Histological Research
Frida Kosofsky
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Rapid and effective molecular subtyping of pancreatic adenocarcinoma (PDAC) is important for prognosis and treatment. Here, the authors develop PACpAInt, a deep learning model for PDAC molecular subtyping from whole-slide histological imaging that enables the analysis of heterogeneity and prognostic predictions.
Multiplexed imaging technologies can reveal the complex cellular and molecular profiles of tissue. Here, the authors develop and implement a denoising pipeline to significantly enhance imaging mass cytometry quality and improve single-cell analyses.
Highly multiplexed tissue imaging continues to show its power for biomedical discovery. In this issue, we publish tools and guidance for implementing this class of methods and reporting subsequent results.
Basic knowledge of tissue preparation, including staining, is important to know when interpreting pathology reports on either in-patient or out-patient biopsies. It is not always the case that the interpreting pathologist has thoroughly analyzed the tissue sample by including appropriate histologic staining, and this deficiency can retard accurate diagnosis.
Four basic types of human tissue can be stained and viewed using various histological techniques. Epithelium, connective tissue, muscle tissue, and nervous tissue have commonalities but look very distinct structurally after staining. Each stain exists to highlight an important feature or component within a tissue type. For example, one of the most common stains, Hematoxylin, is a basic dye that stains proteins a blue color, while Eosin stains proteins a pink color. These two stains are commonly used together to define intracellular organelles and proteins. Because of the variety of the proteins that exist, some stains were created to highlight a particular protein, which this review will discuss in the following sections. The benefit of using a special stain is that it can highlight the specific protein very well. However, because of its specificity, the other structures will not be seen. For this reason, multiple slides will often be created from a given specimen so that multiple stains can be performed to gather the full range of needed information.
Almost all tissue stains are performed on tissue that has been removed from the body. However, in rare instances, very specialize stains called vital stains can work on tissue remaining in the body. These stains are used for the identification of specific types of tissue and identification of abnormal tissue, so a subsequent biopsy can be more accurate in obtaining abnormal tissue.
Before specific staining can occur, tissue samples must undergo preparation through the following stages: Fixation, processing, embedding, sectioning, and sometimes antigen retrieval. In modern histology laboratories, most of these steps are automated.
Fixation: Fixation uses chemicals to preserve the structure of the tissue in its natural form and protects it from degradation by irreversibly cross-linking proteins. Although several specialized fixatives are available, Neutral Buffered Formalin is a common choice for this step. The fixation step is vital to the rest of the histologic staining procedure because by retaining the chemical composition of the tissue, the sample is hardened and makes the sectioning phase easier. Paraffin-formalin is another effective fixative. Its benefit is that it is the fixative of choice for immunostaining; however, it requires preparation at the time of the fixation. Bouin is a fixative used for examining embryo and brain tissue because of its superior preservation of delicate nuclei and glycogen. Its downside is that it does not preserve kidney tissues well and also distorts mitochondrial structure.[1]
Dehydration: The addition of ethanol accomplishes the dehydration of a sample. It removed water from the sample and further hardens the tissue for eventual light microscopy. After ethanol is applied, and following the completion of tissue dehydration, xylene is used to remove the ethanol.[1]
Embedding: Embedding is the process of putting the sample into a paraffin wax or a plastic resin to enhance the process of extracting cellular structures. This step is to be performed with caution if the goal is to perform immunostaining because the paraffin wax will inhibit the penetration of antibodies, and lead to a false result.[1]
Sectioning: Sectioning involves mounting the specimen on a microtome and cutting it into sections. The preferred thickness is 4-5 micrometers so that it can be stained and put on a microscope slide for examination.[1]
Antigen Retrieval: This step is to retrieve antigens that could have been covered in the fixation and embedding stages. If the cross-linking of proteins conceals the antigen sites, there may not be as robust of an immunohistochemical response. Antigen retrieval is achieved through heating and proteolytic methods to break down the cross-links and reveal the epitopes and antigens that were previously covered.[1] Although this step carries the risk of denaturing both the fixative and the antigens themselves, a successful antigen retrieval method can lead to a much more effective immunostaining intensity.
