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PubMed2005

New aspects of laser microdissection in research and routine.

Laser microdissection has opened a window to new technologies. The scientific fields of genomics, transcriptomics, and proteomics need pure samples for rendering reliable results. Homogeneous sample preparation is a prerequisite for modern molecular analyses, both qualitative and quantitative. Laser microdissection and pressure catapulting (LMPC) is a tool for isolating specific cells from complex tissues in a non-contact and contamination-free manner. Because LMPC technology is an optimal method for obtaining fast and reliable access to single cells, the possibility of automatic isolation of single fetal cells has the promise of being a big step forward in developing protocols for non-invasive prenatal diagnosis.

Animals↗
PubMed2005

Microdissection-derived murine mcb probes from somatic cell hybrids.

The multicolor-banding (mcb) technique is a fluorescence in situ hybridization (FISH)-banding approach, which is based on region-specific microdissection libraries producing changing fluorescence intensity ratios along the chromosomes. The latter are used to assign different pseudocolors to specific chromosomal regions. Here we present the first three available mcb-probe sets for the Mus musculus chromosomes 3, 6, and 18. In the present work, the creation of the microdissection libraries was done for the first time on mouse/human somatic cell hybrids. During creation of the mcb-probes, the latter enabled an unambiguous identification of the, otherwise in GTG-banding, hardly distinguishable murine chromosomes.

Animals↗
PubMed2005

Intracellular localization of oxidized low-density lipoproteins in atherosclerotic plaque cells revealed by electron microscopy combined with laser capture microdissection.

Recently, laser capture microdissection (LCM) has become a powerful tool for investigating the genome and protein contents of cells populating normal and pathologically altered tissues. The present work reports a technique for the preparation of tissue specimens for further LCM combined with electron microscopy. In this work, atherosclerotic plaque cells containing oxidized low-density lipoproteins (LDL) were microdissected from human carotid arteries and the intracellular distribution of oxidized LDL was examined, providing novel information about the association of microvesicles containing oxidized LDL with "lipid droplets" in macrophage foam cells.

Aged↗
PubMed2005

An introduction to laser-based tissue microdissection techniques.

The development and application of laser-based tissue microdissection techniques has provided a major impetus to the sensitive and specific molecular analysis of solid tissues and tumors. This chapter provides an overview of the different laser-based microdissection systems and an introduction to the principles involved in the function and applications of these individual systems.

Animals↗
PubMed2005

Methacarn fixation for genomic DNA analysis in microdissected cells.

We have found methacarn, a non-crosslinking protein-precipitating fixative, to be useful for the analysis of DNA from microdissected specimens of wax-embedded tissue. In this chapter, we present the procedure regarding genomic DNA analysis in methacarn-fixed wax-embedded microdissected rat tissue. Using nested polymerase chain reaction (PCR), and a rapid extraction procedure, fragments of DNA up to 2.8 kb in size can be amplified from a 1 x 1 mm area of a 10-microm-thick tissue section. Target fragments of about 500 bp can be amplified from a single cell, but 10-20 cells are necessary for practical detection by nested PCR. Although tissue staining with hematoxylin and eosin inhibits the PCR, amplification of about 500-bp fragments is successful with 150-270 cells by single-step PCR. Immunostaining results in a substantial decrease of yield and degradation of extracted DNA. However, even after immunostaining, fragments of about 180 bp can be amplified with 150-270 cells by single-step PCR. These features demonstrate the suitability of methacarn-fixed wax-embedded tissue for practical genomic DNA analysis in terms of tissue handling, extraction efficiency, and satisfactory PCR results.

Acetic Acid↗
PubMed2005

Multiplex quantitative real-time PCR of laser microdissected tissue.

This chapter describes a method for the rapid assessment of gene copy number in laser microdissected material using multiplex real-time polymerase chain reaction (PCR). Here a putative oncogene (ZNF217) was evaluated in a series of colon tumors, but the method is applicable to any locus for which a nucleic acid sequence is available. The preparation, laser microdissection, and optimum storage of snap-frozen tumor material from freshly resected tissue is described. A set of guidelines specific for real-time PCR assays is included to assist with optimum primer and probe design. In this assay multiplex real-time PCR was performed and our experience has demonstrated that a multiplex reaction allows for a more accurate assessment of gene copy number than a "singleplex" assay because it removes the need for an external control.

Animals↗
PubMed2005

Whole-genome allelotyping using laser microdissected tissue.

