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Boottanun P, Nagai-Okatani C, Nagai M, Ungkulpasvich U, Yamane S, Yamada M, Kuno A. An improved evanescent fluorescence scanner suitable for high-resolution glycome mapping of formalin-fixed paraffin-embedded tissue sections. Anal Bioanal Chem 2023; 415:6975-6984. [PMID: 37395746 DOI: 10.1007/s00216-023-04824-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/25/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023]
Abstract
Lectin microarray (LMA) is a high-throughput platform that enables the rapid and sensitive analysis of N- and O-glycans attached to glycoproteins in biological samples, including formalin-fixed paraffin-embedded (FFPE) tissue sections. Here, we evaluated the sensitivity of the advanced scanner based on the evanescent-field fluorescence principle, which is equipped with a 1× infinity correction optical system and a high-end complementary metal-oxide semiconductor (CMOS) image sensor in digital binning mode. Using various glycoprotein samples, we estimated that the mGSR1200-CMOS scanner has at least fourfold higher sensitivity for the lower limit of linearity range than that of a previous charge-coupled device scanner (mGSR1200). A subsequent sensitivity test using HEK293T cell lysates demonstrated that cell glycomic profiling could be performed with only three cells, which has the potential for the glycomic profiling of cell subpopulations. Thus, we examined its application in tissue glycome mapping, as indicated in the online LM-GlycomeAtlas database. To achieve fine glycome mapping, we refined the laser microdissection-assisted LMA procedure to analyze FFPE tissue sections. In this protocol, it was sufficient to collect 0.1 mm2 of each of the tissue fragments from 5-μm-thick sections, which differentiated the glycomic profile between the glomerulus and renal tubules of a normal mouse kidney. In conclusion, the improved LMA enables high-resolution spatial analysis, which expands the possibilities of its application classifying cell subpopulations in clinical FFPE tissue specimens. This will be used in the discovery phase for the development of novel glyco-biomarkers and therapeutic targets, and to expand the range of target diseases.
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Affiliation(s)
- Patcharaporn Boottanun
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan
| | - Chiaki Nagai-Okatani
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan.
| | - Misugi Nagai
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan
| | - Umbhorn Ungkulpasvich
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan
| | - Shinjiro Yamane
- GlycoTechnica Ltd, 101 Hiranobiru3, 5-28-6 Utsukushigaoka, Aoba-Ku, Yokohama, Kanagawa, 225-0002, Japan
| | - Masao Yamada
- EMUKK LLC, 2-21-19, Matsunoki, Kuwana, Mie, 511-0902, Japan
| | - Atsushi Kuno
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan.
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Lysov Y, Barsky V, Urasov D, Urasov R, Cherepanov A, Mamaev D, Yegorov Y, Chudinov A, Surzhikov S, Rubina A, Smoldovskaya O, Zasedatelev A. Microarray analyzer based on wide field fluorescent microscopy with laser illumination and a device for speckle suppression. BIOMEDICAL OPTICS EXPRESS 2017; 8:4798-4810. [PMID: 29188082 PMCID: PMC5695932 DOI: 10.1364/boe.8.004798] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/07/2017] [Accepted: 09/29/2017] [Indexed: 06/07/2023]
Abstract
A microarray analyzer was developed to obtain images and measure the fluorescence intensity of microarrays at three wavelengths from 380 nm to 850 nm. The analyzer contains lasers to excite fluorescence, barrier filters, optics to project images on an image detector, and a device for suppressing laser speckles on the microarray support. The speckle suppression device contains a fibre-optic bundle and a rotating mirror positioned in a way to change the distance between the bundle butt and mirror surface during each mirror revolution. The analyzer provides for measurements with accuracy within ± 5%. Obtaining images at several exposure times allowed a significant expansion in the range of measured fluorescence intensities. The analyzer is useful for high throughput analysis of the same type of microarrays.
