Paraffin-embedded tissue (PET) is a standard laboratory method used in pathology reports for preserving biological samples. This technique transforms soft, perishable tissue, obtained through biopsy or surgery, into a durable, solid block. The process stabilizes cellular components and tissue architecture, allowing pathologists and researchers to study the sample’s structure and composition. This preservation method is foundational to modern medicine, enabling both immediate clinical diagnosis and long-term scientific investigation.
From Biopsy to Block: The Embedding Process
The transformation of a fresh tissue sample into a stable paraffin block begins immediately with fixation. This initial step, most often utilizing a chemical solution like formalin, halts cellular decay and prevents the degradation of tissue components. Formalin works by chemically cross-linking proteins within the cells, creating stabilizing methylene bridges that provide the fragile tissue with necessary structural rigidity.
Fixed tissue contains water, which is chemically incompatible with paraffin wax, necessitating dehydration. The tissue is sequentially passed through a series of increasing concentrations of alcohol, typically starting around 70% ethanol and progressing to absolute (100%) ethanol. This graded process slowly removes all the water from the cells and the surrounding extracellular matrix, replacing it entirely with the alcohol solution.
Following water removal, a chemical intermediary, such as xylene, is introduced in the clearing step. Xylene is used because it can mix with both the remaining alcohol and the molten paraffin wax, acting as a transition solvent. During this phase, the tissue often becomes translucent, signifying that it is ready to accept the wax.
The final stage involves infiltration and embedding, where the cleared tissue is submerged in molten paraffin wax. The wax is maintained near 60 degrees Celsius, allowing it to fully permeate the tissue structure and fill cellular spaces. Once the tissue is saturated, it is placed into a mold, and the molten wax cools and solidifies. This results in a rigid, rectangular paraffin block containing the preserved tissue sample.
Essential Role in Clinical Pathology
The rigid paraffin block is the foundation for nearly all modern clinical diagnoses derived from tissue samples. The block is mounted onto a microtome, a highly precise instrument designed to shave off extremely thin sections. These delicate ribbons of tissue are typically cut to a thickness of three to five micrometers, which is necessary for light to pass through them effectively under a microscope.
After cutting, these thin sections are floated onto a warm water bath to remove wrinkles and are then mounted onto glass slides. The fundamental step for visual diagnosis is the application of Hematoxylin and Eosin (H&E) stains, which provide the necessary contrast. Hematoxylin is a basic dye that strongly binds to acidic structures, such as the nuclei containing DNA and RNA, staining them in shades of blue or purple.
This nuclear staining contrasts sharply with the Eosin dye, which is acidic and preferentially binds to basic components, including proteins in the cytoplasm and the extracellular matrix. Eosin renders these areas in shades of pink, creating the classic pink-and-purple visual pattern that pathologists rely upon. This technique allows for the clear visualization of cellular architecture and overall tissue morphology.
The pathologist performs a microscopic examination of the stained slide to evaluate the size, shape, and arrangement of the cells. They look for morphological changes, such as disorganized cell growth, abnormal nuclear features, or the presence of inflammatory cells. This analysis identifies and classifies disease states like benign tumors, cancer, or chronic inflammatory conditions, confirming the presence of disease and determining its type and grade.
When the H&E stain is not specific enough to determine the origin or type of a lesion, immunohistochemistry (IHC) is employed. IHC utilizes specific antibodies designed to chemically bind to targeted proteins, or antigens, present within or on the surface of the cells. This technique allows for the precise identification of molecular markers unique to certain cell types or disease processes.
The binding of the antibody to the antigen is made visible using a chromogen, which deposits a detectable color change at the site of the protein marker. IHC is routinely used to determine the lineage of a tumor, such as distinguishing between a carcinoma and a lymphoma. It also identifies hormone receptors on breast cancer cells, which directly influences the patient’s treatment strategy.
The Archival Value of Tissue Blocks
Beyond the immediate clinical diagnosis, paraffin-embedded tissue blocks hold immense value as a stable and permanent biological archive. Once the wax solidifies, the tissue is protected from degradation, allowing the blocks to be stored safely at ambient room temperature for decades. This durability makes them a foundational component of global biobanking efforts.
This archival stability is important for research, enabling scientists to conduct retrospective studies spanning long periods. Researchers can retrieve samples from patients diagnosed years or decades ago to study the natural history of a disease, track its progression, or evaluate long-term outcomes associated with historical treatment protocols. Comparing older samples with contemporary ones provides valuable insights into how diseases evolve.
The material within these blocks is not limited solely to visual, morphological examination; it also serves as a resource for advanced molecular testing. Despite the chemical cross-linking caused by the fixation process, specialized laboratory techniques successfully extract nucleic acids, including DNA and RNA, from the archived tissue.
While the extracted genetic material is often chemically modified and fragmented due to the fixation process, it remains suitable for modern genomic analysis. Techniques such as next-generation sequencing can identify specific gene mutations, chromosomal rearrangements, or gene expression patterns. This molecular information guides precision medicine, helping clinicians select targeted therapies based on the molecular signature of a patient’s disease. These archived blocks also provide a resource for obtaining second opinions or re-evaluating an initial diagnosis years later using newer diagnostic methods.