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Cartilage and bone are specialized skeletal tissues composed of unique extracellular matrices. Bone, in particular, has a highly calcified or mineralized matrix that makes microtomy and standard histological studies very challenging. Therefore, methods to appropriately fix and decalcify mineralized skeletal tissues have been developed to allow for paraffin processing and standard microtomy. In this chapter, we will illustrate methods for tissue grossing, fixation, decalcification, paraffin processing, embedding, sectioning, and routine histological staining of demineralized murine skeletal tissues. We will also discuss methods for decalcified frozen sectioning of skeletal tissues with and without the use of a tape-transfer system.

Immunofluorescence staining of tissues has become a reliable and informative technique used in a diverse set of applications, ranging from simple detection of an antigen of interest in a specific location to the semiquantitative analysis of spatial relationships between multiple antigens and/or cell types. During complement activation, circulating complement proteins are covalently fixed to target tissues, providing a durable marker of complement activation in the tissue, and many of these proteins can be readily detected by immunofluorescence microscopy. In general, staining for complement fragments is much like staining for other noncomplement epitopes. However, one key difference is the diligence with which unfixed tissues must be handled when staining for complement fragment. Here we explain the process of dual staining frozen mouse kidney sections for the complement proteins C3 and C4. Throughout the protocol, we will emphasize important steps for preserving complement protein integrity as well as tips to improve the signal-to-noise ratio to improve overall image quality.

A method for preparing frozen sections with an adhesive film is described. In order to observe fine structures and weak fluorescence of samples, new types of adhesive films [Cryofilm type 3C(16UF) and 4D(16UF)] are used. The adhesive film is made with very clear and very low autofluorescence. For gene analysis, a very thin adhesive film (LMD film) is used to cut by means of the laser microdissection (LMD). For MALDI mass spectrometry imaging (MALDI-MSI), a conductive adhesive film (Cryofilm type MS) is used to avoid electric charge of the sample. A biological sample is frozen quickly and freeze-embedded. The frozen sample is cut with a very sharp disposable blade made from fine tungsten carbide. The combination of the adhesive films and the blade can generate 3 micrometer thick sections from samples including bone, while it is also possible to generate 1 μm thick sections. The morphology of bone and soft tissues are preserved using this method. Cells such as osteoblasts, fibroblasts, and osteoclasts are clearly observed with an oil immersion lens at high magnification. Sections generated using the Cryofilm type 3C(16UF) shows weak fluorescent signals more clearly than sections generated with the previously reported adhesive films [Cryofilm type 2C(9) and 2C(10)]. Furthermore fluorescence of the fine structures in cells is clearly shown using a super-high-resolution microscope. Several staining and experimental methods such as histology, histochemistry, enzyme histochemistry, immunohistochemistry, and in situ hybridization can be performed on these sections. This method is also useful for preparing frozen sections of large sample such as a whole-body mouse and rat. In gene analysis, gene quality of sample collected from the section made with the LMD film is superior to that of sample made by a conventional method. The Cryofilm type MS makes almost complete section from tissues including hard tissues and large samples. The satisfactory signals are detected from the section with MALDI-MSI.

Pathological assessment of frozen sections of tissues is important in the clinical management (intraoperative consultation) and research in patients with esophageal squamous cell carcinoma. Frozen sections may be used in the assessment of status of resection margins, extent of cancer metastasis (pathological staging), confirmation of the pathology, and increased volume of cancer cells for tissue banking. However, the applications of frozen sections have many technical limitations. Thus, interpretation of frozen sections needs expertise, collaborations, and attention to proper technical skills in the sectioning.

Type 1 diabetes is an autoimmune disease resulting in the loss of insulin production and, consequently, hyperglycemia. The nonobese diabetic (NOD) mouse develops spontaneous diabetes with considerable similarity to the disease in humans. Immunological studies using the NOD mouse model allow for the investigation of the natural history of the disease and leukocyte and lymphocyte pathogenic and regulatory functions, as well as testing potential therapies for intervention. The analyses of the cellular events leading up to diabetes may utilize different in vitro cellular assays, immunohistochemistry, and in vivo adoptive transfer, to study mechanisms of the disease and the effects of therapeutic intervention. In this chapter, we describe some common techniques for phenotyping and mechanistic analyses of function, particularly of CD8+ T cells.

Many cancers harbor a large fraction of nonmalignant stromal cells intermixed with neoplastic tumor cells. While single-cell transcriptional profiling methods have begun to address the need to distinguish biological programs in different cell types, such methods do not enable the analysis of spatial information available through histopathological examination. Laser capture microdissection offers a means to separate cellular samples based on morphological criteria. We present here an optimized method to retrieve intact RNA from laser capture microdissected tissue samples, using pancreatic ductal adenocarcinoma as an example, in order to separately profile tumor epithelial and stromal compartments. This method may also be applied to nonmalignant tissues to isolate cellular samples from any morphologically identifiable structure.