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Affiliation(s)
- Yuri Lysov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Victor Barsky
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Dmitriy Urasov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Roman Urasov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Alecksey Cherepanov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Dmitryi Mamaev
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Yegor Yegorov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Alexander Chudinov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Sergey Surzhikov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Alla Rubina
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Olga Smoldovskaya
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
| | - Alexander Zasedatelev
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
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Gopinath SC, Tang TH, Chen Y, Citartan M, Lakshmipriya T. Bacterial detection: From microscope to smartphone. Biosens Bioelectron 2014; 60:332-42. [DOI: 10.1016/j.bios.2014.04.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/13/2014] [Accepted: 04/07/2014] [Indexed: 01/15/2023]
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Li XZ, Kim S, Cho W, Lee SY. Optical detection of nanoparticle-enhanced human papillomavirus genotyping microarrays. BIOMEDICAL OPTICS EXPRESS 2013; 4:187-192. [PMID: 23413051 PMCID: PMC3567705 DOI: 10.1364/boe.4.000187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 12/03/2012] [Accepted: 12/19/2012] [Indexed: 06/01/2023]
Abstract
In this study, we propose a new detection method of nanoparticle-enhanced human papillomavirus genotyping microarrays using a DVD optical pick-up with a photodiode. The HPV genotyping DNA chip was labeled using Au/Ag core-shell nanoparticles, prepared on a treatment glass substrate. Then, the bio information of the HPV genotyping target DNA was detected by measuring the difference of the optical signals between the DNA spots and the background parts for cervical cancer diagnosis. Moreover the approximate linear relationship between the concentration of the HPV genotyping target DNA and the optical signal depending on the density of Au/Ag core-shell nanoparticles was obtained by performing a spot finding algorithm. It is shown that the nanoparticle-labeled HPV genotyping target DNA can be measured and quantified by collecting the low-cost photodiode signal on the treatment glass chip, replacing high-cost fluorescence microarray scanners using a photomultiplier tube.
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Affiliation(s)
- Xue Zhe Li
- Nanostorage Inc., #714 DMC Hi-Tech Industry Center, 1580,
Sangam-Dong, Mapo-Ku, Seoul 121-270, Korea
| | - Sookyung Kim
- Nanostorage Inc., #714 DMC Hi-Tech Industry Center, 1580,
Sangam-Dong, Mapo-Ku, Seoul 121-270, Korea
| | - Wonhyung Cho
- Nanostorage Inc., #714 DMC Hi-Tech Industry Center, 1580,
Sangam-Dong, Mapo-Ku, Seoul 121-270, Korea
| | - Seung-Yop Lee
- Department of Mechanical Engineering, Sogang University, Shinsu-Dong,
Mapo-Ku, Seoul 121-742, Korea
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Magbanua MJM, Sosa EV, Scott JH, Simko J, Collins C, Pinkel D, Ryan CJ, Park JW. Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer. BMC Cancer 2012; 12:78. [PMID: 22373240 PMCID: PMC3395839 DOI: 10.1186/1471-2407-12-78] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 02/28/2012] [Indexed: 11/30/2022] Open
Abstract
Background The number of circulating tumor cells (CTCs) in metastatic prostate cancer patients provides prognostic and predictive information. However, it is the molecular characterization of CTCs that offers insight into the biology of these tumor cells in the context of personalized treatment. Methods We developed a novel approach to isolate CTCs away from hematopoietic cells with high purity, enabling genomic analysis of these cells. The isolation protocol involves immunomagnetic enrichment followed by fluorescence activated cell sorting (IE/FACS). To evaluate the feasibility of isolation of CTCs by IE/FACS and downstream genomic profiling, we conducted a pilot study in patients with metastatic castration resistant prostate cancer (CRPC). Twenty (20) sequential CRPC patients were assayed using CellSearch™. Twelve (12) patients positive for CTCs were subjected to immunomagnetic enrichment and fluorescence activated cell sorting (IE/FACS) to isolate CTCs. Genomic DNA of CTCs was subjected to whole genome amplification (WGA) followed by gene copy number analysis via array comparative genomic hybridization (aCGH). Results CTCs from nine (9) patients successfully profiled were observed to have multiple copy number aberrations including those previously reported in primary prostate tumors such as gains in 8q and losses in 8p. High-level copy number gains at the androgen receptor (AR) locus were observed in 7 (78%) cases. Comparison of genomic profiles between CTCs and archival primary tumors from the same patients revealed common lineage. However, high-level copy number gains in the AR locus were observed in CTCs, but not in the matched archival primary tumors. Conclusions We developed a new approach to isolate prostate CTCs without significant leukocyte admixture, and to subject them to genome-wide copy number analysis. Our assay may be utilized to explore genomic events involved in cancer progression, e.g. development of castration resistance and to monitor therapeutic efficacy of targeted therapies in clinical trials in a relatively non-invasive manner.
