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Wu Y, Gu Q, Wang Z, Tian Z, Liu H, Liu S. Ultrasensitive Electrochemiluminescence Imaging Detection of Multiple miRNAs in Single Cells with a Closed Bipolar Electrode Array Chip. Anal Chem 2024; 96:12112-12119. [PMID: 38989957 DOI: 10.1021/acs.analchem.4c02186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
In situ sensitive detection of multiple biomarkers in a single cell was highly necessary for understanding the pathogenesis mechanism and facilitating disease diagnosis. Herein, a bipolar electrode (BPE)-electrochemiluminescence (ECL) imaging chip was designed for ultrasensitive in situ detection of multiple miRNAs in single cells based on a dual-signal amplification strategy. A single cell was trapped and lysed within the microtrap of the cathode chamber and an HCR amplification process and nanoprobes (Fc/DNA/Fe3O4) were introduced, leading to a large number of electroactive molecules (Fc) being modified on the surface. Under a suitable potential, Fc+ in the cathodic chamber was reduced to Fc and L-012 was oxidized in the anodic chamber according to the electric neutrality principle of the bipolar electrode system, resulting in the ECL signal recorded by EMCCD. Ascribed to the dual-signal amplification, sensitive visual detection of miRNA-21 and miRNA-155 in single cells was achieved. For MCF-7 cells, miRNA-21 and miRNA-155 were calculated to be 4385 and 1932 copies/cell (median), respectively. For HeLa cells, miRNA-21 and miRNA-155 were calculated to be 1843 and 1012 copies/cell (median), respectively. The comprehensive evaluation of two kinds of miRNA could effectively eliminate error signals, and the detection precision was improved by 10%.
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Affiliation(s)
- Yafeng Wu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, State Key Laboratory of Digital Medical Engineering, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Qinglin Gu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, State Key Laboratory of Digital Medical Engineering, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Zhi Wang
- Wuxi Institute of Inspection, Testing and Certification, Wuxi 214125, China
| | - Zhaoyan Tian
- State Key Laboratory for Macromolecule Drugs and Large-Scale Manufacturing, School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China
| | - Hui Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, State Key Laboratory of Digital Medical Engineering, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, State Key Laboratory of Digital Medical Engineering, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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2
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Cong H, Loo J, Chen J, Wang Y, Kong SK, Ho HP. Target trapping and in situ single-cell genetic marker detection with a focused optical beam. Biosens Bioelectron 2019; 133:236-242. [PMID: 30953882 DOI: 10.1016/j.bios.2019.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/04/2019] [Accepted: 02/12/2019] [Indexed: 01/01/2023]
Abstract
Optical trapping of single particles or cells with the capability of in situ bio-sensing or genetic profiling opens the possibility of rapid screening of biological specimens. However, common optical tweezers suffer from the lack of long-range forces. Consequently, their application areas are predominantly limited to target manipulation instead of biological diagnostics. To solve this problem, we herein report an all-in-one approach by combining optical forces and convective drag forces generated through localized optothermal effect for long-range target manipulation. The device consists of a 2D array of gold coated polydimethylsiloxane (PDMS) micro-wells, which are immersed by colloidal particles or cell solution. Upon excitation of a 785-nm laser, the hydrodynamic convective force and optical forces will drag the targets of interest into their designated micro-wells. Moreover, the plasmonic thermal dissipation provides a constant temperature environment for following cell analysis procedures of cell isolation, lysis and isothermal nucleic acid amplification for the detection of genetic markers. With the merits of fabrication simplicity, short sample-to-answer cycle time and the compatibility with optical microscopes, the reported technique offers an attractive and highly versatile approach for on-site single cell analysis systems.
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Affiliation(s)
- Hengji Cong
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Jacky Loo
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China; Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Jiajie Chen
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China.
| | - Yuye Wang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Siu-Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China.
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3
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Chen L, Diao Z, Xu Z, Zhou J, Yan G, Sun H. The clinical application of NGS-based SNP haplotyping for PGD of Hb H disease. Syst Biol Reprod Med 2017; 63:212-217. [PMID: 28340305 DOI: 10.1080/19396368.2017.1296501] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Linjun Chen
- Reproductive Medical Center, Drum Tower Hospital Affiliated to Nanjing University Medical College, Nanjing, People’s Republic of China
| | - Zhenyu Diao
- Reproductive Medical Center, Drum Tower Hospital Affiliated to Nanjing University Medical College, Nanjing, People’s Republic of China
| | - Zhipeng Xu
- Reproductive Medical Center, Drum Tower Hospital Affiliated to Nanjing University Medical College, Nanjing, People’s Republic of China
| | - Jianjun Zhou
- Reproductive Medical Center, Drum Tower Hospital Affiliated to Nanjing University Medical College, Nanjing, People’s Republic of China
| | - Guijun Yan
- Reproductive Medical Center, Drum Tower Hospital Affiliated to Nanjing University Medical College, Nanjing, People’s Republic of China
| | - Haixiang Sun
- Reproductive Medical Center, Drum Tower Hospital Affiliated to Nanjing University Medical College, Nanjing, People’s Republic of China
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Ok CY, Singh RR, Salim AA. Single-Cell Quantitative PCR: Advances and Potential in Cancer Diagnostics. Methods Mol Biol 2016; 1392:153-9. [PMID: 26843054 DOI: 10.1007/978-1-4939-3360-0_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Tissues are heterogeneous in their components. If cells of interest are a minor population of collected tissue, it would be difficult to obtain genetic or genomic information of the interested cell population with conventional genomic DNA extraction from the collected tissue. Single-cell DNA analysis is important in the analysis of genetics of cell clonality, genetic anticipation, and single-cell DNA polymorphisms. Single-cell PCR using Single Cell Ampligrid/GeXP platform is described in this chapter.
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Affiliation(s)
- Chi Young Ok
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 8515 Fannin Street, Houston, TX, 77054, USA.
| | - Rajesh R Singh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 8515 Fannin Street, Houston, TX, 77054, USA.
| | - Alaa A Salim
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 8515 Fannin Street, Houston, TX, 77054, USA.
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Hamilton PB, Lefebvre KE, Bull RD. Single cell PCR amplification of diatoms using fresh and preserved samples. Front Microbiol 2015; 6:1084. [PMID: 26528252 PMCID: PMC4604310 DOI: 10.3389/fmicb.2015.01084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/22/2015] [Indexed: 11/18/2022] Open
Abstract
Single cell Chelex® DNA extraction and nested PCR amplification were used to examine partial gene sequences from natural diatom populations for taxonomic and phylogenetic studies at and above the level of species. DNA was extracted from cells that were either fresh collected or stored in RNAlater. Extractions from Lugol's fixation were also attempted with limited success. Three partial gene sequences (rbcL, 18S, and psbA) were recovered using existing and new primers with a nested or double nested PCR approach with amplification and success rates between 70 and 96%. An rbcL consensus tree grouped morphologically similar specimens and was consistent across the two primary sample treatments: fresh and RNAlater. This tool will greatly enhance the number of microscopic diatom taxa (and potentially other microbes) available for barcoding and phylogenetic studies. The near-term increase in sequence data for diatoms generated via routine single cell extractions and PCR will act as a multiproxy validation of longer-term next generation genomics.
