1
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Jenike AE, Bunkelman B, Perzel Mandell KA, Oduor CI, Chin D, Mair D, Jenike KM, Kim DH, Bailey JA, Rafailovich MH, Rosenberg AZ, Halushka MK. Expression Microdissection for the Analysis of miRNA in a Single-Cell Type. J Transl Med 2023; 103:100133. [PMID: 36990152 PMCID: PMC10524025 DOI: 10.1016/j.labinv.2023.100133] [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: 10/04/2022] [Revised: 02/19/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Cell-specific microRNA (miRNA) expression estimates are important in characterizing the localization of miRNA signaling within tissues. Much of these data are obtained from cultured cells, a process known to significantly alter miRNA expression levels. Thus, our knowledge of in vivo cell miRNA expression estimates is poor. We previously demonstrated expression microdissection-miRNA-sequencing (xMD-miRNA-seq) to acquire in vivo estimates, directly from formalin-fixed tissues, albeit with a limited yield. In this study, we optimized each step of the xMD process, including tissue retrieval, tissue transfer, film preparation, and RNA isolation, to increase RNA yields and ultimately show strong enrichment for in vivo miRNA expression by qPCR array. These method improvements, such as the development of a noncrosslinked ethylene vinyl acetate membrane, resulted in a 23- to 45-fold increase in miRNA yield, depending on the cell type. By qPCR, miR-200a increased by 14-fold in xMD-derived small intestine epithelial cells, with a concurrent 336-fold reduction in miR-143 relative to the matched nondissected duodenal tissue. xMD is now an optimized method to obtain robust in vivo miRNA expression estimates from cells. xMD will allow formalin-fixed tissues from surgical pathology archives to make theragnostic biomarker discoveries.
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Affiliation(s)
- Ana E Jenike
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brady Bunkelman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kira A Perzel Mandell
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cliff I Oduor
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Deborah Chin
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Devin Mair
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Katharine M Jenike
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Deok-Ho Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Miriam H Rafailovich
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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2
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Johann DJ, Shin IJ, Roberge A, Laun S, Peterson EA, Liu M, Steliga MA, Muesse J, Emmert-Buck MR, Tangrea MA. Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples. J Histochem Cytochem 2022; 70:643-658. [PMID: 36129255 PMCID: PMC9527476 DOI: 10.1369/00221554221124163] [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: 05/25/2021] [Accepted: 08/12/2022] [Indexed: 11/22/2022] Open
Abstract
Immunohistochemical (IHC) staining is an established technique for visualizing proteins in tissue sections for research studies and clinical applications. IHC is increasingly used as a targeting strategy for procurement of labeled cells via tissue microdissection, including immunodissection, computer-aided laser dissection (CALD), expression microdissection (xMD), and other techniques. The initial antigen retrieval (AR) process increases epitope availability and improves staining characteristics; however, the procedure can damage DNA. To better understand the effects of AR on DNA quality and quantity in immunodissected samples, both clinical specimens (KRAS gene mutation positive cases) and model system samples (lung cancer patient-derived xenograft tissue) were subjected to commonly employed AR methods (heat induced epitope retrieval [HIER], protease digestion) and the effects on DNA were assessed by Qubit, fragment analysis, quantitative PCR, digital droplet PCR (ddPCR), library preparation, and targeted sequencing. The data showed that HIER resulted in optimal IHC staining characteristics, but induced significant damage to DNA, producing extensive fragmentation and decreased overall yields. However, neither of the AR methods combined with IHC prevented ddPCR amplification of small amplicons and gene mutations were successfully identified from immunodissected clinical samples. The results indicate for the first time that DNA recovered from immunostained slides after standard AR and IHC processing can be successfully employed for genomic mutation analysis via ddPCR and next-generation sequencing (NGS) short-read methods.
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Affiliation(s)
- Donald J. Johann
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ik Jae Shin
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Sarah Laun
- Avoneaux Medical Institute, Baltimore,
Maryland
- Alvin & Lois Lapidus Cancer Institute,
Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, Maryland
| | - Erich A. Peterson
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Meei Liu
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Matthew A. Steliga
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jason Muesse
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Michael A. Tangrea
- Alvin & Lois Lapidus Cancer Institute,
Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, Maryland
- Biology Department, Loyola University
Maryland, Baltimore, Maryland
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3
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Han CM, Waks E, Shapiro B. Mathematical modeling and experimental validation for expression microdissection. APPLIED OPTICS 2020; 59:5870-5880. [PMID: 32672729 DOI: 10.1364/ao.395864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Using laser excitation, expression microdissection (xMD) can selectively heat cancer cells targeted via immunohistochemical staining to enable their selective retrieval from tumor tissue samples, thus reducing misdiagnoses caused by contamination of noncancerous cells. Several theoretical models have been validated for the photothermal effect in highly light absorbing and scattering media. However, these models are not generally applicable to the physics behind the process of xMD. In this study, we propose a thermal model that can analyze the transient temperature distribution and heat melt zone in an xMD sample medium composed of a thermoplastic film and a tumor tissue sample sandwiched between two glass slides. Furthermore, we experimentally examined the model using an ink layer with controllable optical properties to serve as a microscale-thin, tissue-mimicking phantom and found the experimentally measured film temperature is in good agreement with the model predictions. The validated model can help researchers to optimize cell retrieval by xMD for improved diagnostics of cancer and other diseases.
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4
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Legrès LG. [Laser microdissection applications in histology: an open way to molecular studies]. Med Sci (Paris) 2019; 35:871-879. [PMID: 31845879 DOI: 10.1051/medsci/2019166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One of the most fascinating aspects of the use of a laser beam in the field of biology has emerged with the development of devices able to perform fine dissections of biological tissues. Laser microdissection can collect phenotypically identical cells from tissue regions laid on a microscope slide in order to make differential molecular analyses on these microdissected cells. Laser microdissection can be used many areas including oncology to specify molecular mechanisms that enable to adapt a treatment related to diagnosis and research in biology, but also forensic science for tissue selection, neurology for post-mortem studies on patients with Alzheimer's disease, for clonality studies from cell cultures and cytogenetics to decipher chromosomal rearrangements. This technology represents the missing link between clinical observations and the intrinsic physiological mechanisms of biological tissues and its major applications will be addressed here.