As the name implies, it is two stains done in subsequent steps. The hematoxylin is a basic dye that stains acidic structures. The resulting color is a purple/blue hue, and structures that are targeted with this dye are named Basophilic. Basophilic structures include DNA in cell nuclei, RNA in ribosomes, and the rough endoplasmic reticulum.[1]
Eosin is a counterstain done after hematoxylin and is an acidic dye that targets basic structures. The resulting color is a pink/red hue, and structures that attract eosin are called eosinophilic.[1] The cytoplasm is an example of an eosinophilic structure.
The gram stain is a sequential staining technique invented for differentiating bacterial species. Its major utility lies in determining the causative organism of bacterial infection by staining the cell wall.[2] While not all bacteria have a cell wall and thus cannot be stained with this method, it is still a very useful and commonly performed stain. A bacterial sample can be heat-fixed and undergo gram stain with these four steps: Primary staining with crystal violet, secondary staining with grams iodine, decolorized with alcohol or acetone, and counterstained with safranin. Gram-positive bacteria are those that contain a thick layer of peptidoglycan, making them retain the violet stain and appear purple. Alternatively, the gram-negative bacteria have a thin layer of peptidoglycan and more lipids in the cell wall, so the decolorizing step washes out the violet more, and the sample appears pink.[2]
The Giemsa stain is commonly used in hematology for its superior ability to stain bone marrow, plasma cells, and mast cells. It is also very popular for identifying blood parasites.[3] The Giemsa stain can also help to visualize chromosome abnormalities through "Giemsa-Based Banding," or observing the alternating darker and lighter nucleotide portions on chromosomes during mitosis.[3]
The periodic acid Schiff Reaction Stain, often called the PAS stain, is a way to examine structures containing high amounts of carbohydrate molecules, such as the intestinal brush border, renal tubular cells, mucus, and reticular fibers of connective tissue. [4] The glycogen, glycoprotein, glycolipids, and mucins stain red or magenta color when the stain is complete. The periodic acid, a highly oxidized iodine, oxidizes the hydroxyl groups of adjacent sugar molecules to produce aldehydes. After this step, the Schiff reagent attaches to the aldehyde and forms a red magenta color for visualization.[5][6]
Masson's Trichrome Stain is a stain that can yield a multicolor result on the tissue. Even though it has red counterstains, it is popular for its ability to stain collagen fibers blue. Masson's Trichrome can identify cardiac fibrosis, pulmonary fibrosis, chronic kidney disease, and muscular dystrophy.[7]
Congo red is a water-soluble blue dye that produces a red solution at a pH of 3.0-5.0. Its many aromatic rings can stack together through hydrophobic interactions and collect in tissue. Most notably, Congo red can stain amyloid fibers red and orange color, making it a useful study in amyloidosis. When viewed under polarized light in a microscope, Congo-red-stained tissues high in amyloid will show with bright "apple" green birefringence. PMID:[8]
The Prussian blue stain is useful for identifying iron stores in the body.[7][9] The stain works by first staining the tissue with hydrochloric acid and then seeing the ferric ions react to form the insoluble bright blue pigment. It is useful in diagnosing iron accumulation states like hemochromatosis or hemosiderosis through staining liver tissue and seeing the build-up of iron near the peri-portal hepatocytes or along the sinusoidal lining.[10][11] An overabundance in iron stores within bone marrow could signal ineffective erythropoiesis, like in anemia of chronic disease. Alternatively, absent reaction to the Prussian blue stain could indicate low iron levels, like in iron deficiency anemia.
Mucicarmine stains mucin, a secretion produced in epithelial and connective tissue cells.[12] The aluminum and carmine combine to form a positively charged chelating complex. The newly positive charge binds the mucin, stains it red, and allows visualization. It is useful in identifying potential carcinomas and inflammatory conditions, where there is excessive mucin production.[12] In surgery, mucicarmine staining can also determine a primary tumor location by staining the mucus-secreting epithelium in a site not containing mucin-producing cells.[13] Mucicarmine also stains the gelatinous capsule of fungi Cryptococcus.[12]
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