Learn: immunohistochemistry - The Human Protein Atlas (2022)

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Immunohistochemistry (IHC) is a powerful microscopy-based technique for visualizing cellular components, for instance proteins or other macromolecules in tissue samples. The strength of IHC is the intuitive visual output that reveals the existence and localization of the target-protein in the context of different cell types, biological states, and/or subcellular localization within complex tissues.

The IHC technique was invented during the 1940s (Coons, Creech, & Jones, 1941) and is routinely used as an important tool in health care and pathology for e.g. diagnostic purposes or to stratify patients for optimized treatment regimes. IHC is also widely used in research where molecules of interest are analyzed to study their roles in both healthy and diseased cells and tissues on the molecular, cellular or tissue level. There are many different ways to perform visualization of targets in tissues using IHC or IHC-based methods, and numerous protocols exist for different applications and assays. Even though IHC is generally a robust and established method, new assays often need careful optimization depending on the tissue or on the properties of the target protein, binder-molecule and/or reporter system. Many years of technical development and the hugely increased availability for specific binding-molecules have greatly improved the usefulness and areas of applications for IHC. The progress in the field of IHC-based techniques and reagents has enabled scientists and health care providers with more precise tools, assays and biomarkers. In addition, technical advances have enabled e.g. highly sensitive simultaneous detection of multiple proteins in the same sample, and the detection of protein-protein interactions (see Proximity Ligation Assay).

The classical IHC assay is illustrated in Figure 1 and involves detection of epitopes expressed by a single protein-target within a tissue sample using a "primary antibody" capable of binding those epitopes with high specificity. After the epitope-antibody binding event, a "secondary antibody" capable of binding the primary antibody with high specificity is added. The secondary antibody is coupled to a reporter molecule and after the antibody-antibody binding event, a chemical substrate is added which reacts with the reporter molecule to produce a colored precipitate at the site of the whole epitope-antibody complex.

Figure 1. The basic principle of immunohistochemistry.

(Video) Introducing the Human Protein Atlas

In the schematic illustration (Figure 1) a formalin-fixed paraffin embedded tissue section is stained using a primary antibody directed towards a specific protein target. A solution containing the primary antibody is added to the tissue section and the antibodies are allowed some time to find and bind to their target. After this step, unbound and surplus antibodies are washed away and the secondary antibody is added. The secondary antibody, which carries a linker molecule with horseradish peroxidase (HRP) enzymes, is also allowed some time to bind to the primary antibody, followed by another washing step. After this, 3,3' Diaminobenzidine (DAB) is added. The HRP enzyme transforms the DAB substrate into a brownish precipitate that is deposited in the tissue at the site of the reaction, thus producing a visual representation of where the primary antibody first bound its target.


Tissue preparation

The tissue plays a central role in the experiment and it is important that it is processed so that epitopes and proper morphology is preserved. The most common processing for IHC is to prepare formalin-fixed paraffin-embedded (FFPE) tissue blocks. The purpose of formalin fixation is to produce chemical cross-linking of proteins within the tissue. This terminates all cellular processes and freezes the cellular components at the place and in the conformation they were in at the time of fixation and also prevent degradation. After adequate fixation, the tissue is further processed and ultimately embedded in paraffin blocks, which are then sectioned into thin slices (usually 4-10µm) using a microtome. The sections are transferred to glass slides and allowed to adhere prior to further processing.

Other methods for fixation besides formalin are sometimes used. These include other types of aldehydes or using different alcohol solutions. The best choice of fixative is very much dependent on the assay. A common alternative to FFPE is to prepare frozen tissue samples. In this case, the tissue is embedded in a cryoprotective medium and frozen, and fixation is performed post-sectioning. Frozen tissues are sectioned in cryostats and have the advantage of short processing times and of better preservation of sensitive epitopes, but can often be inferior to FFPE tissues in terms of preserving histological morphology.

Antigen (epitope) retrieval

A concern associated with cross-linking fixatives like formalin, or too long time spent in fixative medium is the masking of epitopes, which can obstruct the primary antibody from binding to its target. Especially with FFPE samples, there is often a need to revert some of the chemical crosslinking and "retrieve" the epitopes before proceeding to the actual IHC. There are several antigen retrieval protocols available and the main strategies include treating the tissue slide with heat, digestive enzymes, detergents, or combinations thereof. The most common method for antigen retrieval in FFPE samples is to pressure-boil the tissue slides in an acidic citrate buffer for around 15-20 minutes.

