Laser capture microdissection coupled with on-column extraction LC-MS(n) enables lipidomics of fluorescently labeled Drosophila neurons.

We have used laser capture microdissection (LCM) and fluorescence microscopy to isolate genetically labeled neurons from the Drosophila melanogaster brain. From native thin sections, regions of interest could be analyzed with a spatial resolution better than 50 µm. To exploit the specificity of LCM for lipidomics, catapulted tissue patches were directly collected on a reversed phase column and analyzed using an on-column extraction (OCE) that was directly coupled with liquid chromatography-multistage mass spectrometry (LC-MS(n)). With this approach, more than 50 membrane lipids belonging to 9 classes were quantified in tissue regions equivalent to a sample amount of 50 cells. Using this method, the limit of quantitation and the extraction efficiency could be estimated enabling a reliable evaluation of acquired lipid profiles. The lipid profiles of cell body- and synapse-enriched regions of the Drosophila brain were determined and found to be distinct. We argue that this workflow represents a tremendous improvement for tissue lipidomics by integrating genetics, fluorescence microscopy, LCM and LC-MS(n).

Expression of Intermediate Filaments and Germ Cell Markers in the Developing Bovine Ovary: An Immunohistochemical and Laser-Assisted Microdissection Study.

In the present investigation, bovine ovary prenatal development was studied using immunohistochemistry and laser-assisted microdissection (LAM). A major aim of this study was to evaluate the protein expression pattern of intermediate filaments (IF) and distinguish S100 protein (S100 alpha and S100 beta protein) isoforms during prenatal follicle differentiation, subsequently correlating them with germ cell marker expression. A development-specific expression pattern of different keratins as well as vimentin was detected in the prenatal bovine ovary; K18-specific expression was found during all developmental stages (i.e. in surface epithelium, germ cell cord somatic cells, and follicle cells), and keratins 5, 7, 8, 14, and 19 and vimentin had a stage-specific expression pattern in the different cell populations of the prenatal ovaries. Additionally, our results represent new data on the expression pattern of germ cell markers during bovine ovary prenatal development. S100 alpha and beta protein was localized to oocyte cytoplasm of different follicle stages, and S100 alpha staining could be observed in granulosa cells. Furthermore, through isolation of characteristic ovary cell populations using LAM, specific confirmation of some genes of interest (KRT8, KRT18, S100 alpha, S100 beta, and OCT4, DDX4) could be obtained by RT-PCR in single cell groups of the developing bovine ovary.

Cellular expression and localization of estrogen receptor α and progesterone receptor mRNA in the bovine oviduct combining laser-assisted microdissection, quantitative PCR, and in situ hybridization.

The importance of using techniques that allow the study of pure populations of cells has been increasingly recognized. The authors used laser-assisted microdissection (LAM) in combination with quantitative real-time PCR (qPCR) to assess the relative expression of mRNAs encoding estrogen receptor α (ERα) and progesterone receptor (PR) in the different compartments of the bovine oviduct (epithelium, stroma, smooth muscle coat) during the follicular and mid-luteal phases of the estrus cycle. The localization of receptor mRNA was further studied using non-radioactive in situ hybridization (NISH). A special focus was on whether formalin fixation and paraffin embedding influence the quality and quantity of mRNA obtained from microdissected material. Distinct cyclic changes of the mRNA in the bovine oviduct were observed with elevated levels of PR mRNA transcripts in the epithelium and smooth muscle coat during the follicular phase. The expression of PR mRNA did not vary significantly in the stroma of the bovine oviduct during follicular and mid-luteal phases. In conclusion, the authors found that LAM with qPCR can precisely locate and accurately quantify mRNA expression in specific cell populations from formalin-fixed and paraffin-embedded oviductal tissue.

Enhanced molecular analyses by combination of the HOPE-technique and laser microdissection.

As part of an investigation aimed at illuminating the possibilities and limits of the HOPE-fixation and paraffin-embedding technique we here describe a novel procedure which was developed in order to combine the benefits of the HOPE-technique with the capabilities of laser microdissection. The presented procedure avoids the need for amplification of template-RNA thus facilitating reliable and reproducible results. The excellent preservation of nucleic acids, proteins, and morphology in HOPE-fixed, paraffin-embedded tissues enhances the molecular applications available to date with materials acquired by laser microdissection when compared to formalin fixed, paraffin-embedded tissues, thus substantially extending the methodological panel in tissue based research.

Noncontact laser microdissection and pressure catapulting: sample preparation for genomic, transcriptomic, and proteomic analysis.

