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A Device for Isolation of Selected Single Adherent Cells. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4303586. [PMID: 36567910 PMCID: PMC9780011 DOI: 10.1155/2022/4303586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 10/29/2022] [Accepted: 11/12/2022] [Indexed: 12/23/2022]
Abstract
In recent years, extensive research has been focused on the field of single cell analysis. The isolation of single cells is the first step in this type of research. However, the techniques used for direct isolation and acquisition of single adherent cells are limited. Here, we present a method of obtaining selected single adherent cells using a separation device. Compared with other single cell isolation methods, this method has the advantages of simple operation, low cost, minimal cell damage, and preservation of cell morphology. Our methodology is, therefore, suitable for the collection of selected single adherent cells.
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Parra-Medina R, Ramírez-Clavijo S. Why not to use punch biopsies in formalin-fixed paraffin-embedded samples of prostate cancer tissue for DNA and RNA extraction? AFRICAN JOURNAL OF UROLOGY 2021. [DOI: 10.1186/s12301-021-00257-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractExtraction of DNA and RNA from formalin-fixed paraffin-embedded (FFPE) tissue blocks is a critical process in molecular oncology testing. Using FFPE, it is possible to choose the portion of tissue to study, taking into account the cell morphology, storage stability and storage conditions at room temperature, and make retrospective studies with clinical and pathological information. In prostate cancer tissue, in contrast with macroscopic tumors, it is not easy to identify the tumor; therefore, it is very important to make a microscopic diagnosis. We do not recommend punching this tissue because it can choose normal tissue for molecular analysis. In the present article we review the differences between punch biopsy and microdissection.
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Cortés-Llanos B, Wang Y, Sims CE, Allbritton NL. A technology of a different sort: microraft arrays. LAB ON A CHIP 2021; 21:3204-3218. [PMID: 34346456 PMCID: PMC8387436 DOI: 10.1039/d1lc00506e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A common procedure performed throughout biomedical research is the selection and isolation of biological entities such as organelles, cells and organoids from a mixed population. In this review, we describe the development and application of microraft arrays, an analysis and isolation platform which enables a vast range of criteria and strategies to be used when separating biological entities. The microraft arrays are comprised of elastomeric microwells with detachable polymer bases (microrafts) that act as capture and culture sites as well as supporting carriers during cell isolation. The technology is elegant in its simplicity and can be implemented for samples possessing tens to millions of objects yielding a flexible platform for applications such as single-cell RNA sequencing, subcellular organelle capture and assay, high-throughput screening and development of CRISPR gene-edited cell lines, and organoid manipulation and selection. The transparent arrays are compatible with a multitude of imaging modalities enabling selection based on 2D or 3D spatial phenotypes or temporal properties. Each microraft can be individually isolated on demand with retention of high viability due to the near zero hydrodynamic stress imposed upon the cells during microraft release, capture and deposition. The platform has been utilized as a simple manual add-on to a standard microscope or incorporated into fully automated instruments that implement state-of-the-art imaging algorithms and machine learning. The vast array of selection criteria enables separations not possible with conventional sorting methods, thus garnering widespread interest in the biological and pharmaceutical sciences.
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Morlote D, Janowski KM, Siniard RC, Guo RJ, Winokur T, DeFrank G, Harada S. Effects of Improved DNA Integrity by Punch From Tissue Blocks as Compared to Pinpoint Extraction From Unstained Slides on Next-Generation Sequencing Quality Metrics. Am J Clin Pathol 2019; 152:27-35. [PMID: 30892602 DOI: 10.1093/ajcp/aqz014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To compare the effects of two methods of formalin-fixed paraffin-embedded (FFPE) tissue harvesting on DNA quality and next-generation sequencing (NGS) quality metrics. METHODS DNA integrity number (DIN) and NGS quality metrics resulting from DNA extraction and sequencing of 199 sequential samples harvested via the Pinpoint Slide DNA Isolation System and the punch method were compared. RESULTS DNA extracted from FFPE tissue punches had higher DIN than that extracted from Pinpoint samples (mean ± SD, 6.18 ± 0.83 vs 5.09 ± 0.91; P < .0001), indicating less degradation. Lower DIN correlated with lower-quality metrics of NGS, that is lower percentage of unique on-target reads, average depth of coverage, and percentage of positions with coverage depth greater than or equal to 100×, 400×, and 1,000×. CONCLUSIONS Our study demonstrated methods to harvest tissue from FFPE blocks may affect quality of DNA, which in turn has an effect on other NGS quality metrics.