Antibody binding

The quality and specificity of the binding molecule is crucial for any IHC based technique, and the choice of binder can directly affect the outcome, reliability, and possibly also the interpretation of the assay. Antibodies are by far the most common type of binding-molecule used for IHC, and although most antibodies are able to adequately detect the correct molecule of interest, they may also vary greatly in their specificity for their intended target. Antibodies with high specificity are therefore more reliable when interpreting "on-target" binding, since they produce little or no "off-target" binding or "background". Antibodies that are less specific can produce more off-target binding, and the resulting background will possibly interfere with the correct interpretation of the true on-target signals. There are two main types of antibodies; polyclonal antibodies which is a heterogeneous mix of antibodies that bind different epitopes on the target and monoclonal antibodies that all bind the same epitope. Polyclonal antibodies are often very potent due to their ability to detect and bind multiple epitopes on the same target. However, the epitopes they bind are often poorly defined and with multiple and varying epitope-specificities comes the increased likelihood of off-target binding events and background noise. However, the potency of polyclonal antibodies can be advantageous since the concentration of binding events around the on-target molecule usually outweighs potential background noise. A drawback is that polyclonal antibodies are usually limited resources since they are derived from animal sera. Monoclonal antibodies, by contrast, have more continuity since they can be produced in hybridoma cell lines. Monoclonal antibodies are also often well defined in terms of epitope binding, but can still generate results that are hard to interpret if the specificity is low or if the target epitope is present in low abundance.

Careful optimization and titration of antibody concentration for each assay is needed, since the result is dependent not only on the antibody's specificity and affinity for the target, but also on the concentration and availability of on-target and potential off-target epitopes present in the sample. Adding too much antibodies to the sample will increase the number of possible low-affinity off-target binding events once the on-target epitope(s) are saturated with binders. By lowering the antibody concentration, off-target binding events become rarer as they usually have lower affinity than on-target binding events. The risk when attempting to reduce background while using a low-affinity antibody is that the on-target signals are concomitantly weakened to the point of providing a false negative result.

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Other types of binder molecules sometimes used in IHC-based techniques include affibodies, peptides, antibody fragments or other small molecules.

Detection systems

The whole purpose of performing IHC is to obtain a visual representation of where the target can be found within the experimental tissue, and preferably also gain information about the target's expression pattern among heterogeneous cell populations and/or subcellular localizations. This is exemplified in Figure 2, which illustrates how different antibodies are used to visualize different cellular or tissue compartments within a complex tissue. To visualize the target-antibody interaction, some kind of detection system that produces an observable stain or signal is needed. The most common method for introducing a detection system to the experiment is to use a secondary antibody that carries a pre-bound reporter molecule, i.e. enzyme or fluorophore. Secondary antibodies are usually targeted specifically towards antibody molecules from a different animal species. For example, if the primary antibody is raised in a rabbit, then the secondary antibody must be raised in another animal and targeted specifically towards rabbit antibodies.

Hematoxylin staining

No antibody staining

Nuclear staining

Membranous staining

Cytoplasmic staining
LAMB2 (Laminin)

Connective tissue

Figure 2. Visualizing different protein targets in complex tissues. The right column shows a magnification of the corresponding images in the left column.

In the IHC image (Figure 2), consecutive sections of human esophagus stained using four different antibodies allows for direct comparison of different protein expression patterns within the tissue and within subcellular compartments. The top images are only counterstained for hematoxylin for comparison. The p63 antibody stains cell nuclei in a population of cells that reside in the basal part of the esophageal epithelium. The EGFR (Epidermal growth factor receptor) antibody appears to stain the same cell population as p63, but stains cellular membranes instead of nuclei. The G6PD (Glucose-6-phosphate dehydrogenase) antibody stains the cytoplasm of a wider repertoire of esophageal epithelial cells and also cells residing in the connective tissue. The Laminin (LAMB2) antibody stains only cells and structures in the connective tissue underlying the esophagus.

