Comparative spatial whole transcriptome analysis of matched frozen and formalin-fixed paraffin-embedded colorectal cancer tissues

Abstract

Spatial transcriptomic technology enables resolving a tumor microenvironment heterogeneity of colorectal cancer (CRC) tissue samples. However, there is limited evidence regarding the relative strengths and weaknesses of different CRC sample types and preservation methods, including formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF) and snap frozen (SF). Here, we examine gene expression profiles in 36 tissue areas, FFPE, FF and SF samples, derived from a patient with stage IV CRC, using spatial analysis of the whole transcriptome. The tissue samples obtained from surgical resection of the cancer were subjected to a detailed histological evaluation and spatial transcriptomics analysis to compare the quality of the sample between different preservation methods. Spatial transcriptomic analysis demonstrated that FFPE tissue samples offered improved resolution of cellular morphology in the tumor microenvironment, facilitating greater detail of gene expression and cell types. In contrast, gene expression analysis of FF and SF tissues embedded in optimal cutting temperature compound revealed a high level of CRC gene expression. FFPE, FF and SF samples shared a significant overlap among the top 300 genes that were strongly associated with key biological processes in CRC. In summary, the spatial analysis of the whole transcriptome across FFPE, FF and SF CRC tissues revealed intratumoral heterogeneity and highlighted key transcriptomic signatures, suggesting the specific value of different tissue preservation methods in the profiling of CRC.