The pan-cancer analysis of whole genomes The expansion of whole-genome sequencing studies from individual ICGC and TCGA working groups presented the opportunity to undertake a meta-analysis of genomic features across tumour types. To achieve this, the PCAWG Consortium was established. A Technical Working Group implemented the informatics analyses by aggregating the raw sequencing data from different working groups that studied individual tumour types, aligning the sequences to the human genome and delivering a set of high-quality somatic mutation calls for downstream analysis (Extended Data Fig. 1). Given the recent meta-analysis

Summary The aberrant transcription factor EWS-FLI1 drives Ewing sarcoma yet its molecular function is incompletely understood. We find that EWS-FLI1 reprograms gene regulatory circuits in Ewing sarcoma by directly inducing or repressing enhancers. At GGAA repeat elements, which lack evolutionary conservation and regulatory potential in other cell types, EWS-FLI1 multimers induce chromatin opening and create de novo enhancers that physically interact with target promoters. Conversely, EWS-FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild type ETS transcription factors. These divergent chromatin-remodeling patterns repress tumor suppressors and mesenchymal lineage regulators, while activating oncogenes and new potential therapeutic targets, such as the kinase VRK1. Our findings demonstrate how EWS-FLI1 establishes an oncogenic regulatory program governing both tumor survival and differentiation.

Programmed cell death 1 ligand 1 (PD-L1, B7H1) is a cell-surface protein that suppresses the cytotoxic CD8+ T cell-mediated immune response. PD-L1 expression and its clinical relevance in sarcomas are not well understood. Therefore, we sought to measure RNA expression levels for PD-L1 in 38 clinically annotated osteosarcoma tumor samples, and aimed to determine if PD-L1 expression correlates with clinical features and tumor-infiltrating T-lymphocytes (TILs). Quantitative real-time RT-PCR for PD-L1 was optimized in 18 cell lines, of which 5 were osteosarcoma-derived. qRT-PCR results were validated via flow cytometry and immunohistochemistry (IHC) in select cell lines. Total RNA was isolated from 38 human osteosarcoma samples for qRT-PCR analysis. Clinical data were sorted and significance was determined by Student t-test. TILs were examined in patient samples by tissue microarray (TMA) hematoxylin-eosin (HE) staining. We confirmed the constitutive PD-L1 mRNA expression in cell lines by qRT-PCR, flow cytometry, and IHC. Across human osteosarcoma samples, PD-L1 mRNA gene expression ranged over four-log (>5000-fold difference). Relative expression levels were evaluated against clinical factors such as age/gender, metastasis, recurrence, chemotherapy, percent necrosis, and survival; no significant associations were identified. The presence of TILs was associated with high PD-L1 expression (R2=0.37, P=0.01). In summary, we developed an RNA-based assay to determine PD-L1 expression levels, and we show for the first time that high levels of PD-L1 are expressed in a subset of osteosarcoma, and PD-L1 expression is positively correlated with TILs. There are multiple agents targeting PD-1/PD-L1 in clinical development, and this may be a novel immunotherapeutic strategy for osteosarcoma clinical trials.

Understanding the biological pathways critical for common neurofibromatosis type 1 (NF1) peripheral nerve tumours is essential, as there is a lack of tumour biomarkers, prognostic factors and therapeutics. We used gene expression profiling to define transcriptional changes between primary normal Schwann cells (n = 10), NF1-derived primary benign neurofibroma Schwann cells (NFSCs) (n = 22), malignant peripheral nerve sheath tumour (MPNST) cell lines (n = 13), benign neurofibromas (NF) (n = 26) and MPNST (n = 6). Dermal and plexiform NFs were indistinguishable. A prominent theme in the analysis was aberrant differentiation. NFs repressed gene programs normally active in Schwann cell precursors and immature Schwann cells. MPNST signatures strongly differed; genes up-regulated in sarcomas were significantly enriched for genes activated in neural crest cells. We validated the differential expression of 82 genes including the neural crest transcription factor SOX9 and SOX9 predicted targets. SOX9 immunoreactivity was robust in NF and MPSNT tissue sections and targeting SOX9 – strongly expressed in NF1-related tumours – caused MPNST cell death. SOX9 is a biomarker of NF and MPNST, and possibly a therapeutic target in NF1.