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Affiliation(s)
- Mark Jesus M Magbanua
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, USA
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Haga T, Takahashi S, Sonehara T, Kumazaki N, Anazawa T. Dual-view imaging system using a wide-range dichroic mirror for simultaneous four-color single-molecule detection. Anal Chem 2011; 83:6948-55. [PMID: 21805964 DOI: 10.1021/ac2000797] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A dual-view imaging system for simultaneous four-color single-molecule (SM) detection was developed. As for the detection procedure, four species of SM fluorophores, namely, Alexa 488, 555, 647, and 680, are immobilized on different slides and excited by evanescent-wave illumination. Fluorescence emitted from an SM fluorophore is split by a wide-range dichroic mirror (WR DM) in a dual-view optics and imaged as two SM fluorescence spots (SM spots) on an electron-multiplying charge-coupled device (EM-CCD) at 100 Hz. The transmittance of the WR DM changes gradually over the wavelength range of 500 to 700 nm so that the signal ratios of the two SM spots for the four fluorophore species differ. A method for classifying SM fluorophores into four species in accordance with their signal ratios was developed. It was used to classify 597 SM fluorophores at an accuracy of above 98% for all the species. This accuracy is comparable to that of a conventional four-color SM detection system. To classify four species, the conventional system disperses SM fluorescence with a prism and provides an elongated SM spot that uses more pixels of an EM-CCD chip than that of the developed system. The developed system can thus detect 1.5-fold more SM spots with the same-size EM-CCD chip, so it can achieve 1.5-fold higher throughput. Moreover, the developed system is based on a simple and practical approach, namely, replacing an ordinary dichroic mirror in a commercially available dual-view optics with a WR DM. This replacement transforms a dual-view imaging system for two-color detection into a system for four-color detection. The developed system is suitable for detection systems of next-generation DNA sequencers and DNA microarray-chip analyzers.
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Affiliation(s)
- Takanobu Haga
- Central Research Laboratory, Hitachi, Ltd., Kokubunji-shi, Tokyo, Japan.
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Real-time detection of DNA hybridization on microarray using a CCD-based imaging system equipped with a rotated microlens array disk. Biosens Bioelectron 2011; 26:1942-6. [DOI: 10.1016/j.bios.2010.07.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/24/2010] [Accepted: 07/06/2010] [Indexed: 11/24/2022]
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Davari P, Hebert JL, Albertson DG, Huey B, Roy R, Mancianti ML, Horvai AE, McDaniel LD, Schultz RA, Epstein EH. Loss of Blm enhances basal cell carcinoma and rhabdomyosarcoma tumorigenesis in Ptch1+/- mice. Carcinogenesis 2009; 31:968-73. [PMID: 19995795 DOI: 10.1093/carcin/bgp309] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Basal cell carcinomas (BCCs) have relative genomic stability and relatively benign clinical behavior but whether these two are related causally is unknown. To investigate the effects of introducing genomic instability into murine BCCs, we have compared ionizing radiation-induced tumorigenesis in Ptch1(+/-) mice versus that in Ptch1(+/-) mice carrying mutant Blm alleles. We found that BCCs in Ptch1(+/-) Blm(tm3Brd/tm3Brd) mice had a trend toward greater genomic instability as measured by array comprehensive genomic hybridization and that these mice developed significantly more microscopic BCCs than did Ptch1(+/-) Blm(+/tm3Brd) or Ptch1(+/-) Blm(+/+) mice. The mutant Blm alleles also markedly enhanced the formation of rhabdomyosarcomas (RMSs), another cancer to which Ptch1(+/)(-) mice and PTCH1(+/)(-) (basal cell nevus syndrome) patients are susceptible. Highly recurrent but different copy number changes were associated with the two tumor types and included losses of chromosomes 4 and 10 in all BCCs and gain of chromosome 10 in 80% of RMSs. Loss of chromosome 11 and 13, including the Trp53 and Ptch1 loci, respectively, occurred frequently in BCCs, suggesting tissue-specific selection for genes or pathways that collaborate with Ptch deficiency in tumorigenesis. Despite the quantitative differences, there was no dramatic qualititative difference in the BCC or RMS tumors associated with the mutant Blm genotype.