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Snow AN, Stence AA, Pruessner JA, Bossler AD, Ma D. A simple and cost-effective method of DNA extraction from small formalin-fixed paraffin-embedded tissue for molecular oncologic testing. BMC Clin Pathol 2014; 14:30. [PMID: 25067909 PMCID: PMC4110377 DOI: 10.1186/1472-6890-14-30] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/01/2014] [Indexed: 02/14/2023] Open
Abstract
Background Extraction of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is a critical step in molecular oncologic testing. As molecular oncology testing becomes more important for prognostic and therapeutic decision making and tissue specimens become smaller due to earlier detection of suspicious lesions and the use of fine needle aspiration methods for tissue collection, it becomes more challenging for the typical molecular pathology laboratory to obtain reliable test results. We developed a DNA extraction method to obtain sufficient quantity and high quality genomic DNA from limited FFPE tissue for molecular oncology testing using a combination of H&E stained slides, a matrix capture method and the Qiagen DNA column. Methods Three DNA extraction methods were compared: our standard procedure of manually scraping tissue from unstained slides followed by DNA extraction using the QIAamp FFPE column (Qiagen, Valencia, CA), a glue capture method (Pinpoint Solution, Zymo Research Corp, Inc) on H&E stained slides followed by DNA extraction using either the QIAamp column or the column included with the Pinpoint kit (Zymo Research). The DNA extraction protocol was optimized. Statistical analysis was performed using the paired two-sample student’s t-test. Results The combination of the matrix capture method with the QIAamp column gave an equivalent amount of DNA as our standard extraction method using the unstained slides and a 4.6-fold higher DNA yield than using the Zymo column included in the Pinpoint Slide Solution kit. Several molecular tests were performed and DNA purified using the new method gave the same results as for the previous methods. Conclusions Using H&E stained slides allows visual confirmation of tumor cells during microdissection. The Pinpoint solution made removal of specific tissue from the slides easier and reduced the risk of contamination and tissue loss. This DNA extraction method is simple, cost-effective, and blends with our current workflow requiring no additional equipment.
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Affiliation(s)
- Anthony N Snow
- Department of Pathology, Brown University, Rhode Island Hospital, Providence, Rhode Island 02806, USA
| | - Aaron A Stence
- Department of Pathology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, BT6008GH, Iowa City, IA 52242, USA
| | - Jonathan A Pruessner
- Department of Pathology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, BT6008GH, Iowa City, IA 52242, USA
| | - Aaron D Bossler
- Department of Pathology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, BT6008GH, Iowa City, IA 52242, USA
| | - Deqin Ma
- Department of Pathology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, BT6008GH, Iowa City, IA 52242, USA
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Wang Y, Phillips C, Xu W, Pai JH, Dhopeshwarkar R, Sims CE, Allbritton N. Micromolded arrays for separation of adherent cells. LAB ON A CHIP 2010; 10:2917-24. [PMID: 20838672 PMCID: PMC2994190 DOI: 10.1039/c0lc00186d] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We present an efficient, yet inexpensive, approach for isolating viable single cells or colonies from a mixed population. This cell microarray platform possesses innovations in both the array manufacture and the manner of target cell release. Arrays of microwells with bases composed of detachable concave elements, termed microrafts, were fabricated by a dip-coating process using a polydimethylsiloxane mold as the template and the array substrate. This manufacturing approach enabled the use of materials other than photoresists to create the array elements. Thus microrafts possessing low autofluorescence could be fabricated for fluorescence-based identification of cells. Cells plated on the microarray settled and attached at the center of the wells due to the microrafts' concavity. Individual microrafts were readily dislodged by the action of a needle inserted through the compliant polymer substrate. The hard polymer material (polystyrene or epoxy resin) of which the microrafts were composed protected the cells from damage by the needle. For cell analysis and isolation, cells of interest were identified using a standard inverted microscope and microrafts carrying target cells were dislodged with the needle. The released cells/microrafts could be efficiently collected, cultured and clonally expanded. During the separation and collection procedures, the cells remained adherent and provided a measure of protection during manipulation, thus providing an extremely high single-cell cloning rate (>95%). Generation of a transfected cell line based on expression of a fluorescent protein demonstrated an important application for performing on-chip cell separations.