For FFPE tissue samples the most common detection method is to use enzymatic reactions to generate a colored precipitate at the site of antibody binding. The secondary antibodies then carry an enzyme, e.g. horseradish peroxidase (HRP) or alkaline phosphatase (AP), that are capable of converting chromogens like 3,3' Diaminobenzidine (DAB) or 5-bromo-4-chloro-3-indolyl phosphate/ p-nitroblue tetrazolium chloride (BCIP/NBT) into brown or bluish precipitates that are deposited in the tissue at the site of the reaction. Chromogenic stains are observable in light-microscopy and are usually very stable over long periods of time, which is beneficial if the experiment needs to be archived or reviewed at a later time point.

For frozen tissue sections it is more common to use fluorophore-linked secondary antibodies that emit a specific color (usually green, red, or blue) when excited by the correct wavelengths of light. Moreover, fluorophores are usually not stable for long periods of time. However, the benefit of using fluorophores is that they provide an easy method for performing double-labeling experiments where several antibodies towards multiple targets are assayed in the same sample. The secondary antibodies need to be targeted towards different primary antibodies and also to be coupled to different fluorophores. The different secondary antibodies are then observed separately by exciting them sequentially with different wavelengths of light. These different excitation results are saved as separate images (or color channels) and may later be overlaid to infer protein co-localizations etc.

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Using reporter-carrying secondary antibodies for detection is in itself an amplification step since several secondary antibodies are able to bind a single primary antibody, but sometimes further amplification steps are desired to increase the signal and sensitivity of the experiment. In such cases, the secondary antibody may instead carry "linker molecules", for instance biotin polymers, which are able to recruit a larger number of reporter molecules in subsequent steps. This strategy for amplifying signals is useful for both enzymatic and fluorescent detection methods.


Immunohistochemical staining using chromogens often benefits from having a counterstain applied that enhances the contrast and facilitates the observation of histological features. The most common type of counterstain used for FFPE samples is hematoxylin that stains cellular cytoplasm with a pale bluish color, and stain cell nuclei in a darker bluish nuance. Fluorescent stainings are usually not counterstained with hematoxylin, since the detection method is not based on light microscopy. Instead, the most common way to obtain counterstaining for fluorescence is to label cell nuclei by adding fluorescent dyes that bind nucleic acids. After the actual immunohistochemical reaction, the only remaining steps are to coverslip and seal the sample for protection and longterm storage. The most common way is to "glue" the coverslip to the sample using commercially available purpose-made resins.

Specific examples

IHC is widely used in both research and clinical practice. The Human Protein Atlas (HPA) project is a prime example of how high-throughput IHC is used to achieve large-scale mapping of the human proteome in a multitude of tissues, cancers and cells. In the HPA project, a streamlined in-house large scale antibody production chain facilitates the generation of specific antibodies, which after passing basic characterization and validation regimes, are used to systematically stain tissue microarrays containing hundreds of tissue cores within a single experiment. The system for IHC employed by HPA relies heavily on standardization of protocols and automatisation using machines, but the evaluation of the optimal titration for each antibody is performed manually before the antibody is approved for staining on the full set of tissues. Each stained tissue core is annotated with respect to immunohistochemical staining in tissues and cell types, and thereafter published as a high resolution image on the web portal to be freely viewed by anyone.

In clinical practice, IHC is mainly used within pathology to aid physicians to evaluate tissue specimens with respect to healthy and or diseased states, to set diagnoses, and to define the molecular subtype of different types of cancer. A specific example where IHC is used diagnostically is when pathologists are presented with a metastatic tumor sample and the tissue origin of the primary tumor is unknown. In these cases, pathologists use a panel of different antibodies that target tissue specific proteins, such as prostate-specific antigen for prostate cancer, or estrogen receptor for gynecological cancers, or cytokeratin 20 for gastrointestinal cancers (Gremel et al., 2014). Once a broad classification is made, additional tissue specific antibodies are used to further pinpoint the origin of the primary tumor. This information is useful for choosing the best or most appropriate strategy for drug therapy and/or to locate the primary tumor for radiation therapy and/or surgery.