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Affiliation(s)
- Parastoo Davari
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
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Sukumaran SM, Potsaid B, Lee MY, Clark DS, Dordick JS. Development of a fluorescence-based, ultra high-throughput screening platform for nanoliter-scale cytochrome p450 microarrays. ACTA ACUST UNITED AC 2009; 14:668-78. [PMID: 19525490 DOI: 10.1177/1087057109336592] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Cytochrome P450 enzyme (CYP450s) assays are critical enzymes in early-stage lead discovery and optimization in drug development. Currently available fluorescence-based reaction assays provide a rapid and reliable method for monitoring CYP450 enzyme activity but are confined to medium-throughput well-plate systems. The authors present a high-throughput, integrated screening platform for CYP450 assays combining enzyme encapsulation techniques, microarraying methods, and wide-field imaging. Alginate-containing microarrays consisting of up to 1134 CYP450 reaction elements were fabricated on functionalized glass slides (reaction volumes 20 to 80 nL, total enzyme content in pg) and imaged to yield endpoint activity, stability, and kinetic data. A charge-coupled device imager acquired quantitative, high-resolution images of a 20x20 mm area/snapshot using custom-built wide-field optics with telecentric lenses and easily interchangeable filter sets. The imaging system offered a broad dynamic intensity range (linear over 3 orders of magnitude) and sensitivity down to fluorochrome quantities of <5 fmols, with read accuracy similar to a laser scanner or a fluorescence plate reader but with higher throughput. Rapid image acquisition enabled analysis of CYP450 kinetics. Fluorogenic assays with CYP3A4, CYP2C9, and CYP2D6 on the alginate microarrays exhibited Z' factors ranging from 0.75 to 0.85, sensitive detection of inhibitory compounds, and reactivity comparable to that in solution, thereby demonstrating the reliability and accuracy of the microarray platform. This system enables for the first time a significant miniaturization of CYP enzyme assays with significant conservation of assay reagents, greatly increased throughput, and no apparent loss of enzyme activity or assay sensitivity.
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Affiliation(s)
- Sumitra M Sukumaran
- Department of Chemical and Biological Engineering and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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Erfurth F, Tretyakov A, Nyuyki B, Mrotzek G, Schmidt WD, Fassler D, Saluz HP. Two-Laser, Large-Field Hyperspectral Microarray Scanner for the Analysis of Multicolor Microarrays. Anal Chem 2008; 80:7706-13. [DOI: 10.1021/ac801014m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florian Erfurth
- Department of Photonics and Sensors, Innovative Bio-, Medical- and Environmental Technologies (GMBU e.V.), Felsbachstrasse 7 D-07745 Jena, Germany, and Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, D-07745 Jena, Germany
| | - Alexander Tretyakov
- Department of Photonics and Sensors, Innovative Bio-, Medical- and Environmental Technologies (GMBU e.V.), Felsbachstrasse 7 D-07745 Jena, Germany, and Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, D-07745 Jena, Germany
| | - Berla Nyuyki
- Department of Photonics and Sensors, Innovative Bio-, Medical- and Environmental Technologies (GMBU e.V.), Felsbachstrasse 7 D-07745 Jena, Germany, and Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, D-07745 Jena, Germany
| | - Grit Mrotzek
- Department of Photonics and Sensors, Innovative Bio-, Medical- and Environmental Technologies (GMBU e.V.), Felsbachstrasse 7 D-07745 Jena, Germany, and Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, D-07745 Jena, Germany
| | - Wolf-Dieter Schmidt
- Department of Photonics and Sensors, Innovative Bio-, Medical- and Environmental Technologies (GMBU e.V.), Felsbachstrasse 7 D-07745 Jena, Germany, and Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, D-07745 Jena, Germany
| | - Dieter Fassler