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Affiliation(s)
- Paul B. Hamilton
- Research and Collections, Canadian Museum of NatureOttawa, ON, Canada
| | - Keely E. Lefebvre
- Research and Collections, Canadian Museum of NatureOttawa, ON, Canada
- Biology and Environmental Science, Center for Advanced Research in Environmental Genomics, University of OttawaOttawa, ON, Canada
| | - Roger D. Bull
- Research and Collections, Canadian Museum of NatureOttawa, ON, Canada
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Kwon H, Park HS, Yu J, Hong S, Choi Y. Spatio-temporally controlled transfection by quantitative injection into a single cell. Biomaterials 2015. [PMID: 26222285 DOI: 10.1016/j.biomaterials.2015.07.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Transfection-based cellular control has been widely used in biology; however, conventional transfection methods cannot control spatio-temporal differences in gene expression or the quantity of delivered materials such as external DNA or RNA. Here, we present a non-viral and spatio-temporally controlled transfection technique of a quantitative injection into a single cell. DNA was quantitatively injected into a single cell at a desired location and time, and the optimal gene delivery and expression conditions were determined based on the amount of the delivered DNA and the transfection efficacy. Interestingly, an injection of 1500 DNAs produced an about average 30% gene expression efficiency, which was the optimal condition, and gene expression was sustained for more than 14 days. In a single cell, fluorescent intensity and polymerase chain reaction (PCR) results were compared for the quantity of gene expression. The high coincidence of both results suggests that the fluorescence intensity can reveal gene expression level which was investigated by PCR. In addition, 3 multiple DNA genes were successfully expressed in a single cell with different ratio. Overall, these results demonstrate that spatio-temporally controlled transfection by quantitative transfection is a useful technique for regulating gene expression in a single cell, which suggests that this technique may be used for stem cell research, including the creation of induced pluripotent stem (iPS) cells.
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Affiliation(s)
- Hyosung Kwon
- Department of Bio-convergence Engineering, Korea University, Seoul 136-701, South Korea
| | - Hang-soo Park
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 136-701, South Korea
| | - Jewon Yu
- Department of Biomedical Engineering, Korea University, Seoul 136-701, South Korea
| | - Sunghoi Hong
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 136-701, South Korea; School of Biosystem and Biomedical Science, Korea University, Seoul 136-701, South Korea.
| | - Yeonho Choi
- Department of Bio-convergence Engineering, Korea University, Seoul 136-701, South Korea; Department of Biomedical Engineering, Korea University, Seoul 136-701, South Korea.
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Lane CE, Benton MG. Detection of the enzymatically-active polyhydroxyalkanoate synthase subunit gene, phaC, in cyanobacteria via colony PCR. Mol Cell Probes 2015; 29:454-460. [PMID: 26162861 DOI: 10.1016/j.mcp.2015.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 11/26/2022]
Abstract
A colony PCR-based assay was developed to rapidly determine if a cyanobacterium of interest contains the requisite genetic material, the PHA synthase PhaC subunit, to produce polyhydroxyalkanoates (PHAs). The test is both high throughput and robust, owing to an extensive sequence analysis of cyanobacteria PHA synthases. The assay uses a single detection primer set and a single reaction condition across multiple cyanobacteria strains to produce an easily detectable positive result - amplification via PCR as evidenced by a band in electrophoresis. In order to demonstrate the potential of the presence of phaC as an indicator of a cyanobacteria's PHA accumulation capabilities, the ability to produce PHA was assessed for five cyanobacteria with a traditional in vivo PHA granule staining using an oxazine dye. The confirmed in vivo staining results were then compared to the PCR-based assay results and found to be in agreement. The colony PCR assay was capable of successfully detecting the phaC gene in all six of the diverse cyanobacteria tested which possessed the gene, while exhibiting no undesired product formation across the nine total cyanobacteria strains tested. The colony PCR quick prep provides sufficient usable DNA template such that this assay could be readily expanded to assess multiple genes of interest simultaneously.
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Affiliation(s)
- Courtney E Lane
- Louisiana State University, Cain Department of Chemical Engineering, 110 Chemical Engineering, South Stadium Drive, Baton Rouge, LA 70803, USA
| | - Michael G Benton
- Louisiana State University, Cain Department of Chemical Engineering, 110 Chemical Engineering, South Stadium Drive, Baton Rouge, LA 70803, USA.
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8
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Choi YH, Penedo MCT, Daftari P, Velez IC, Hinrichs K. Accuracy of preimplantation genetic diagnosis in equine in vivo-recovered and in vitro-produced blastocysts. Reprod Fertil Dev 2015; 28:RD14419. [PMID: 25775205 DOI: 10.1071/rd14419] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/19/2015] [Indexed: 02/28/2024] Open
Abstract
Preimplantation genetic diagnosis has great potential in the horse, but information on evaluation of equine embryo biopsy samples is limited. Blastocysts were biopsied using a Piezo drill and methods for whole-genome amplification (WGA) investigated. Results for 33 genetic loci were then compared between biopsy samples from in vitro-produced (IVP) and in vivo-recovered (VIV) blastocysts. Under the experimental conditions described, WGA using the Qiagen Repli-g Midi kit was more accurate than that using the Illustra Genomiphi V2 kit (98.2% vs 25.8%, respectively). Using WGA with the Qiagen kit, three biopsy samples were evaluated from each of eight IVP and 19 VIV blastocysts, some produced using semen from stallions carrying the genetic mutations associated with the diseases hereditary equine regional dermal asthenia (HERDA), hyperkalemic periodic paralysis (HYPP) or polysaccharide storage myopathy 1 (PSSM1). Three of 81 biopsy samples (3.7%) returned 95% overall accuracy in IVP and VIV embryos, and this technique is suitable for use in a clinical setting.
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9
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Levy A, Gomez-Roca C, Massard C, Planchard D, Albiges L, Bahleda R, Bourgier C, Deutsch E, Soria JC, Besse B. Clinical benefit for patients with non-small cell lung cancer enrolled in phase I trials. Oncol Res Treat 2013; 36:357-62. [PMID: 23774150 DOI: 10.1159/000351257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
AIM To analyze the clinical features and outcomes of advanced non-small cell lung cancer (NSCLC) patients treated in phase I trials. PATIENTS AND METHODS The clinical characteristics, efficacy and toxicity data of 70 pretreated NSCLC patients enrolled in 17 phase I trials between January 2005 and June 2010 were analyzed at our institution. RESULTS The histological types were: adenocarcinoma (79%), squamous cell carcinoma (13%), and others. Patients received a median number of 3 prior lines of treatment before inclusion. 1 complete response (CR), 11 (16%) partial responses (PRs), and 29 (41%) stable diseases (SDs) were observed (according to Response Evaluation Criteria in Solid Tumors (RECIST)). The median overall survival (OS) time was 18 months and the median progression-free survival (PFS) time was 4.1 months. The median PFS of these patients within their prior therapy line before phase I inclusion was 4.3 months. A performance status score of 0 and the number of prior lines of treatment were significant for OS and PFS in multivariate analysis, respectively. Grade 3/4 toxicities were observed in 20 (27%) patients, and there was 1 treatment-related death. CONCLUSION Patients in good general condition and with limited pretreatment derived an improved benefit, suggesting that phase I studies may be a valid option for pretreated NSCLC patients.
