PATHOLOGY SHIFT 1 TISSUE PROCESSING, MICROTOMY, AND STAINING 24 AUG 2022 AY 2022-2023 Dra. Celestine Marie G. Trinidad, MD, DPSP 03 TABLE OF CONTENTS Tissue Processing Methods…………….………………1 1.1. Producing Small Tissue Sections 1.2. Methods of Tissue Processing 2. Steps in Tissue Processing.……………………….……2 2.1. Fixation 2.2. Dehydration 2.3. Clearing 2.4. Infiltration 3. Factors Affecting Tissue Processing……..……..……4 3.1. Tissue Density and Thickness 3.2. Agitation 3.3. Temperature 3.4. Pressure 3.5. Vacuum 3.6. Other Technical Considerations 4. Embedding/Casting/Blocking….………………….…….1 4.1. Embedding Molds 4.2. Embedding Machine 4.3. Steps in Embedding 5. Sectioning/Microtomy………..……..…………........……4 5.1. Parts of a Microtome 5.2. Steps in Sectioning 5.3. Artifacts 6. Staining……………………………..………….……….......6 6.1. Types of Stains 7. Mounting of Tissue Sections........................................7 7.1. Steps in Mounting 8. Labeling..........................................................................8 9. Stains for Cellular Components and Contents...........8 9.1. Periodic Acid Schiff (PAS) Stain 9.2. Masson’s Trichrome 9.3. Alcian Blue Stain 9.4. Reticulin Stain 9.5. Perl’s Prussian Blue 9.6. Lipid Stains 9.7. Amyloid Sstains 10. Stains for Organisms....................................................9 10.1. PAS Stain 10.2. Grocott-Gomori Methenamine Silver 10.3. Giemsa Stain 10.4. Warthin Starry 10.5. Gram Stain 10.6. Mycobacterial Stain (Acid Fast Stain) 1. Fig 1. Tissue cassette (Source: Instructor’s slide) • Fig 2. Paraffin blocks (Source: Instructor’s slide) Fig 3. Smaller sections on a glass slide (Source: Instructor’s slide) • LEGEND Take note 1. Textbook From Prof Previous Trans TISSUE PROCESSING METHODS MABB; ADG 1.1 PRODUCING SMALL TISSUE SECTIONS MABB • After placing samples of tissue in tissue cassettes, we turn them into even smaller sections that we can place on a glass slide and view under the microscope. . We embed these tissues in paraffin blocks. o These tissues have to be embedded in a solid medium firm enough to support the tissue, give it enough rigidity to be cut, and yet soft enough not to damage the knife or the tissue itself. • Tissue Processing o Various steps to produce tissue sections o Tissue must be adequately prepared and set in a paraffin block ready for cutting o Ensures that the tissue is firm enough and completely embedded for sectioning o Good quality tissue sections ensure adequate interpretation of microscopic cellular changes Steps in Tissue Processing o Fixation o Dehydration o Clearing o Infiltration o Embedding 1 PATHOLOGY SHIFT 1 | LESSON 3 | TISSUE PROCESSING, MICROTOMY, AND STAINING 1.2. METHODS OF TISSUE PROCESSING MABB; ADG 1.2.1 Manual Method • For small batches of tissue • You do everything by hand • Convenient backup in the event of a power interruption or breakdown of the tissue processor 4 5 FLUID TRANSFER PROCESSOR Fig 5. Tissue Transfer Processor Fig 6. Fluid Transfer Processor “Dip-and dunk” machine Also known as Enclosed tissue processor Cassettes stay in a single chamber and fluids are pumped in and out as required Specimens do not dry out within the chamber Reagent vapors are vented through filters or retained in a closed-loop system Preferably used 2. STEPS IN TISSUE PROCESSING MABB Table 2. Sample Processing Schedule Most tissue processors follow this one. STATION 1 2 3 REAGENT 10% neutral buffered formalin 70% alcohol 80% alcohol 1 hour 1 hour 1 hour 1 hour Clearing Infiltration 1 hour 1 hour 1 hour 1 hour 1 h o u r 12 STATIONS lasting 1 hour each Each station has a corresponding reagent that corresponds to a particular step in tissue processing “What I want you to remember from this slide [Table 1] is that the entire process takes 12 HOURS. So you DON’T instantly get a paraffin block right after you submit a specimen. Processing takes time. It would be some time before you get the block and slides as well.” (Trinidad, 2022) Table 1. Types of Automated Tissue Processors Specimen-containing cassettes are moved from one container to another Paraffin wax 7 • • TISSUE TRANSFER PROCESSOR 12 6 1.2.2 