Members of the nuclear factor-κB (NF-κB) family of transcriptional regulators are central mediators of the cellular inflammatory response. Although constitutive NF-κB signalling is present in most human tumours, mutations in pathway members are rare, complicating efforts to understand and block aberrant NF-κB activity in cancer. Here we show that more than two-thirds of supratentorial ependymomas contain oncogenic fusions between RELA, the principal effector of canonical NF-κB signalling, and an uncharacterized gene, C11orf95. In each case, C11orf95–RELA fusions resulted from chromothripsis involving chromosome 11q13.1. C11orf95–RELA fusion proteins translocated spontaneously to the nucleus to activate NF-κB target genes, and rapidly transformed neural stem cells—the cell of origin of ependymoma—to form these tumours in mice. Our data identify a highly recurrent genetic alteration of RELA in human cancer, and the C11orf95–RELA fusion protein as a potential therapeutic target in supratentorial ependymoma.
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Sequence and array data were deposited in the European Bioinformatics Institute (EBI) under accession number EGAS00001000254.
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This research was supported as part of the St. Jude Children’s Research Hospital, Washington University Pediatric Cancer Genome Project. This work was supported by grants from the National Institutes of Health (R01CA129541, P01CA96832 and P30CA021765 to R.J.G), the Collaborative Ependymoma Research Network (CERN), and by the American Lebanese Syrian Associated Charities (ALSAC). We are grateful to S. Temple for the gift of reagents and the staff of the Hartwell Center for Bioinformatics and Biotechnology, Animal Imaging Center, and Flow Cytometry and Cell Sorting Shared Resource at St. Jude Children’s Research Hospital for technical assistance.
The authors declare no competing financial interests.
Extended data figures and tables
a, Coverage for whole-genome sequenced cases. Percent of the genome (left) and exome (right) covered at 10×, 20× and 30× depth in tumour and germline samples. b, RNA-seq coverage. Coverage below the red line is considered poor quality; those with 20× depth, above the green line, are considered very high quality.
Extended Data Figure 2 Comparison of genomic aberrations among ependymomas analysed by whole genome sequencing.
a, The large majority of ependymomas have less than ten coding SNVs. Samples with more than 20 coding SNVs and their corresponding sample number from Fig. 1 are shown. b, Comparison of total number of structural variations in posterior fossa and supratentorial (ST) samples (Wilcox ranked sum test, P = 0.0006). c, Circos plot depicting SVs discovered across all supratentorial (red, outer plot) and posterior fossa (blue, inner plot) ependymomas. Each dot represents a validated or putative SV breakpoint detected by CREST in the WGS discovery cohort. Note the highly focal clustering of SVs on Chr11q in supratentorial ependymomas.
Extended Data Figure 3 Chromothripsis in supratentorial ependymomas resulting in C11orf95–RELA translocations.
Circos plots for the eight supratentorial (ST) ependymomas analysed using WGS that contained C11orf95–RELA translocations (sample numbers as Fig. 1). From the outer ring to the inner ring: chromosome, CNV calls, softclip count histogram, SVs (red, both sides with ≥10 softclips; blue, one side with >10 softclips; grey, <10 supporting softclips on either side).
a, Breakpoints of structural rearrangements (red loops) at 11q13.1 in tumours ST1 to ST8. b, Exemplary C11orf95–RELA translocation and fusion transcript in sample ST5. Top, RNA-seq coverage; middle, DNA sequence across the fusion breakpoint; bottom, RNA sequence. c, Derivative chromosome generated by chromothripsis in tumour ST6 highlighting the locations of C11orf95 ‘break-apart’ FISH probes. Yellow block arrows represent chromosome fragments rearranged by chromothripsis. Numbers indicate fragment order on normal chromosome 11. FISH result, right. Arrows, transcription orientation.
Extended Data Figure 5 Translocation fusions: transcripts and predicted protein products detected in ependymoma.
a, Reverse transcription PCR products of the indicated transcripts detected in tumour samples (sample numbers as in Fig. 1a). b, Predicted protein products of wild-type translocation partners (top) and fusion products (bottom).
RNA-seq contig maps demonstrating the various fusion products generated through splicing of the primary C11orf95–RELA translocation transcript.
Extended Data Figure 7 Analysis of C11orf95–RELA translocation and expression in formalin-fixed paraffin-embedded human and mouse ependymoma.
a, Formalin-fixed paraffin-embedded (FFPE) cohort (top) and results (middle) of break-apart FISH and RT–PCR analysis of the C11orf95–RELA translocation and transcript, respectively. Tumours with ‘unavailable’ data had insufficient material for analysis. b, GFAP, p-Ser276-RELA, CCND1 and L1CAM immunohistochemistry in human and mouse RELAFUS1–7-positive and -negative cases. The mouse tumours recapitulate the ‘vascular-variant’ of human supratentorial ependymoma (see haematoxylin and eosin (H&E) images). This subtype is characterized by a branching network of capillaries (white arrows) and cytoplasmic clearing (black arrows). ***P < 0.0005. Scale bar, 50 μm
Extended Data Figure 8 C11orf95–RELA fusion protein spontaneously activates an NF-κB transcriptional reporter.
NF-κB–green fluorescence reporter (GFP) activity in 293T cells transduced with the indicated virus, treated for 60 min with TNF (50 ng ml–1) or vehicle control.
This file contains Supplementary Methods and Materials, Supplementary Results, Supplementary Figures 1-15 additional references. (PDF 3496 kb)
This file contains Supplementary Tables 1-6 and comprises Table 1: Clinical, pathological and validated genetic abnormalities of all 177 tumors in the study cohort ; Table 2: Coverage data for tumours analyzed by whole genome sequencing; Table 3: Coverage data for tumors analyzed by RNASeq; able 4: Tier 1 validated and putative high quality SNV and indel mutations; Table 5: Tier 2 validated and putative high quality SNV and indel mutations; and Table S6: Tier 3 validated and putative high-quality SNVs and indel mutations. (ZIP 954 kb)
This file contains Supplementary Tables 7-12 and comprises Table 7: Numbers of high quality validated and putative Tier1 SNVs and indel mutations detected by WGS; Table 8: Copy number variations in tumors from the discovery series analyzed by WGS; Table 9: Copy number alterations detected by SNP 6 arrays; Table 10: Summary of All Genetic Aberrations Found by WGS; Table 11: Counts of structural variations detected by CREST in samples analyzed by WGS; and Table 12: Statistical analysis of chromothripsis status within 11q13.1. (ZIP 525 kb)
This file contains Supplementary Tables 13-18 and comprises Table 13: Validated and uncovered fusion builder predictions from WGS; Table 14: Primers used for SV validation; Table 15: iFISH probes; Table 16a: C11orf95-RELA fusions predicted by RNA-seq; Table 16b: Fusions involving C11orf95 but not RELA; Table 16c: Additional fusions not involving C11orf95; Table 17a: Significantly activated transcription regulators identified by Ingenuity Pathway Analysis; Table 17b: Significant networks identified by analysis of differential gene expression data or RNASeq data & highlighting NF-kB; Table 18a: Pathway analysis of genes upregulated by RELAWT in NSCs and Table 18b: Pathway analysis of genes upregulated by RELAFUS1 in NSCs (ZIP 107 kb)
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Parker, M., Mohankumar, K., Punchihewa, C. et al. C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma. Nature 506, 451–455 (2014). https://doi.org/10.1038/nature13109
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