Benefits of FFPE Tissue Storage


FFPE tissue storage is a great way to ensure your samples are stored safely and in the best conditions. Using a tissue bank also means you have access to selections at all times. This makes it easy to conduct tests with a quick turnaround time.

Microbiome research

FFPEs, or Formalin-Fixed Paraffin-Embedded tissue, are human-derived biospecimens that display unique storage capacities for disease-relevant molecular information. This makes them an essential source for innovative biomedical research. In the field of microbiome research, these samples can help to diagnose critical illnesses. In addition, they may also be used as a biomarker for establishing the characteristics of diseases.

In breast cancer research, a large amount of data has been gathered on the role of breast microbiota in carcinogenesis. However, most studies have compared the microbial composition of tumor tissue to that of healthy tissue. In these studies, there was evidence of differences in the microbial composition of benign and malignant tumors, and there were no significant differences between women with different stages of cancer.

The microbial composition of breast tumors is enriched with bacteria that are not present in healthy tissue. 

In addition to its usefulness as a disease marker, the microbiota of breast cancer can serve as a therapeutic target. Another benefit of FFPE tissue storage is its convenient storage conditions. Unlike frozen collections, FFPEs can be stored at room temperature for long periods. This makes them ideal for post-biopsy pathological analysis. This preparation requires less maintenance and time and is compatible with surgical procedures.

As a result, FFPEs are a significant sample in biobanks. However, their quality may not be as stable as frozen collections. The second verification step is necessary before being used for research purposes. This process, called fixation, involves toxic solutions to modify the native structure of proteins. The fixation results are partially free from bias and can be influenced by the preparation methods.

DNA extraction

FFPE tissue is a type of tissue that has been fixed in formalin. This preserves a wide variety of tissues but has limitations. This type of tissue is not always heat-sensitive and can degrade over time. FFPE tissue provides an excellent source of information. But it is essential to be careful when handling and storing FFPE tissue samples. Many researchers prefer to use FFPE samples for their tissue analyses. They believe that the quality of an FFPE sample is more stable at ambient temperatures. But there is no guarantee that the samples will retain their integrity during diagnostics and subsequent molecular applications. For instance, RNA tends to break down after a certain point. This can impact the extraction of proteins for proteomics studies. Therefore, strict quality management is a must. This may be particularly critical for analyzing next-generation sequencing data.

Formaldehyde fixation

FFPE tissue storage and formaldehyde fixation are used to preserve and store a wide range of clinical samples. There are several advantages to using FFPE tissue. These include the preservation of macromolecules, the ability to protect cellular morphology, and the ability to store the sample at room temperature. In addition, FFPE tissue has extensive cross-linking that can mask sensitive antigens. During the process of formaldehyde fixation, methylene bridges are formed between amino groups. This reaction is a chemical reaction that deactivates proteases. It also results in a highly reactive methylol adduct that affects endopeptidase digestion. Moreover, formaldehyde forms a cross-link between lysine and arginine. These cross-links are challenging to extract, and some proteins remain intact after formaldehyde processing. This issue is essential because of the possibility of reversed formaldehyde-induced modifications. Identifying these modifications is a real challenge, and FFPE tissue storage and formaldehyde fixing benefits are more comprehensive than identifying disease-associated improvements. In addition to cross-linking, formaldehyde fixation can have other physical effects on a sample. These changes may limit the identification of proteins or prevent them from being accurately identified. They can also alter the secondary structure of the tissue. In addition, physical changes such as boiling and coagulation with organic solvents can change the FFPE tissue. These material changes may be reflected in the spectral count of the protein extract.


FFPE tissue has emerged as a famous specimen in biobanks. It offers an excellent information preservation system. However, its suitability for research is dependent on the molecular target. Usually, tissue samples are fixed in formalin. This process denatures proteins, causing them to lose their natural structure. It also damages epitopes. This can affect the assay performance. For instance, unstained FFPE sections can lose their antigenicity within a few weeks. It is, therefore, essential to perform chemical extractions as soon as possible. Recently, several researchers have used non-destructive molecular extraction techniques to extract proteins from FFPE samples. These methods include heat-induced antigen retrieval and radio-immunoprecipitation assay buffer. Interestingly, DNA and RNA molecules can be removed from FFPE tissue blocks. Using these techniques, researchers have found a range of proteins from benign prostatic hyperplasia.

FFPE tissue is also an attractive option for immunohistochemistry (IHC) experiments. In this method, the sample is bathed in a solution of antibodies. The antibody then binds to the proteins and structures in the model. A fluorescence scanner then examines this. Compared to frozen samples, FFPEs show better morphology and a higher degree of cross-linkage. This may mask sensitive antigens, making them more challenging to see in the microscope. It has been found that double-stranded DNA is relatively stable in FFPE blocks. FFPE tissue is also more durable than frozen tissue. In addition, FFPEs are less expensive to store than frozen tissues. These benefits are likely to increase as complementary techniques are developed.

Muhammad Sakhawat is a premium content writer and has expertise in writing content on various niches. He is currently working with as a full-time content writer. You can follow him on Twitter. @im_sakhawat_

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