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Affiliation(s)
- Antonin Levy
- SITEP (Service des Innovations Therapeutiques Precoces), Department of Medicine, Institut Gustave Roussy, Paris XI University, Villejuif, France
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10
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Shi X, Lin LI, Chen SY, Chao SH, Zhang W, Meldrum DR. Real-time PCR of single bacterial cells on an array of adhering droplets. LAB ON A CHIP 2011; 11:2276-2281. [PMID: 21607246 DOI: 10.1039/c1lc20207c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Real-time PCR at the single bacterial cell level is an indispensable tool to quantitatively reveal the heterogeneity of isogenetic cells. Conventional PCR platforms that utilize microtiter plates or PCR tubes have been widely used, but their large reaction volumes are not suited for sensitive single-cell analysis. Microfluidic devices provide high density, low volume PCR chambers, but they are usually expensive and require dedicated equipment to manipulate liquid and perform detection. To address these limitations, we developed an inexpensive chip-level device that is compatible with a commercial real-time PCR thermal cycler to perform quantitative PCR for single bacterial cells. The chip contains twelve surface-adhering droplets, defined by hydrophilic patterning, that serve as real-time PCR reaction chambers when they are immersed in oil. A one-step process that premixed reagents with cell medium before loading was applied, so no on-chip liquid manipulation and DNA purification were needed. To validate its application for genetic analysis, Synechocystis PCC 6803 cells were loaded on the chip from 1000 cells to one cell per droplet, and their 16S rRNA gene (two copies per cell) was analyzed on a commercially available ABI StepOne real-time PCR thermal cycler. The result showed that the device is capable of genetic analysis at single bacterial cell level with C(q) standard deviation less than 1.05 cycles. The successful rate of this chip-based operation is more than 85% at the single bacterial cell level.
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Affiliation(s)
- Xu Shi
- Center for Biosignatures Discovery Automation, Arizona State University, PO Box 876501. Tempe, AZ, USA
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Gunn NM, Chang R, Westerhof T, Li GP, Bachman M, Nelson EL. Ferromagnetic micropallets for magnetic capture of single adherent cells. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:17703-11. [PMID: 20968293 PMCID: PMC2981060 DOI: 10.1021/la101960v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We present a magnetic micropallet array and demonstrate its capacity to recover specific, individual adherent cells from large populations and deliver them for downstream single cell analysis. A ferromagnetic photopolymer was formulated, characterized, and used to fabricate magnetic micropallets, which are microscale pedestals that provide demarcated cell growth surfaces with preservation of biophysical properties including photopatternability, biocompatibility, and optical clarity. Each micropallet holds a single adherent cell in culture, and hundreds of thousands of micropallets comprise a single micropallet array. Any micropallet in the array can be recovered on demand, carrying the adhered cell with it. We used this platform to recover selectively single cells, which were subsequently analyzed using single-cell RT-qPCR.
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Affiliation(s)
- Nicholas M. Gunn
- School of Engineering, Department of Biomedical Engineering, University of California at Irvine, Irvine, CA 92697
| | - Ruth Chang
- Department of Medicine, University of California at Irvine, Irvine, CA 92697
| | - Trisha Westerhof
- School of Biological Sciences, University of California at Irvine, Irvine, CA 92697
| | - Guann-Pyng Li
- Department of Electrical and Computer Science, University of California at Irvine, Irvine, CA 92697
- Integrated Nanosystems Research Facility, University of California at Irvine, Irvine, CA 92697
- California Institute for Telecommunications and Information Technology (CalIT), University of California at Irvine, Irvine, CA 92697
| | - Mark Bachman
- Department of Electrical and Computer Science, University of California at Irvine, Irvine, CA 92697
- Integrated Nanosystems Research Facility, University of California at Irvine, Irvine, CA 92697
- California Institute for Telecommunications and Information Technology (CalIT), University of California at Irvine, Irvine, CA 92697
| | - Edward L. Nelson
- School of Medicine, Department of Medicine, Division of Hematology/Oncology, University of California at Irvine, Irvine, CA 92697
- Institute for Immunology, University of California at Irvine, Irvine, CA 92697
- School of Biological Sciences, Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA 92697
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12
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Diversity of phytoplankton nitrate transporter sequences from isolated single cells and mixed samples from the East China Sea and mRNA quantification. Appl Environ Microbiol 2010; 77:122-30. [PMID: 21075880 DOI: 10.1128/aem.01315-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcript abundances of nitrate transporter genes (Nrt2) were proposed as potential markers for nitrogen deficiency in marine diatoms. To correctly quantify diatom Nrt2 mRNA in the East China Sea (ECS), we utilized both mixed-species sequencing and single-cell PCR to expand the sequence database for this region. Using the single-cell method of PCR, 9 new diatom Nrt2 sequences belonging to 5 genera, the Nrt2 sequences of which have never been reported before, were obtained. On the other hand, 291 sequences homologous to Nrt2 were retrieved from mixed-species sequencing using degenerate primers, and these sequences were clustered into 12 major groups according to a phylogenetic analysis. Based on sequence alignments, 11 pairs of group-specific PCR primers were designed to detect Nrt2 mRNA levels in the ECS, and 3 of these primer pairs showed high specificity to target species. In ECS phytoplankton samples, environmental RNA was amplified via antisense RNA amplification followed by cDNA production. Subsequently, Nrt2 transcript levels were readily detected using quantitative PCR. Our results indicated that investigating sequence diversity followed by careful primer design and evaluation is a good strategy to quantify the expression of genes of ecologically important phytoplankton.
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Giorgi EE, Funkhouser B, Athreya G, Perelson AS, Korber BT, Bhattacharya T. Estimating time since infection in early homogeneous HIV-1 samples using a poisson model. BMC Bioinformatics 2010; 11:532. [PMID: 20973976 PMCID: PMC2975664 DOI: 10.1186/1471-2105-11-532] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 10/25/2010] [Indexed: 01/03/2023] Open
Abstract
Background The occurrence of a genetic bottleneck in HIV sexual or mother-to-infant transmission has been well documented. This results in a majority of new infections being homogeneous, i.e., initiated by a single genetic strain. Early after infection, prior to the onset of the host immune response, the viral population grows exponentially. In this simple setting, an approach for estimating evolutionary and demographic parameters based on comparison of diversity measures is a feasible alternative to the existing Bayesian methods (e.g., BEAST), which are instead based on the simulation of genealogies. Results We have devised a web tool that analyzes genetic diversity in acutely infected HIV-1 patients by comparing it to a model of neutral growth. More specifically, we consider a homogeneous infection (i.e., initiated by a unique genetic strain) prior to the onset of host-induced selection, where we can assume a random accumulation of mutations. Previously, we have shown that such a model successfully describes about 80% of sexual HIV-1 transmissions provided the samples are drawn early enough in the infection. Violation of the model is an indicator of either heterogeneous infections or the initiation of selection. Conclusions When the underlying assumptions of our model (homogeneous infection prior to selection and fast exponential growth) are met, we are under a very particular scenario for which we can use a forward approach (instead of backwards in time as provided by coalescent methods). This allows for more computationally efficient methods to derive the time since the most recent common ancestor. Furthermore, the tool performs statistical tests on the Hamming distance frequency distribution, and outputs summary statistics (mean of the best fitting Poisson distribution, goodness of fit p-value, etc). The tool runs within minutes and can readily accommodate the tens of thousands of sequences generated through new ultradeep pyrosequencing technologies. The tool is available on the LANL website.