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Affiliation(s)
- Luc G Legrès
- Institut de recherche Saint-Louis, Paris, France, UMR_S 976 Inserm, Université de Paris, Hôpital Saint-Louis, 1 avenue Claude-Vellefaux, F-75010 Paris, France
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5
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Hipp JD, Johann DJ, Chen Y, Madabhushi A, Monaco J, Cheng J, Rodriguez-Canales J, Stumpe MC, Riedlinger G, Rosenberg AZ, Hanson JC, Kunju LP, Emmert-Buck MR, Balis UJ, Tangrea MA. Computer-Aided Laser Dissection: A Microdissection Workflow Leveraging Image Analysis Tools. J Pathol Inform 2018; 9:45. [PMID: 30622835 PMCID: PMC6298131 DOI: 10.4103/jpi.jpi_60_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/16/2018] [Indexed: 01/05/2023] Open
Abstract
Introduction The development and application of new molecular diagnostic assays based on next-generation sequencing and proteomics require improved methodologies for procurement of target cells from histological sections. Laser microdissection can successfully isolate distinct cells from tissue specimens based on visual selection for many research and clinical applications. However, this can be a daunting task when a large number of cells are required for molecular analysis or when a sizeable number of specimens need to be evaluated. Materials and Methods To improve the efficiency of the cellular identification process, we describe a microdissection workflow that leverages recently developed and open source image analysis algorithms referred to as computer-aided laser dissection (CALD). CALD permits a computer algorithm to identify the cells of interest and drive the dissection process. Results We describe several "use cases" that demonstrate the integration of image analytic tools probabilistic pairwise Markov model, ImageJ, spatially invariant vector quantization (SIVQ), and eSeg onto the ThermoFisher Scientific ArcturusXT and Leica LMD7000 microdissection platforms. Conclusions The CALD methodology demonstrates the integration of image analysis tools with the microdissection workflow and shows the potential impact to clinical and life science applications.
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Affiliation(s)
- Jason D Hipp
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Google Inc., Mountain View, CA, USA
| | - Donald J Johann
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yun Chen
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Anant Madabhushi
- Department of Biomedical Engineering, Center for Computational Imaging and Personalized Diagnostics, Case Western Reserve University, Cleveland, OH, USA
| | | | - Jerome Cheng
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jaime Rodriguez-Canales
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Medimmune, LLC, Gaithersburg, MD, USA
| | | | - Greg Riedlinger
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Division of Translational Pathology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Avi Z Rosenberg
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jeffrey C Hanson
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Lakshmi P Kunju
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Michael R Emmert-Buck
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Avoneaux Medical Institute, LLC, Baltimore, MD, USA
| | - Ulysses J Balis
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Tangrea
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Alvin and Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
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6
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Kumar B, Rosenberg AZ, Choi SM, Fox-Talbot K, De Marzo AM, Nonn L, Brennen WN, Marchionni L, Halushka MK, Lupold SE. Cell-type specific expression of oncogenic and tumor suppressive microRNAs in the human prostate and prostate cancer. Sci Rep 2018; 8:7189. [PMID: 29739972 PMCID: PMC5940660 DOI: 10.1038/s41598-018-25320-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/19/2018] [Indexed: 02/06/2023] Open
Abstract
MiR-1 and miR-143 are frequently reduced in human prostate cancer (PCa), while miR-141 and miR-21 are frequently elevated. Consequently, these miRNAs have been studied as cell-autonomous tumor suppressors and oncogenes. However, the cell-type specificity of these miRNAs is not well defined in prostate tissue. Through two different microdissection techniques, and droplet digital RT-PCR, we quantified these miRNAs in the stroma and epithelium of radical prostatectomy specimens. In contrast to their purported roles as cell-autonomous tumor suppressors, we found miR-1 and miR-143 expression to be predominantly stromal. Conversely, miR-141 was predominantly epithelial. miR-21 was detected in both stroma and epithelium. Strikingly, the levels of miR-1 and miR-143 were significantly reduced in tumor-associated stroma, but not tumor epithelium. Gene expression analyses in human cell lines, tissues, and prostate-derived stromal cultures support the cell-type selective expression of miR-1, miR-141, and miR-143. Analyses of the PCa Genome Atlas (TCGA-PRAD) showed a strong positive correlation between stromal markers and miR-1 and miR-143, and a strong negative correlation between stromal markers and miR-141. In these tumors, loss of miR-1 and gain of miR-21 was highly associated with biochemical recurrence. These data shed new light on stromal and epithelial miRNA expression in the PCa tumor microenvironment.
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Affiliation(s)
- Binod Kumar
- The James Buchanan Brady Urologic Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Avi Z Rosenberg
- The Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Su Mi Choi
- The James Buchanan Brady Urologic Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Karen Fox-Talbot
- The Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Angelo M De Marzo
- The James Buchanan Brady Urologic Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,The Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Larisa Nonn
- The Department of Pathology, University of Illinois, Chicago, IL, USA
| | - W Nathaniel Brennen
- The Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Luigi Marchionni
- The Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Marc K Halushka
- The Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.,The Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Shawn E Lupold
- The James Buchanan Brady Urologic Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA. .,The Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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7
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Bevilacqua C, Ducos B. Laser microdissection: A powerful tool for genomics at cell level. Mol Aspects Med 2017; 59:5-27. [PMID: 28927943 DOI: 10.1016/j.mam.2017.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/18/2022]
Abstract
Laser microdissection (LM) has become widely democratized over the last fifteen years. Instruments have evolved to offer more powerful and efficient lasers as well as new options for sample collection and preparation. Technological evolutions have also focused on the post-microdissection analysis capabilities, opening up investigations in all disciplines of experimental and clinical biology, thanks to the advent of new high-throughput methods of genome analysis, including RNAseq and proteomics, now globally known as microgenomics, i.e. analysis of biomolecules at the cell level. In spite of the advances these rapidly developing methods have allowed, the workflow for sampling and collection by LM remains a critical step in insuring sample integrity in terms of histology (accurate cell identification) and biochemistry (reliable analyzes of biomolecules). In this review, we describe the sample processing as well as the strengths and limiting factors of LM applied to the specific selection of one or more cells of interest from a heterogeneous tissue. We will see how the latest developments in protocols and methods have made LM a powerful and sometimes essential tool for genomic and proteomic analyzes of tiny amounts of biomolecules extracted from few cells isolated from a complex tissue, in their physiological context, thus offering new opportunities for understanding fundamental physiological and/or patho-physiological processes.
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Affiliation(s)
- Claudia Bevilacqua
- GABI, Plateforme @BRIDGE, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, 78350 Jouy en Josas, France.
| | - Bertrand Ducos
- LPS-ENS, CNRS UMR 8550, UPMC, Université Denis Diderot, PSL Research University, 24 Rue Lhomond, 75005 Paris France; High Throughput qPCR Core Facility, IBENS, 46 Rue d'Ulm, 75005 Paris France; Laser Microdissection Facility of Montagne Sainte Geneviève, CIRB Collège de France, Place Marcellin Berthelot, 75005 Paris France.
