Arginine-axis transcriptomics define three neuroblastoma subtypes and a fixed four-gene prognostic signature with...

Metabolic plasticity shapes neuroblastoma (NB) heterogeneity and therapy response. Arginine (Arg) sits at the crossroads of the urea cycle, nitric-oxide signaling, polyamine biosynthesis, and proline-collagen metabolism, yet, pathway-level organization of the Arg/proline ("Arg-axis") program in NB and its clinical relevance remain incompletely defined. This study aimed to define Arg-axis transcriptomic subtypes in NB and to develop and externally validate an Arg-axis-derived prognostic risk score with immune correlates.

We prespecified a 54-gene Arg/proline-metabolism panel and used it as the feature space for discovery in GSE49710 (microarray) and validation in E-MTAB-8248 (microarray); two immunotherapy RNA sequencing (RNA-seq) cohorts (MEL_PRJEB23709, GSE78220) were analyzed for out-of-domain evaluation. Consensus clustering delineated Arg-axis subtypes. Tumor stemness was quantified by one-class logistic regression (OCLR)-derived messenger RNA (mRNA) expression-based stemness index (mRNAsi). Cluster-derived features were reduced by random forest and entered into multivariable Cox modeling to derive a fixed-coefficient four-gene signature. Discrimination, calibration, and clinical utility were assessed by receiver operating characteristic (ROC), calibration, and decision-curve analysis (DCA). Immune contexture was inferred by Estimation of STromal and Immune cells in MAlignant Tumors using Expression data (ESTIMATE), Microenvironment Cell Populations-counter (MCP-counter), and Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT); checkpoint response was predicted by using Tumor Immune Dysfunction and Exclusion (TIDE) [2025] and immunophenoscore (IPS). Connectivity Map (CMap 2.0) prioritized compounds using the top |log fold change| 150 up/down genes per cohort with cross-cohort aggregation.

Fifty of 54 panel genes were expressed in the discovery cohort. Consensus clustering supported three subtypes with stepwise overall-survival separation, higher mRNAsi in the poorest-prognosis group, and concordant clinicogenomic features [age, International Neuroblastoma Staging System (INSS) stage, MYCN]. gseGO highlighted cell-cycle/replication programs in high-risk states and antigen-presentation/T-cell-inflamed programs in favorable states. The fixed four-gene model stratified outcome in discovery and reproduced risk separation in the external NB cohort, retaining independence from age, stage, and MYCN, and showing added net benefit on DCA. Across risk strata, immune deconvolution indicated myeloid/extracellular matrix (ECM)-dominant microenvironments at higher scores vs. T-cell-inflamed phenotypes at lower scores; TIDE/IPS were concordant. In two immunotherapy cohorts, a higher RiskScore was associated with inferior overall survival, consistent with the in-silico response metrics. Aggregated CMap analysis nominated histone deacetylase (HDAC) inhibition, with entinostat (MS-275) ranking highest as a candidate to reverse the high-risk transcriptomic program.

An Arg-axis-anchored approach resolves biologically coherent NB subtypes and yields a parsimonious, fixed-coefficient four-gene signature that generalizes across cohorts, aligns with immune contexture, and proposes testable therapeutic hypotheses. These results support metabolism-informed risk stratification in NB and motivate prospective validation with standardized processing, mechanistic flux assays, and rational combination studies.