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Affiliation(s)
- Elena E Giorgi
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Chung KF, Sicard F, Vukicevic V, Hermann A, Storch A, Huttner WB, Bornstein SR, Ehrhart-Bornstein M. Isolation of neural crest derived chromaffin progenitors from adult adrenal medulla. Stem Cells 2010; 27:2602-13. [PMID: 19609938 DOI: 10.1002/stem.180] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromaffin cells of the adrenal medulla are neural crest-derived cells of the sympathoadrenal lineage. Unlike the closely-related sympathetic neurons, a subpopulation of proliferation-competent cells exists even in the adult. Here, we describe the isolation, expansion, and in vitro characterization of proliferation-competent progenitor cells from the bovine adrenal medulla. Similar to neurospheres, these cells, when prevented from adherence to the culture dish, grew in spheres, which we named chromospheres. These chromospheres were devoid of mRNA specific for smooth muscle cells (MYH11) or endothelial cells (PECAM1). During sphere formation, markers for differentiated chromaffin cells, such as phenylethanolamine-N-methyl transferase, were downregulated while neural progenitor markers nestin, vimentin, musashi 1, and nerve growth factor receptor, as well as markers of neural crest progenitor cells such as Sox1 and Sox9, were upregulated. Clonal analysis and bromo-2'-deoxyuridine-incorporation analysis demonstrated the self-renewing capacity of chromosphere cells. Differentiation protocols using NGF and BMP4 or dexamethasone induced neuronal or endocrine differentiation, respectively. Electrophysiological analyses of neural cells derived from chromospheres revealed functional properties of mature nerve cells, such as tetrodotoxin-sensitive sodium channels and action potentials. Our study provides evidence that proliferation and differentiation competent chromaffin progenitor cells can be isolated from adult adrenal medulla and that these cells might harbor the potential for the treatment of neurodegenerative diseases, such as Parkinson's disease.
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Affiliation(s)
- Kuei-Fang Chung
- Carl Gustav Carus University Medical School, Medical Clinic III, Dresden University of Technology, Dresden, Germany
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15
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Lynn DH, Pinheiro M. A survey of polymerase chain reaction (PCR) amplification studies of unicellular protists using single-cell PCR. J Eukaryot Microbiol 2009; 56:406-12. [PMID: 19737192 DOI: 10.1111/j.1550-7408.2009.00439.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We surveyed a variety of studies that have used single-cell polymerase chain reaction (SC-PCR) to examine the gene sequences of a diversity of unicellular protists. Representatives of all the Super-Groups of eukaryotes have been subjected to SC-PCR with ciliates and dinoflagellates being most commonly examined. The SC-PCR was carried out either by directly amplifying a single lysed cell or by first extracting DNA and following this with amplification of the DNA extract. Cell lysis methods included heating, freezing, mechanical rupture, and enzyme digestion. Cells fixed or preserved with ethanol, methanol, and Lugol's have also been used successfully. Heminested or seminested PCR might follow the initial PCR, whose products were then directly sequenced or cloned and then sequenced. The methods are not complicated. This should encourage protistologists to use SC-PCR in the description of new or revised taxa, especially rare and unculturable forms, and it should also enable the probing of gene expression in relation to life history stages.
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Affiliation(s)
- Denis H Lynn
- Department of Integrative Biology, University of Guelph, Ontario, Canada.
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16
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Kroneis T, Gutstein-Abo L, Kofler K, Hartmann M, Hartmann P, Alunni-Fabbroni M, Walcher W, Dohr G, Petek E, Guetta E, Sedlmayr P. Automatic retrieval of single microchimeric cells and verification of identity by on-chip multiplex PCR. J Cell Mol Med 2009; 14:954-69. [PMID: 19453769 PMCID: PMC3823127 DOI: 10.1111/j.1582-4934.2009.00784.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The analysis of rare cells is not an easy task. This is especially true when cells representing a fetal microchimerism are to be utilized for the purpose of non-invasive prenatal diagnosis because it is both imperative and difficult to avoid contaminating the minority of fetal cells with maternal ones. Under these conditions, even highly specific biochemical markers are not perfectly reliable. We have developed a method to verify the genomic identity of rare cells that combines automatic screening for enriched target cells (based on immunofluorescence labelling) with isolation of single candidate microchimeric cells (by laser microdissection and subsequent laser catapulting) and low-volume on-chip multiplex PCR for DNA fingerprint analysis. The power of the method was tested using samples containing mixed cells of related and non-related individuals. Single-cell DNA fingerprinting was successful in 74% of the cells analysed (55/74), with a PCR efficiency of 59.2% (860/1452) for heterozygous loci. The identification of cells by means of DNA profiling was achieved in 100% (12/12) of non-related cells in artificial mixtures and in 86% (37/43) of cells sharing a haploid set of chromosomes and was performed on cells enriched from blood and cells isolated from tissue. We suggest DNA profiling as a standard for the identification of microchimerism on a single-cell basis.
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Affiliation(s)
- Thomas Kroneis
- Institute of Cell Biology, Histology and Embryology, Center for Molecular Medicine, Medical University of Graz, Graz, Austria
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Whole genome amplification of the rust Puccinia striiformis f. sp. tritici from single spores. J Microbiol Methods 2009; 77:229-34. [PMID: 19233233 DOI: 10.1016/j.mimet.2009.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 02/11/2009] [Indexed: 11/24/2022]
Abstract
Rust fungi are obligate parasites and cannot be routinely cultured to obtain sufficient biomass for DNA extractions. Multiple displacement amplification (MDA) was demonstrated in this study for whole genome amplification from single spores of the rust fungus, Puccinia striiformis. The genomic DNA coverage and fidelity of this method was evaluated by PCR amplification and sequencing of two genetic markers: portions of the multi-copy nuclear ribosomal DNA internal transcribed spacer region (ITS) and the single copy beta-tubulin gene from two geographical diverse isolates. Our results show that MDA is a valuable tool for whole genome amplification from single spores, and we propose that MDA-amplified DNA can be used for molecular genetic analysis of the wheat yellow rust fungus.