The understanding of the molecular mechanisms of cellular metabolism and proliferation necessitates accurate identification, isolation, and finally characterization of a specific cell or a population of cells and subsequently their subsets of biomolecules. For the simultaneous analysis of thousands of molecular parameters within a single experiment, as realized by DNA, RNA, and protein microarray technologies, a defined number of homogeneous cells derived from a distinct morphological origin is required. Sample preparation is therefore a very crucial step for high-resolution downstream applications. Laser microdissection and laser pressure catapulting (LMPC) enables such pure and homogeneous sample preparation, resulting in an eminent increase in the specificity of molecular analyses. For microdissection, the force of focused laser light is used to excise selected cells or large tissue areas from object slides or from living cell culture down to a resolution of individual single cells and subcellular components like organelles or chromosomes, respectively. After microdissection this sample is directly catapulted into an appropriate collection device. As the entire process works without any mechanical contact, it enables pure sample retrieval from morphologically defined origin without cross contamination. Wherever homogenous samples are required for subsequent analysis of, e.g., cell areas, single cells, or chromosomes, the PALM MicroBeam system is an indispensable tool. The integration of image analysis platforms fully automates screening, identification, and finally subsequent high-throughput sample handling. These samples can be directly linked into versatile downstream applications, such as single-cell mRNA-extraction, different PCR methods, microarray techniques, and many others. Acceleration in sample generation vastly increases the throughput in molecular laboratories and leads to an increasing knowledge about differentially regulated mRNAs and expressed proteins, providing new insights into cellular mechanisms and therefore enabling the development of systems for tumor biomarker identification, early detection of disease-causing alterations, therapeutic targeting and/or patient-tailored therapy.

Extraction and processing of high quality RNA from impalpable and macroscopically invisible prostate cancer for microarray gene expression analysis.

Molecular analyses of early-stage prostate cancers are necessary to assess their potential clinical significance based on established and/or novel biomarkers for tailored clinical management. A prerequisite for the application of RNA-based analyses of such, mostly macroscopically-undetectable, small prostate carcinomas is the recovery and preservation of sufficient RNA quantities and quality. Furthermore, in prostate cancer, heterogeneity is a common phenomenon that includes a juxtaposition of different tissue compositions and variable histological grades within the same tumor focus. To better understand the molecular mechanisms of prostate cancer, it is essential to correlate molecular data with a specific cell type. Here, we present a tissue collecting protocol which is aligned with the preoperative evaluation of tumor localization. In combination with the technique of laser microdissection and pressure catapulting, we are able to preserve RNA of high quality from homogeneous cell populations of macroscopically-undetectable small prostate carcinomas. To obtain the necessary RNA quantities for whole genome cDNA microarrays, the isolated total RNAs were amplified by T7-based RNA-polymerase in vitro transcription. The microarray analyses (Human Unigene Set RZPD3.1) resulted in 216 differentially expressed genes (191 down-regulated, 25 up-regulated). Among these were several known prostate cancer relevant genes, such as AMACR, TARP, LIM, GPR160 (all up-regulated), CAV1, NTN1, MT1X; CLU, TRIM29, SPARCL1 and HSPB8 (all down-regulated).

Cellular protein and mRNA expression patterns of matrix metalloproteinases-2, -3 and -9 in human breast cancer: correlation with tumour growth.

The expression of matrix metalloproteinases (MMPs) with type IV collagenase activity has been associated with tumour invasion and metastatic potential in experimental models. We studied whether the cellular localization of MMP expression provides useful information on tumour behaviour in human breast cancer. Immunohistochemistry and non-radioisotopic-detected in situ hybridization were used to study protein and mRNA expression profiles for MMPs-2, -3 and -9 in paraffin sections of 70 invasive breast carcinomas. Protein and mRNA expression of the MMPs was observed in tumour as well as in peritumoural stromal cells. MMP protein expression was increased at the invasive border (p < 0.05). Grade 3 carcinomas expressed MMP-2 mRNA in significantly more tumour cells than grade 2 carcinomas (p = 0.006). Ductal carcinomas with an extensive intraductal component were characterized by the lowest percentages of MMPs-2 and -3 mRNA expressing peritumoural stromal cells (p < 0.05). No correlation was observed between MMP protein/mRNA expression and pTNM classification. In conclusion our results indicate that the expression of MMPs is associated with tumour behaviour. The correlation of MMPs-2 and -3 expression in peritumoural stromal cells with tumour type, shown for the first time, suggests that transcriptional regulation of these MMPs in stromal cells is important for the growth pattern of breast cancer.

High frequency of TGF-beta-receptor-II mutations in microdissected tissue samples from laryngeal squamous cell carcinomas.

In this study we analyze 105 paraformaldehyde-fixed and paraffin-embedded tumor samples from 12 patients with invasive squamous cell carcinoma of the larynx for the presence of gene mutations of the complete TGF-beta-receptor-II (TBR-II) gene. This study was conducted on tissue samples following separation of tumor cell groups from adjacent stroma cell compartments by laser microdissection, resulting in pure tumor cell complexes of approximately 50 to 500 cells. We detected 35 different mutations in 5 of the 12 patients analyzed but none in numerous samples of the normal peritumoral stroma or in normal epithelium. Twelve of the mutations were silent and nonfunctional, whereas the 23 relevant mutations were either bp replacements leading to amino acid exchanges or deletions leading to frame shifts and premature stop codons. Except for the so-called "big polyadenine tract" in exon 3 with several similar mutations, no further mutational hot spot was found. In addition we found a correlation between mutations and a loss of typical TGF-beta effects in tumor cells (high cell proliferation rate) but not in the stroma cells (low proliferative capacity, significant de novo deposition of matrix material). This study is the first to identify a high mutational rate of the TBR-II gene in laryngeal squamous cell carcinoma. We show that that only small tumor-cell groups are affected. The molecular abnormalities are variable, and only one hot spot of mutations can be identified (exon 3, big polyadenine tract). These defects and possibly comparable mutations in other proteins of the TGF-beta-signaling cascade seem to be associated with enhanced cell proliferation rates and alterations of the peritumoral matrix.