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8
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Optimized expression-based microdissection of formalin-fixed lung cancer tissue. J Transl Med 2017; 97:863-872. [PMID: 28436954 DOI: 10.1038/labinvest.2017.31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/10/2017] [Accepted: 03/02/2017] [Indexed: 01/07/2023] Open
Abstract
Analysis of specific DNA alterations in precision medicine of tumors is crucially important for molecular targeted treatments. Lung cancer is a prototypic example and one of the leading causes of cancer-related deaths worldwide. One major technical problem of detecting DNA alterations in tissue samples is cellular heterogeneity, that is, mixture of tumor and normal cells. Microdissection is an important tool to enrich tumor cells from heterogeneous tissue samples. However, conventional laser capture microdissection has several disadvantages like user-dependent selection of regions of interest (ROI), high costs for dissection systems and long processing times. ROI selection in expression-based microdissection (xMD) directly relies on cancer cell-specific immunostaining. Whole-slide irradiation leads to localized energy absorption at the sites of most intensive staining and melting of a membrane covering the slide, so that tumor cells can be isolated by removing the complete membrane. In this study, we optimized xMD of lung cancer tissue by enhancing staining intensity of tumor cell-specific immunostaining and processing of the stained samples. This optimized procedure did not alter DNA quality and resulted in enrichment of mutated EGFR DNA from lung adenocarcinoma specimens after xMD. We here also introduce a quality control protocol based on digital whole-slide scanning and image analysis before and after xMD to quantify selectivity and efficiency of the procedure. In summary, this study provides a workflow for xMD, adapted and tested for lung cancer tissue that can be used for lung tumor cell dissection before diagnostic or investigatory analyses.
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9
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Appleby-Mallinder C, Wyles MD, Simpson JE, Wharton SB, Ince PG, Heath PR. Expression microdissection isolation of enriched cell populations from archival brain tissue. J Neurosci Methods 2016; 268:125-30. [PMID: 27178137 DOI: 10.1016/j.jneumeth.2016.05.007] [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] [Received: 01/05/2016] [Revised: 04/26/2016] [Accepted: 05/04/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Laser capture microdissection (LCM) is an established technique for the procurement of enriched cell populations that can undergo further downstream analysis, although it does have limitations. Expression microdissection (xMD) is a new technique that begins to address these pitfalls, such as operator dependence and contamination. NEW METHOD xMD utilises immunohistochemistry in conjunction with a chromogen to isolate specific cell types by extending the fundamental principles of LCM to create an operator-independent method for the procurement of specific CNS cell types. RESULTS We report how xMD enables the isolation of specific cell populations, namely neurones and astrocytes, from rat formalin fixed-paraffin embedded (FFPE) tissue. Subsequent reverse transcriptase-polymerase chain reaction (RT-PCR) analysis confirms the enrichment of these specific populations. RIN values after xMD indicate samples are sufficient to carry out further analysis. COMPARISON WITH EXISTING METHOD xMD offers a rapid method of isolating specific CNS cell types without the need for identification by an operator, reducing the amount of unintentional contamination caused by operator error, whilst also significantly reducing the time required by the current basic LCM technique. CONCLUSIONS xMD is a superior method for the procurement of enriched cell populations from post-mortem tissue, which can be utilised to create transcriptome profiles, aiding our understanding of the contribution of these cells to a range of neurological diseases. xMD also addresses the issues associated with LCM, such as reliance on an operator to identify target cells, which can cause contamination, as well as addressing the time consuming nature of LCM.
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Affiliation(s)
- C Appleby-Mallinder
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK
| | - M D Wyles
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK
| | - J E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK
| | - S B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK
| | - P G Ince
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK
| | - P R Heath
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK.
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10
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Rosenberg AZ, Armani MD, Fetsch PA, Xi L, Pham TT, Raffeld M, Chen Y, O’Flaherty N, Stussman R, Blackler AR, Du Q, Hanson JC, Roth MJ, Filie AC, Roh MH, Emmert-Buck MR, Hipp JD, Tangrea MA. High-Throughput Microdissection for Next-Generation Sequencing. PLoS One 2016; 11:e0151775. [PMID: 26999048 PMCID: PMC4801357 DOI: 10.1371/journal.pone.0151775] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/03/2016] [Indexed: 01/02/2023] Open
Abstract
Precision medicine promises to enhance patient treatment through the use of emerging molecular technologies, including genomics, transcriptomics, and proteomics. However, current tools in surgical pathology lack the capability to efficiently isolate specific cell populations in complex tissues/tumors, which can confound molecular results. Expression microdissection (xMD) is an immuno-based cell/subcellular isolation tool that procures targets of interest from a cytological or histological specimen. In this study, we demonstrate the accuracy and precision of xMD by rapidly isolating immunostained targets, including cytokeratin AE1/AE3, p53, and estrogen receptor (ER) positive cells and nuclei from tissue sections. Other targets procured included green fluorescent protein (GFP) expressing fibroblasts, in situ hybridization positive Epstein-Barr virus nuclei, and silver stained fungi. In order to assess the effect on molecular data, xMD was utilized to isolate specific targets from a mixed population of cells where the targets constituted only 5% of the sample. Target enrichment from this admixed cell population prior to next-generation sequencing (NGS) produced a minimum 13-fold increase in mutation allele frequency detection. These data suggest a role for xMD in a wide range of molecular pathology studies, as well as in the clinical workflow for samples where tumor cell enrichment is needed, or for those with a relative paucity of target cells.
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Affiliation(s)
- Avi Z. Rosenberg
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael D. Armani
- Pathogenetics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Patricia A. Fetsch
- Cytopathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Liqiang Xi
- Molecular Diagnostics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tina Thu Pham
- Molecular Diagnostics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark Raffeld
- Molecular Diagnostics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yun Chen
- Pathogenetics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Neil O’Flaherty
- Pathogenetics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rebecca Stussman
- Pathogenetics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Adele R. Blackler
- Pathogenetics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Qiang Du
- Pathogenetics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffrey C. Hanson
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark J. Roth
- Cytopathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Armando C. Filie
- Cytopathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael H. Roh
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael R. Emmert-Buck
- Pathogenetics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Avoneaux Medical Institute, Oxford, Maryland, United States of America
- * E-mail: (MREB); (MAT)
| | - Jason D. Hipp
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael A. Tangrea
- Pathogenetics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital, Baltimore, Maryland, United States of America
- * E-mail: (MREB); (MAT)
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11
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Frost AR, Eltoum I, Siegal GP, Emmert‐Buck MR, Tangrea MA. Laser Microdissection. ACTA ACUST UNITED AC 2015; 112:25A.1.1-25A.1.30. [DOI: 10.1002/0471142727.mb25a01s112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andra R. Frost
- Department of Pathology, University of Alabama at Birmingham Birmingham Alabama
| | - Isam‐Eldin Eltoum
- Department of Pathology, University of Alabama at Birmingham Birmingham Alabama
| | - Gene P. Siegal
- Department of Pathology, University of Alabama at Birmingham Birmingham Alabama
| | | | - Michael A. Tangrea
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital Baltimore Maryland
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12
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Multiplex quantitative measurement of mRNAs from fixed tissue microarray sections. Appl Immunohistochem Mol Morphol 2014; 22:323-30. [PMID: 24809843 DOI: 10.1097/pdm.0000000000000039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The development of prognostic and diagnostic biomarkers, such as those from gene expression studies, requires independent validation in clinical specimens. Immunohistochemical analysis on tissue microarrays (TMAs) of formalin-fixed paraffin-embedded tissue is often used to increase the statistical power, and it is used more often than in situ hybridization, which can be technically limiting. Herein, we introduce a method for performing quantitative gene expression analysis across a TMA using an adaptation of 2D-RT-qPCR, a recently developed technology for measuring transcript levels in a histologic section while maintaining 2-dimensional positional information of the tissue sample. As a demonstration of utility, a TMA with tumor and normal human prostate samples was used to validate expression profiles from previous array-based gene discovery studies of prostate cancer. The results show that 2D-RT-qPCR expands the utility of TMAs to include sensitive and accurate gene expression measurements.