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Affiliation(s)
- Yuli Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
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Pai JH, Xu W, Sims CE, Allbritton NL. Microtable arrays for culture and isolation of cell colonies. Anal Bioanal Chem 2010; 398:2595-604. [PMID: 20644916 DOI: 10.1007/s00216-010-3984-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 06/07/2010] [Accepted: 06/29/2010] [Indexed: 01/09/2023]
Abstract
Cell microarrays with culture sites composed of individually removable microstructures or micropallets have proven benefits for isolation of cells from a mixed population. The laser energy required to selectively remove these micropallets with attached cells from the array depends on the microstructure surface area in contact with the substrate. Laser energies sufficient to release micropallets greater than 100 μm resulted in loss of cell viability. A new three-dimensional culture site similar in appearance to a table was designed and fabricated using a simple process that relied on a differential sensitivity of two photoresists to UV-mediated photopolymerization. With this design, the larger culture area rests on four small supports to minimize the surface area in contact with the substrate. Microtables up to 250 × 250 μm were consistently released with single 10-μJ pulses to each of the four support structures. In contrast, microstructures with a 150 × 150-μm surface area in contact with the substrate could not be reliably released at pulse energies up to 212 μJ. Cassie-Baxter wetting is required to provide a barrier of air to localize and sequester cells to the culture sites. A second asset of the design was an increased retention of this air barrier under conditions of decreased surface tension and after prolonged culture of cells. The improved air retention was due to the hydrophobic cavity created beneath the table and above the substrate which entrapped air when an aqueous solution was added to the array. The microtables proved an efficient method for isolating colonies from the array with 100% of selected colonies competent to expand following release from the array.
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Affiliation(s)
- Jeng-Hao Pai
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
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Shadpour H, Sims CE, Allbritton NL. Enrichment and expansion of cells using antibody-coated micropallet arrays. Cytometry A 2009; 75:609-18. [PMID: 19504569 DOI: 10.1002/cyto.a.20741] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Positive selection, sorting, and collection of single cells from within a heterogeneous population are required for many biological studies. We recently demonstrated a miniaturized cell array for this purpose; however, on-chip pre-enrichment and isolation of specific target cells would provide significant value for cell isolation. In the current work, mixed cell samples of fewer than 30,000 cells were used for panning by means of on-array antibody-capture to pre-enrich the target population. The cell surface receptors Fc(epsilon)R(1), c-Kit, and ErbB2 were used for positive selection of RBL, RBL, and SK-BR-3 cells, respectively, from the mixed population. The capture efficiency, selectivity, and enrichment for the target cells were calculated and compared with fibronectin-coated controls. As expected, the capture efficiency depended on the frequency of the target cell in the mixed population over the range of 0.3-33%. For a frequency of 5% target cells, the capture efficiency was 39%-53% for the three conditions, while the selectivity varied between 78% and 98% with 16-20-fold enrichment. Furthermore, single-cell cloning studies demonstrated a high cloning efficiency of target cells selectively isolated from the array. Antibody-based pre-enrichment in combination with micropallet-based cell selection will be a valuable tool for isolation and expansion of rare cells from small heterogeneous populations.
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Affiliation(s)
- Hamed Shadpour
- Department of Chemistry, University of North Carolina, Chapel Hill, 27599, USA
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Li Y, Fester T, Taylor CG. Transcriptomic Analysis of Nematode Infestation. CELL BIOLOGY OF PLANT NEMATODE PARASITISM 2009. [DOI: 10.1007/978-3-540-85215-5_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Wang Y, Salazar GT, Pai JH, Shadpour H, Sims CE, Allbritton NL. Micropallet arrays with poly(ethylene glycol) walls. LAB ON A CHIP 2008; 8:734-40. [PMID: 18432343 PMCID: PMC2596887 DOI: 10.1039/b800286j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Arrays of releasable micropallets with surrounding walls of poly(ethylene glycol) (PEG) were fabricated for the patterning and sorting of adherent cells. PEG walls were fabricated between the SU-8 pallets using a simple, mask-free strategy. By utilizing the difference in UV-transmittance of glass and SU-8, PEG monomer was selectively photopolymerized in the space surrounding the pallets. Since the PEG walls are composed of a cross-linked structure, the stability of the walls is independent of the pallet array geometry and the properties of the overlying solution. Even though surrounded with PEG walls, the individual pallets were detached from the array by the mechanical force generated by a focused laser pulse, with a release threshold of 6 microJ. Since the PEG hydrogels are repellent to protein adsorption and cell attachment, the walls localized cell growth to the pallet top surface. Cells grown in the microwells formed by the PEG walls were released by detaching the underlying pallet. The released cells/pallets were collected, cultured and clonally expanded. The micropallet arrays with PEG walls provide a platform for performing single cell analysis and sorting on chip.
