Fig. 7.
PCF11-derived TREND signatures predict superior patient outcome. a Predictive potential of TREND signatures (red) compared to common stratifiers in neuroblastoma (blue, Supplementary Table 6) with (n = 493, left) or without (n = 401, right) MYCN amplification (p-values, Supplementary Table 7, Cox-modelling Supplementary Figure 7e). Receiver-operating characteristic (ROC) curve reflecting the ratio of short-to-long isoform abundance of PCF11-TREND-affected genes (with AUC > 0.7) for predicting death (upper panels) or association with high risk (lower panels). Red line depicts predictive power of a combined TREND pattern (multifactor ROC) compared to ROC based on expression of established risk markers (MYCN and ALK82; grey lines reflect ROC for 3′end isoform patterns of individual TREND-affected genes, GSE4971044; Supplementary Table 6). b ROC curves reflecting TREND alterations (red) of genes belonging to the neurodifferentiation TREND operon highlight the predictive power of deregulated TREND signatures compared to the poor sensitivity and specificity of the mere mRNA abundance (orange; n = 493, raw data same as for a; TREND isoforms and mRNA abundance of RBM17, ELP2 and AKT2 (lower row) serve as control confirming absence of analytical bias in favour of TREND). c High-level PCF11 mRNA expression in other paediatric malignancies with embryonic origin including medulloblastomas (GSE35493), Ewing sarcomas (GSE17679) and primitive neuroectodermal tumours (PNET, GSE17679) compared to respective controls (red; expression data obtained from R2 (http://r2.amc.nl)). For box plots, centre line depicts median, hinges show 25th and 75th percentile, whiskers depict interquartile range (IQR = 1.5), two-sided t-test. **p < 0.01, ***p < 0.001. d Integrated model for PCF11-dependent TREND regulation in neuroblastoma governing neurodifferentiation (details see text). Briefly, (1) postnatal downregulation of PCF11 is believed to (2) reduce efficiency of transcription termination20,21, facilitating (3) alternative polyadenylation (APA) at distal (3′ located) polyadenylation (pA) signals (red), affecting TREND of >900 RNAs (4). This includes a neurodifferentiation TREND operon (Fig. 3b), shaping (5) WNT signalling to induce neurodifferentiation. Conversely, sustained (postnatal) high-level PCF11 expression arrests neuronal precursors in an undifferentiated state by promoting polyadenylation at proximal pA (blue), thereby controlling protein output of the neurodifferentiation TREND operon. Transcript isoform regulation of GNB1, a modulator of various transmembrane signalling pathways48 with a role in development63, malignant transformation64 and neurodevelopmental disorders65 is prerequisite for PCF11-dependent regulation of neurodifferentiation. Notably, GNB1 was previously identified as marker for spontaneous neuroblastoma regression41