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18
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Toriello NM, Douglas ES, Mathies RA. Microfluidic device for electric field-driven single-cell capture and activation. Anal Chem 2007; 77:6935-41. [PMID: 16255592 DOI: 10.1021/ac051032d] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A microchip that performs directed capture and chemical activation of surface-modified single cells has been developed. The cell capture system is comprised of interdigitated gold electrodes microfabricated on a glass substrate within PDMS channels. The cell surface is labeled with thiol functional groups using endogenous RGD receptors, and adhesion to exposed gold pads on the electrodes is directed by applying a driving electric potential. Multiple cell types can thus be sequentially and selectively captured on desired electrodes. Single-cell capture efficiency is optimized by varying the duration of field application. Maximum single-cell capture is attained for the 10-min trial, with 63 +/- 9% (n = 30) of the electrode pad rows having a single cell. In activation studies, single M1WT3 CHO cells loaded with the calcium-sensitive dye fluo-4 AM were captured; exposure to the muscarinic agonist carbachol increased the fluorescence to 220 +/- 74% (n = 79) of the original intensity. These results demonstrate the ability to direct the adhesion of selected living single cells on electrodes in a microfluidic device and to analyze their response to chemical stimuli.
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Affiliation(s)
- Nicholas M Toriello
- Department of Chemistry and UC Berkeley/UCSF Joint Graduate Group in Bioengineering, University of California, Berkeley, California 94720, USA
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19
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Lin DM, Loveall B, Ewer J, Deitcher DL, Sucher NJ. Characterization of mRNA expression in single neurons. Methods Mol Biol 2007; 399:133-152. [PMID: 18309930 DOI: 10.1007/978-1-59745-504-6_10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
How neurons differ from each other is largely determined by their specific repertoire of mRNAs. The genes expressed by a given neuron reflect its developmental history, its interaction with other cells, and its synaptic activity. Since the introduction of reverse transcription polymerase chain reaction (RT-PCR), it has been possible to identify specific mRNAs present in small samples of total RNA. But isolating RNA from only those cells of interest, and not others, represents a significant challenge. Several approaches can be used to isolate RNA from selected neurons. Following whole-cell patch-clamp recording, mRNA can be harvested from living cells by aspirating the cytoplasm into the patch-clamp pipette. Transcripts expressed in the recorded neuron can then be amplified by RT-PCR. Another way of isolating identified neurons is to use cell-specific promoters to drive the expression of a marker gene such as green fluorescent protein (GFP). RNA can then be isolated from GFP-positive cells. In a tissue context, laser microdissection can also be used to excise the cells of interest directly into an RNA isolation solution. The above methods of RNA isolation can also be combined with RNA amplification and microarray technology to identify specific transcripts that are unique to the cell type being studied. Here we provide detailed protocols for harvesting RNA from single cells, methods for RNA purification, and PCR amplification.
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Affiliation(s)
- David M Lin
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
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20
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Choi D, Fung A, Moon H, Ho D, Chen Y, Kan E, Rheem Y, Yoo B, Myung N. Transport of living cells with magnetically assembled nanowires. Biomed Microdevices 2006; 9:143-8. [PMID: 17111225 DOI: 10.1007/s10544-006-9008-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We present a technique of transporting and positioning living cells internalized by nickel (Ni) nanowires guided by magnetic field. Nanoscale magnetic nanowires are internalized by the Rat Neuroblastoma (ATCC number CRL-2754) and the cells are transported and positioned by magnetic fields from the magnetic material-coated electrodes. This technique may enable the interfacing between neurons and electronic devices to empower investigations pertaining to non-invasive neuron probing as well as nanofabricated neural pharmacological technologies.
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Affiliation(s)
- D Choi
- Mechanical & Aerospace Engineering Department, University of California at Los Angeles, CA 90095, USA.
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21
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A. Ali B, . HHS, . THH, . QDX. Detection of Full Length Hb S Gene (1.2 Kb) in One- and Two-cell Embryo Originated from Hamster Oocyte and Human Spermatozoa by Using Nested-PCR. JOURNAL OF MEDICAL SCIENCES 2006. [DOI: 10.3923/jms.2006.1015.1020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Pinard R, de Winter A, Sarkis GJ, Gerstein MB, Tartaro KR, Plant RN, Egholm M, Rothberg JM, Leamon JH. Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics 2006; 7:216. [PMID: 16928277 PMCID: PMC1560136 DOI: 10.1186/1471-2164-7-216] [Citation(s) in RCA: 224] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 08/23/2006] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs) or large scale (CGH array, FISH) methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes. Halobacterium species NRC-1 DNA and Campylobacter jejuni were amplified by several common, commercially available protocols: multiple displacement amplification, primer extension pre-amplification and degenerate oligonucleotide primed PCR. The amplification-induced bias of each method was assessed by sequencing both genomes in their entirety using the 454 Sequencing System technology and comparing the results with those obtained from unamplified controls. RESULTS All amplification methodologies induced statistically significant bias relative to the unamplified control. For the Halobacterium species NRC-1 genome, assessed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 119 times greater than those from unamplified material, 164.0 times greater for Repli-G, 165.0 times greater for PEP-PCR and 252.0 times greater than the unamplified controls for DOP-PCR. For Campylobacter jejuni, also analyzed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 15 times greater than those from unamplified material, 19.8 times greater for Repli-G, 61.8 times greater for PEP-PCR and 220.5 times greater than the unamplified controls for DOP-PCR. CONCLUSION Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.
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Affiliation(s)
- Robert Pinard
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
| | - Alex de Winter
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
| | - Gary J Sarkis
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
| | - Mark B Gerstein
- MB&B Department, Yale University, 266 Whitney Ave., New Haven CT 06520, USA
| | | | - Ramona N Plant
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
| | - Michael Egholm
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
| | | | - John H Leamon
- 454 Life Sciences, 20 Commercial Street, Branford CT 06405, USA
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Saker A, Benachi A, Bonnefont JP, Munnich A, Dumez Y, Lacour B, Paterlini-Brechot P. Genetic characterisation of circulating fetal cells allows non-invasive prenatal diagnosis of cystic fibrosis. Prenat Diagn 2006; 26:906-16. [PMID: 16832834 DOI: 10.1002/pd.1524] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVES Cystic fibrosis (CF) is an autosomal recessive disease due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The purpose of this study was to develop a molecular method to characterise both paternal and maternal CFTR alleles in DNA from circulating fetal cells (CFCs) isolated by ISET (isolation by size of epithelial tumour/trophoblastic cells). METHODS The molecular protocol was defined by developing the F508del mutation analysis and addressing it both to single trophoblastic cells, isolated by ISET and identified by short tandem repeats (STR) genotyping, and to pooled trophoblastic genomes, thus avoiding the risk of allele drop out (ADO). This protocol was validated in 100 leucocytes from F508del carriers and subsequently blindly applied to the blood (5 mL) of 12 pregnant women, at 11 to 13 weeks of gestation, whose offspring had a 1/4 risk of CF. Ten couples were carriers of F508del mutation, while two were carriers of unknown CFTR mutations. RESULTS Results showed that one fetus was affected, seven were heterozygous carriers of a CFTR mutation, and four were healthy homozygotes. These findings were consistent with those obtained by chorionic villus sampling (CVS). CONCLUSION Our data show that the ISET-CF approach affords reliable prenatal diagnosis (PND) of cystic fibrosis and is potentially applicable to pregnant women at risk of having an affected child, thus avoiding the risk of iatrogenic miscarriage.