Automated Method • Using a tissue processor • Method used by most laboratories Fig 4. Tissue processor (Source: Instructor’s slide) 8 9 10 11 95% alcohol 95% alcohol 100% (absolute) alcohol 100% (absolute) alcohol Xylene Xylene Xylene Paraffin wax PURPOSE TIME Fixation 1 hour Dehydration 1 hour 1 hour 2.1. FIXATION MABB; ADG • Done even before submitting it to the histopathology laboratory • Also part of tissue processing o 1st step o 1 hour in 10% neutral buffered formalin • Alteration of tissues by stabilizing proteins so that the tissues become resistant to change • Essentially kill the tissues o Stop all metabolic processes 2.1.1. Fixative of Choice • 10% Neutral Buffered Formalin • Change the soluble contents of the cells into insoluble structures • Prevent autolysis (decay of tissue due to the action of cellular enzymes) and putrefaction (bacterial attack) • Stabilize structures to maintain the proper relationship of cells and their stroma 2.1.2. Role of Fixation in Tissue Processing • Allows thin sectioning of tissues by hardening tissue • Protects tissue from the subsequent processing steps • Improves cell avidity for special stains 2.1.3. Must Dos in Fixation • Suboptimal/ delayed fixation = Irreversible tissue damage and damage of sections • Tissue should be fixed in a sufficient volume of solution (10:1 to 20:1) • Fixatives diluted and/or contaminated by bodily fluids must be replaced to ensure effectiveness o Quality control of tissue processing 2 PATHOLOGY SHIFT 1 | LESSON 3 | TISSUE PROCESSING, MICROTOMY, AND STAINING • Fixation time o Time tissue is exposed to formalin o Acceptable range: 6 to 48 hours o Failure to meet this range adversely affects staining qualities o Overfixation hardens the tissue and makes it difficult to cut 2.2. DEHYDRATION MABB; ADG • Takes about 6 hours (Stations 2 to 7) 2.2.1. Definition Process of removing intracellular and extracellular water from the tissue following fixation and prior to wax impregnation • Most of the water in a specimen must be removed before it can be infiltrated with wax o Because wax does not mix with water o Wax cannot infiltrate inside a specimen if it still has water o To help remember the concept: o Liquids: “Like dissolves like” o Miscible: polar liquids dissolve in polar liquids; non-polar liquids dissolve in non-polar liquids o Wax is a non-polar substance and water is a polar substance • 2.2.2. Reagent For Dehydration Step • Alcohol (Ethyl alcohol/ Ethanol) • Recommended for routine dehydration of tissues • Fast-acting, mixes with water and many organic solvents • Penetrates tissues easily • Not poisonous and not very expensive 2.2.3. Dehydration Process • Involve slow substitution of the water in the tissue with the organic solvent • Entails immersing the specimen in a series of ethanol solutions in graded concentration o 70% → 90% → 100% (absolute alcohol) o Graded in order to minimize some shrinkage and extraction of cell components • Some components are drawn out alongside water: o Water soluble proteins: removed at lower alcohol concentrations o Certain lipids may be dissolved: 100% alcohol concentration o Fatty tissues esp. those with benign neoplasms of fat (lipoma): acetone or isopropanol should be added first before the final absolute ethanol ▪ 100% (absolute alcohol) ensures complete dehydration • Volume of ethanol: should not be less than 10x the volume of tissue o To ensure complete penetration of the tissue 2.3. CLEARING CMB; ADG • A.k.a. de-alcoholization • Takes 3 hours to complete; 3 stations (Stations 8, 9, 10) o All use the same reagent (Xylene) in 3 different changes or batches o Is new in each station to completely clear the specimen • After dehydration, tissues are water-free, but still cannot be infiltrated with wax o wax and ethanol are immiscible Ethanol is polar Wax is non-polar • Intermediate solvent that is fully miscible with both the ethanol and wax is needed to remove alcohol and other dehydrating solutions from tissues prior to embedding o Is of intermediate polarity that can mix with both ethanol and wax 2.3.1. Definition • Process whereby alcohol