Metabolic dysfunction-associated steatohepatitis (MASH) progresses through macrophage activation and hepatic stellate cell (HSC)-driven fibrogenesis. As cell-level single-cell discoveries often suffer from pseudoreplication and fail to replicate across cohorts, in this study we critically re-evaluated human liver single-nucleus RNA-sequencing data using a rigorous per-donor statistical framework to dissociate invariant biological signals from technical artifacts. Macrophage and HSC compartments from dataset GSE202379 were profiled across clinical stages (healthy, metabolic dysfunction-associated steatotic liver disease, MASH). Cell-level statistics were aggregated into per-donor metrics, and continuous phenotypic shifts evaluated via the Jonckheere–Terpstra (JT) trend test. Key findings were tested for cross-cohort reproducibility in two independent cohorts (GSE136103 and GSE244832). A 249-gene scar-associated macrophage (SAMac) program showed reproducible, stage-dependent expansion in the discovery cohort (per-donor Jonckheere–Terpstra trend across the disease-only spectrum, MASLD to advanced MASH, z = 2.23, p = 0.026 [primary]; z = 2.74, p = 0.006 across all four stages including the healthy baseline) and directional replication in external data. Cell–cell communication analysis replicated the receptor-side topology of a conserved macrophage-to-HSC PDGF axis in both external cohorts and the ligand-driven PDGFC→PDGFRB edge in the external snRNA-seq cohort (GSE244832), with PDGFRB being a high-degree hub within the HSC fibrogenic interaction network. Importantly, a previously published global HSC activation module failed to validate (JT p = 0.77); however, its core extracellular matrix and RUNX1/2 sub-axis remained robust, whereas the widely claimed AP-1/JUNB regulatory driver was not supported at the transcript level in the single-nucleus RNA-seq cohort data. These findings are consistent with an isolation-associated immediate-early gene response in enzymatically dissociated scRNA-seq data, given the flat-to-downward transcript-level trend in cryopreserved-tissue cohorts; transcript-level data cannot, however, exclude protein- or phosphorylation-level AP-1 activity. Targetable downstream components within the validated core architecture were annotated. By implementing per-donor verification, we successfully separated robust pathological features of MASH from platform-dependent artifacts. The validated SAMac program and the macrophage–HSC PDGF axis, together with an associated RUNX subprogram, represent high-confidence, reproducibility-filtered candidate therapeutic nodes that require functional validation. These findings establish a reproducibility-first standard for single-cell translational research, and the validated programs are consistent with emerging models of inter-organ inflammatory circuitry in MASH.

Although papillary thyroid carcinoma (PTC) is widely considered an immunologically cold tumor, detectable T-cell infiltration can influence disease progression in selected patients. Previous bulk analyses have linked cAMP-responsive element modulator (CREM) expression to a favorable progression-free interval and an inverse correlation with regulatory T-cell infiltration but have not resolved the cellular origin or functional state. In this study, we integrate single-cell RNA-sequencing data from a 23-sample PTC atlas with bulk Cancer Genome Atlas Thyroid Carcinoma (TCGA–THCA) validation. We show that CREM marks a T-cell receptor (TCR)-driven immediate early gene activation state in tumor-infiltrating T cells rather than a cAMP program; this state is consistently and modestly enriched within the FOXP3⁺ regulatory T-cell compartment, challenging the interpretation that bulk inverse Treg–CREM correlations reflect Treg-intrinsic repression. CREM-high T cells upregulate ANXA1, and permutation-controlled analysis identifies a candidate paracrine axis from CD4/CD8 T cells to the epithelial epidermal growth factor receptor (EGFR). At the bulk level, CREM expression correlates with reduced proliferation programs and is associated with a prolonged progression-free interval (multivariate HR 0.56, 95% CI 0.31–1.00, p = 0.050), with the effect direction preserved after immune and sex adjustment. Genome-wide differential expression and gene-set enrichment in an independent cohort (GSE193581) confirm that CREM-detected T cells are enriched for a TCR-driven immediate early transcriptional program, supporting the reinterpretation of CREM as a marker of TCR-driven IEG activation.