References and Links

Original reference describing the IHC technique:Coons, A. H., Creech, H. J., & Jones, R. N. (1941). Immunological Properties of an Antibody Containing a Fluorescent Group.Experimental Biology and Medicine, 47(2), 200-202. DOI:10.3181/00379727-47-13084P

Commonly used antibodies for cancer diagnostics:
Gremel G et al., A systematic analysis of commonly used antibodies in cancer diagnostics.Histopathology. (2014)
PubMed: 24330150DOI: 10.1111/his.12255

(Video) Production: Tissue Microarrays & Digitalization Within Human Protein Atlas l Protocol Preview

A review on validating antibodies for IHC:
O'Hurley G et al., Garbage in, garbage out: a critical evaluation of strategies used for validation of immunohistochemical biomarkers.Mol Oncol. (2014)
PubMed: 24725481DOI: 10.1016/j.molonc.2014.03.008

"The Immunohistochemical Staining Methods Education Guide" - a free handbook provided by Dako:

Antibodypedia - An open-access database of publicly available antibodies and their usefulness in various applications:

IHC world - Protocols, Forum, Products, and more:

A video-clip describing tissue microarrays, IHC, and the Protein Atlas website:

A YouTube clip illustrating IHC from BioGenexLaboratories:

(Video) How to explore antibody stainings on the Human Protein Atlas -old


What is the human protein atlas used for? ›

The Human Protein Atlas is a unique world-leading effort to map all the human proteins in cells, tissues, and organs in the human body using antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology.

What is the Human Protein Atlas project? ›

The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology.

How do you read immunohistochemistry? ›

The IHC test gives a score of 0 to 3+ that measures the amount of HER2 receptor protein on the surface of cells in a breast cancer tissue sample. If the score is 0 to 1+, it's called HER2 negative. If the score is 2+, it's called borderline. A score of 3+ is called HER2 positive.

What is the difference between Elisa and IHC? ›


These assays enable the detection of low amounts of target protein from cell lysates. In general, ELISA assays are more sensitive quantitatively than IHC assays. However, IHC assays provide results in context giving a semiquantitative overview of the tissue.

How many proteins are in the human body? ›

Proteome: It is now estimated that the human body contains between 80,000 and 400,000 proteins. However, they aren't all produced by all the body's cells at any given time. Cells have different proteomes depending on their cell type.

How much protein is in a human body? ›

Protein is a functionally important component at the molecular level of body composition. Protein mass in healthy adults is relatively large, representing 10.6 kg, or 15.1%, of body mass in the reference man (1).

When was the HPA Brain Atlas launched? ›

The Brain Atlas database is the latest released by the Human Protein Atlas (HPA) program which started in 2003 with the aim to map the entirety of the human proteome.

What are the different proteins? ›

There are seven types of proteins: antibodies, contractile proteins, enzymes, hormonal proteins, structural proteins, storage proteins, and transport proteins.

Which of the following human protein is used to treat emphysema? ›

Complete answer:

> The option (c) $\alpha$- 1- antitrypsin is correct. A human protein that is obtained from transgenic animals and is widely used to treat emphysema is $\alpha$−1-antitrypsin.

How do you analyze IHC images? ›

For IHC images stained with 3,3'-diaminobenzidine (DAB) and hematoxylin (H), select the “H DAB” vector option.
IHC image post-threshold.
  1. Go to “Analyze” and select “Set Measurements”.
  2. A “Set Measurement” pop up window will open. ...
  3. Select “Okay” in the Set Measurement window. ...
  4. Go to “Analyze” and select “Measure”.
Dec 20, 2019

What can immunohistochemistry detect? ›

Immunohistochemistry is used to help diagnose diseases, such as cancer. It may also be used to help tell the difference between different types of cancer.

What are immunohistochemistry techniques? ›

Immunohistochemistry (IHC) is a powerful technique that exploits the specific binding between an antibody and antigen to detect and localize specific antigens in cells and tissue, most commonly detected and examined with the light microscope.

How are IHC antibodies made? ›

Antibody types

Monoclonal antibodies are made by injecting the animal and then taking a specific sample of immune tissue, isolating a parent cell, and using the resulting immortalized line to create antibodies. This causes the antibodies to show specificity for a single epitope.