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Affiliation(s)
- Yuli Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA. E-mail: ; Fax: +1 (919) 962−2388; Tel: +1 (919) 966−2291
| | - Georgina To'a Salazar
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA. E-mail: ; Fax: +1 (919) 962−2388; Tel: +1 (919) 966−2291
- Department of Biomedical Engineering, University of California, Irvine, California, 92697, USA
| | - Jeng-Hao Pai
- Department of Chemical Engineering and Materials Science, University of California, Irvine, California, 92697, USA
| | - Hamed Shadpour
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA. E-mail: ; Fax: +1 (919) 962−2388; Tel: +1 (919) 966−2291
| | - Christopher E. Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA. E-mail: ; Fax: +1 (919) 962−2388; Tel: +1 (919) 966−2291
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA. E-mail: ; Fax: +1 (919) 962−2388; Tel: +1 (919) 966−2291
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Salazar GT, Wang Y, Sims CE, Bachman M, Li G, Allbritton NL. Characterization of the laser-based release of micropallets from arrays. JOURNAL OF BIOMEDICAL OPTICS 2008; 13:034007. [PMID: 18601552 PMCID: PMC2536741 DOI: 10.1117/1.2937475] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The micropallet array system uses a pulsed laser to release pallets tens of microns to hundreds of micrometers in size from a larger array, enabling selective isolation of single cells adherent to the pallets. We characterize the laser-based release of pallets with respect to pallet array and laser parameters. The threshold laser energy required for pallet release increases linearly with the area of the pallet in contact with the underlying glass substrate. The spacing of the pallets within an array as well as the thickness or height of the pallet does not impact the energy required to release a pallet. Delivery of multiple laser pulses decreases the energy/pulse required for pallet release when the pallets were 100 microm or greater on a side. In addition to the square pallets, complex structures such as cantilevers and spirals could be released without damage using the pulsed laser. Identification of the pallet-array variables influencing the energy required for pallet release as well as strategies to minimize this energy will prove critical in optimizing the release of pallets with cells on the arrays.
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Affiliation(s)
- Georgina To’a Salazar
- Department of Biomedical Engineering, University of California, Irvine, California, 92697
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599
| | - Yuli Wang
- Integrated Nanosystems Research Facility, University of California, Irvine, California, 92697
| | - Christopher E. Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599
| | - Mark Bachman
- Integrated Nanosystems Research Facility, University of California, Irvine, California, 92697
| | - G.P. Li
- Integrated Nanosystems Research Facility, University of California, Irvine, California, 92697
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599
- * Corresponding author NLA: 919-966-2291, , Fax: 919-962-2388
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12
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Sims CE, Bachman M, Li GP, Allbritton NL. Choosing one from the many: selection and sorting strategies for single adherent cells. Anal Bioanal Chem 2007; 387:5-8. [PMID: 16955263 DOI: 10.1007/s00216-006-0612-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Christopher E Sims
- Department of Physiology & Biophysics, School of Health Sciences, University of California, Irvine, CA 92697, USA
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Wang Y, Young G, Bachman M, Sims CE, Li GP, Allbritton NL. Collection and Expansion of Single Cells and Colonies Released from a Micropallet Array. Anal Chem 2007; 79:2359-66. [PMID: 17288466 DOI: 10.1021/ac062180m] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to selectively grow out individual cells possessing unique characteristics from within a mixed population is of widespread importance for biomedical investigations. Generation of genetically engineered cell lines, transformation studies, cell-based assays, and stem cell studies are examples where single-cell cloning is of immense value. The vast majority of mammalian cells grow adherent to a surface; therefore, positive selection followed by cloning of cells while the cells remain adherent to their growth surface is an important goal. We recently demonstrated a microfabricated cell array combined with laser-based release of individual array elements for positive selection of single cells. In the current work, a strategy to collect single cells for clonal expansion is described. The system enabled cloning of individual cells with 80-90% efficiency. Single cells were selected and cloned from small populations of fewer than 10,000 cells. Strategies used by cells to migrate from the pallets to form colonies on the surface of the collection device were examined. Implementation of encoded array elements made it possible to follow specific cells throughout the selection, collection, and cloning procedure. Thus, a particular cell can be identified by any number of imaging techniques, isolated, and clonally expanded to generate a homogeneous cell line or a pure sample for genetic or biochemical analysis.
