Pediatric and adult sonic hedgehog medulloblastomas are clinically and molecularly distinct

Abstract

Recent integrative genomic approaches have defined molecular subgroups of medulloblastoma that are genetically and clinically distinct. Sonic hedgehog (Shh) medulloblastomas account for one-third of all cases and comprise the majority of infant and adult medulloblastomas. To discern molecular heterogeneity among Shh-medulloblastomas, we analyzed transcriptional profiles from four independent Shh-medulloblastoma expression datasets (n = 66). Unsupervised clustering analyses demonstrated a clear distinction between infant and adult Shh-medulloblastomas, which was reliably replicated across datasets. Comparison of transcriptomes from infant and adult Shh-medulloblastomas revealed deregulation of multiple gene families, including genes implicated in cellular development, synaptogenesis, and extracellular matrix maintenance. Furthermore, metastatic dissemination is a marker of poor prognosis in adult, but not in pediatric Shh-medulloblastomas. Children with desmoplastic Shh-medulloblastomas have a better prognosis than those with Shh-medulloblastomas and classic histology. Desmoplasia is not prognostic for adult Shh-medulloblastoma. Cytogenetic analysis of a large, non-overlapping cohort of Shh-medulloblastomas (n = 151) revealed significant over-representation of chromosome 10q deletion (P < 0.001) and MYCN amplification (P < 0.05) in pediatric Shh cases compared with adults. Adult Shh-medulloblastomas harboring chromosome 10q deletion, 2 gain, 17p deletion, 17q gain, and/or GLI2 amplification have a much worse prognosis as compared to pediatric cases exhibiting the same aberrations. Collectively, our data demonstrate that pediatric and adult Shh-medulloblastomas are clinically, transcriptionally, genetically, and prognostically distinct.

Fig. 1

Transcriptional heterogeneity among Shh-medulloblastomas. a Frequency plot of Shh-medulloblastoma incidence reveals a bimodal age distribution. Shh-medulloblastomas from our expression cohort (n = 33) are plotted as a percentage of the total number of tumors (n = 102) according to their respective age category: infants (≤3 years), children (4–15 years), and adults (≥16 years). b Unsupervised HCL of Shh-medulloblastomas identifies three distinct clusters. HCL was performed using 1,450 high SD genes. Pairwise significance values for the three sample clusters as determined using SigClust are shown in the legend. Patient age, gender, and histology are listed below the dendrogram. c Upper panel PCA of Shh-medulloblastomas reveals separation of samples according to patient age category. PCA was performed using the same 1,450 high SD genes utilized in b. Lower panel PCA of infant and adult Shh-medulloblastomas demonstrates clear separation between the two age groups. d Left panel Unsupervised NMF clustering of infant and adult Shh-medulloblastomas identifies two stable classes in the dataset that are indicative of patient age category. The ‘infant’ cluster is comprised solely of infant cases, whereas the ‘adult’ cluster consists of all analyzed adult cases and one infant case (asterisk, *). Right panel NMF clustering performed on a validation dataset of 26 Shh-medulloblastomas recapitulates the ‘infant’ and ‘adult’ clusters identified in our dataset. Infant cases clustering with the ‘adult’ cluster are marked with an asterisk (*). Lower panel SubMap analysis comparing the two Shh subclasses in the current dataset (‘Northcott Data’) to those present in the validation cohort (‘Validation Data’) demonstrates that they are transcriptionally equivalent

Fig. 2

Infant and adult Shh-medulloblastomas exhibit distinct transcriptional profiles. a Heatmap showing the top 100 differentially expressed genes between infant (n = 13) and adult (n = 10) Shh-medulloblastoma as determined using t test statistics applied to our expression cohort. Genes determined to be significantly differentially expressed in the same class (i.e. upregulated in adult Shh-medulloblastoma) in the validation cohort (n = 26) are highlighted in bold/red, whereas genes not present on the array platform used in the validation cohort are highlighted in orange. b GSEA enrichment plots and heatmaps showing enrichment of genes involved in skeletal system morphogenesis (upper panel) and synaptogenesis (lower panel) are significantly correlated with adult Shh-medulloblastoma. c GSEA enrichment plot and heatmap demonstrating a positive correlation between infant Shh-medulloblastoma and genes involved in ECM function. d Significant functional themes identified among adult and infant Shh-medulloblastomas. Venn diagrams illustrate the overlap of significant genes between our Shh expression dataset (‘Northcott Data’) and the validation cohort (‘Validation Data’). Genes identified as significant across all datasets were input according to age category into IPA to determine top functional themes

Fig. 3

Prognostic significance of clinicopathological features in Shh-medulloblastoma. a Age distribution of pediatric (n = 55) and adult (n = 96) Shh-medulloblastomas in our MB TMA cohort (n = 151). Lower panels Gender, tumor location, and metastatic frequency in our MB TMA cohort. b OS and PFS probabilities for pediatric and adult Shh-medulloblastomas included in the cohort. c OS and PFS probabilities for Shh-medulloblastomas stratified by metastatic status. d OS and PFS probabilities for Shh-medulloblastomas stratified by histological subtype (classic vs. desmoplastic)

Fig. 4

Prognostic significance of chromosome 10q deletion and GLI2 amplification among Shh-medulloblastomas. a OS and PFS probabilities for Shh-medulloblastomas stratified by chromosome 10q deletion status. b OS and PFS probabilities for Shh-medulloblastomas stratified by GLI2 amplification status