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Jensen E. Laser-Capture Microdissection. Anat Rec (Hoboken) 2013; 296:1683-7. [DOI: 10.1002/ar.22791] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/06/2013] [Indexed: 11/08/2022]
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Blackler AR, Morgan NY, Gao B, Olano LR, Armani MD, Romantseva E, Kakareka JW, Bonner RF, Mukherjee S, Xiao B, Tran K, Pohida TJ, Emmert-Buck MR, Tangrea MA, Markey SP. Proteomic analysis of nuclei dissected from fixed rat brain tissue using expression microdissection. Anal Chem 2013; 85:7139-45. [PMID: 23799655 DOI: 10.1021/ac400691k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Expression microdissection (xMD) is a high-throughput, operator-independent technology that enables the procurement of specific cell populations from tissue specimens. In this method, histological sections are first stained for cellular markers via either chemical or immuno-guided methods, placed in close contact with an ethylene vinyl acetate (EVA) film, and exposed to a light source. The focal, transient heating of the stained cells or subcellular structures melts the EVA film selectively to the targets for procurement. In this report, we introduce a custom-designed flashcube system that permits consistent and reproducible microdissection of nuclei across an FFPE rat brain tissue section in milliseconds. In addition, we present a method to efficiently recover and combine captured proteins from multiple xMD films. Both light and scanning electron microscopy demonstrated captured nuclear structures. Shotgun proteomic analysis of the samples showed a significant enrichment in nuclear localized proteins, with an average 25% of recovered proteins localized to the nucleus, versus 15% for whole tissue controls (p < 0.001). Targeted mass spectrometry using multiple reaction monitoring (MRM) showed more impressive data, with a 3-fold enrichment in histones, and a concurrent depletion of proteins localized to the cytoplasm, cytoskeleton, and mitochondria. These data demonstrate that the flashcube-xMD technology is applicable to the proteomic study of a broad range of targets in molecular pathology.
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Affiliation(s)
- A R Blackler
- National Cancer Institute, NIH, Bethesda, Maryland 20892, United States
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Laser-assisted microdissection in translational research: theory, technical considerations, and future applications. Appl Immunohistochem Mol Morphol 2013; 21:31-47. [PMID: 22495368 DOI: 10.1097/pai.0b013e31824d0519] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Molecular profiling already exerts a profound influence on biomedical research and disease management. Microdissection technologies contribute to the molecular profiling of diseases, enabling investigators to probe genetic characteristics and dissect functional physiology within specific cell populations. Laser-capture microdissection (LCM), in particular, permits collation of genetic, epigenetic, and gene expression differences between normal, premalignant, and malignant cell populations. Its selectivity for specific cell populations promises to greatly improve the diagnosis and management of many human diseases. LCM has been extensively used in cancer research, contributing to the understanding of tumor biology by mutation detection, clonality analysis, epigenetic alteration assessment, gene expression profiling, proteomics, and metabolomics. In this review, we focus on LCM applications for DNA, RNA, and protein analysis in specific cell types and on commercially available LCM platforms. These analyses could clinically be used as aids to cancer diagnosis, clinical management, genomic profile studies, and targeted therapy. In this review, we also discuss the technical details of tissue preparation, analytical yields, tissue selection, and selected applications using LCM.
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Yan W, Shih J, Rodriguez-Canales J, Tangrea MA, Player A, Diao L, Hu N, Goldstein AM, Wang J, Taylor PR, Lippman SM, Wistuba II, Emmert-Buck MR, Erickson HS. Three-dimensional mRNA measurements reveal minimal regional heterogeneity in esophageal squamous cell carcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 182:529-39. [PMID: 23219752 DOI: 10.1016/j.ajpath.2012.10.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 09/24/2012] [Accepted: 10/15/2012] [Indexed: 12/11/2022]
Abstract
The classic tumor clonal evolution theory postulates that cancers change over time to produce unique molecular subclones within a parent neoplasm, presumably including regional differences in gene expression. More recently, however, this notion has been challenged by studies showing that tumors maintain a relatively stable transcript profile. To examine these competing hypotheses, we microdissected discrete subregions containing approximately 3000 to 8000 cells (500 to 1500 μm in diameter) from ex vivo esophageal squamous cell carcinoma (ESCC) specimens and analyzed transcriptomes throughout three-dimensional tumor space. Overall mRNA profiles were highly similar in all 59 intratumor comparisons, in distinct contrast to the markedly different global expression patterns observed in other dissected cell populations. For example, normal esophageal basal cells contained 1918 and 624 differentially expressed genes at a greater than twofold level (95% confidence level of <5% false positives), compared with normal differentiated esophageal cells and ESCC, respectively. In contrast, intratumor regions had only zero to four gene changes at a greater than twofold level, with most tumor comparisons showing none. The present data indicate that, when analyzed using a standard array-based method at this level of histological resolution, ESCC contains little regional mRNA heterogeneity.
