of unique resources, among them recombinant DNA libraries, physical maps, and data-mining tools. Here, we demonstrate how bioinformatics tools can become an integral part of simple, yet powerful approaches to devise diagnostic strategies for detection of aneuploidy in interphase cells. Our strategy involving initial in silico optimization steps offers remarkable savings in time and costs during probe generation, while at the same time significantly increasing the assay’s specificity, sensitivity, and reproducibility.
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Affiliation(s)
- Benjamin O'Brien
- William Harvey Research Institute, Queen Mary University London, UK.
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Weier HUG, Ito Y, Kwan J, Smida J, Weier JF, Hieber L, Lu CM, Lehmann L, Wang M, Kassabian HJ, Zeng H, O'Brien B. Delineating chromosomal breakpoints in radiation-induced papillary thyroid cancer. Genes (Basel) 2011; 2:397-419. [PMID: 22096618 PMCID: PMC3216054 DOI: 10.3390/genes2030397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 05/23/2011] [Accepted: 06/16/2011] [Indexed: 12/11/2022] Open
Abstract
Recurrent translocations are well known hallmarks of many human solid tumors and hematological disorders, where patient- and breakpoint-specific information may facilitate prognostication and individualized therapy. In thyroid carcinomas, the proto-oncogenes RET and NTRK1 are often found to be activated through chromosomal rearrangements. However, many sporadic tumors and papillary thyroid carcinomas (PTCs) arising in patients with a history of exposure to elevated levels of ionizing irradiation do not carry these known abnormalities. We developed a rapid scheme to screen tumor cell metaphase spreads and identify candidate genes of tumorigenesis and neoplastic progression for subsequent functional studies. Using a series of overnight fluorescence in situ hybridization (FISH) experiments with pools comprised of bacterial artificial chromosome (BAC) clones, it now becomes possible to rapidly refine breakpoint maps and, within one week, progress from the low resolution Spectral Karyotyping (SKY) maps or Giemsa-banding (G-banding) karyotypes to fully integrated, high resolution physical maps including a list of candiate genes in the critical regions.
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Affiliation(s)
- Heinz-Ulrich G. Weier
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; E-Mails: (H.-U.G.W.); (J.K.); (H.J.K.); (H.Z.)
| | - Yuko Ito
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; E-Mails: (H.-U.G.W.); (J.K.); (H.J.K.); (H.Z.)
- National Institute of Science and Technology Policy (NISTEP), Ministry of Education, Culture, Sports, Science and Technology, Tokyo 100-0005, Japan; E-Mail:
| | - Johnson Kwan
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; E-Mails: (H.-U.G.W.); (J.K.); (H.J.K.); (H.Z.)
| | - Jan Smida
- Clinical Cooperation Group Osteosarcoma, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; E-Mail:
| | - Jingly F. Weier
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; E-Mails: (H.-U.G.W.); (J.K.); (H.J.K.); (H.Z.)
- Clinical Labs–Cytogenetics, University of California, 185 Berry Street Suite 290, San Francisco, CA 94143-0100, USA; E-Mail:
| | - Ludwig Hieber
- Department of Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr.1, Neuherberg 85764, Germany; E-Mail:
| | - Chun-Mei Lu
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; E-Mails: (H.-U.G.W.); (J.K.); (H.J.K.); (H.Z.)
- Department of Chemical and Materials Engineering, National Chin-Yi University of Technology, No.35, Lane 215, Section 1, Chungshan Road, Taiping City, Taichung 411, Taiwan; E-Mail:
| | - Lars Lehmann
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; E-Mails: (H.-U.G.W.); (J.K.); (H.J.K.); (H.Z.)
- Department of Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr.1, Neuherberg 85764, Germany; E-Mail:
- Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany; E-Mail:
| | - Mei Wang
- Department of Diabetes, City of Hope, 1500 Duarte Road, Duarte, CA 91010-3012, USA; E-mail:
| | - Haig J. Kassabian
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; E-Mails: (H.-U.G.W.); (J.K.); (H.J.K.); (H.Z.)
| | - Hui Zeng
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; E-Mails: (H.-U.G.W.); (J.K.); (H.J.K.); (H.Z.)
| | - Benjamin O'Brien
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; E-Mails: (H.-U.G.W.); (J.K.); (H.J.K.); (H.Z.)
