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Lemke KH, Weier JF, Weier HUG, Lawin-O'Brien AR. High Performance DNA Probes for Perinatal Detection of Numerical Chromosome Aberrations. ACTA ACUST UNITED AC 2015; 3. [PMID: 26855976 PMCID: PMC4739796 DOI: 10.4172/2379-1764.1000155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human reproduction is a tightly controlled process of stepwise evolution with multiple, mostly yet unknown milestones and checkpoints. Healthy halpoid gametes have to be produced by the parents, which will fuse to form the diploid zygote that implants in the female uterus and grows to become first an embryo, then a fetus and finally matures into a newborn. There are several known risk factors that interfere with normal production of gametes, spermatocytes or oocytes, and often cause embryonic mortality and fetal demise at an early stage. Yet some embryos with chomosomal abnormalities can develop beyond the critical first trimester of pregnancy and, while those with supernumary chromosomes in their hyperdiploid cells will be spontaneously aborted, a small fraction of fetuses with an extra chromosome continues to grow to term and will be delivered as a liveborn baby. While minor clinical symptoms displayed by children with trisomies are manageable for many parents, the burden of caring for a child with numerical chromosome abnormalities can be overwhelming to partners or individual families. It also poses a significant financial burden to the society and poses ethical dilemma. In this communication, we will review the progress that has been made in the development of molecular techniques to test individual fetal cells for chromosomal imbalances. We will focus our discussion on the direct visualization of chromosome-specific DNA sequences in live or fixed specimens using fluorescence in situ hybridization (FISH) and, more specifically, talk about the groundbreaking progress that in recent years has been achieved towards an improved diagnosis with novel, chromosome-specific DNA probes.
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Affiliation(s)
- Kalistyn H Lemke
- Life Sciences Division, University of California, E.O. Lawrence Berkeley National Laboratory (LBNL), Berkeley, USA
| | - Jingly F Weier
- Life Sciences Division, University of California, E.O. Lawrence Berkeley National Laboratory (LBNL), Berkeley, USA; Dermatopathology Service, School of Medicine, University of California, San Francisco, USA
| | - Heinz-Ulrich G Weier
- Life Sciences Division, University of California, E.O. Lawrence Berkeley National Laboratory (LBNL), Berkeley, USA
| | - Anna R Lawin-O'Brien
- Centre for Fetal Care, Queen Charlotte's and Chelsea Hospital, Imperial College Healthcare, London, UK
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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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Multi-Color Spectral Transcript Analysis (SPECTRA) for Phenotypic Characterization of Tumor Cells. Biomolecules 2013; 3:180-97. [PMID: 24970164 PMCID: PMC4030878 DOI: 10.3390/biom3010180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 01/31/2013] [Accepted: 02/04/2013] [Indexed: 11/16/2022] Open
Abstract
Many human tumors show significant changes in their signal transduction pathways and, thus, the way the cells interact with their environment. Often caused by chromosomal rearrangements, including gene amplifications, translocations or deletions, the altered levels of gene expression may provide a tumor-specific signature that can be exploited for diagnostic or therapeutic purposes. We investigated the utility of multiplexed fluorescence in situ hybridization (FISH) using non-isotopically labeled cDNA probes detected by Spectral Imaging as a sensitive and rapid procedure to measure tumor-specific gene expression signatures. We used a commercially available system to acquire and analyze multicolor FISH images. Initial investigations used panels of fluorescent calibration standards to evaluate the system. These experiments were followed by hybridization of five-to-six differently labeled cDNA probes, which target the transcripts of tyrosine kinase genes known to be differently expressed in normal cells and tumors of the breast or thyroid gland. The relatively simple, yet efficient, molecular cytogenetic method presented here may find many applications in characterization of solid tumors or disseminated tumor cells. Addressing tumor heterogeneity by means of multi-parameter single cell analyses is expected to enable a wide range of investigations in the areas of tumor stem cells, tumor clonality and disease progression.
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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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