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Affiliation(s)
- Wusheng Yan
- Pathogenetics Unit, National Institutes of Health, Bethesda, Maryland 20892, USA
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Hipp J, Cheng J, Hanson JC, Yan W, Taylor P, Hu N, Rodriguez-Canales J, Hipp J, Tangrea MA, Emmert-Buck MR, Balis U. SIVQ-aided laser capture microdissection: A tool for high-throughput expression profiling. J Pathol Inform 2011; 2:19. [PMID: 21572509 PMCID: PMC3073068 DOI: 10.4103/2153-3539.78500] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 02/22/2011] [Indexed: 11/15/2022] Open
Abstract
Introduction: Laser capture microdissection (LCM) facilitates procurement of defined cell populations for study in the context of histopathology. The morphologic assessment step in the LCM procedure is time consuming and tedious, thus restricting the utility of the technology for large applications. Results: Here, we describe the use of Spatially Invariant Vector Quantization (SIVQ) for histological analysis and LCM. Using SIVQ, we selected vectors as morphologic predicates that were representative of normal epithelial or cancer cells and then searched for phenotypically similar cells across entire tissue sections. The selected cells were subsequently auto-microdissected and the recovered RNA was analyzed by expression microarray. Gene expression profiles from SIVQ–LCM and standard LCM–derived samples demonstrated highly congruous signatures, confirming the equivalence of the differing microdissection methods. Conclusion: SIVQ–LCM improves the work-flow of microdissection in two significant ways. First, the process is transformative in that it shifts the pathologist's role from technical execution of the entire microdissection to a limited-contact supervisory role, enabling large-scale extraction of tissue by expediting subsequent semi-autonomous identification of target cell populations. Second, this work-flow model provides an opportunity to systematically identify highly constrained cell populations and morphologically consistent regions within tissue sections. Integrating SIVQ with LCM in a single environment provides advanced capabilities for efficient and high-throughput histological-based molecular studies.
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Affiliation(s)
- Jason Hipp
- Department of Pathology, University of Michigan School of Medicine, Division of Pathology Informatics, M4233 Med Sci I, 1301 Catherine, Ann Arbor, MI 48109-0602, USA
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Tangrea MA, Mukherjee S, Gao B, Markey SP, Du Q, Armani M, Kreitman MS, Rosenberg AM, Wallis BS, Eberle FC, Duncan FC, Hanson JC, Chuaqui RF, Rodriguez-Canales J, Emmert-Buck MR. Effect of immunohistochemistry on molecular analysis of tissue samples: implications for microdissection technologies. J Histochem Cytochem 2011; 59:591-600. [PMID: 21430260 DOI: 10.1369/0022155411404704] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Laser-based tissue microdissection is an important tool for the molecular evaluation of histological sections. The technology has continued to advance since its initial commercialization in the 1990s, with improvements in many aspects of the process. More recent developments are tailored toward an automated, operator-independent mode that relies on antibodies as targeting probes, such as immuno-laser capture microdissection or expression microdissection (xMD). Central to the utility of expression-based dissection techniques is the effect of the staining process on the biomolecules in histological sections. To investigate this issue, the authors analyzed DNA, RNA, and protein in immunostained, microdissected samples. DNA was the most robust molecule, exhibiting no significant change in quality after immunostaining but a variable 50% to 75% decrease in the total yield. In contrast, RNA in frozen and ethanol-fixed, paraffin-embedded samples was susceptible to hydrolysis and digestion by endogenous RNases during the initial steps of staining. Proteins from immunostained tissues were successfully analyzed by one-dimensional electrophoresis and mass spectrometry but were less amenable to solution phase assays. Overall, the results suggest investigators can use immunoguided microdissection methods for important analytic techniques; however, continued improvements in staining protocols and molecular extraction methods are key to further advancing the capability of these methods.
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Affiliation(s)
- Michael A Tangrea
- Pathogenetics Unit, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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Abstract
Laser-based microdissection facilitates the isolation of specific cell populations from clinical or animal model tissue specimens for molecular analysis. Expression microdissection (xMD) is a second-generation technology that offers considerable advantages in dissection capabilities; however, until recently the method has not been accessible to investigators. This protocol describes the adaptation of xMD to commonly used laser microdissection instruments and to a commercially available handheld laser device in order to make the technique widely available to the biomedical research community. The method improves dissection speed for many applications by using a targeting probe for cell procurement in place of an operator-based, cell-by-cell selection process. Moreover, xMD can provide improved dissection precision because of the unique characteristics of film activation. The time to complete the protocol is highly dependent on the target cell population and the number of cells needed for subsequent molecular analysis.
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Armani M, Rodriguez-Canales J, Gillespie J, Tangrea M, Erickson H, Emmert-Buck MR, Shapiro B, Smela E. 2D-PCR: a method of mapping DNA in tissue sections. LAB ON A CHIP 2009; 9:3526-3534. [PMID: 20024032 PMCID: PMC2910845 DOI: 10.1039/b910807f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A novel approach was developed for mapping the location of target DNA in tissue sections. The method combines a high-density, multi-well plate with an innovative single-tube procedure to directly extract, amplify, and detect the DNA in parallel while maintaining the two-dimensional (2D) architecture of the tissue. A 2D map of the gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was created from a tissue section and shown to correlate with the spatial area of the sample. It is anticipated that this approach may be easily adapted to assess the status of multiple genes within tissue sections, yielding a molecular map that directly correlates with the histology of the sample. This will provide investigators with a new tool to interrogate the molecular heterogeneity of tissue specimens.
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Affiliation(s)
- Michael Armani
- Bioengineering Graduate Program, University of Maryland, College Park, MD, USA
- Fischell Department of Bio-Engineering, University of Maryland, College Park, MD, USA
- Pathogenetics Unit, Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Jaime Rodriguez-Canales
- Laser Microdissection Core, Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | | | - Michael Tangrea
- Pathogenetics Unit, Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Heidi Erickson
- University of Texas, M. D. Anderson Cancer Center, Department of Thoracic Head & Neck Medical Oncology, Houston, TX, USA
| | - Michael R. Emmert-Buck
- Pathogenetics Unit, Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Benjamin Shapiro
- Bioengineering Graduate Program, University of Maryland, College Park, MD, USA
- Fischell Department of Bio-Engineering, University of Maryland, College Park, MD, USA
| | - Elisabeth Smela
- Bioengineering Graduate Program, University of Maryland, College Park, MD, USA
- Department of Mechanical Engineering, University of Maryland, 2176 Martin Hall, College Park, MD, 20742, USA
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21
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Erickson HS, Albert PS, Gillespie JW, Rodriguez-Canales J, Marston Linehan W, Pinto PA, Chuaqui RF, Emmert-Buck MR. Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples. Nat Protoc 2009; 4:902-22. [PMID: 19478806 DOI: 10.1038/nprot.2009.61] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is a valuable tool for measuring gene expression in biological samples. However, unique challenges are encountered when studies are performed on cells microdissected from tissues derived from animal models or the clinic, including specimen-related issues, variability of RNA template quality and quantity, and normalization. qRT-PCR using small amounts of mRNA derived from dissected cell populations requires adaptation of standard methods to allow meaningful comparisons across sample sets. The protocol described here presents the rationale, technical steps, normalization strategy and data analysis necessary to generate reliable gene expression measurements of transcripts from dissected samples. The entire protocol from tissue microdissection through qRT-PCR analysis requires approximately 16 h.
