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

Why do patients with cancer die?

Cancer is a major cause of global mortality, both in affluent countries and increasingly in developing nations. Many patients with cancer experience reduced life expectancy and have metastatic disease at the time of death. However, the more precise causes of mortality and patient deterioration before death remain poorly understood. This scarcity of information, particularly the lack of mechanistic insights, presents a challenge for the development of novel treatment strategies to improve the quality of, and potentially extend, life for patients with late-stage cancer. In addition, earlier deployment of existing strategies to prolong quality of life is highly desirable. In this Roadmap, we review the proximal causes of mortality in patients with cancer and discuss current knowledge about the interconnections between mechanisms that contribute to mortality, before finally proposing new and improved avenues for data collection, research and the development of treatment strategies that may improve quality of life for patients.

Assessment role of total phenols and flavonoids extracted from Pleurotus columbinus mushroom on the premature ovarian failure induced by chemotherapy in rats

Background

Many species of mushroom contain an assortment of free radical scavengers (Phenolics and Flavonoids compounds) that have made them nutritionally beneficial and a source of expansion of drug production. In this study, we examined the preventive and remedial role of total phenol extract from Pleurotus columbines (TP) in alleviating the consequences of cyclophosphamide (CTX) on the ovaries of female rats. Rats were randomly assigned to four groups: healthy controls, cyclophosphamide (CTX), received a TP (100 mg/kg) orally daily for 14 days and curative group: CTX-TP, we determined and identified a total phenol from a mushroom extract and examined it as an antioxidant agent. To investigate the therapeutic influence, it was administrated 2 weeks after CTX. To assess the impact of TP on ovarian damage caused by CTX, ovarian hormone tests were performed such as luteinizing hormone (LH), 17-β-estradiol (E2), and anti-mullerian hormone (AMH). Besides, follicle-stimulating hormone (FSH) in serum was evaluated, and histopathological analysis of the ovary was examined.

Results

This study indicates that treatment with TP decreased the severity of cyclophosphamide-induced ovary injury by reducing inflammation and apoptotic effects and increasing the activity of antioxidants.

Conclusions

TP could be used to alleviate cyclophosphamide-induced ovary injury.

Improved immunohistochemical detection of phosphorylated mitogen-activated protein kinases in the injured rat optic nerve head

The activity of mitogen-activated protein kinases (MAPKs) is largely controlled by addition or removal of phosphate groups, which are carried out by kinase or phosphatase enzymes, respectively. Determining the phosphorylation status of MAPK isoenzymes, therefore, aids elucidation of the physiological and pathological roles of this enzyme. In practical terms, however, end-point procurement of appropriate experimental tissues produces conditions where MAPK phosphorylation status can rapidly alter, thus giving rise to aberrant data. We therefore attempted to instigate a means of stabilising end-point MAPK phosphorylation levels when procuring tissues for analysis. We employed a well-described rat model of ocular hypertension in which MAPK isoenzyme activation occurs in the optic nerve head (ONH), but can vary according to the level of resultant tissue pathology. Animals were appropriately treated and after 3 days were perfused in the presence or absence of a cocktail of phosphatase inhibitors (PIs), immediately prior to tissue fixation, in order to prevent dephosphorylation of phosphorylated MAPKs. Immunohistochemical labelling for phosphorylated MAPKs in untreated ONH sections was unaffected by the presence of PIs in the perfusate. MAPK activation was detected by immunohistochemistry in the treated ONH, but findings varied considerably, particularly in animals with less extensive tissue damage. The presence of PIs in the perfusate, however, significantly reduced this variation and enabled consistent changes to be detected, particularly in the animals with less extensive tissue damage. Thus, the addition of PIs to the perfusate is suggested when studying MAPK activation by immunohistochemistry, especially in the ONH.