Immunohistochemistry (IHC) is a routinely used technique in clinical diagnosis of pathological conditions and in basic and translational research. It combines anatomical, immunological, and biochemical methods and relies on the specific binding of an antibody to an antigen. Using the technique with mineralized tissues is more challenging than with soft tissues. Demineralizing the samples allows for embedding in paraffin wax, and also facilitates cryosectioning. This chapter describes methods for IHC on formaldehyde-fixed, demineralized, paraffin-embedded, or frozen sections to detect antigens in skeletal tissues.

Cutting frozen sections is a technique that allows for the rapid diagnosis of unfixed frozen tissue. A thin slice of tissue is cut from a frozen biospecimen and then stained typically with hematoxylin and eosin. The applications of this technique range from clinical diagnosis to quality assurance in the procurement or the use of biobanking specimens. It is important that the quality of the frozen section is of the highest possible caliber in order to optimize the pathologist's interpretation, whether the result is used for surgical management or to validate the tissue being collected for research. Herein, we describe a step-by-step method to cut frozen sections.

The heterogeneity present in solid tumors adds significant difficulty to scientific analysis and improved understanding. Fundamentally, solid tumor formation consists of cancer cells proper along with stromal elements. The burgeoning malignant process is dependent upon modified stromal elements. Collectively, the stroma forms an essential microenvironment, which is indispensable for the survival and growth of the malignant neoplasm. This cellular heterogeneity makes molecular profiling of solid tumors via mass spectrometry (MS)-based proteomics a daunting task. Laser capture microdissection (LCM) is commonly used to obtain distinct histological cell types (e.g., tumor parenchymal cells, stromal cells) from tumor tissue and attempt to address the tumor heterogeneity interference with downstream liquid chromatography (LC) MS analysis. To provide optimal LC-MS analysis of micro-scale and/or nano-scale tissue sections, we modified and optimized a silver-stained one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D-SDS-PAGE) protocol for the LC-MS analysis of LCM-procured fresh-frozen tissue specimens. Presented is a detailed in-gel digestion protocol adjusted specifically to maximize the proteome coverage of amount-limited LCM samples, and facilitate in-depth molecular profiling. Following LCM, targeted tissue sections are further fractionated using silver-stained 1D-SDS-PAGE to resolve and visualize tissue proteins prior to in-gel digestion and subsequent LC-MS analysis.

Laser Capture Microdissection has earned a permanent place among modern techniques connecting histology and molecular biology. Laser Capture Microdissection has become an invaluable tool in medical research as a means for collection of specific cell populations isolated from their environment. Such genomic sample enrichment dramatically increases the sensitivity and precision of downstream molecular assays used for biomarker discovery, monitoring disease onset and progression, and in the development of personalized medicine. The diversity of research targets (cancerous and precancerous lesions in clinical and animal research, cell pellets, rodent embryos, frozen tissues, archival repository slides, etc.) and scientific objectives present a challenge in establishing standard protocols for Laser Capture Microdissection. In the present chapter, we share our experiences in design and successful execution of numerous diverse microdissection projects, and provide considerations to be taken into account in planning a microdissection study. Our workflow and protocols are standardized for a wide range of animal and human tissues and adapted to downstream analysis platforms.

Intraoperative consultation (IOC) in gynecologic pathology is aimed at providing or confirming the diagnosis at the time of surgery and evaluating the extent of disease in order to assist the surgeon in determining the surgical procedure being performed. This chapter discusses the main indications for IOC in gynecologic pathology and describes how to submit and process these specimens in order to obtain optimal material. In addition, diagnostic pitfalls and ancillary testing related to IOC in gynecologic pathology are summarized.

In situ hybridization-assisted punches (IFAP) are a low-cost method for extracting tissue from frozen slide-mounted sections as thin as 12 μm. The method synergizes well with standard histological workflows and uses in situ hybridization to target corresponding slide-mounted cryosections that contain the region of interest. Liquid beads of M-1 embedding matrix are applied and snap frozen, binding the matrix to the underlying tissue. Bead-tissue complexes are removed and DNA extracted using a high-salt method. IFAP-extracted DNA is suitable for downstream DNA methylation analysis.

MicroRNAs are an abundant class of small noncoding RNAs that regulate and fine-tune the expression of protein-coding genes. Each microRNA regulates around 100 genes, and they are mostly conserved and abundant within the multicellular organisms. Even though microRNAs have a role in many biological processes and diseases, the function of each single microRNA is still yet to be explored in all tissues and cells they are present. Therefore, an efficient in situ hybridization method, combining locked nucleic acid technology and tyramide signal amplification system, has been developed and presented for detection of microRNAs in frozen section at a cellular resolution and with high sensitivity.

