Comprehensive multi-omics profiling reveals molecular heterogeneity and developmental signatures in solid pseudopapillary neoplasm of the pancreas

Solid pseudopapillary neoplasm (SPN) of the pancreas is a rare, low-grade malignant tumor that predominantly affects young women. Although previous studies have applied omics approaches, including whole-exome sequencing, transcriptomics, and DNA methylation profiling to characterize SPN, its tumorigenesis and cell of origin remain elusive. Apart from the recurrent CTNNB1 hotspot mutation, which is currently considered the only canonical driver, SPN is typically diploid and exhibits few recurrent genomic alterations. Moreover, because of its low incidence, previous small-cohort studies have been insufficient for robust molecular subtyping or integrative analysis. To comprehensively characterize the molecular landscape of SPN, we performed multi-omics analyses on 80 tumors using whole-genome sequencing (WGS), whole-transcriptome sequencing, and whole-genome enzymatic methyl-sequencing (EM-seq). Unsupervised hierarchical clustering based on the top 1,000 genes ranked by median absolute deviation (MAD) across transcriptomes identified two robust molecular subtypes: a developmentally reprogrammed type and an immune-enriched type: The immune-enriched subtype exhibited significant activation of immune-associated pathways, including immunoglobulin-mediated and adaptive immune responses, whereas the developmentally reprogrammed subtype showed enrichment of embryonic skeletal system development and morphogenesis signatures. Furthermore, SPN tumors displayed a genome-wide hypermethylated pattern compared with normal pancreatic tissues, highlighting their distinct epigenetic state. Beyond expression-based stratification, we systematically examined fusion events, genome-wide somatic mutations, structural variants, mitochondrial genome alterations, numtogenesis, retrotransposon activity, and methylation entropy across the cohort. Notably, a recurrent TVP23C-CDRT4 fusion was detected in 61% of cases, suggesting a potential novel genomic hallmark of SPN. This study represents the largest integrative multi-omics analysis of SPN to date, revealing distinct transcriptomic and epigenomic subtypes, a recurrent fusion event, and marked molecular heterogeneity. Ongoing integrative analyses aim to clarify the developmental origin and oncogenic evolution of this rare pancreatic neoplasm.