or dehydrating agent is removed from the tissue and replaced with a substance that will dissolve in the wax • Removes a substantial amount of fat from the tissue to ensure a complete wax infiltration (aside from some fatty tissue already removed during dehydration) o Clearing removes most of the fat from the tissue 2.3.2. Reagent For Clearing Step • Xylene o Colorless clearing agent that is most commonly used in histopathology o Cost-effective • Tissue is immersed in 1-3 different changes of xylene solutions to gradually replace the ethanol with xylene o Xylene dissolves alcohol and replaces it in the tissue 2.4. INFILTRATION CMB; ADG • A.k.a. impregnation • Takes 2 hours in 2 stations o changes (paraffin wax) 2.4.1. Definition • Process whereby the clearing agent is completely removed from the tissue and replaced by a medium that completely fills the tissue cavities and gives a firm consistency to the specimen • Allows easier handling and cutting of suitably thin sections without any damage or distortion to the tissue and cellular components 3 PATHOLOGY SHIFT 1 | LESSON 3 | TISSUE PROCESSING, MICROTOMY, AND STAINING 2.4.2. Infiltration Process • Tissue is infiltrated with a suitable histological wax (paraffin) • Paraffin is liquid at high temp (60°C) → solidify when cooled (20°C) o Allows sections to be cut • Wax o Mixture of purified paraffin wax and additives (resins) o Allows thin sectioning on microtomes Fig 8. Perpendicular fluid flow through tissue cassettes (Source: instructor’s slides) 3.3. TEMPERATURE CMB; NADG • Must be kept at 37 – 45 °C • High temperature can cause tissue to shrink and become hard and brittle Fig 7. Dehydration-Clearing-Infiltration Process (Source: Instructor’s slides) 3. FACTORS AFFECTING TISSUE PROCESSING CMB; NADG • Factors that impact the duration of tissue processing and extent of infiltration: o Tissue density and thickness o Agitation o Temperature o Vacuum and pressure 3.1. TISSUE DENSITY AND THICKNESS CMB; NADG • Spongy tissues: more rapidly infiltrated by wax than hard and dense tissues • Hard and dense tissues: take longer time to finish their processing • Tissue thickness: influences the rate of reagent diffusion and processing time • The thicker the block, the longer time it takes for tissue processing to be over • Recommended is typically not more than 4 mm thick • When samples are put in cassettes, it shouldn’t be too thick as it would take longer to process 3.2. AGITATION (VERTICAL OR ROTARY OSCILLATION MECHANISMS) CMB; NADG In the chambers, in the tissue processor, there are vertical or rotary oscillation mechanisms (Trinidad, 2022). • • • Increases the flow of fresh fluids in and around tissues (speeds up fluid exchange) Increases the surface area available for fluid exchange Cassette perforations should be perpendicular to the fluid flow • Low temperature increases the viscosity of reagents used in tissue processing • ↓ rate of diffusion (rate the substances move through the tissue) • ↑ processing time 3.4. PRESSURE CMB; NADG • The baskets or chambers have corresponding pressures which must be controlled Reduced pressure High pressure • increased (↑) • facilitates infiltration of dense specimens with infiltration rate the more viscous • decreased (↓) embedding media tissue processing time 3.5. VACUUM CMB; NADG Chambers also have a vacuum mechanism in them (Trinidad, 2022). • • Improves processing quality and aid in removal of trapped air from porous tissue Can reduce the infiltration time when dealing with dense and fatty tissues 3.6. OTHER TECHNICAL CONSIDERATIONS CMB;NADG • Baskets and metal cassettes should be cleaned and wax-free • Tissues (inside baskets or chambers) should not be packed too tightly in baskets Ensure that there is some space within and that the fluid can completely infiltrate the tissues (Trinidad, 2022). • Processors must be free of spilled fluids and accumulated wax 4 PATHOLOGY SHIFT 1 | LESSON 3 | TISSUE PROCESSING, MICROTOMY, AND STAINING • • Fluid levels must be higher than the specimen containers o Check the level of fluid within the baskets. Timing and delay mechanism must