Laser Dissection Microscopy (LDM) is a valuable technique to identify the genetic event that underlies cutaneous mosaicism. Isolation of a selected cell population is key to the detection of a somatic mutation. Advantages of the LDM technique are that stored skin biopsies can be analyzed without the necessity of culturing cells. Here, we describe the preparation of skin sections and cells for LDM, followed by dissection, and subsequent DNA and RNA analysis in order to detect the underlying somatic mutation.

The introduction of large-scale gene expression profiling studies has greatly increased the need to rapidly obtain high-quality cellular expression patterns of genes found to exhibit differential expression. The use of large-scale nonradioactive RNA in situ hybridization makes this possible, and greatly increases the general usefulness of this data. Here, we describe protocols for parallel analysis of up to 50 different gene-specific probes in mouse retinal sections.

β-galactosidase (β-gal) is among the most frequently used markers for studying a wide variety of biological mechanisms, e.g., gene expression, cell migration, stem cell conversion to different cell types, and gene silencing. Many of these studies require the histochemical detection of relative β-gal levels in tissue cross-sections mounted onto glass slides and visualized by microscopy. This is particularly useful for the analysis of promoter activity in skeletal muscle tissue since the β-gal levels can vary dramatically between different anatomical muscles and myofiber types. The differences in promoter activity can be due to a myofiber's developmental history, innervation, response to normal or experimental physiological signals, and its disease state. It is thus important to identify the individual fiber types within muscle cross-sections and to correlate these with transgene expression signals. Here, we provide a detailed description of how to process and analyze muscle tissues to determine the fiber-type composition and β-gal transgene expression within cryosections.

Immunohistochemistry is a classic technique used for the localization of antigenic target molecules in -tissue. The method exploits the principle that the target antigen is recognized by specific antibody and is visualized using different detection systems. The subject of this chapter is simultaneous immunohistochemical detection of protein antigens and proliferation marker BrdU in the developing tooth.

Laser capture microdissection (LCM) has become a powerful technique that allows analyzing gene expression in specific target cells from complex tissues. It is widely used in animal research, yet few studies on plants have been carried out. We have applied this technique to the plants-nematode interaction by isolating feeding cells (giant cells; GCs) immersed inside complex swelled root structures (galls) induced by root-knot nematodes. For this purpose, a protocol that combines good morphology preservation with RNA integrity maintenance was developed, and successfully applied to Arabidopsis and tomato galls. Specifically, early developing GCs at 3 and 7 days post infection (dpi) were analyzed; RNA from LCM GCs was amplified and used successfully for microarray assays.

Terminal deoxynucleotidyl transferase (TdT) dUTP Nick-End Labeling (TUNEL) assay has been designed to detect apoptotic cells that undergo extensive DNA degradation during the late stages of apoptosis. The method is based on the ability of TdT to label blunt ends of double-stranded DNA breaks independent of a template. This chapter describes an assay for detection of apoptotic cells during mouse odontogenesis using a colorimetric TUNEL system.

In situ zymography is a unique laboratory technique that enables the localisation of matrix-degrading metalloproteinase (MMP) activity in histological sections. Frozen sections are placed on glass slides coated with fluorescently labelled matrix proteins. After incubation MMP activity can be observed as black holes in the fluorescent background due to proteolysis of the matrix protein. Alternatively frozen sections can be incubated with matrix proteins conjugated to quenched fluorescein. Proteolysis of the substrate by MMPs leads to the release of fluorescence. This technique can be combined with immunohistochemistry to enable co-location of proteins such as cell type markers or other proteins of interest. Additionally, this technique can be adapted for use with cell cultures, permitting precise location of MMP activity within cells, time-lapse analysis of MMP activity and analysis of MMP activity in migrating cells.

The analysis of frozen tissue by antibodies can be accomplished by the quick freezing of a small tissue sample in liquid nitrogen. Super-cooled isopentane can also be used to further the preservation process. Freezing preserves the available proteins in a near-native state for their identification by antibodies raised against naturally folded proteins. The tissues are sectioned onto charged glass slides where they can be optimally fixed in weakly or non-denaturing solutions such as acetone or those that are alcohol-based. Following mild pretreatment steps to allow for antibody use with low background, (the endogenous peroxidase enzyme or oxidative compounds quenched in a hydrogen peroxide solution and available charged sites blocked by incubation in a normal serum solution) the sections are ready for antigen detection.

In situ hybridization is well suited to obtaining specific topological information on gene transcripts and thereby to relating such observations to a particular function. In spite of the technical and practical difficulties, the application of molecular biological techniques such as in situ hybridization to the cochlea can provide important insights. However, the rarity of gene products (mRNA and proteins) in the cochlea and its fragile structure require the refinement and adaptation of in situ hybridization methods. The present chapter provides a detailed in situ hybridization protocol adapted to frozen tissue sections collected from adult and neonatal stages of the vertebrate cochlea.