Spatial transcriptomic profiling of macroregenerative and high-grade dysplastic nodules in cirrhotic liver: A pilot study

High-grade dysplastic nodules (HGDN) are recognized precursors of hepatocellular carcinoma in cirrhosis, yet their distinction from macro-regenerative nodules (MRN) relies entirely on morphologic features that exist along a continuum rather than as discrete thresholds, with no ancillary marker available to adjudicate this boundary. Whether these lesions represent distinct molecular states remains unknown. We performed whole-transcriptome spatial profiling (GeoMx Digital Spatial Profiler, Bruker) of MRN and HGDN within their native cirrhotic microenvironment in FFPE explant specimens from three patients. Fifteen regions of interest spanning background cirrhosis ( n = 2), MRN ( n = 3), HGDN ( n = 4), and the HGDN–cirrhotic interface ( n = 6) underwent exploratory differential expression and gene set enrichment analyses; because MRN and HGDN derived from different patients, lesion class and donor could not be separated. MRN showed a quiescent regenerative program characterized by HGFAC upregulation, depletion of inflammatory and immunoglobulin transcripts, and no significant upregulation of canonical hepatocellular carcinoma markers. HGDN showed PZP, DEPP1, and CDHR5 upregulation and enrichment of interferon signaling. Spatially, HGDN separated into a metallothionein-enriched core and an MHC-I/interferon-enriched interface expressing HLA-B, HLA-C, and IFI6, a pattern that bulk profiling would be expected to obscure; the core–interface distinction persisted when analysis was restricted to a single patient. In this pilot cohort, morphologically defined regenerative and premalignant hepatocellular nodules showed distinct transcriptional profiles, providing preliminary, hypothesis-generating molecular support for a difficult morphologic distinction. These observations, including the MHC-I/interferon-enriched dysplastic interface, identify candidate targets for validation in larger cohorts with paired lesions.