- William Harvey Research Institute, Translational Medicine and Therapeutics, Barts and The London School of Medicine, Charterhouse Square, London, EC1M 6BQ, UK
- Department of Anesthesiology, German Heart Institute Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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O'Brien B, Jossart GH, Ito Y, Greulich-Bode KM, Weier JF, Munne S, Clark OH, Weier HUG. 'Chromosomal Rainbows' Detect Oncogenic Rearrangements of Signaling Molecules in Thyroid Tumors. THE OPEN CELL SIGNALING JOURNAL 2010; 2:13-22. [PMID: 22328910 DOI: 10.2172/1011038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Altered signal transduction can be considered a hallmark of many solid tumors. In thyroid cancers the receptor tyrosine kinase (rtk) genes NTRK1 (Online Mendelian Inheritance in Man = OMIM *191315, also known as 'TRKA'), RET ('Rearranged during Transfection protooncogene', OMIM *164761) and MET (OMIM *164860) have been reported as activated, rearranged or overexpressed. In many cases, a combination of cytogenetic and molecular techniques allows elucidation of cellular changes that initiate tumor development and progression. While the mechanisms leading to overexpression of the rtk MET gene remain largely unknown, a variety of chromosomal rearrangements of the RET or NTKR1 gene could be demonstrated in thyroid cancer. Abnormal expressions in these tumors seem to follow a similar pattern: the rearrangement translocates the 3'- end of the rtk gene including the entire catalytic domain to an expressed gene leading to a chimeric RNA and protein with kinase activity. Our research was prompted by an increasing number of reports describing translocations involving ret and previously unknown translocation partners.We developed a high resolution technique based on fluorescence in situ hybridization (FISH) to allow rapid screening for cytogenetic rearrangements which complements conventional chromosome banding analysis. Our technique applies simultaneous hybridization of numerous probes labeled with different reporter molecules which are distributed along the target chromosome allowing the detection of cytogenetic changes at near megabasepair (Mbp) resolution. Here, we report our results using a probe set specific for human chromosome 10, which is altered in a significant portion of human thyroid cancers (TC's). While rendering accurate information about the cytogenetic location of rearranged elements, our multi-locus, multi-color analysis was developed primarily to overcome limitations of whole chromosome painting (WCP) and chromosome banding techniques for fine mapping of breakpoints in papillary thyroid cancer (PTC).
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Affiliation(s)
- Benjamin O'Brien
- Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Weier HUG, Kwan J, Lu CM, Ito Y, Wang M, Baumgartner A, Hayward SW, Weier JF, Zitzelsberger HF. Kinase expression and chromosomal rearrangements in papillary thyroid cancer tissues: investigations at the molecular and microscopic levels. JOURNAL OF PHYSIOLOGY AND PHARMACOLOGY 2010; 60 Suppl 4:47-55. [PMID: 20083851 DOI: 10.2172/983010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 09/10/2009] [Indexed: 11/02/2022]
Abstract
Structural chromosome aberrations are known hallmarks of many solid tumors. In the papillary form of thyroid cancer (PTC), for example, activation of the receptor tyrosine kinase (RTK) genes, ret or the neurotrophic tyrosine kinase receptor type I (NTRK1) by intra- or interchromosomal rearrangements have been suggested as a cause of the disease. The 1986 accident at the nuclear power plant in Chernobyl, Ukraine, led to the uncontrolled release of high levels of radioisotopes. Ten years later, the incidence of childhood papillary thyroid cancer (chPTC) near Chernobyl had risen by two orders of magnitude. Tumors removed from some of these patients showed aberrant expression of the ret RTK gene due to a ret/PTC1 or ret/PTC3 rearrangement involving chromosome 10. However, many cultured chPTC cells show a normal G-banded karyotype and no ret rearrangement. We hypothesize that the "ret-negative" tumors inappropriately express a different oncogene or have lost function of a tumor suppressor as a result of chromosomal rearrangements, and decided to apply molecular and cytogenetic methods to search for potentially oncogenic chromosomal rearrangements in Chernobyl chPTC cases. Knowledge of the kind of genetic alterations may facilitate the early detection and staging of chPTC as well as provide guidance for therapeutic intervention.
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Affiliation(s)
- H-U G Weier
- Life Sciences Division, University of California, E.O. Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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