A WHO-Grade-Derived Meningioma Transcriptomic Program: Cross-Cohort Recurrence Association and Single-Cell Contextualization

Transcriptomic programs may complement histopathologic grading in meningioma, but their reproducibility across platforms and cellular context remain uncertain.We derived a fixed 200-gene WHO grade I-versus-II program in GSE136661, tested retrospective recurrence associations in GSE16581 and GSE74385 using covariate-adjusted Firth models, and examined the program in two single-cell cohorts.The program was higher in recurrent tumors and retained grade-adjusted associations in GSE16581 (odds ratio per 1-SD increase, 14.74; 95% CI, 2.77-224.07; 10 recurrence events) and GSE74385 after simultaneous grade and batch adjustment (odds ratio, 5.18; 95% CI, 1.40-25.83;22 events).The wide GSE16581 interval indicates substantial uncertainty in effect magnitude despite directionally stable sensitivity analyses.Component decomposition identified a coordinated proliferation-associated, extracellular-matrix/mesenchymal-down axis, with both the up-regulated and down-regulated components tracking grade.Patient-level tumor/tumor-like-cell pseudobulk scores in GSE206647 reproduced the grade association (Spearman rho=0.87;rho=0.83after lineage-marker exclusion).Of 159 measurable program genes, 58 reached FDR<0.10 and 56 were directionally concordant with discovery; PI3 (elafin) and PITX1 (a paired-like homeodomain transcription factor) emerged as grade-associated candidates for tissue validation.Patient-resolved non-negative matrix factorization recovered a cell-cycle metaprogram in 6 of 15 eligible tumors; after scoring across all 15 tumors, it was the only positively grade-associated metaprogram surviving multiple-testing correction and remained identifiable across cell-filtering and construction-parameter sensitivity analyses.Together, these findings establish cross-cohort reproducibility and single-cell context for a fixed grade-derived expression axis, demonstrate retrospective recurrence relevance without establishing gradeindependent prediction, and prioritize PI3 and PITX1 for orthogonal tissue evaluation.Prospective timeto-event studies using a prespecified, calibrated single-sample assay are warranted to test clinical utility.