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Affiliation(s)
- Heidi S Erickson
- Pathogenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, National Cancer Institute, NIH, Bethesda, MD, USA
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Abstract
Cancer therapy is in the midst of a major paradigm shift. Traditionally, cancer treatments have focused on tumour cells. However, studies over the past few decades have demonstrated that cancer is a vastly complex entity with multiple components affecting a tumour's growth, invasion and metastasis. These components, collectively termed the 'tumour microenvironment', include endothelial cells, pericytes, fibroblasts, inflammatory cells, leucocytes and elements of the extracellular matrix (ECM). Biological agents that target components of the tumour microenvironment may provide an interesting alternative to traditional tumour cell-directed therapy. Because of the complexity of the tumour milieu, the most beneficial therapy will likely involve the combination of one or more agents directed at this new target. This review highlights recent preclinical and clinical studies involving agents that target tumour vasculature, leucocytes, pericytes, cancer-associated fibroblasts and ECM components. We pay particular attention to combination therapies targeting multiple components of the tumour microenvironment, and aim to demonstrate that this strategy holds promise for the future of cancer treatment.
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Affiliation(s)
- E Hanna
- Tumour Angiogenesis Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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23
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Spurrier B, Honkanen P, Holway A, Kumamoto K, Terashima M, Takenoshita S, Wakabayashi G, Austin J, Nishizuka S. Protein and lysate array technologies in cancer research. Biotechnol Adv 2008; 26:361-9. [PMID: 18514460 DOI: 10.1016/j.biotechadv.2008.04.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2007] [Revised: 03/24/2008] [Accepted: 04/03/2008] [Indexed: 01/03/2023]
Abstract
Capturing quantitative proteomic information provides new insights for enhancing the understanding of cancer biology. There have been several protein microarray formats, and each has an advantage depending on what is being detected. However, in contrast to nucleotide printing, the production of protein arrays generally requires the capability of handling viscous solutions, and the mishandling of various factors, such as temperature and humidity, adversely affect protein status. The requirement for such specifications is critical when increasing the throughput for monitoring a large number of samples for rigorous quantitation. In particular, a new solid pin arrayer has been extremely powerful when highly viscous cell lysates printed for high-density, "reverse-phase" protein arrays, and acquired data allows for theoretical models of protein signaling networks to be constructed. In this review, applications of currently available protein microarray technology to cancer research are discussed including the advantages of the new solid pin architecture for opening up powerful proteomic applications.
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Affiliation(s)
- Brett Spurrier
- Molecular Translational Technology, Molecular Therapeutics Program, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
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Proteomics of Cancer of Hormone-Dependent Tissues. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 630:133-47. [DOI: 10.1007/978-0-387-78818-0_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Abstract
Procurement of pure populations of cells from heterogeneous histological sections can be accomplished utilizing tissue microdissection. At present, a variety of different manual and laser-based dissection tools are available and each method has particular strengths and weaknesses. The types of biomolecular analyses that can be performed on microdissected cells depend not only on the method of cell procurement, but also on the effects of upstream tissue handling and processing. Tissue preparation protocols include two major approaches; snap-freezing, or, fixation and embedding. Snap-freezing generally provides the best quality tissue for subsequent study, including proteomic analyses such as two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Tissue fixatives include either precipitating reagents or biomolecular cross-linkers. The fixed samples are then further processed and embedded in a wax medium. In general, the biomolecules recovered from fixed and embedded tissue specimens are lower in both quantity and quality than those from snap-frozen specimens, although they are useful for certain types of analyses. The protocols provided here for tissue handling and processing, preparation of tissue sections, and microdissection are derived from our experience at the Pathogenetics Unit of the National Cancer Institute.
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The critical role of histology in an era of genomics and proteomics: a commentary and reflection. Adv Anat Pathol 2007; 14:375-400. [PMID: 18049128 DOI: 10.1097/pap.0b013e318159479d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The role of histologic examination in lymphoma diagnosis has been called into question by proponents of new technologies, such as genomics and proteomics. We review the history and salient features of morphologic evaluation in lymphoid diseases, and discuss the general and specific limitations of mature ancillary techniques, such as immunohistochemistry, flow cytometry, and molecular studies. We then speculate on the future relationship between morphology and the new genomic and proteomic technologies as they become integrated into clinical practice.
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Abstract
Deciphering the cellular and molecular interactions that drive disease within the tissue microenvironment holds promise for discovering drug targets of the future. In order to recapitulate the in vivo interactions through molecular analysis, one must be able to analyze specific cell populations within the context of their heterogeneous tissue microecology. Laser capture microdissection is a method to procure subpopulations of tissue cells under direct microscopic visualization. Laser capture microdissection technology can harvest the cells of interest directly or can isolate specific cells by cutting away unwanted cells to give histologically pure enriched cell populations. A variety of downstream applications exist: DNA genotyping and loss-of-heterozygosity analysis, RNA transcript profiling, cDNA library generation, mass spectrometry proteomics discovery and signal pathway profiling.
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Affiliation(s)
- Virginia Espina
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA 20110, USA.
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28
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Abstract
Proteomics holds the promise of evaluating global changes in protein expression and post-translational modification in response to environmental stimuli. However, difficulties in achieving cellular anatomic resolution and extracting specific types of proteins from cells have limited the efficacy of these techniques. Laser capture microdissection has provided a solution to the problem of anatomical resolution in tissues. New extraction methodologies have expanded the range of proteins identified in subsequent analyses. This review will examine the application of laser capture microdissection to proteomic tissue sampling, and subsequent extraction of these samples for differential expression analysis. Statistical and other quantitative issues important for the analysis of the highly complex datasets generated are also reviewed.
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Affiliation(s)
- Howard B Gutstein
- MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 110, Houston, TX 77030-4009, USA.
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29
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Espina V, Wulfkuhle JD, Calvert VS, VanMeter A, Zhou W, Coukos G, Geho DH, Petricoin EF, Liotta LA. Laser-capture microdissection. Nat Protoc 2007; 1:586-603. [PMID: 17406286 DOI: 10.1038/nprot.2006.85] [Citation(s) in RCA: 496] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Deciphering the cellular and molecular interactions that drive disease within the tissue microenvironment holds promise for discovering drug targets of the future. In order to recapitulate the in vivo interactions thorough molecular analysis, one must be able to analyze specific cell populations within the context of their heterogeneous tissue microecology. Laser-capture microdissection (LCM) is a method to procure subpopulations of tissue cells under direct microscopic visualization. LCM technology can harvest the cells of interest directly or can isolate specific cells by cutting away unwanted cells to give histologically pure enriched cell populations. A variety of downstream applications exist: DNA genotyping and loss-of-heterozygosity (LOH) analysis, RNA transcript profiling, cDNA library generation, proteomics discovery and signal-pathway profiling. Herein we provide a thorough description of LCM techniques, with an emphasis on tips and troubleshooting advice derived from LCM users. The total time required to carry out this protocol is typically 1-1.5 h.