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Affiliation(s)
- Yuli Wang
- Department of Physiology and Biophysics, Integrated Nanosystems Research Facility, Department of Electrical Engineering and Computer Science, and Department of Biomedical Engineering, University of California, Irvine, California 92697, USA
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Dafna B, Rina S, Irena S. Laser Capture Microdissection and Laser Pressure Catapulting as Tools to Study Gene Expression in Individual Cells of a Complex Tissue. Methods Cell Biol 2007; 82:675-87. [PMID: 17586276 DOI: 10.1016/s0091-679x(06)82024-8] [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: 05/15/2023]
Abstract
Laser capture microdissection (LCM) method allows the selection of individual or clustered cells from intact tissues. LCM enables to pick cells from tissues that are difficult to study individually, to sort the anatomical complexity of tissues, and to make the cells available for molecular analyses. This technology provides an opportunity to uncover the molecular control of cellular fate in the natural microenvironment. It is a difficult task to obtain cells from skeletal tissues, such as cartilage, periost, bone, and muscle, that are structured together and do not exist as individual organs. LCM allows isolation of desired cells from the native tissue environment for the analysis of gene expression. We earlier described the selection of cells from skeletal tissues that were analyzed for expression of transcription factors, receptors for cytokines, nuclear receptors, and functional genes such as alkaline phosphatase and structural proteins. Current results acquired using the LCM technology demonstrate expression of known genes that are in agreement with their reported in vivo and in vitro function in skeletal cells. The obtained knowledge will provide molecular information in the context of the cell and tissue biology. Such analysis will enable a reliable interpretation of function of known and novel genes expression in the skeletal tissues under various physiological conditions.
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Affiliation(s)
- Benayahu Dafna
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Israel
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15
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Wang Y, Young G, Aoto PC, Pai JH, Bachman M, Li GP, Sims CE, Allbritton NL. Broadening cell selection criteria with micropallet arrays of adherent cells. Cytometry A 2007; 71:866-74. [PMID: 17559133 DOI: 10.1002/cyto.a.20424] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A host of technologies exists for the separation of living, nonadherent cells, with separation decisions typically based on fluorescence or immunolabeling of cells. Methods to separate adherent cells as well as to broaden the range of possible sorting criteria would be of high value and complementary to existing strategies. Cells were cultured on arrays of releasable pallets. The arrays were screened and individual cell(s)/pallets were released and collected. Conventional fluorescence and immunolabeling of cells were compatible with the pallet arrays, as were separations based on gene expression. By varying the size of the pallet and the number of cells cultured on the array, single cells or clonal colonies of cells were isolated from a heterogeneous population. Since cells remained adherent throughout the isolation process, separations based on morphologic characteristics, for example cell shape, were feasible. Repeated measurements of each cell in an array were performed permitting the selection of cells based on their temporal behavior, e.g. growth rate. The pallet array system provides the flexibility to select and collect adherent cells based on phenotypic and temporal criteria and other characteristics not accessible by alternative methods.
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Affiliation(s)
- Yuli Wang
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
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Nakamura N, Ruebel K, Jin L, Qian X, Zhang H, Lloyd RV. Laser capture microdissection for analysis of single cells. METHODS IN MOLECULAR MEDICINE 2007; 132:11-8. [PMID: 17876072 DOI: 10.1007/978-1-59745-298-4_2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Laser capture microdissection (LCM) can be used to obtain single cells or a homogeneous population of cells for molecular analysis. This approach becomes even more powerful when it is combined with immunocytochemical staining using specific antibodies to label the cells of interest before LCM (referred to as immuno-LCM). These techniques have been applied in our laboratory to the analysis of pituitary cells from dissociated tissues and from cultured populations of heterogeneous pituitary, thyroid, and carcinoid tumor cells, as well as for the analysis of single cells in various sarcomas. When combined with reverse transcriptase polymerase chain reaction (RT-PCR) and Southern blot analysis, the sensitivity of this method is increased, allowing the reproducible analysis of gene expression from 1 to 10 cells. These methods show the utility of immuno-LCM as well as LCM combined with RT-PCR for cellular and molecular studies of gene expression.
