Elucidating disease pathogenesis using formalin-fixed paraffin-embedded samples: Integrating genomics, spatial transcriptomics, and histology – A focus on vascular anomalies

Formalin-fixed paraffin-embedded (FFPE) samples are widely used for pathological diagnosis because they enable histological evaluation, special staining, and immunohistochemistry. The advent of next-generation sequencing (NGS) technologies has expanded their applications to comprehensive molecular analyses including genomic mutation profiling and spatial transcriptomics. FFPE samples present challenges hampering full realization of their extensive utility including nucleic acid degradation and interlaboratory variability, which necessitate standardized workflows to ensure reproducible and reliable molecular analysis results. Although FFPE-based molecular analytical methods are maturing, a unified workflow for multilayered and comprehensive pathological investigations, from FFPE sample preparation to NGS-based molecular analyses, has not been established. NGS-based genomic mutation profiling identifies key gene mutations underlying disease-driving mechanisms, using FFPE-derived DNA for large-scale gene panel analyses. This approach facilitates tailored therapeutic selection and offers considerable diagnostic and prognostic insights. Spatial transcriptomics complements these genomic analyses by providing spatially resolved gene expression data, coupling molecular findings with tissue architecture. FFPE samples expand access to spatial transcriptomics, informing hypothesis generation and detailed analyses of cellular dynamics. This review emphasizes the integration of NGS-based genomic mutation profiling and spatial transcriptomics using FFPE samples. Combining these complementary methodologies facilitates elucidation of multilayered disease mechanisms, driving innovations in diagnostic accuracy, personalized treatment strategies, and unraveling intricate biological processes. Overcoming current challenges, including nucleic acid degradation and workflow inconsistencies, will allow researchers and clinicians to achieve comprehensive pathological insights with unprecedented precision. • Advances in NGS have expanded the potential of archival FFPE samples for analysis. • FFPE samples are vital for linking genotypes to phenotypes through multi-omics. • Nucleic acid degradation and workflow variability hinder FFPE analyses. • Standardized pre-analytical and analytical protocols ensure reliable results. • A multidisciplinary team is essential for successful FFPE-based multi-omics.