In-situ hybridizations and FFPE slides.

Here's an example of the difference between what you could do with an FFPE, H&E slide 15 years ago versus today. This illustrates WHY archives of FFPE tissue have become so much more useful in recent years. In this example we are looking at a sagittal section of an embryonic mouse:

Abbreviations: Br – brain; DMO – dorsal region medulla oblongata; IC – internal capsule; K – kidney; Li – liver with blood vessels; Lu – lung; Ma – mandible; NCh – nasal chamber; NPhD – nasopharangeal duct; PhU – phallic part of urethra; (s) – sense. 

So, you can see that the mouse has cells, tissues, organs, the usual, yup, it's definitely a mouse, and honestly that's about all you can tell from the above image.

Now imagine you are interested in a specific gene, and you want to know where that gene is most actively expressed. Today you can do that using a technique called in situ hybridization (ISH).  The image below was taken from a study of a gene I will simply call "GENE X"  which is believed to code for a transcription factor protein. In humans, GENE X mutations cause severe diseases including neonatal diabetes mellitus.  The purpose of this ISH analysis was to localize GENE X mRNA at the anatomical and cellular levels in order to help scientists learn something of its likely function.  The formaldehyde fixed sections were mounted on glass slides then hybridized with 35S-labeled cRNA probes. Patterns of gene expression were analyzed by x-ray film autoradiography and  darkfield illumination. The image below is of the same section as the one above.

The results provided evidence for the presence of GENE A mRNA at various concentrations in several tissues including specific brain regions, structures related to the nasal chamber, lung, liver blood vessels, kidney, ureter and pancreas. In the pancreatic islets, the hybridization intensity was comparable to that of the kidney cortex. I won't bore you with all the details of what this experiment suggests, but the point here is that now the scientist has the option to ask questions about what specific genes might be doing in specific places and at specific times during the development of the organism. Pretty neat huh?

FFPE specimens

The process of creating formalin fixed paraffin embedded (FFPE) tissue and and fixed, H&E stained slides has been around for over a hundred years. It's a standard tool used by clinicians, pathologists and researchers in many life-science fields. Fixed material is stable at room temperature and can be conveniently stored for long periods. Since these techniques has been around for a while, hospitals and research labs all over the world have tended to accumulate huge archives of fixed material containing many millions of specimens and dating back many decades. In hospitals, this can include tissue removed as biopsies, resected material removed from patients during surgery and samples collected post-mortem. Hospitals keep these samples as a way to keep track of patient histories, monitor long-term changes of a patient's condition, ensure and improve the accuracy of diagnosis of disease and to meet legal record-keeping obligations. Only a tiny proportion of the massive global stockpile of preserved tissue has ever been used for research purposes, and for smaller community hospitals with no research labs on site, we can assume that virtually none of the tissue collected yields any research benefit to anyone once it's clinical purpose has been fulfilled. After a certain amount of time has elapsed, some organizations simply dispose of old samples, or move them to long-term storage facilities, never again to see the light of day.  Until recently, the research value of old, preserved tissue specimens seemed dubious anyway, since preserved tissue is biologically inactive and samples are of sufficiently small size as to make the extraction of useful biochemicals impractical using traditional approaches.