- Department of Photonics and Sensors, Innovative Bio-, Medical- and Environmental Technologies (GMBU e.V.), Felsbachstrasse 7 D-07745 Jena, Germany, and Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, D-07745 Jena, Germany
| | - Hans Peter Saluz
- Department of Photonics and Sensors, Innovative Bio-, Medical- and Environmental Technologies (GMBU e.V.), Felsbachstrasse 7 D-07745 Jena, Germany, and Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, D-07745 Jena, Germany
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Clark SM, Hamilton GE, Nordmeyer RA, Uber D, Cornell EW, Brown N, Segraves R, Davis R, Albertson DG, Pinkel D. High-efficiency microarray printer using fused-silica capillary tube printing pins. Anal Chem 2008; 80:7639-42. [PMID: 18763810 DOI: 10.1021/ac8010395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a contact printing approach for microarrays that uses fused-silica capillary tubes with tapered tips for printing pins and a pressure/vacuum system to control pin loading, printing, and cleaning. The printing process is insensitive to variable environmental factors such as humidity, and the small diameter of the pins allows routine printing from 1536 well source plates. Pin load capacity, 0.2 microL in the current system, is adjustable by controlling pin length. More than 2000 spots can be printed per 0.2-microL pin load (<100 pl/spot), and densities of >12,000 spots/cm(2) are readily achievable. Solutions with a wide range of viscosities and chemical properties can be printed. The system can print tens of thousands of different solutions at high speed, due to the ability to use large numbers of pins simultaneously, and can produce a large number of replicate arrays since all of the solution picked up by the pins is available for deposition.
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Affiliation(s)
- Steve M Clark
- University of California San Francisco, Box 0808, San Francisco, California 94143, USA
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12
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Gajduskova P, Snijders AM, Kwek S, Roydasgupta R, Fridlyand J, Tokuyasu T, Pinkel D, Albertson DG. Genome position and gene amplification. Genome Biol 2008; 8:R120. [PMID: 17584934 PMCID: PMC2394771 DOI: 10.1186/gb-2007-8-6-r120] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 05/15/2007] [Accepted: 06/21/2007] [Indexed: 01/05/2023] Open
Abstract
Genomic analyses of human cells expressing dihydrofolate reductase provide insight into the effects of genome position on the propensity for a drug-resistance gene to amplify in human cells.
Background Amplifications, regions of focal high-level copy number change, lead to overexpression of oncogenes or drug resistance genes in tumors. Their presence is often associated with poor prognosis; however, the use of amplification as a mechanism for overexpression of a particular gene in tumors varies. To investigate the influence of genome position on propensity to amplify, we integrated a mutant form of the gene encoding dihydrofolate reductase into different positions in the human genome, challenged cells with methotrexate and then studied the genomic alterations arising in drug resistant cells. Results We observed site-specific differences in methotrexate sensitivity, amplicon organization and amplification frequency. One site was uniquely associated with a significantly enhanced propensity to amplify and recurrent amplicon boundaries, possibly implicating a rare folate-sensitive fragile site in initiating amplification. Hierarchical clustering of gene expression patterns and subsequent gene enrichment analysis revealed two clusters differing significantly in expression of MYC target genes independent of integration site. Conclusion These studies suggest that genome context together with the particular challenges to genome stability experienced during the progression to cancer contribute to the propensity to amplify a specific oncogene or drug resistance gene, whereas the overall functional response to drug (or other) challenge may be independent of the genomic location of an oncogene.