Protein Markers Associated with an ALDH Sub-Population in Colorectal Cancer

ALDH has been shown to be a marker that denotes a sub-population of cancer stem cells in colorectal and other cancers. This sub-population of cells shows an increased risk for tumor initiation, metastasis, and resistance to chemotherapy and radiation resulting in recurrence and death. It is thus essential to identify the important signaling pathways related to ALDH1+ CSCs in colon cancer. The essential issue becomes to isolate pure sub-populations of cells from heterogeneous tissues for further analysis. To achieve this goal, tissues from colorectal cancer Stage III patients were immuno-stained with ALDH1 antibody. Target ALDH1+ and ALDH1- cells from the same tissue were micro-dissected using Laser Capture Microdissection (LCM). Captured cells were lysed and analyzed using LC-MS/MS where around 20,000 cells were available for analysis. This analysis resulted in 134 proteins which were differentially expressed between ALDH1+ and ALDH1- cells in three patient sample pairs. Based on these differentially expressed proteins an IPA pathway analysis was performed that showed two key pathways in cell to cell signaling and organismal injury and abnormalities. The IPA analysis revealed β-catenin, NFκB (p65) and TGFβ1 as important cancer-related proteins in these pathways. A TMA validation using immunofluorescence staining of tissue micro-arrays including 170 cases was used to verify that these key proteins were highly overexpressed in ALDH1+ cells in colon cancer tissues compared to ALDH1- cells.

Simplified and versatile method for isolation of high-quality RNA from pancreas

Isolation of high-quality RNA from pancreas is challenging because the organ contains large quantities of RNases and undergoes autolysis upon harvest. Here we present a simplified perfusion method of the pancreas using an RNase inhibitor. The technique consistently yields high-quality RNA from stored pancreas samples suitable for molecular biology applications, including quantitative RT-PCR. Yields are comparable to RNA isolated from pancreas immediately, but superior to RNA isolated from stored samples that were snap-frozen or immersed in an RNase inhibitor solution. In addition, when compared to the previously reported in situ ductal perfusion technique, our method does not cause histological artifacts.

Why is it crucial to reintegrate pathology into cancer research?

The integration of pathology with molecular biology is vital if we are to enhance the translational value of cancer research. Pathology represents a bridge between medicine and basic biology, it remains the gold standard for cancer diagnosis, and it plays an important role in discovery studies. In the past, pathology and cancer research were closely associated; however, the molecular biology revolution has shifted the focus of investigators toward the molecular alterations of tumors. The reductionist approach taken in molecular studies is producing great insight into the inner workings of neoplasia, but it can also minimize the importance of histopathology and of understanding the disease as a whole. In turn, pathologists can underestimate the role of molecular studies in developing new ancillary techniques for clinical diagnosis. A multidisciplinary approach that integrates pathology and molecular biology within a translational research system is needed. This process will require overcoming cultural barriers and can be achieved through education, a more effective incorporation of pathology into biological research, and conversely an integration of biological research into the pathology laboratory.

Setting up a Prospective Thyroid Biobank for Translational Research: Practical Approach of a Single Institution (2004-2009, Pasteur Hospital, Nice, France)

In the last few years, conditions for setting up a human biobank in France have been upgraded by taking into account (1) the new laws and regulations that integrate the ethical and societal dimension of biobanking and delineate the risks for patients associated with the procurement of human cells and tissues, (2) the increasing request by scientists for human samples with proven biological quality and sophisticated sets of annotations, including information produced through the evergrowing use of molecular biology in pathology, and (3) establishment of procedures concerning the safety of the personnel working with biological products. For this purpose, health authorities and national research institutes in France have provided significant support for the set up of biobanks. The present work was conducted to describe how we set up a biobank targeting diseases of a specific organ (thyroid gland), with the aim of rapidly developing translational research projects. The prospective experience of a single institution (Pasteur Hospital, Nice, France) over a 6-year period (2004-2009) is presented from the practical point of view of a surgical pathology laboratory. We describe different procedures required to obtain high-quality thyroid biological resources and clinical annotations. The procedures were established for the management of biological products obtained from 1454 patients who underwent thyroid surgery. The preanalytical steps leading to the storage of frozen specimens were carried out in parallel with diagnostic procedures. As the number of international networks for research programs using biological products is steadily increasing, it is crucial to harmonize the procedures used by biobanks. In this regard, the described thyroid biobank has been set up using criteria established by the French National Cancer Institute (Institut National du Cancer) to guarantee the quality of different collections stored in biobanks.