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Affiliation(s)
- Ali Saker
- INSERM, Unité 807, Paris, France, Université Réné Descartes, Paris, France
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24
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Yang YH, Yang ES, Kwon JY, Kim IK, Park YW. Prenatal Diagnosis of Trisomy 21 with Fetal Cells in Maternal Blood Using Comparative Genomic Hybridization. Fetal Diagn Ther 2005; 21:125-33. [PMID: 16354990 DOI: 10.1159/000089062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Accepted: 01/18/2005] [Indexed: 11/19/2022]
Abstract
OBJECTIVE This study was undertaken to determine the clinical use of comparative genomic hybridization (CGH) for detection of fetal trisomy 21 from fetal ceIls (nucleated red blood cells; nRBCs) isolated from maternal peripheral venous blood. METHODS Maternal peripheral venous blood samples were collected in sterile tubes containing heparin. After triple density gradient centrifugation, magnetic activated cell sorting using CD45 and CD71 was used to isolate the fetal nRBCs. Fetal nRBCs were successfully isolated from maternal peripheral blood in all cases. After laser-microdissecting fetal nRBCs, degenerate oligonucleotide-primed polymerase chain reaction, and nick translation, DNA size was suitable for hybridization. RESULTS By CGH analysis, we diagnosed one normal male, one normal female, and one trisomy 21 male fetus. These results were confirmed by amniocentesis. CONCLUSIONS Prenatal diagnosis from fetal cells in maternal peripheral blood by CGH shows clinical promise as an alternative or as a supplement to fluorescence in situ hybridization with chromosome-specific probes but further studies are warranted.
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Affiliation(s)
- Young Ho Yang
- Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea.
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25
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Csako G. Present and future of rapid and/or high-throughput methods for nucleic acid testing. Clin Chim Acta 2005; 363:6-31. [PMID: 16102738 DOI: 10.1016/j.cccn.2005.07.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 07/03/2005] [Accepted: 07/03/2005] [Indexed: 12/21/2022]
Abstract
BACKGROUND Behind the success of 'completing' the human genome project was a more than 30-year history of technical innovations for nucleic acid testing. METHODS Discovery of specific restriction endonucleases and reverse transcriptase was followed shortly by the development of the first diagnostic nucleic acid tests in the early 1970s. Introduction of Southern, Northern and dot blotting and DNA sequencing later in the 1970s considerably advanced the diagnostic capabilities. Nevertheless, it was the discovery of the polymerase chain reaction (PCR) in 1985 that led to an exponential growth in molecular biology and the introduction of practicable nucleic acid tests in the routine laboratory. The past two decades witnessed a continuing explosion of technological innovations in molecular diagnostics. In addition to classic PCR and reverse transcriptase PCR, numerous variations of PCR and alternative amplification techniques along with an ever-increasing variety of detection chemistries, closed tube (homogeneous) assays, and automated systems were developed. Discovery of real-time quantitative PCR and the development of oligonucleotide microarrays, the 'DNA chip', in the 1990s heralded the beginning of another revolution in molecular biology and diagnostics that is still in progress.
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Affiliation(s)
- Gyorgy Csako
- Department of Laboratory Medicine, W.G. Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892-1508, USA.
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26
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Katz-Jaffe MG, Mantzaris D, Cram DS. DNA identification of fetal cells isolated from cervical mucus: potential for early non-invasive prenatal diagnosis. BJOG 2005; 112:595-600. [PMID: 15842283 DOI: 10.1111/j.1471-0528.2004.00506.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To develop a reliable method to isolate fetal cells for genetic diagnosis. DESIGN Aspiration of cervical mucus from pregnant women in the first trimester. SETTING Pregnant women were recruited before an elective termination of pregnancy. POPULATION Sixty pregnant women (7-10 weeks of gestation). METHODS Fetal cells were isolated from aspirated cervical mucus of pregnant women using a combination of enzymatic digestion, fluorescent immunohistochemistry, micromanipulation and single-cell DNA allelic profiling. MAIN OUTCOME MEASURES The isolation and identification of fetal cells. RESULTS The transformation of the tenacious cervical mucus into a single-cell suspension enabled the isolation and identification of fetal cells by fluorescent immunohistochemistry. Confirmation of fetal origin was accomplished by single-cell DNA allelic profiling alongside known maternal cells. CONCLUSIONS This novel non-invasive method is rapid and efficient with results attainable within 24 hours as early as seven weeks of gestation. The technique would offer earlier reassurance and the option of first trimester therapeutic abortions to both high and low risk pregnant women.
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Affiliation(s)
- Mandy G Katz-Jaffe
- Monash Institute of Reproduction and Development, Monash University and Monash IVF, Melbourne, Australia
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27
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Hong JW, Studer V, Hang G, Anderson WF, Quake SR. A nanoliter-scale nucleic acid processor with parallel architecture. Nat Biotechnol 2004; 22:435-9. [PMID: 15024389 DOI: 10.1038/nbt951] [Citation(s) in RCA: 377] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2003] [Accepted: 01/15/2004] [Indexed: 02/07/2023]
Abstract
The purification of nucleic acids from microbial and mammalian cells is a crucial step in many biological and medical applications. We have developed microfluidic chips for automated nucleic acid purification from small numbers of bacterial or mammalian cells. All processes, such as cell isolation, cell lysis, DNA or mRNA purification, and recovery, were carried out on a single microfluidic chip in nanoliter volumes without any pre- or postsample treatment. Measurable amounts of mRNA were extracted in an automated fashion from as little as a single mammalian cell and recovered from the chip. These microfluidic chips are capable of processing different samples in parallel, thereby illustrating how highly parallel microfluidic architectures can be constructed to perform integrated batch-processing functionalities for biological and medical applications.
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Sanchez JA, Pierce KE, Rice JE, Wangh LJ. Linear-after-the-exponential (LATE)-PCR: an advanced method of asymmetric PCR and its uses in quantitative real-time analysis. Proc Natl Acad Sci U S A 2004; 101:1933-8. [PMID: 14769930 PMCID: PMC357030 DOI: 10.1073/pnas.0305476101] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Conventional asymmetric PCR is inefficient and difficult to optimize because limiting the concentration of one primer lowers its melting temperature below the reaction annealing temperature. Linear-After-The-Exponential (LATE)-PCR describes a new paradigm for primer design that renders assays as efficient as symmetric PCR assays, regardless of primer ratio. LATE-PCR generates single-stranded products with predictable kinetics for many cycles beyond the exponential phase. LATE-PCR also introduces new probe design criteria that uncouple hybridization probe detection from primer annealing and extension, increase probe reliability, improve allele discrimination, and increase signal strength by 80-250% relative to symmetric PCR. These improvements in PCR are particularly useful for real-time quantitative analysis of target numbers in small samples. LATE-PCR is adaptable to high throughput applications in fields such as clinical diagnostics, biodefense, forensics, and DNA sequencing. We showcase LATE-PCR via amplification of the cystic fibrosis CFDelta508 allele and the Tay-Sachs disease TSD 1278 allele from single heterozygous cells.