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Affiliation(s)
- Pavla Gajduskova
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská, Brno, 612 65, Czech Republic
| | - Antoine M Snijders
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Serena Kwek
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Ritu Roydasgupta
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Jane Fridlyand
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Taku Tokuyasu
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Daniel Pinkel
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Donna G Albertson
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
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Home-built integrated microarray system (IMAS). A three-laser confocal fluorescence scanner coupled with a microarray printer. Anal Bioanal Chem 2008; 390:1563-73. [DOI: 10.1007/s00216-008-1842-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Revised: 12/20/2007] [Accepted: 01/08/2008] [Indexed: 11/26/2022]
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14
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Boland E, Clayton-Smith J, Woo VG, McKee S, Manson FDC, Medne L, Zackai E, Swanson EA, Fitzpatrick D, Millen KJ, Sherr EH, Dobyns WB, Black GCM. Mapping of deletion and translocation breakpoints in 1q44 implicates the serine/threonine kinase AKT3 in postnatal microcephaly and agenesis of the corpus callosum. Am J Hum Genet 2007; 81:292-303. [PMID: 17668379 PMCID: PMC1950798 DOI: 10.1086/519999] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 05/02/2007] [Indexed: 12/08/2022] Open
Abstract
Deletions of chromosome 1q42-q44 have been reported in a variety of developmental abnormalities of the brain, including microcephaly (MIC) and agenesis of the corpus callosum (ACC). Here, we describe detailed mapping studies of patients with unbalanced structural rearrangements of distal 1q4. These define a 3.5-Mb critical region extending from RP11-80B9 to RP11-241M7 that we hypothesize contains one or more genes that lead to MIC and ACC when present in only one functional copy. Next, mapping of a balanced reciprocal t(1;13)(q44;q32) translocation in a patient with postnatal MIC and ACC demonstrated a breakpoint within this region that is situated 20 kb upstream of AKT3, a serine-threonine kinase. The murine orthologue Akt3 is required for the developmental regulation of normal brain size and callosal development. Whereas sequencing of AKT3 in a panel of 45 patients with ACC did not demonstrate any pathogenic variations, whole-mount in situ hybridization confirmed expression of Akt3 in the developing central nervous system during mouse embryogenesis. AKT3 represents an excellent candidate for developmental human MIC and ACC, and we suggest that haploinsufficiency causes both postnatal MIC and ACC.
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Affiliation(s)
- Elena Boland
- Academic Unit of Medical Genetics and Regional Genetic Service, St. Mary's Hospital, and Centre for Molecular Medicine, The University of Manchester, M13 0JH, UK
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Benz CC, Fedele V, Xu F, Ylstra B, Ginzinger D, Yu M, Moore D, Hall RK, Wolff DJ, Disis ML, Eppenberger-Castori S, Eppenberger U, Schittulli F, Tommasi S, Paradiso A, Scott GK, Albertson DG. Altered promoter usage characterizes monoallelic transcription arising with ERBB2 amplification in human breast cancers. Genes Chromosomes Cancer 2006; 45:983-94. [PMID: 16883574 DOI: 10.1002/gcc.20364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Analysis of a collection of human breast cancers (n = 150), enriched in ERBB2-positive cases (n = 57) and involving tumor genotyping relative to population-matched blood genotyping (n = 749) for a common ERBB2 single nucleotide polymorphism Ala(G)1170Pro(C), revealed that ERBB2 amplification in breast cancer is invariably monoallelic. Analysis of paired breast cancer and blood samples from informative (G1170C heterozygotic) ERBB2-positive (n = 12) and ERBB2-negative (n = 17) cases not only confirmed monoallelic amplification and ERBB2 transcriptional overexpression but also revealed that most low ERBB2 expressing breast cancers (12/17) exhibit unbalanced allelic transcription, showing 3-fold to nearly 5,000-fold preferential expression from one of two inherited alleles. To explore cis-acting transcriptional mechanisms potentially selected during ERBB2 amplification, levels of four different ERBB2 transcript variants (5.2, 4.7, 2.1, and 1.4 kb) were correlated with total (4.6 kb) ERBB2 mRNA levels in ERBB2-positive (n = 14) versus ERBB2-negative (n = 43) primary breast cancers. Relative expression of only the 2.1 kb extracellular domain-encoding splice variant and a 4.7 kb mRNA variant that uses an alternative start site were significantly increased in association with ERBB2-positivity, implicating altered promoter usage and selective transcript regulation within the ERBB2 amplicon. Altogether, these findings provide new mechanistic insights into the development of ERBB2-positive breast cancer and strong rationale for delineating candidate cis-acting regulatory elements that may link allele-specific ERBB2 transcription in premalignant breast epithelia with subsequent development of breast cancers bearing monoallelic ERBB2 amplicons.
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