Investigation 007
What the Slide Cannot Say
Three parasites cause cancer. Nobody is checking for a fourth.
Cancer, found and missed
Formalin fixation
Formaldehyde stops biology mid-sentence by cross-linking protein. It preserves shape beautifully and shreds DNA doing it.
What we are reading
Gathered for the investigation and not yet written up. Each note says what the paper does and does not show.
- Reid KM, Maistry S, Ramesar R, Heathfield LJ. A review of the optimisation of the use of formalin fixed paraffin embedded tissue for molecular analysis in a forensic post-mortem setting.10.1016/j.forsciint.2017.09.020 · PMID 29078160
The cost of fixation, stated without euphemism: 'The preservation of tissue in formalin is KNOWN TO DAMAGE DNA through crosslinking activity. This results in the extraction of SEVERELY FRAGMENTED DNA of variable yields, which subsequently REDUCES THE ABILITY TO PERFORM DOWNSTREAM MOLECULAR ANALYSES.' 111 studies reviewed on how to work around it. This is the single most important fact for the parasite question: the step that makes the tissue readable by eye is the same step that degrades the molecules a PCR would need to name an organism nobody suspected.
- Matsunaga H, Arikawa K, Yamazaki M, Wagatsuma R, Ide K, Samuel AZ, Takamochi K, Suzuki K, Hayashi T, Hosokawa M, Kambara H, Takeyama H. Reproducible and sensitive micro-tissue RNA sequencing from formalin-fixed paraffin-embedded tissues for spatial gene expression analysis.10.1038/s41598-022-23651-6 · PMID 36376423
The counterweight, and the reason the episode should not end in despair. Yes, FFPE tissue 'may be severely damaged by methylene crosslinking'. But this group recovered roughly 7,000 genes from a 100-micrometre punch, 10 micrometres thick, from mouse liver fixed TWO YEARS earlier, and characterised the tumour microenvironment in human lung cancer blocks fixed SIX YEARS earlier. Every hospital in the developed world holds decades of these blocks at room temperature. The archive is readable. Nobody has read it for this.
- Boon ME, Kok LP. Theory and practice of combining coagulant fixation and microwave histoprocessing.10.1080/10520290802553476 · PMID 19031284
The history, and the reason it is formalin at all. F. Blum introduced formaldehyde as a fixative in 1893; it became standard because it hardened and preserved gross specimens, and because it was CHEAPER than the ethyl alcohol Dutch scientists had used since the eighteenth century. Alcohol-based coagulant fixatives do not cross-link, so they do not compromise immunostaining and do not damage DNA or RNA. Over 40,000 skin biopsies and 100,000 cervical samples have been processed this way in one Leiden laboratory. The authors' prediction, made in 2008 and still not realised: formalin will eventually be legislated out once health authorities 'realize that formalin invalidates expensive tests'.
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