be correctly set and checked against the appropriate processing schedule Processing usually takes overnight (Trinidad, 2022). • Quality Assurance Program: keep a processor log (records) o Number of specimens processed o Processing reagent changes o Temperature checks on the wax baths (kept at a certain temperature for infiltration) o • Completion of the routine maintenance schedule After 12 hours, tissue processing is done. Fig 9. Correct Orientation in Embedding (yellow arrow) (Source: Instructor’s slide) 4.1. EMBEDDING MOLDS PDEF; NADG • Plastic Molds o “Peel-away” type of plastic mold o Disposable GENERAL STEPS Tissue Cassette → Paraffin Blocks → Small Tissue Sections Fig 10. Plastic molds / “peel-aways” (Source: Instructor’s slide) • 4. EMBEDDING/CASTING/BLOCKING PDEF; NADG • Embedding o Also known as casting or blocking o The last step in tissue processing o Process by which the impregnated tissue is placed into a precisely arranged position in a mold containing a medium which is then allowed to solidify Metal Molds o Used with a tissue cassette o Reusable o NOT disposable “This tissue has been impregnated by paraffin, and we now need to put it in a mold containing the same medium as well.” (Trinidad, 2022) • • The tissue is oriented and placed in a mold that is filled with molten wax to form a solid tissue block. The CORRECT orientation of the tissue in a mold is the most important step in embedding. o Embedded with the surface to be cut facing down in the mold “It is important that you embed the tissue properly so that what you [are] looking at is what you will be cutting first.” (Trinidad, 2022) Fig 11. Metal molds and tissue cassettes (Source: Instructor’s slide) 4.2. EMBEDDING MACHINE PDEF; NADG Figure 12. Embedding machine used in UST-FMS (Source: Instructor’s slide) 5 PATHOLOGY SHIFT 1 | LESSON 3 | TISSUE PROCESSING, MICROTOMY, AND STAINING • Paraffin Wax – used for embedding o Simplest, most common, & BEST embedding medium used for routine tissue processing o Also used in infiltration step Figure 13. Parts of an embedding machine (Source: Instructor’s slide) Embedding machine • This is the standard method to produce blocks of tissue for section cutting. • Usually, this procedure is performed using an embedding machine, surrounding the tissues by a medium such as paraffin wax, which when cooled and solidified will provide sufficient support for section cutting. Fig 14. Paraffin Wax (Source: Instructor’s slide) 4.3. STEPS IN EMBEDDING PDEF; NADG • STEP 1: Open the tissue cassette o To expose the tissue Table 3. Parts of an embedding machine PART DESCRIPTION Wax Dispenser Molten wax is placed here and is dispensed by this mechanism. Forceps Warmer Where forceps are warmed. Tissue Warmer Hot Plate Cold Plate Where tissues are placed first before they are placed in the embedding machine. To maintain the heat or to heat objects/samples with controlled heating usually up to 65˚C. To cool the processed block (see step 7 of embedding) usually up to a temperature of 20˚C PICTURE Fig 15. Open the tissue cassette (Source: Instructor’s slide) • STEP 2: Select the mold that fits the tissue o Plastic or metal mold depends on size & shape o Allowance: at least 2 mm margin of wax “You need to place the tissue in the middle and you need it to have at least 2 mm of margin of wax all around, so choose the right mold for the tissues.” (Trinidad, 2022) Fig 16. Select the mold that fits the tissue (Source: Instructor’s slide) • STEP 3: Dispense wax in the mold o about 1/2 or 2/3 full Fig 17. Dispense wax in mold (Source: Instructor’s slide) 6 PATHOLOGY SHIFT 1 | LESSON 3 | TISSUE PROCESSING, MICROTOMY, AND STAINING • STEP 4: Using clean and warm forceps, select the tissue and orient on the mold, gently pressing it flat on the wax o This is the significance of the forceps warmer part of the embedding machine Fig 22. Remove the block from the mold when the wax is completely cooled and hardened (Source: Instructor’s slide) Fig 18. Using a clean and warm forceps, select the tissue and orient on the mold, gently pressing it flat on the wax (Source: Instructor’s