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Affiliation(s)
- J Aquiles Sanchez
- Department of Biology, MS 008, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
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Heinmöller E, Bockholt A, Werther M, Ziemer M, Müller A, Ghadimi BM, Rüschoff J. Laser microdissection of small tissue samples--application to chronic pancreatitis tissues. Pathol Res Pract 2003; 199:363-71. [PMID: 12924436 DOI: 10.1078/0344-0338-00432] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Laser microdissection is considered to be the gold standard of tissue sampling, especially if a defined small tissue area consisting of single or few cells within a heterogeneous tissue compartment is of interest. This sophisticated technique offers the opportunity of rapid and contamination-free tissue sampling for RNA- or DNA-based molecular genetic studies. We have applied laser microdissection to a molecular genetic study of pancreatic intraductal lesions (PanINs) in tissues of chronic pancreatitis, where an exact microdissection of small ducts within a dense fibrous tissue is of paramount importance for following analysis. From nine patients suffering from chronic pancreatitis, formalin-fixed, paraffin-embedded tissue specimens were laser microdissected, and a total of 202 normal ducts and PanINs of grade PanIN-1A to grade PanIN-2 were harvested. After whole genome amplification by improved primer extension and preamplification PCR (I-PEP-PCR), microsatellite-PCR based loss of heterozygosity analysis (LOH) of the tumor suppressor gene loci TP53, p16INK4, and DPC4 was performed. One of 85 informative duct lesions (1.2%) had LOH of TP53, 1 of 76 duct lesions (1.3%) had LOH of DPC4, and 2/29 duct lesions (6.9%) showed LOH of p16INK4. Microsatellite instability (MSI) was seen in 2 of 178 duct lesions (1.1%). Immunohistochemical staining of p53 protein and DPC4 protein revealed no aberrant expression. These preliminary data indicate that LOH of tumor suppressor genes, important in pancreatic cancer genesis or MSI, can be found in chronic pancreatitis tissues, but their incidence is low.
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30
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Gale JM, Romero CP, Tafoya GB, Conia J. Application of optical trapping for cells grown on plates: optimization of PCR and fidelity of DNA sequencing of p53 gene from a single cell. Clin Chem 2003; 49:415-24. [PMID: 12600953 DOI: 10.1373/49.3.415] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Optical trapping has traditionally been used to visually select and isolate nonadherent cells grown in suspension because cells grown in monolayers will rapidly reattach to surfaces if suspended in solution. We explored methods to slow cell reattachment that are also compatible with high-fidelity PCR. METHODS Using HeLa cells grown on plates and suspended after trypsinization, we measured the efficiency of capture by retention and movement of the cell by the laser. Success for removing a captured cell by pipette was determined by PCR amplification of the 5S rRNA gene. After optimizing PCR amplification of a 2049-bp region of the p53 gene, we determined PCR fidelity by DNA sequencing. RESULTS Addition of bovine serum albumin to suspended cells slowed reattachment from seconds to minutes and allowed efficient trapping. The success rate of removing a cell from the trap by pipette to a PCR tube was 91.5%. The 5S PCR assay also revealed that DNA and RNA that copurify with polymerases could give false-positive results. Sequence analysis of four clones derived from a single cell showed only three polymerase errors in 7200 bp of sequence read and revealed difficulties in reading the correct number in a run of 16 A:T. Comparison of the HeLa and wild-type human sequences revealed several previously unreported base differences and an (A:T)(n) length polymorphism in p53 introns. CONCLUSIONS These results represent the first use of optical trapping on adherent cells and demonstrate the high accuracy of DNA sequencing that can be achieved from a single cell.
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Affiliation(s)
- James M Gale
- Department of Cell Biology and Physiology, Steve Schiff Center for Skin Cancer University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
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Guetta E, Gordon D, Simchen MJ, Goldman B, Barkai G. Hematopoietic progenitor cells as targets for non-invasive prenatal diagnosis: detection of fetal CD34+ cells and assessment of post-delivery persistence in the maternal circulation. Blood Cells Mol Dis 2003; 30:13-21. [PMID: 12667983 DOI: 10.1016/s1079-9796(03)00008-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Culture expansion of fetal cells from the maternal circulation will provide an increased number of cells for non-invasive prenatal diagnosis. Hematopoietic CD34+ cells are potential candidates for this application. More information is needed regarding the frequency of these cells and the phenomenon of post-delivery persistence in the maternal circulation. In this study we assessed the number of fetal CD34+ cells in the maternal circulation, the effect of culture expansion on the number of fetal cells and the persistence of fetal CD34+ cells from previous pregnancies. Fetal cells were identified by the presence of Y-chromosome sequences detected by FISH and nested PCR. Fetal CD34+ cells were detected in all samples from women carrying a male fetus. A low number of residual fetal cells from previous pregnancies was detected (1-3 XY cells in 20 ml blood) in less than 1/3 of the samples from both non-pregnant women and those pregnant with a female fetus. Culturing of CD34+ cells resulted in a significant increase in fetal cell numbers. However, the number of fetal cells persisting from previous pregnancies also increased after culture. It is proposed that information derived from CD34+ cells could potentially support data derived from other cell types for more accurate non-invasive prenatal diagnosis.
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Affiliation(s)
- E Guetta
- Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer 52621, Israel.
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Westphal G, Burgemeister R, Friedemann G, Wellmann A, Wernert N, Wollscheid V, Becker B, Vogt T, Knüchel R, Stolz W, Schütze K. Noncontact laser catapulting: a basic procedure for functional genomics and proteomics. Methods Enzymol 2002; 356:80-99. [PMID: 12418190 DOI: 10.1016/s0076-6879(02)56925-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Affiliation(s)
- Sinuhe Hahn
- Laboratory for Prenatal Medicine, Department of Obstetrics and Gynecology, University of Basel, CH-4031 Basel, Switzerland
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Hahn S, Holzgreve W. Prenatal diagnosis using fetal cells and cell-free fetal DNA in maternal blood: what is currently feasible? Clin Obstet Gynecol 2002; 45:649-56; discussion 730-2. [PMID: 12370604 DOI: 10.1097/00003081-200209000-00008] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Sinuhe Hahn
- Department of Obstetrics and Gynecology, University of Basel, Switzerland.