Isolation of guard cells from fresh epidermis using a piezo-power micro-dissection system with vibration-attenuated needles

The Eppendorf Piezo-Power Microdissection (PPMD) system uses a tungsten needle (MicroChisel) oscillating in a forward-backward (vertical) mode to cut cells from surrounding tissue. This technology competes with laser-based dissection systems, which offer high accuracy and precision, but are more expensive and require fixed tissue. In contrast, PPMD systems can dissect freshly prepared tissue, but their accuracy and precision is lower due to unwanted lateral vibrations of the MicroChisel. Especially in tissues where elasticity is high, these vibrations can limit the cutting resolution or hamper the dissection. Here we describe a cost-efficient and simple glass capillary-encapsulation modification of MicroChisels for effective attenuation of lateral vibrations. The use of modified MicroChisels enables accurate and precise tissue dissection from highly elastic material.

Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples

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.

Imaging aspects of cardiovascular disease at the cell and molecular level

Cell and molecular imaging has a long and distinguished history. Erythrocytes were visualized microscopically by van Leeuwenhoek in 1674, and microscope technology has evolved mightily since the first single-lens instruments, and now incorporates many types that do not use photons of light for image formation. The combination of these instruments with preparations stained with histochemical and immunohistochemical markers has revolutionized imaging by allowing the biochemical identification of components at subcellular resolution. The field of cardiovascular disease has benefited greatly from these advances for the characterization of disease etiologies. In this review, we will highlight and summarize the use of microscopy imaging systems, including light microscopy, electron microscopy, confocal scanning laser microscopy, laser scanning cytometry, laser microdissection, and atomic force microscopy in conjunction with a variety of histochemical techniques in studies aimed at understanding mechanisms underlying cardiovascular diseases at the cell and molecular level.

Laser-capture microdissection in prostate cancer research: establishment and validation of a powerful tool for the assessment of tumour-stroma interactions

OBJECTIVES

To describe our experience with the optimization and validation of laser-capture microdissection (LCM) for biomarker analysis in prostate tissues. As LCM allows the separation of benign and malignant epithelial structures and stromal elements, it not only allows identification of the source of the biomarker, but might also accentuate gene or protein expression changes by reducing contamination by other cellular elements.

MATERIALS AND METHODS

In all, 19 fresh-frozen prostate tissue samples were subjected to LCM, with the cDNA being analysed using quantitative polymerase chain reaction for several genes, to identify the optimum number of cells for capture, as well as gene markers assessing for the purity of the captured cells. The localization was further confirmed by in situ hybridization.

RESULTS

Prostate-specific antigen (PSA) and cytokeratin 8, were expressed solely by epithelial cells, whereas hepatocyte growth factor (HGF) and tissue inhibitor of metalloproteinases-3 (TIMP3) were expressed only by stromal cells, and the levels of transcripts of these genes were unaltered between benign and malignant tissues.

CONCLUSIONS

These data suggest that PSA, cytokeratin 8, HGF and TIMP3 are reliable gene markers of purity of epithelial and stromal compartments for LCM of prostate tumours. Although this technique is not new and is increasingly used in laboratories, it needs optimization and stringent validation criteria before data analysis. This applies to all tissue types subjected to LCM.

Tissue integrity and RNA quality of laser microdissected phloem of potato

The phloem is an important conduit for the transport of signaling molecules including RNA. Phloem sap has served as a source of RNA to profile uncontaminated phloem transcriptomes but its collection is difficult in many species. Laser capture microdissection techniques offer a valuable alternative for isolating RNA from specific vascular cells. In potato (Solanum tuberosum L.), there are seven BEL1-like transcription factors expressed throughout the plant with diverse functions. The RNA of one of these, StBEL5, moves through the phloem from the leaf to stolon tips to regulate tuber formation. In this study, the presence of several BEL RNAs and one Knotted1-like RNA was determined in phloem cells collected by laser microdissection coupled to laser pressure catapulting (LMPC). Three fixatives were compared for their effect on cell morphology and RNA quality in transverse sections of stems of potato. For optimum tissue integrity and quality of RNA from potato stem sections, the best results were achieved using ethanol acetate as the fixative. In addition, the RT-PCR results demonstrated the presence of six out of seven of the StBEL RNAs and a potato Knox RNA in phloem cells.