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Affiliation(s)
- Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10900 University Blvd. MS 4E3, Manassas, Virginia, USA
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30
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Chimge NO, Ruddle F, Bayarsaihan D. Laser-assisted microdissection (LAM) in developmental biology. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2007; 308:113-8. [PMID: 17016827 DOI: 10.1002/jez.b.21133] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The analysis of gene expression in developing organs is a valuable tool for the assessment of genetic fingerprints during the various stages of differentiation. Complex processes in developing tissues are particularly difficult to understand in terms of biochemical phenomena. Laser-assisted microdissection (LAM) allows the efficient and precise capture of cells or groups of cells from developing tissues in sufficient quantities and within the context of time and space to permit the subsequent molecular characterization of the targeted tissue. The technique development has dramatically increased the ease of isolating specific cells which, together with progress in tissue preparation and microextraction protocols, allows for broad-range down-stream applications in the fields of genomics, transcriptomics and proteomics. This review gives an overview of the LAM technology and its application in developmental biology.
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Affiliation(s)
- Nyam-Osor Chimge
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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31
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Papadopoulos N, Kinzler KW, Vogelstein B. The role of companion diagnostics in the development and use of mutation-targeted cancer therapies. Nat Biotechnol 2006; 24:985-95. [PMID: 16900147 DOI: 10.1038/nbt1234] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Among all the known differences between cancer and normal cells, it is only the genetic differences that unequivocally distinguish the former from the latter. It is therefore not surprising that recent therapeutic advances are based on agents that specifically target the products of the genes that are mutated in cancer cells. The ability to identify the patients most likely to benefit from such therapies is a natural outgrowth of these discoveries. Development of companion diagnostic tests for this identification is proceeding but should receive much more attention than it currently does. These tests can simplify the drug discovery process, make clinical trials more efficient and informative, and be used to individualize the therapy of cancer patients.
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Affiliation(s)
- Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute, The Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, 1650 Orleans Street, CRB1, Baltimore, MD 21231, USA.
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32
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Grover AC, Tangrea MA, Woodson KG, Wallis BS, Hanson JC, Chuaqui RF, Gillespie JW, Erickson HS, Bonner RF, Pohida TJ, Emmert-Buck MR, Libutti SK. Tumor-associated endothelial cells display GSTP1 and RARbeta2 promoter methylation in human prostate cancer. J Transl Med 2006; 4:13. [PMID: 16512911 PMCID: PMC1420331 DOI: 10.1186/1479-5876-4-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 03/02/2006] [Indexed: 11/22/2022] Open
Abstract
Background A functional blood supply is essential for tumor growth and proliferation. However, the mechanism of blood vessel recruitment to the tumor is still poorly understood. Ideally, a thorough molecular assessment of blood vessel cells would be critical in our comprehension of this process. Yet, to date, there is little known about the molecular makeup of the endothelial cells of tumor-associated blood vessels, due in part to the difficulty of isolating a pure population of endothelial cells from the heterogeneous tissue environment. Methods Here we describe the use of a recently developed technique, Expression Microdissection, to isolate endothelial cells from the tumor microenvironment. The methylation status of the dissected samples was evaluated for GSTP1 and RARβ2 promoters via the QMS-PCR method. Results Comparing GSTP1 and RARβ2 promoter methylation data, we show that 100% and 88% methylation is detected, respectively, in the tumor areas, both in epithelium and endothelium. Little to no methylation is observed in non-tumor tissue areas. Conclusion We applied an accurate microdissection technique to isolate endothelial cells from tissues, enabling DNA analysis such as promoter methylation status. The observations suggest that epigenetic alterations may play a role in determining the phenotype of tumor-associated vasculature.
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Affiliation(s)
- Amelia C Grover
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Tangrea
- Pathologenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Karen G Woodson
- Cancer Prevention Studies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Benjamin S Wallis
- Pathologenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Jeffrey C Hanson
- Cancer Prevention Studies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Rodrigo F Chuaqui
- Pathologenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - John W Gillespie
- Pathologenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Heidi S Erickson
- Pathologenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Robert F Bonner
- Laboratory of Integrative and Medical Biophysics, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J Pohida
- Computational Bioscience and Engineering Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD USA
| | - Michael R Emmert-Buck
- Pathologenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Steven K Libutti
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Rupp C, Dolznig H, Puri C, Schweifer N, Sommergruber W, Kraut N, Rettig WJ, Kerjaschki D, Garin-Chesa P. Laser Capture Microdissection of Epithelial Cancers Guided by Antibodies Against Fibroblast Activation Protein and Endosialin. ACTA ACUST UNITED AC 2006; 15:35-42. [PMID: 16531767 DOI: 10.1097/00019606-200603000-00006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Transcriptional profiling of cancer biopsies is used extensively to identify expression signatures for specific cancer types, diagnostic and prognostic subgroups, and novel molecular targets for therapy. To broaden these applications, several challenges remain. For example, the integrity of RNA extracted even from small tissue samples has to be insured and monitored. Moreover, total tumor RNA may hide the marked histologic heterogeneity of human cancers. A principle approach to this heterogeneity has been provided by laser capture microdissection performed on antibody-stained tissue sections (immuno-LCM; iLCM). In this study, we have established a procedure to assess the quality of RNA obtained from tissue sections, coupled with immunostaining using antibodies to different tumor stromal markers, and subsequent iLCM to selectively capture the cancer stroma compartments. The procedure was applied to 53 frozen specimens of human epithelial cancers. Sections were stained for histopathological evaluation, and RNA was isolated from adjacent serial sections. RNA quality was assessed by the Agilent-Bioanalyzer (Agilent, Palo Alto, CA) and by multiplex RT-PCR. Two thirds of the specimens were found to yield good to excellent RNA quality. For microdissection of the tumor stroma with reactive fibroblasts and tumor blood vessels, a rapid incubation protocol with antibodies against fibroblast activation protein (FAP) and against endosialin was developed to ensure RNA integrity for subsequent iLCM. Using these procedures, RNA from distinct tumor compartments can be isolated, analyzed, amplified, and used for transcription profiling.
