Purpose: A risk-adapted treatment strategy, the ISG/OS-2 trial, evaluated the use of mifamurtide in patients with P-glycoprotein (Pgp)–positive localized osteosarcoma. The primary objective was the identification of prognostic classifiers based on tumor microenvironment (TME) gene profiling in all patients and in those undergoing mifamurtide treatment. Experimental Design: RNA from pretreatment formalin-fixed, paraffin-embedded nondecalcified tissues of 62 patients was analyzed with the PanCancer Immune Profiling Panel (NanoString Technologies). Thirty-three (53%) of 62 Pgp-positive patients underwent chemotherapy + mifamurtide; 29 (47%) of 62 Pgp-negative patients received chemotherapy alone. Univariate Cox regression, ROC curve, and CIBERSORTx algorithm gene deconvolution analyses were performed. Results: A 21-gene signature able to stratify all patients into high risk (Hi-R) and low risk (Lo-R) was identified: 5-year overall survival (OS) of 47% for Hi-R and 92% for Lo-R (P = 3e−06). TME of Lo-R compared with Hi-R was significantly enriched in CD8 T cells, regulatory T cells, and NK-activated cells and diminished in CD4 T cells. The 21-gene signature was validated in two independent sets: TARGET-OS The Cancer Genome Atlas (n = 62) and GSE33382 (n = 57). For patients treated with chemotherapy + mifamurtide, 31 mifamurtide-related genes able to distinguish Hi-R and Lo-R in terms of OS (P = 1e−09) and event-free survival (P = 3e−06) were also identified. After multivariate analysis, the 21- and 31-gene mifamurtide-related signatures were independently associated with OS (P = 0.00044 and P = 0.000079, respectively). Conclusions: A validated osteosarcoma TME prognostic gene signature has been identified, regardless of mifamurtide treatment. Importantly, a mifamurtide-related signature was also developed. Tumor–immune interactions possibly implicated in disease progression and treatment response were shown.

Ewing sarcoma (EwS), a highly aggressive malignancy affecting children and young adults, is primarily driven by a distinctive oncogenic fusion, the EWSR1‐ETS, whose activity is a key source of epigenetic and clinical heterogeneity. CD99 is constantly present in EwS cells, known to modulate the EwS genetic profile and tumor malignancy. However, the relevance of CD99 alone, or in association with EWSR1‐ETS chimeras, is poorly understood. We explored the dynamic relationship between CD99 and EWS::FLI1, the main fusion observed in EwS, by means of model systems with inducible expression of either molecule. The transcriptomic dynamics of cells with or without expression of EWS::FLI1 or CD99 were analyzed and correlated with tumor cell growth. The CD99‐associated EwS gene profile was found to have commonalities with the profile induced by EWS::FLI1, but also peculiar differences. Both EWS::FLI1 and CD99 are regulated targets of the DREAM complex, but the CD99 expression specifically impacted genes that are the targets of FOXM1 and are involved in the setting of the G2/M phase of the cell cycle. Most CD99‐regulated FOXM1‐targeted genes were found to correlate with bad prognosis in two public clinical datasets (R2 platform), further supporting the clinical relevance of CD99‐mediated regulation of EwS gene expression.

Corrigendum: Denatonium as a Bitter Taste Receptor Agonist Modifies Transcriptomic Profile and Functions of Acute Myeloid Leukemia Cells

Supplementary Figure S3: ROC curves depicting risk prediction signature score performance in discovery cohorts. AUC value is shown. The optimal cut-off value used to stratify patients was 2.49

Supplementary Figure S1: Study Design

Cox regression output , 31 genes selected based on LogRank≤0.05 significantly associated with overall survival (OS) in 33 localized primary high-grade osteosarcoma underwent chemotherapy (CT) combined with mifamurtide treatment