Laser-based microdissection technologies have been recently developed and applied to procure homogenous populations of tumor cells from paraffin-embedded and frozen tissue sections. When combined with whole-genomic amplification techniques, sufficient amounts of DNA can be generated from a small number of tumor cells procured by laser-based microdissection. Amplified DNA can then be used to perform high-throughput genome-wide allelotyping using fluorescent-labeled microsatellite markers spanning the whole genome. Loss of heterozygosity can be assessed by Genescan and Genotyper software (ABI Prism).

Alleles↗
PubMed2005

Laser-assisted microdissection of membrane-mounted tissue sections.

Biological tissues (in particular those affected by disease) are inherently complex mixtures of different cell types and matrices. This heterogeneity can complicate the interpretation of molecular biological studies performed on whole-tissue extracts if the precise cellular origin of the molecules being tested is not known. Laser-assisted microdissection (LAM) has emerged as a leading histological technique for obtaining samples enriched for specific target cell populations or tissue components for subsequent molecular (especially polymerase chain reaction-based) analysis. This method allows the identification and study of target-specific molecular alterations in heterogeneous specimens, and enables more accurate detection and quantification of target molecules. In this chapter, we focus on tissue microdissection performed with an ultraviolet laser system and describe protocols for the basic procedure and for handling of the samples.

Animals↗
PubMed2005

Gene expression profiling of primary tumor cell populations using laser capture microdissection, RNA transcript amplification, and GeneChip microarrays.

Gene expression profiling from microdissected cell populations is a powerful approach to explore molecular processes involved in development and solid tumor biology. In this chapter, we detail robust and validated methods for tissue preparation and isolation of high-quality RNA from microdissected cell populations. A protocol is also provided for linear transcript amplification using as little as 10 ng of total RNA to produce labeled cRNA targets for hybridization to GeneChip high-density oligonucleotide microarrays. Particular emphasis is placed on troubleshooting each technical step in the protocol and measures of quality assurance for both RNA isolation and resulting microarray data.

Animals↗
PubMed2005

Laser capture microdissection of hepatic stages of the human parasite Plasmodium falciparum for molecular analysis.

Despite the sequencing of parasite genomes and development of DNA microarray technology, gene profiling of parasites remains a difficult task. For example, transcriptome analysis cannot currently be applied to the hepatic stages of the malaria parasite Plasmodium falciparum due to difficulties in obtaining sufficient amounts of parasite material that lies among the large excess of host cell RNA. Here, we describe the isolation of P. falciparum-infected human hepatocytes by a laser capture microdissection approach. Reverse transcriptase polymerase chain reaction amplification of several P. falciparum transcripts demonstrates the high quality of the RNA recovered after microdissection. This approach should enable analysis of P. falciparum transcriptome during its hepatic development, a major step toward the identification of new therapeutic and vaccine targets.

Animals↗
PubMed2006

Microdissection with PCR in situ.

In situ amplification techniques are designed to increase the mass of DNA in a fixed target, either whole cells or tissue sections. When combined with fluorescently labeled nucleotides, they can be used for locus detection. They also can be used to increase target mass for subsequent operations, such as cellular or chromosomal isolation by microdissection. When combined with chromosome microdissection, these techniques allow libraries to be made from single copies of chromosomes, chromosome fragments, or even bacteria.

Bacteria↗
PubMed2005

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This article reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies, and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing, and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high quality, appropriately anatomically tagged scientific results. In optimized protocols is a source of inefficiency in current life science research. Improvement in this area will significantly increase life science quality and productivity. The article is divided into introduction, materials, protocols, and notes sections. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this article, readers are advised to read through the entire article first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.

Biomarkers↗
PubMed2005

Use of laser-capture microdissection for the identification of marker genes for the ventromedial hypothalamic nucleus.

The ventromedial hypothalamic nucleus (VMH) plays an important role in the control of feeding and energy homeostasis. In contrast to other hypothalamic nuclei that are also known to regulate energy balance, there is a paucity of nucleus-specific marker genes for the VMH, limiting the application of molecular approaches for analyzing VMH information processing, function, and circuitry. Here, we report the use of laser-capture microdissection to isolate a set of cDNAs that are enriched in the VMH relative to two adjacent hypothalamic nuclei, the arcuate and dorsomedial hypothalamus. The relative expression levels of nine of the 12 most robustly expressed VMH-enriched genes were confirmed by real-time PCR analysis using separate RNAs from these three nuclei. Three of these VMH-enriched genes were further characterized by in situ hybridization histochemistry, including pituitary adenylate cyclase activating polypeptide, cerebellin 1, and an expressed sequence tag named LBH2. Finally, to test whether some of these genes were coordinately regulated, we monitored their expression in steroidogenic factor 1 (SF-1) knock-out mice. SF-1 is a transcription factor that controls the development of the VMH. The RNA levels for four of these genes were reduced in these knock-out animals, further suggesting that they are direct or indirect targets of this orphan nuclear receptor. The VMH-enriched genes identified here provide a basis for a functional analysis of VMH neuronal subpopulations via the use of bacterial artificial chromosome transgenics and related technologies. These results also demonstrate the utility of laser-capture microdissection coupled with microarray technology to identify nucleus-specific transcriptional networks.