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Affiliation(s)
- Christian Rupp
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria
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Hanson JA, Gillespie JW, Grover A, Tangrea MA, Chuaqui RF, Emmert-Buck MR, Tangrea JA, Libutti SK, Linehan WM, Woodson KG. Gene promoter methylation in prostate tumor-associated stromal cells. J Natl Cancer Inst 2006; 98:255-61. [PMID: 16478744 DOI: 10.1093/jnci/djj051] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Gene expression can be silenced through the methylation of specific sites in the promoter region. This mechanism of gene silencing has an important role in the carcinogenesis of prostate and other cancers. Although tumor-associated stromal cells also exhibit changes in gene expression, promoter methylation has not been described in these cells. METHODS Tumor epithelia, tumor-associated stroma and normal epithelia, and stroma adjacent to tumor tissues were isolated from whole-mount prostatectomy specimens (two per patient) of patients (n = 5) with localized prostate cancer and from normal epithelia and stroma from benign prostate hyperplasia specimens (two per patient) from men (n = 5) without prostate cancer by using laser capture microdissection or expression microdissection. The methylation status of three genes important in prostate carcinogenesis, GSTP1, RARbeta2, and CD44, were evaluated using quantitative methylation-sensitive polymerase chain reaction. RESULTS GSTP1 and RARbeta2 were methylated in the tumor epithelium of all five prostate cancer patients and in the tumor-associated stroma in four of the five patients. CD44 was methylated in the tumor epithelium from four of the five patients but not in the tumor stroma. GSTP1 and RARbeta2 were methylated in normal epithelium of two and four patients, respectively, and in normal stroma of one and two patients, respectively, that were isolated from regions adjacent to the tumors and may have resulted from a tumor-field effect; CD44 methylation was not observed in normal epithelium or stroma. In contrast, normal epithelia and stroma from benign prostate hyperplasia specimens showed no promoter methylation in GSTP1, RARbeta2, or CD44. CONCLUSIONS The observation of promoter methylation in the non-neoplastic cells of the prostate tumor microenvironment may advance our understanding of prostate cancer development and progression and lead to new diagnostic and prognostic markers and therapeutic targets.
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Affiliation(s)
- Jeffrey A Hanson
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Pinzani P, Orlando C, Pazzagli M. Laser-assisted microdissection for real-time PCR sample preparation. Mol Aspects Med 2006; 27:140-59. [PMID: 16480765 DOI: 10.1016/j.mam.2005.12.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Laser-assisted microdissection (LMD) has been developed to procure precisely the cells of interest in a tissue specimen, in a rapid and practical manner. Together with real-time PCR and RT-PCR techniques, it is now feasible to study genetic alterations, gene expression features and proteins in defined cell populations from complex normal and diseased tissues. The process that brings from sample collection to the final quantitative results is articulated in several steps, each of which requires optimal choices in order to end up with high-quality nucleic acid or protein that allows successful application of the final quantitative assays. This review will describe shortly the development of LMD technologies and the principles they are based on. Trying to highlight the advantages and disadvantages of LMD, the main problems related to specimens collection and processing, section preparation and extraction of bio-molecules from microdissected tissue samples have been analysed.
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Affiliation(s)
- P Pinzani
- Department of Clinical Physiopathology, Clinical Biochemistry Unit, University of Florence, Italy
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Nelson T, Tausta SL, Gandotra N, Liu T. Laser microdissection of plant tissue: what you see is what you get. ANNUAL REVIEW OF PLANT BIOLOGY 2006; 57:181-201. [PMID: 16669760 DOI: 10.1146/annurev.arplant.56.032604.144138] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Laser microdissection (LM) utilizes a cutting or harvesting laser to isolate specific cells from histological sections; the process is guided by microscopy. This provides a means of removing selected cells from complex tissues, based only on their identification by microscopic appearance, location, or staining properties (e.g., immunohistochemistry, reporter gene expression, etc.). Cells isolated by LM can be a source of cell-specific DNA, RNA, protein or metabolites for subsequent evaluation of DNA modifications, transcript/protein/metabolite profiling, or other cell-specific properties that would be averaged with those of neighboring cell types during analysis of undissected complex tissues. Plants are particularly amenable to the application of LM; the highly regular tissue organization and stable cell walls of plants facilitate the visual identification of most cell types even in unstained tissue sections. Plant cells isolated by LM have been the starting point for a variety of genomic and metabolite studies of specific cell types.
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Affiliation(s)
- Timothy Nelson
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA.
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Abstract
It is not easy to write a critical review of the methods available for labeling RNA and DNA "extracts" for microarray studies. There are a number of reasons for this: Suppliers of the reagents and kits used for this purpose do research and development, quality control, and validation and then they provide a hard-wired, "optimized" product. They often give few details about the compositions of these products, are inclined to put the best face they can on what they sell and gloss over any deficiencies, and have no interest in paying for direct comparisons of their product to those of other companies. These comparisons can be expensive to perform, and there are few good examples in the literature. When comparative experiments have been done, it is not clear that each of the individual methods tested was executed with equal proficiency. Many experiments can be required to determine how best to hybridize any given labeled extract to a particular array and how to block, wash, and postprocess (e.g., stain) the array so that the signal-to-noise ratio is maximized. In addition, authors of comparative studies used different arrays, technical protocols (some of which are out of date), experimental designs, and analyses. Finally, some new techniques, which seem quite promising, have been employed so little that their strengths and shortcomings are difficult to assess.
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Day RC, Grossniklaus U, Macknight RC. Be more specific! Laser-assisted microdissection of plant cells. TRENDS IN PLANT SCIENCE 2005; 10:397-406. [PMID: 16027030 DOI: 10.1016/j.tplants.2005.06.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Revised: 05/24/2005] [Accepted: 06/24/2005] [Indexed: 05/03/2023]
Abstract
Laser-assisted microdissection (LAM) is a powerful tool for isolating specific tissues, cell types and even organelles from sectioned biological specimen in a manner conducive to the extraction of RNA, DNA or protein. LAM, which is an established technique in many areas of biology, has now been successfully adapted for use with plant tissues. Here, we provide an overview of the processes involved in conducting a successful LAM study in plants and review recent developments that have made this technique even more desirable. We also discuss how the technology might be exploited to answer some pertinent questions in plant biology.
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Affiliation(s)
- Robert C Day
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Bhattacherjee V, Greene R, Pisano MM. Cambridge Healthtech Institute's 3rd Annual Laser Capture Microscopy: cutting edge applications. May 2-3 2005, World Trade Center, Boston, MA, USA. Expert Rev Mol Diagn 2005; 5:487-91. [PMID: 16013966 DOI: 10.1586/14737159.5.4.487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Vasker Bhattacherjee
- The Laboratory of Craniofacial Development, University of Louisville Birth Defects Center, 501 S. Preston Street, Suite 301, Louisville, KY 40202, USA.
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De Falco M, De Luca A. Meeting report on the 12th International Congress of Histochemistry and Cytochemistry (ICHC). J Cell Physiol 2005; 204:407-11. [PMID: 15895396 PMCID: PMC7166837 DOI: 10.1002/jcp.20418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The International Congress of Histochemistry and Cytochemistry (ICHC) promoted in San Diego La Jolla (CA, USA), the 12th meeting where researchers of all over the world presented their work and the most innovative methods in histochemical disciplines. A summary of the last meeting is reported. © 2005 Wiley‐Liss, Inc.
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Affiliation(s)
- Maria De Falco
- Department of Evolutionary and Comparative Biology, University of Naples “Federico II”, Naples, Italy
| | - Antonio De Luca
- Department of Medicine and Public Health, Section of Clinical Anatomy, Second University of Naples, Naples, Italy
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