High quality RNA retrieved from samples obtained by using LMPC (laser microdissection and pressure catapulting) technology.

Isolation of intact RNA in high quality is the first and often the most critical step in performing many fundamental molecular biology experiments, and is essential for many techniques used in gene expression analysis. As many factors influence nucleic acid preservation, RNA isolation should include some important steps before and after the actual RNA extraction. We tested the influence of fixation and staining protocols regarding RNA integrity and concentration. A factor that is often underestimated is the absolute necessity for homogenous starting materials. Application of the LMPC technology allows for a rapidand highly precise procurement of purified cell populations suitable for a variety of downstream analyses.

Glycosaminoglycan therapy prevents TGF-beta1 overexpression and pathologic changes in renal tissue of long-term diabetic rats.

Chronic induction of the prosclerotic cytokine transforming growth factor beta (TGF-beta) has been implicated in the pathogenesis of diabetic nephropathy. In a rat model of diabetes mellitus-induced glomerulosclerosis, daily administration of a modified heparin (mH) glycosaminoglycan (GAG) preparation with low anticoagulant activity prevented glomerular and tubular matrix accumulation, as well as overexpression of TGF-beta1 mRNA and albuminuria, without obvious side effects. To elucidate the molecular mechanisms of GAG/mH inhibitory actions on TGF-beta1, studies using cultured mesangial cells were also performed. In these cells, high glucose-induced, dose-dependent increases in TGF-beta1 mRNA and bioactive TGF-beta protein expression were inhibited by GAG/mH treatment, whereas basal TGF-beta1 expression was not affected. Both the heparin-derived GAG and dermatan sulfate were effective, indicating that the heparin chemical structure is not necessary for inhibitory activity. Coincubation of GAG with active TGF-beta1 demonstrated no inhibitory effect on TGF-beta1 bioactivity, excluding a neutralizing effect of GAG on TGF-beta1 a the protein level. Furthermore, it was demonstrated that GAG inhibited phorbol myristate acetate-induced translocation of protein kinase C-alpha (PKC-alpha) and -beta1 and activation of PKC-alpha, as well as high glucose-induced activation of PKC-alpha. These results suggest that GAG inhibit TGF-beta1 overexpression at the transcriptional level, possibly via inhibition of high glucose-activated PKC. The findings indicate the potential of GAG therapy for the prevention of diabetic glomerulosclerosis by the inhibition of chronic disease-induced TGF-beta1 mRNA overexpression.

AP-1 proteins mediate hyperglycemia-induced activation of the human TGF-beta1 promoter in mesangial cells.

Hyperglycemia-induced overproduction of the prosclerotic cytokine transforming growth factor-beta1 (TGF-beta1) has been implicated in the pathogenesis of diabetic nephropathy. Because high glucose and phorbol esters (PMA) increase TGF-beta1 mRNA levels in mesangial cells, this study was designed to characterize these effects on the human TGF-beta1 promoter activity. With the use of luciferase reporter gene constructs containing TGF-beta1 5'-flanking sequence (from -453 to +11 bp) transfected into mesangial cells, it was found that 30 mM glucose induced a nearly twofold increase in TGF-beta1 promoter activity after 24 h of incubation in human and porcine mesangial cells. Stimulation by PMA was more effective (2.3-fold). Mutagenesis in either one of the two or both activating protein-1 (AP-1) binding sites abolished the high glucose and the PMA effect. Furthermore, addition of the AP-1 inhibitor curcumin obliterated the glucose response. Corresponding experiments revealed that the transcription factor stimulating protein 1 was not involved in mediating the glucose effect. The high glucose-induced TGF-beta1 promoter activation was also prevented by inhibitors of protein kinase C and p38 mitogen-activated proteinkinase. Electrophoretic mobility shift assays with oligonucleotides containing one of the two AP-1 binding sites showed that glucose treatment markedly enhanced the binding activity of nuclear proteins of mesangial cells, particularly to box B. Supershift assays demonstrated that JunD and c-Fos were present in the protein-DNA complexes under control and hyperglycemic conditions. The functional and structural results show that glucose regulates human TGF-beta1 gene expression through two adjacent AP-1 binding sites and gives rise to the involvement of protein kinase C and p38 mitogen-activated protein kinase in hyperglycemia-induced TGF-beta1 gene expression.