Animals↗
PubMed2004

Laser capture microdissection, microarrays and the precise definition of a cancer cell.

Most expression profiling studies of solid tumors have used biopsy samples containing large numbers of contaminating stromal and other cell types, thereby complicating any precise delineation of gene expression in nontumor versus tumor cell types. Combining laser capture microdissection, RNA amplification protocols, microarray technologies and our knowledge of the human genome sequence, it is possible to isolate pure populations of cells or even a single cell and interrogate the expression of thousands of sequences for the purpose of more precisely defining the biology of the tumor cell. Although many of the studies that currently allow for characterization of small sample preparations and single cells were performed utilizing noncancer cell types, and in some cases isolation protocols other than laser capture microdissection, a list of protocols are described that could be used for the expression analysis of individual tumor cells. Application of these experimental approaches to cancer studies may permit a more accurate definition of the biology of the cancer cell, so that ultimately, more specific targeted therapies can be developed.

B-Lymphocytes↗
PubMed2003

Automated sequencing of complete mitochondrial genomes from laser-capture microdissected samples.

Mitochondrial DNA mutations have been related to both aging and a variety of diseases such as cancer. Due to the relatively small size of the genome (16 kb) and with the use of automated DNA sequencing, the entire genome can be sequenced from clinical specimens in days. We present a reliable approach to complete mitochondrial genome sequencing from laser-capture microdissected human clinical cancer specimens that overcome the inherent limitations of relatively small tissue samples and partial DNA degradation, which are unavoidable when laser-capture microdissection is used to attain pure populations of cells from heterogeneous tissues obtained from surgical procedures. The acquisition of sufficient template combined with a standard set of 18 pairs of PCR primers allows for the efficient amplification of the genome. Subsequent single-stranded amplification is performed using 36 sequencing primers, and samples are run on an ABI PRISM 3100 Genetic Analyzer. The use of this procedure should allow even investigators with little experience sequencing from clinical specimens success in complete mitochondrial genome sequencing.

Base Sequence↗
PubMed2003

Identification of lung micrometastatic tumor foci in nude mice with implanted tumor using laser capture microdissection and PCR-single-strand conformation polymorphism.

OBJECTIVE: To assess the value of the laser capture microdissection (LCM) combined with polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) technique for diagnosing micrometastatic cancer cells in the lung of nude mice with implanted tumor. METHODS: Isolation of the cells from the suspected tumor loci in the lung of nude mice with implanted tumors was performed using laser capture microdissection technique, and the genomic DNA extracted from the cells was amplified by 2 sequential PCRs. Non-radioisotopic single-strand conformation polymorphism (SSCP) was subsequently performed to analyze the point mutation of K-ras gene. RESULTS: K-ras gene (codon 12) mutation in AGT was identified in the suspected metastatic cancer cells but not in the benign nodular lesion, where wild type K-ras gene (GGT) was detected. CONCLUSION: The utilization of LCM combined with PCR-SSCP technique may serve as a crucial aid for molecular diagnosis of morphologically suspicious cancer cell populations.

Animals↗
PubMed2003

Analysis of osteopontin in mouse growth plate cartilage by application of laser capture microdissection and RT-PCR.

Gene expression of osteopontin (OPN) has been investigated in mice by application of laser capture microdissection (LCM) and reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. LCM permits individual cells to be isolated ("captured") from tissue sections for molecular analyses. In this study, chondrocytes were captured from growth plate zones in frozen sections of tibiae from 1-11-day-old postnatal mice. RNA was extracted from cells, DNAse-treated, and reverse-transcribed. cDNA was amplified by PCR and OPN mRNA was revealed on agarose gels. Whole cartilage and brain (a positive control) from the same animals also were examined. Reactions containing no RT were negative controls, and 18S rRNA standardized expressed message from captured cells. RT-PCR analysis of laser-captured whole cartilage showed a general qualitative loss of OPN mRNA as animal age increased. Youngest mice gave equivalent OPN expression over all laser-microdissected cartilage zones. For 7-11 day-old mice, OPN expression was qualitatively greatest in resting and lowest in hypertrophic regions of cartilage. Expression of OPN correlated with mineral in the tissue suggests that OPN functionally may inhibit normal vertebrate growth plate mineralization, and its loss with increasing tissue maturation appears permissive to mineral development.

Animals↗