Risk-adapted therapy and biological heterogeneity in pineoblastoma: integrated clinico-pathological analysis from the prospective, multi-center SJMB03 and SJYC07 trials

Abstract

Pineoblastoma is a rare embryonal tumor of childhood that is conventionally treated with high-dose craniospinal irradiation (CSI). Multi-dimensional molecular evaluation of pineoblastoma and associated intertumoral heterogeneity is lacking. Herein, we report outcomes and molecular features of children with pineoblastoma from two multi-center, risk-adapted trials (SJMB03 for patients ≥ 3 years; SJYC07 for patients < 3 years) complemented by a non-protocol institutional cohort. The clinical cohort consisted of 58 patients with histologically diagnosed pineoblastoma (SJMB03 = 30, SJYC07 = 12, non-protocol = 16, including 12 managed with SJMB03-like therapy). The SJMB03 protocol comprised risk-adapted CSI (average-risk = 23.4 Gy, high-risk = 36 Gy) with radiation boost to the primary site and adjuvant chemotherapy. The SJYC07 protocol consisted of induction chemotherapy, consolidation with focal radiation (intermediate-risk) or chemotherapy (high-risk), and metronomic maintenance therapy. The molecular cohort comprised 43 pineal parenchymal tumors profiled by DNA methylation array (n = 43), whole-exome sequencing (n = 26), and RNA-sequencing (n = 16). Respective 5-year progression-free survival rates for patients with average-risk or high-risk disease on SJMB03 or SJMB03-like therapy were 100% and 56.5 ± 10.3% (P = 0.007); respective 2-year progression-free survival rates for those with intermediate-risk or high-risk disease on SJYC07 were 14.3 ± 13.2% and 0% (P = 0.375). Of patients with average-risk disease treated with SJMB03/SJMB03-like therapy, 17/18 survived without progression. DNA-methylation analysis revealed four clinically relevant pineoblastoma subgroups: PB-A, PB-B, PB-B-like, and PB-FOXR2. Pineoblastoma subgroups differed in age at diagnosis, propensity for metastasis, cytogenetics, and clinical outcomes. Alterations in the miRNA-processing pathway genes DICER1, DROSHA, and DGCR8 were recurrent and mutually exclusive in PB-B and PB-B-like subgroups; PB-FOXR2 samples universally overexpressed the FOXR2 proto-oncogene. Our findings suggest superior outcome amongst older children with average-risk pineoblastoma treated with reduced-dose CSI. The identification of biologically and clinically distinct pineoblastoma subgroups warrants consideration of future molecularly-driven treatment protocols for this rare pediatric brain tumor entity.

Keywords: Clinical trial; DICER1; FOXR2; MicroRNA processing; Molecular subgroups; Pineoblastoma.

Fig. 1

Cohort compositions and key clinical outcomes (a) Composition of the clinical and molecular cohorts. Patients with histologically diagnosed pineoblastoma (PB) comprised the clinical cohort; patients whose tumors were profiled on methylation array (PB=40, pineal parenchymal tumor of intermediate differentiation [PPTID]=1, pinealocytoma=1, pineal anlage tumor=1) comprised the molecular cohort. (b) Progression-free survival (PFS) and overall survival (OS) of the entire clinical PB cohort (top) or stratified by treatment protocol (middle) and PFS according to risk strata for patients on SJMB03/SJMB03-like therapy and SJYC07 (bottom). PTPR, papillary tumor of pineal region; WES, whole exome sequencing; WGS, whole genome sequencing

Fig. 2

Novel molecular pineoblastoma (PB) subgroups defined by DNA-methylation profiling (a) t-stochastic neighbor embedding (t-SNE) analysis of pineal parenchymal tumors (histological PB, n= 40; PPTID, n = 1; pineal anlage tumor, n = 1; pineocytoma, n = 1) and relevant reference classes from a published brain tumor dataset by Capper et al.[14] Four main PB subgroups, PB-A, PB-B, PB-B–like, and PB-FOXR2, are apparent, with further heterogeneity observed in the outliers. Study samples are colored by their methylation class assignment by the MolecularNeuropathology (MNP) brain tumor classifier, revealing two previously undescribed subgroups (PB-B–like and PB-FOXR2). (b) Summary demographic and clinical features of the newly defined PB subgroups. Differences in age at diagnosis, sex, treatment, propensity for metastasis, and progression-free survival are depicted. Contr-Pineal, control pineal tissue; Contr-Inflamm, control inflammatory tumor; ETMR, embryonal tumor with multilayered rosettes; F, female; M, male; M⁰, non-metastatic; M+, metastatic; MB-G3, medulloblastoma group 3; MB-G4, medulloblastoma group 4; MB-SHH CHL/AD, medulloblastoma SHH-activated (children and adult); MB-SHH INF, medulloblastoma SHH-activated (infant); MB-WNT, medulloblastoma WNT-activated; PB-A, pineoblastoma group A; PB-B, pineoblastoma group B; PB-B–like, pineoblastoma group B–like; PB-FOXR2, pineoblastoma FOXR2-overexpressed; Plex-Ped B, plexus tumor subclass pediatric B; PPT, pineal parenchymal tumor of intermediate differentiation (MNP classifier); PPTID, pineal parenchymal tumor of intermediate differentiation (histology); RETB, retinoblastoma

Fig. 3

Genomic alterations in molecularly defined pineoblastomas (a) Oncoprint depicting loss-of-function mutations and/or allelic deletions in miRNA pathway genes DICER1, DROSHA, and DGCR8 in addition to subgroup-specific chromosomal arm–level copy-number alterations, patient demographics, and outcome. (b) Lollipop plots depicting deleterious somatic and germline mutations in miRNA pathway genes DICER1, DROSHA, and DGCR8. chr, chromosome; fs, frameshift; X, stop codon. (c) Three exemplary copy-number plots highlighting 14q loss involving the DICER1 locus, focal 5p loss involving the DROSHA locus, and focal 22q loss involving the DGCR8 locus. Corresponding chromosomal regions of all samples from the molecular cohort, showcasing the restriction of these cytogenetic events to PB-B and PB-B–like subgroups. Chr, chromosome; F, female; M, male; PD, progressive disease

Fig. 4

Subgroup-specific expression signature and pathway enrichment in pineoblastoma (PB) (a) Heatmap of top differentially expressed genes by subgroup. PB-A was excluded here and from subsequent panels because only one expression profile was available. (b) Expression levels of pinealocyte markers (CRX, NRL, ASMT, ADRB1), DICER1, and FOXR2 among molecularly defined PB subgroups (PB-B, PB-B-like, PB-FOXR2) and outliers (non-PB). P-values were derived from the likelihood ratio test. Mut, mutant; PB-A, pineoblastoma group A; PB-B, pineoblastoma group B; PB-B–like, pineoblastoma group B–like; PB-FOXR2, pineoblastoma FOXR2-overexpressed; WT, wild-type

Fig. 5

Summary of key clinical, genomic, and cytogenetic findings according to molecularly defined pineoblastoma subgroups based on the current dataset Progression-free survival (PFS) for each subgroup is shown. Note that RB1 alteration underlying the PB-A subgroup has not been detected in our study but is included for completeness. M⁰, non-metastatic; M⁺, metastatic; N, number; PB-A, pineoblastoma group A; PB-B, pineoblastoma group B; PB-B-like, pineoblastoma group B–like; PB-FOXR2, pineoblastoma FOXR2-overexpressed; y, years