slide) • Fig 23. Paraffin block (Source: Instructor’s slide) STEP 5: Insert the identifying label on the mold, and place tissue cassette on top 5. SECTIONING/MICROTOMY PDEF, RPT; NADG ● Sectioning / Microtomy – a paraffin-embedded tissue is trimmed and cut into uniformly thin slices using a microtome to facilitate studies under the microscope o The embedded tissues must be cut into thin sections to be placed on a slide Fig 19. Insert the identifying label on the mold, and place cassette on top (Source: Instructor’s slide) • STEP 6: Dispense wax, completely filling the mold Fig 20. Dispense wax, completely filling the mold (Source: Instructor’s slide) • STEP 7: Cool the block on the cold plate Fig 24. A Microtome (Source: Instructor’s slide) 5.1. PARTS OF A MICROTOME PDEF; NADG ● Microtome o Knife and its Holder – knife is inserted here o Block holder (Chuck) o Base (Microtome Body) o Rotary Wheel – turned to make the block holder go nearer to the knife as you cut along the sections Fig 21. Cool the block on the cold plate (Source: Instructor’s slide) • STEP 8: Remove the block from the mold when the wax is completely cooled and hardened o This will take about 30 minutes o END PRODUCT → PARAFFIN BLOCK ROTARY WHEEL 7 PATHOLOGY SHIFT 1 | LESSON 3 | TISSUE PROCESSING, MICROTOMY, AND STAINING • STEP 4: Continue cutting until a ribbon of sections is created Fig 25. Microtome and its Parts (Source: Instructor’s slide) Fig 29. Continue cutting until a ribbon of sections is created (Source: Instructor’s slide) 5.2. STEPS IN SECTIONING PDEF, RPT; KDSC • STEP 1: Insert the knife blade into the holder and tighten o Make sure that it is secure o A loose and unsecured knife may result in imperfect sections Fig 30. Tissue ribbons (Source: Instructor’s slide) Fig 26. Insert the knife blade into the holder and tighten (Source: Instructor’s slide) • STEP 2: Orient the block in the microtome chuck o The block holder is also called the chuck o The long axis of the block should be parallel to the knife • STEP 5: Float the ribbon on the water bath o Remove wrinkles or bubbles o Separate sections from each other by teasing them very carefully apart using forceps in the water bath o Paraffinized ribbons of serial tissue sections can be removed from the microtome knife as they are cut ▪ Slight traction is exerted on the end of the ribbon stretching it gradually over the blade while floating carefully in a warm water bath Fig 27. Orient the block in the microtome chuck (Source: Instructor’s slide) • STEP 3: Turn the wheel on the side of the microtome and start cutting o Block will go nearer to the knife as you turn the wheel o In the initial rough trim of blocks, thickness of the blocks will be 15-30 mm ▪ But it can be adjusted in the microtome o The actual section slices, or the thin slices would be 3-5 microns Fig 28. Turn the wheel on the side of the microtome and start cutting (Source: Instructor’s slide) Fig 31. Float the ribbon on the water bath (Source: Instructor’s slide) o Water bath temperature should be kept 5-10˚C below the melting point of the embedding wax ▪ Too HOT: desiccated-looking section ▪ Too COLD: excessive tissue wrinkling Fig 32. Water bath machine (Source: Instructor’s slide) 8 PATHOLOGY SHIFT 1 | LESSON 3 | TISSUE PROCESSING, MICROTOMY, AND STAINING Table 4. Problems and appearances of ribbons APPEARANCE PROBLEM 5.3. ARTIFACTS RPT • Good microtomy techniques will minimize artifacts that can lead to difficult diagnostic interpretation of special stains Thin Desiccated (dried), almost transparent Thick Too opaque Figure 29. A badly sectioned tissue (Source: Instructor’s slide) Normal • • STEP 6: Mount sections on glass slide o Fish the ribbons out of the water bath carefully into the glass slide Artifacts include: o Tearing o Ripping o Creases o Holes o Folding o Floaters ▪ Extraneous tissue pieces that are not part of the sample ▪ During the fishing out step of the water bath, you can get floating tissue that is not part of your section ▪ May be part of the other samples that have been floating in the water bath “Thus, it is important to regularly change