Is immunohistochemistry the same as Western blot? ›

IHC, unlike Western blot or ELISA, does not require that proteins be extracted from cells or tissues. Instead, sample preparation for IHC focuses on properly fixing, slicing, and mounting the samples. Use these sample preparation guides to learn how to prepare cell cultures and various tissue types for IHC.

What is the longest protein? ›

With its length of ~27,000 to ~35,000 amino acids (depending on the splice isoform), titin is the largest known protein. Furthermore, the gene for titin contains the largest number of exons (363) discovered in any single gene, as well as the longest single exon (17,106 bp).

Which organ has the highest protein concentration? ›

Among all tissues, liver has the highest number of secreted proteins, followed by brain, artery, pancreas, and pituitary.

What are the 3 types of protein? ›

Proteins are the basic component of living cells. They are made of carbon, hydrogen, oxygen, nitrogen, and one or more chains of amino acids. The three structures of proteins are fibrous, globular and membrane, which can also be broken down by each protein's function.

How much protein does a 70 year old woman need daily? ›

The current recommended dietary allowance for women older than 70 years is 0.36 grams for each pound of body weight or 46 grams of protein for a 130-pound woman. This amount is the same for all women 19 and older.

How much protein does an 80 year old need? ›

Protein Requirements for Elderly Adults. Experts in the field of protein and aging recommend a protein intake between 1.2 and 2.0 g/kg/day or higher for elderly adults [3,8,15].

How much protein should a 60 year old woman? ›

For women over 50, experts recommend 1 to 1.5 grams of protein per kilogram of weight (1 kilogram = 2.2 pounds). If you weigh 140 pounds, for instance, you would need at least 63 grams of protein a day.

Which of the following human protein is used to treat emphysema? ›

Complete answer:

> The option (c) $\alpha$- 1- antitrypsin is correct. A human protein that is obtained from transgenic animals and is widely used to treat emphysema is $\alpha$−1-antitrypsin.

What is proteome map? ›

Proteome Mapping is a technique in which the proteome is analysed by LCMS: a combination of chromatography separation and mass spectrometry. Pure protein sample is digested and run through an extended 1- or 2-D LC gradient, and the eluent injected into a LCMS instrument.

When was the HPA Brain Atlas launched? ›

The Brain Atlas database is the latest released by the Human Protein Atlas (HPA) program which started in 2003 with the aim to map the entirety of the human proteome.

What are the different proteins? ›

There are seven types of proteins: antibodies, contractile proteins, enzymes, hormonal proteins, structural proteins, storage proteins, and transport proteins.

Is Alpha-1 antitrypsin a human protein? ›

Key Facts. Alpha-1-antitrypsin (AAT) is a protein produced in the liver that protects the body's tissues from being damaged by infection-fighting agents released by its immune system. In alpha-1 antitrypsin deficiency, the body's normal production of AAT is reduced, resulting in the destruction of sensitive lung tissue ...

Which human protein is produced by the transgenic cow? ›

III. Milk produced by transgenic cow, Rosie contains 2.4 g protein/L and alpha-lactalbumin, human protein.

What causes emphysema? ›

The main cause of emphysema is long-term exposure to airborne irritants, including: Tobacco smoke. Marijuana smoke. Air pollution.

Which organ has the highest protein concentration? ›

Among all tissues, liver has the highest number of secreted proteins, followed by brain, artery, pancreas, and pituitary.

Which is bigger genome or proteome? ›

The proteome is many-fold larger than the genome, given the wide degree of posttranslational modifications and processing that nearly all proteins undergo.

Why is human proteome important? ›

The field of proteomics is particularly important because most diseases are manifested at the level of protein activity. Consequently, proteomics seeks to correlate directly the involvement of specific proteins, protein complexes and their modification status in a given disease state.

Is DNA a protein? ›

No, DNA is not a protein. The major relationship between DNA and protein is that DNA encodes the information that is necessary to synthesize proteins. But DNA itself is not a protein. DNA is composed of long chains of nucleotides.

What are 4 types of proteins? ›

The complete structure of a protein can be described at four different levels of complexity: primary, secondary, tertiary, and quaternary structure.

What are the 2 main types of proteins? ›

There are two main categories (or sources) of proteins – animal and plant based.


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