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Affiliation(s)
- Nobuki Nakamura
- Department of Laboratory Medicine and Pathology, Mayo Clinic Medical College, Rochester, MN, USA
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Salazar GT, Wang Y, Young G, Bachman M, Sims CE, Li GP, Allbritton NL. Micropallet Arrays for the Separation of Single, Adherent Cells. Anal Chem 2006; 79:682-7. [PMID: 17222037 DOI: 10.1021/ac0615706] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The selection and collection of single cells from within a heterogeneous population is required to produce genetically engineered cell lines, to develop new stem cell lines, and for single-cell studies. We describe a new platform for the positive selection of single live mammalian cells while the cells remain adherent to their growth surface. Cells were grown on arrays of microfabricated, releasable elements composed of SU-8 polymer termed "cell pallets". The presence of air between the elements restricted the cells to the top surfaces of the pallets. Single pallets situated within large arrays of pallets were released on demand using a single, focused, laser pulse. The laser pulses were low in energy (2-5 muJ) and did not detach nearby, nontargeted pallets. Since the SU-8 pallets and the underlying glass substrate were optically transparent, the cells on the pallets could be visualized by microscopy before and after release. Over 90% of cells remained attached to the pallet during laser-based release. The feasibility of growing the cells from the released pallets into clonal colonies was demonstrated. The pallet array system permits adherent cells to be inspected using conventional microscopy and selected cells released for further analysis. The ability to assess cells while they remain adherent to a surface will broaden the number of attributes that can be utilized for cell separation, for example, cell shape, cytoskeletal properties, and other attributes.
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Affiliation(s)
- Georgina To'a Salazar
- Department of Physiology and Biophysics, Integrated Nanosystems Research Facility, University of California, Irvine, California 92697, USA
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Holloway AJ, Diyagama DS, Opeskin K, Creaney J, Robinson BWS, Lake RA, Bowtell DDL. A Molecular Diagnostic Test for Distinguishing Lung Adenocarcinoma from Malignant Mesothelioma Using Cells Collected from Pleural Effusions. Clin Cancer Res 2006; 12:5129-35. [PMID: 16951230 DOI: 10.1158/1078-0432.ccr-06-1027] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Patients with malignant mesothelioma or adenocarcinoma of the lung often present with respiratory complications associated with a malignant pleural effusion. Distinguishing between these malignancies is frequently problematic, as many of the clinical, cytologic, and histologic features of the diseases overlap. Following cytologic analysis of pleural effusions, subsequent confirmatory tissue biopsies involve increased patient morbidity and expense. We have therefore designed a gene expression-based test to classify the primary tumor causing a malignant pleural effusion, using cells collected from the effusion itself. EXPERIMENTAL DESIGN We have used microarray data for 190 lung adenocarcinomas and 33 malignant mesotheliomas to identify genes differentially expressed between the two diseases. Genes expressed in normal mesothelial cells were removed, allowing the development of a PCR-based test to measure the expression of genes that discriminate between mesothelioma and lung adenocarcinoma from cytology specimens. RESULTS Applying an real-time PCR-based assay involving 17 genes to 13 independent samples from biopsy-proven malignant mesothelioma and lung adenocarcinomas resulted in the correct identification of all samples. CONCLUSIONS We have developed a test that is able to distinguish between lung adenocarcinoma and mesothelioma in cells collected from pleural effusions.
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Affiliation(s)
- Andrew J Holloway
- Ian Potter Centre for Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia.
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Erwin CR, Jarboe MD, Sartor MA, Medvedovic M, Stringer KF, Warner BW, Bates MD. Developmental characteristics of adapting mouse small intestine crypt cells. Gastroenterology 2006; 130:1324-32. [PMID: 16618423 DOI: 10.1053/j.gastro.2006.02.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2005] [Accepted: 11/30/2005] [Indexed: 01/30/2023]
Abstract
BACKGROUND & AIMS Following massive small bowel resection (SBR), the remnant intestine undergoes an adaptive process characterized by increases in a number of physiologic and morphologic parameters. These changes are the result of a stimulus that increases crypt cell mitosis and augments cellular progression along the villus axis. To better define this process, we identified patterns of gene expression specifically within adapting intestinal crypt cells following SBR. METHODS Laser capture microdissection was used to isolate mouse intestinal crypt cells following SBR or sham operation. Multiple biological and technical complementary DNA microarray replicates allowed rigorous statistical analyses for identification of important expression profiles. Major groups of genes were classified as to site of action, functional pathway, and possible regulatory groups. RESULTS A total of 300 genes differentially expressed at significant levels within adapting crypt enterocytes were analyzed. Comparison of this list of differentially expressed adapting crypt cell genes with a generalized mouse gene expression database (from 82 developing and adult mouse tissues) showed the greatest overlap with developing and immature intestinal tissues. We identified prominent groups of genes involved with cell growth, signal transduction, and nucleic acid binding. Genes not previously shown to be involved with adaptation or development and maturation were identified. CONCLUSIONS Identification of similar genes coordinately regulated during both adaptation and development, processes that share key morphologic features, provides a basis for new mechanistic insights into these shared characteristics.