the water in the water bath.” (Trinidad, 2021) Figure 27. Mount sections on glass slide (Source: Instructor’s slide) • Tissue slide is drained o May be gently heated in a drying oven to evaporate the water between the sections and the glass and to melt the wax and improve adhesion to the slide Figure 30. Contaminant floaters from the fishing process (Source: Instructor’s slide) ● ● Figure 28. Drying oven (Source: Instructor’s slide) 6. STAINING RPT; KDSC Staining – process whereby tissue components are made visible in microscopic sections by direct interactions with a dye or staining solution o Produce a contrast between different tissues and cellular components based on their varying affinities for most dyes or stains Before staining the slides, you need to prepare them first by: o Dewaxing – heat slides in 60C° for at least 30 minutes to soften the wax ▪ Can also be done in the drying oven (the one used to drain tissue slides) 9 PATHOLOGY SHIFT 1 | LESSON 3 | TISSUE PROCESSING, MICROTOMY, AND STAINING o After dewaxing, wash with xylene → absolute alcohol → distilled water (this procedure is the one commonly done in laboratories) ▪ Some laboratory protocols: xylene → absolute alcohol → 70% alcohol → 50% alcohol → distilled water ▪ Thus, protocols vary from lab to lab Figure 31. Staining area in the UST-FMS Pathology lab (Source: Instructor’s slide) ● Basic Principle in Staining: “Opposites Attract” o ACIDIC cell components (nucleus) has greater affinity for Basic Dyes o BASIC cell components (cytoplasm) has greater affinity for Acidic Dyes 6.1. HEMATOXYLIN AND EOSIN STAIN (H&E) RPT; KDSC • aka “the routine stain”; Used for routine histopathologic examination Figure 33. Examples of Other Stains (Source: Instructor’s slide) “Keep in mind that there are many other stains that you can use with different uses depending on what you are looking for in your specimens.” (Trinidad, 2021) ● ● Figure 32. Hematoxylin and Eosin Stain (Source: Instructor’s slide) Table 3. Difference between Hematoxylin and Eosin ● ● ● ● ● ● ● ● ● ● ● HEMATOXYLIN EOSIN Basic dye ● Acidic dye Stains cell nuclei ● Stains cytoplasm purple or blue (basic), connective tissue and other Nuclei is the acidic extracellular component of the cell because it contains substances pink or red nucleic acids (DNA, RNA) OTHER STAINS Periodic Acid Schiff ● Grocott-Gomori (PAS) Methenamine Silver Masson’s Trichrome ● Warthin Starry Alcian Blue ● Giemsa Reticulin ● Gram Oil Red O ● Perl’s Prussian Blue Sudan Black Congo Red Acid Fast ● 7. MOUNTING IN TISSUE SECTIONS RPT; KDSC Last step in tissue processing Results in a permanent histological preparation suitable for microscopy, after adhesion of the sections on to the slide and appropriate staining of the tissue Mounting medium o Applied between the section and coverslip after staining and prevents movement of the coverslip o Protects the stained section from getting scratched o Facilitates easy handling and storage of slides o Prevent bleaching or deterioration of slides ▪ In time, slides usually fade ▪ Putting mounting medium and cover slip slows down the rate of the fading of slides. 7.1 STEPS IN MOUNTING RPT 1. Apply 1 or 2 drops of mounting medium 2. Put the cover slip over the tissue very carefully, avoiding bubbles o Bubbles prevent one from seeing the tissues clearly in the microscope 10 PATHOLOGY SHIFT 1 | LESSON 3 | TISSUE PROCESSING, MICROTOMY, AND STAINING Figure 34. Steps in Mounting of Tissue Sections Stains (Source: Instructor’s slide) • 8. LABELING RPT; KDSC Identification and correctly labeling the tissue blocks and its corresponding slides o Stickers may be used for samples in tissue slides. o Barcodes are the most ideal label because they can directly be inputted in the computer, helping streamline the process. Figure 35. Labeled tissue slides on the upper portion of the glass slide (Instructor’s slide) REFERENCES Main References ● Lecture Powerpoint and Video Recording by Dra. Celestine Marie G. Trinidad, MD, DPSP Supplementary References ● Pathology Trans from LEAPMed Batch 2021 and 2022 TWG EIC TEG EIC M.A.B.B. N.A.D.G. 11 PATHOLOGY