Formalin‐fixed paraffin‐embedded (FFPE) samples help to investigate transcriptomic responses in wildlife disease

• DOI: 10.1111/1755-0998.13805
• Publication Date: 2023-05-08T04:28:31Z
• Authors: Allison K. Miller; Cara L. Brosnahan; Anjali Pande; Cindy F. Baker; Jemma L. Geoghegan; Jane Kitson; Neil J. Gemmell; Edwina J. Dowle

Abstract Infectious diseases impact numerous organisms. Knowledge of host‐pathogen interactions and host responses to infection is crucial for conservation management. Obtaining this knowledge quickly made increasingly possible by a variety genomic approaches, yet, many species the bottleneck understanding this, remains access appropriate samples data. Lack sample availability has also limited our how pathogens immune hosts change over time. Archival materials may provide way explore pathogen emergence multiple—possibly hundreds—of years. Here, we tested whether formalin‐fixed paraffin‐embedded (FFPE) tissue could be used understand an unknown pathology, lamprey reddening syndrome (LRS), affecting pouched lampreys ( Geotria australis ). Our differential expression analyses dermal tissues from four unaffected eight affected collected in 2012 alluded several potential agents associated with LRS. Interestingly, pathways viral infections were overrepresented versus lamprey. Gene ontology non‐affected provided new insights into largely understudied lampreys. work confirms that FFPE can infer information about transcriptional wildlife historical pathologies/syndromes. In addition, use transcriptomics offers opportunities investigate environmental changes. We conclude discussion best utilize these unique archival resources future transcriptomic studies.