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Affiliation(s)
- Christopher R Erwin
- Division of Pediatric and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.
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20
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Abstract
Macrophages are prominent in the stromal compartment of virtually all types of malignancy. These highly versatile cells respond to the presence of stimuli in different parts of tumors with the release of a distinct repertoire of growth factors, cytokines, chemokines, and enzymes that regulate tumor growth, angiogenesis, invasion, and/or metastasis. The distinct microenvironments where tumor-associated macrophages (TAM) act include areas of invasion where TAMs promote cancer cell motility, stromal and perivascular areas where TAMs promote metastasis, and avascular and perinecrotic areas where hypoxic TAMs stimulate angiogenesis. This review will discuss the evidence for differential regulation of TAMs in these microenvironments and provide an overview of current attempts to target or use TAMs for therapeutic purposes.
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Affiliation(s)
- Claire E Lewis
- Academic Unit of Pathology, Division of Genomic Medicine, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, United Kingdom.
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21
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Ivanov D, Dvoriantchikova G, Pestova A, Nathanson L, Shestopalov VI. Microarray analysis of fiber cell maturation in the lens. FEBS Lett 2005; 579:1213-9. [PMID: 15710416 PMCID: PMC1401504 DOI: 10.1016/j.febslet.2005.01.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Revised: 12/23/2004] [Accepted: 01/07/2005] [Indexed: 11/20/2022]
Abstract
The mammalian lens consists of an aged core of quiescent cells enveloped by layers of mature fully elongated cells and younger, continuously elongating transcriptionally active cells. The fiber cell maturation is initiated when fiber cells cease to elongate. The process of maturation represents a radical switch from active elongation to a life-long quiescence and has not been studied previously. It may also include critical stages of preparation for the organelle removal and denucleation. In the present study, we used laser capture microdisection (LCM) microdissection and RNA amplification to compare global gene expression profiles of young elongating and mature, non-elongating fiber cells. Analysis of microarray data from three independent dye-swap experiments identified 65 differentially expressed genes (FDR<0.1) with greater than 2-fold change in expression levels. Microarray array results for a group of randomly selected genes were confirmed by quantitative RT-PCR. These microarray results provide clues to understanding the molecular pathways underlying lens development. The identified changes in the profile of gene expression reflected a shift in cell physiology characterizing the lens fiber maturation.
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Affiliation(s)
- Dmitry Ivanov
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL 33136, USA
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Galina Dvoriantchikova
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL 33136, USA
| | - Anna Pestova
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL 33136, USA
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Lubov Nathanson
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Valery I. Shestopalov
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL 33136, USA
- Department of Cell Biology and Anatomy, University of Miami Miller School of Medicine, Miami, FL, USA
- *Corresponding author. Fax: +1 305 547 3658. E-mail address: (V.I. Shestopalov)
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Mueller A, Merrell DS, Grimm J, Falkow S. Profiling of microdissected gastric epithelial cells reveals a cell type-specific response to Helicobacter pylori infection. Gastroenterology 2004; 127:1446-62. [PMID: 15521014 DOI: 10.1053/j.gastro.2004.08.054] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND AND AIMS Helicobacter pylori colonizes the epithelial lining of the human stomach and is associated with disorders ranging from chronic gastritis to peptic ulcers and gastric cancer. We have explored the transcriptional response of the epithelium globally by applying a whole-genome approach to a murine model of infection. METHODS The 3 major epithelial lineages of the stomach-the parietal, mucus-producing, and chief cells-were harvested from cryosections of infected and uninfected murine stomachs by laser microdissection and subjected to gene expression profiling. The localization and quantity of selected transcripts were verified by in situ hybridization and quantitative real-time reverse-transcription polymerase chain reaction. RESULTS Each cell type is characterized by a transcriptional signature profile. The parietal cell profile is highly enriched for factors involved in mitochondrial energy generation, whereas the chief cell predominantly expresses digestive enzymes and glycosylation-associated proteins. In contrast, the mucus cell signature is distinguished by an abundance of cell-surface receptors, signaling molecules, and factors involved in antigen presentation. All of these indicate a role in sampling, sensing, and responding to environmental stimuli. In line with this biological function, we measured a strong transcriptional response to Helicobacter pylori infection only in this cell type. The genes that are differentially expressed upon infection are implicated in a proinflammatory and mucosal defense response as well as modulation of angiogenesis, iron availability, and tumor suppression. CONCLUSIONS Laser microdissection-assisted transcriptional profiling is a useful tool to explore the biology of specific cell populations and is sensitive enough to measure the transcriptional response to bacterial infection in vivo.