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36
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Yan L, Kaczorowski G, Kohler M. One-tube protocol for single-cell reverse transcriptase-polymerase chain reaction. Anal Biochem 2002; 304:267-70. [PMID: 12009706 DOI: 10.1006/abio.2002.5623] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Lizhen Yan
- Department of Ion Channels, Merck Research Laboratories, RY80N-C31, Rahway, NJ 07065, USA
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37
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Heinmöller E, Liu Q, Sun Y, Schlake G, Hill KA, Weiss LM, Sommer SS. Toward efficient analysis of mutations in single cells from ethanol-fixed, paraffin-embedded, and immunohistochemically stained tissues. J Transl Med 2002; 82:443-53. [PMID: 11950901 DOI: 10.1038/labinvest.3780437] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Only a few studies have demonstrated successful molecular analysis after whole genome amplification using single cells dissected from paraffin-embedded tissues. The results in these studies were limited by low-amplification efficiency and high rates of allele dropout. In the present study, the amplification rate using a thoroughly modified primer extension and preamplification-PCR protocol was improved significantly for single cells microdissected from paraffin-embedded and immunohistochemically stained tissues. Tissue fixation with ethanol (85%) and the addition of 0.2 mmol/L EDTA helped to achieve an amplification rate between 67% (segments 200 to 400 bp) and 72% (segments <200 bp). Normal tissue sections were immunohistochemically double stained for overabundance of p53 protein and proliferating cell nuclear antigen. Microdissection of single cells was performed with a manual micromanipulator equipped with a Tungsten needle. Sequence analysis of the TP53 gene was performed after improved primer extension preamplification-PCR and multiplex PCR from single microdissected cells. The rate of allele dropout was at least 68%. These technical advances facilitate routine mutation analysis using a single cell or a few cells microdissected from routinely processed paraffin-embedded normal and tumor tissues. Allele dropout still represents a serious problem in single-cell mutation analysis, especially in samples with limited template DNA and prone to DNA damage.
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Affiliation(s)
- Ernst Heinmöller
- Department of Molecular Genetics, City of Hope National Medical Center/Beckman Research Center, Duarte, California 91010-0269, USA
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Enrichment, immunomorphological, and genetic characterization of fetal cells circulating in maternal blood. THE AMERICAN JOURNAL OF PATHOLOGY 2002; 160:51-8. [PMID: 11786398 PMCID: PMC1867119 DOI: 10.1016/s0002-9440(10)64348-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fetal cells circulating in the peripheral blood of pregnant women are a potential target for noninvasive genetic analyses. They include epithelial (trophoblastic) cells, which are larger than peripheral blood leukocytes. We enriched circulating trophoblastic cells using the isolation by size of epithelial tumor cells (ISET) method. Peripheral blood was obtained at 11 to 12 weeks of pregnancy. Cells isolated by ISET were stained by hematoxylin and eosin or by immunohistochemistry. Large epithelial cells were microdissected and fetal cell identification was obtained by polymerase chain reaction with short tandem repeats and/or Y-specific primers. By analyzing only 2 ml of blood, we found a variable number (n = 1 to 7) of Y-positive cells (overall 15 of 23) in all of the six mothers carrying a male fetus. In contrast, none of the 26 cells isolated from seven mothers carrying a female fetus scored positive. Eleven cells were analyzed by using short tandem repeat-specific markers: six of them showed a fetal profile and five showed a maternal profile consistently with Y-specific results. Only one-fifth of the single cell DNA was used for fetal cell assessment, leaving enough material for further genetic tests. We also show that the ISET approach allows the performance of fluorescence in situ hybridization analyses and the detection of DNA point mutations in single microdissected cells. We conclude that this is a powerful approach to enrich circulating fetal cells and prove their fetal origin, and that it may have implications for noninvasive prenatal diagnosis of genetic disorders.
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Zabzdyr JL, Lillard SJ. Measurement of single-cell gene expression using capillary electrophoresis. Anal Chem 2001; 73:5771-5. [PMID: 11774920 DOI: 10.1021/ac0155714] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Capillary electrophoresis with laser-induced fluorescence detection was used to monitor gene expression in individual mammalian cells using the reverse transcriptasepolymerase chain reaction. Specifically, beta-actin expression in single LNCaP (prostate cancer) cells was measured. A sieving matrix containing hydroxypropyl methyl cellulose was used to effect size-based separation. Ethidium bromide fluorescence of the product DNA was used as the detection scheme and yielded excellent sensitivity. The beta-actin product, resulting from an individual cell lysed by a freeze-thaw method, gave an average signal-to-noise ratio (S/N) of 77+/-27 (n = 2). Chemical lysis of a single cell, using a dilute solution of SDS, gave a S/N of 26+/-2 (n = 2), roughly 3-fold lower than for freeze-thaw lysis. An initial detection limit (not considering fully optimized conditions) was calculated from an amplified cDNA standard to correspond to a concentration of approximately 133 starting molecules/nL (of beta-actin mRNA).
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Affiliation(s)
- J L Zabzdyr
- Department of Chemistry, University of California, Riverside 92521, USA
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Ling G, Persson A, Berne B, Uhlén M, Lundeberg J, Ponten F. Persistent p53 mutations in single cells from normal human skin. THE AMERICAN JOURNAL OF PATHOLOGY 2001; 159:1247-53. [PMID: 11583952 PMCID: PMC1850504 DOI: 10.1016/s0002-9440(10)62511-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/16/2001] [Indexed: 10/18/2022]
Abstract
Epidermal clones of p53-mutated keratinocytes are abundant in chronically sun-exposed skin and may play an important role in early development of skin cancer. Advanced laser capture microdissection enables genetic analysis of targeted cells from tissue sections without contamination from neighboring cells. In this study p53 gene mutations were characterized in single cells from normal, chronically sun-exposed skin. Biopsies were obtained from skin subjected to daily summer sun and skin totally protected from the sun by blue denim fabric. Using laser capture microdissection, 172 single-cell samples were retrieved from four biopsies and analyzed using single-cell polymerase chain reaction and direct DNA sequencing. A total of 14 different mutations were identified in 26 of 99 keratinocytes from which the p53 gene could be amplified. Mutations displayed a typical UV signature and were detected in both scattered keratinocytes and in a small cluster of p53-immunoreactive keratinocytes. This minute epidermal p53 clone had a diameter of 10 to 15 basal cells. Two missense mutations were found in all layers of epidermis within the p53 clone. The presented data show that p53 mutations are common in normal skin and that a clone of keratinocytes with a mutated p53 gene prevailed despite 2 months of total protection from ultraviolet light.
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Affiliation(s)
- G Ling
- Department of Genetics and Pathology, University Hospital, Uppsala, Sweden
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Abstract
The presence of fetal cells and free fetal DNA in maternal blood offers an exciting opportunity for the development of safe noninvasive forms of prenatal diagnosis. Research in this field has, however, also indicated that their levels in the maternal circulation are increased in certain pregnancy-related disorders, such as preeclampsia. Their closer examination may shed new light on the underlying etiology of this enigmatic disorder.
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Affiliation(s)
- W Holzgreve
- Department of Obstetrics and Gynecology, University of Basel, Basel, Switzerland.
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Abstract
Analysis of organisms using techniques that provide high spatial and temporal resolution is of increasing interest in many disciplines of biomedical research. Although the examination of animal tissues has been the main focus to date, the recent development and improvement of methods for the sampling and handling of single cells and for their biochemical analysis now provide tools for investigating plant as well as animal cells.
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Affiliation(s)
- J Kehr
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14424, Potsdam, Germany.
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