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Affiliation(s)
- Anne Mueller
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Abstract
The "informatics revolution" in both bioinformatics and dental informatics will eventually change the way we practice dentistry. This convergence will play a pivotal role in creating a bridge of opportunity by integrating scientific and clinical specialties to promote the advances in treatment, risk assessment, diagnosis, therapeutics, and oral health-care outcome. Bioinformatics has been an emerging field in the biomedical research community and has been gaining momentum in dental medicine. This area has created a steady stream of large and complex genomic data, which has transformed the way a clinical or basic science researcher approaches genomic research. This application to dental medicine, termed "oral genomics", can aid in the molecular understanding of the genes and proteins, their interactions, pathways, and networks that are responsible for the development and progression of oral diseases and disorders. As the result of the Human Genome Project, new advances have prompted high-throughput technologies, such as DNA microarrays, which have become accepted tools in the biomedical research community. This manuscript reviews the two most commonly used microarray technologies, basic microarray data analysis, and the results from several ongoing oral cancer genomic studies.
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Affiliation(s)
- W P Kuo
- Harvard School of Dental Medicine, Department of Oral Medicine, Infection, and Immunity, 188 Longwood Avenue, Boston, MA 02115, USA.
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Abstract
With completion of the human genome sequence, it is now possible to study the expression of the entire human gene complement of approximately 30,000-35,000 genes. To accomplish this goal, microarrays have become the leading methodology for the analysis of global gene expression. Improvements in technology have increased the sensitivity of microarrays to the point where it is feasible to study gene expression in a small number of cells and even at the single cell level. A summary of developments in the area of expression profiling in single cells will be described, and the rationale for these types of studies will be presented. In addition, from a biologist's point of view, some bioinformatic challenges of expression analysis of single cells will be discussed.
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Affiliation(s)
- Ernest S Kawasaki
- Advanced Technology Center, National Cancer Institute, National Institutes of Health, 8717 Grovemont Circle, Bethesda, MD 20892, USA.
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Jaroszewicz S, Simovici DA, Kuo WP, Ohno-Machado L. The Goodman–Kruskal Coefficient and Its Applications in Genetic Diagnosis of Cancer. IEEE Trans Biomed Eng 2004; 51:1095-102. [PMID: 15248526 DOI: 10.1109/tbme.2004.827267] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Increasing interest in new pattern recognition methods has been motivated by bioinformatics research. The analysis of gene expression data originated from microarrays constitutes an important application area for classification algorithms and illustrates the need for identifying important predictors. We show that the Goodman-Kruskal coefficient can be used for constructing minimal classifiers for tabular data, and we give an algorithm that can construct such classifiers.
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Affiliation(s)
- Szymon Jaroszewicz
- Department of Computer Science, University of Massachusetts, Boston, MA 02125, USA.
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Betsuyaku T, Senior RM. Laser capture microdissection and mRNA characterization of mouse airway epithelium: methodological considerations. Micron 2004; 35:229-34. [PMID: 15003609 DOI: 10.1016/j.micron.2003.11.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2003] [Indexed: 10/26/2022]
Abstract
The use of laser capture microdissection (LCM) to obtain epithelial cells lining the distal airways for gene profiling is described. In the mouse, the distal airways are particularly attractive for LCM as there is very high percentage of a single cell type, Clara cells, lining these airways. It is shown that the RNA from distal airway epithelial cells harvested by LCM is well preserved and that with linear amplification sufficient cRNA for microarray analysis can be attained from small numbers of cells.
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Affiliation(s)
- Tomoko Betsuyaku
- First Department of Medicine, Hokkaido University School of Medicine, Sapporo, Japan.
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Todd R, August M. Molecular approaches to the diagnosis of sporadic and nevoid basal cell carcinoma syndrome-associated odontogenic keratocysts. Oral Maxillofac Surg Clin North Am 2003; 15:447-61. [PMID: 18088695 DOI: 10.1016/s1042-3699(03)00039-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Eskin SG, Horbett TA, McIntire LV, Mitchell RN, Ratner BD, Schoen FJ, Yee A. Some Background Concepts. Biomater Sci 1996. [DOI: 10.1016/b978-012582460-6/50006-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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