A powerful way to discover key genes playing causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here, we report high-resolution analyses of somatic copy-number alterations (SCNAs) from 3131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across multiple cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several gene families are enriched among these regions of focal SCNA, including the BCL2 family of apoptosis regulators and the NF-κB pathway. We show that cancer cells harboring amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend upon expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in multiple cancer types.

Although B-Raf V600E is the most common somatic mutation in papillary thyroid carcinoma (PTC), how it induces tumor aggressiveness is not fully understood. Using gene set enrichment analysis and in vitro and in vivo functional studies, we identified and validated a B-Raf V600E gene set signature associated with tumor progression in PTCs. An independent cohort of B-Raf V600E -positive PTCs showed significantly higher expression levels of many extracellular matrix genes compared with controls. We performed extensive in vitro and in vivo validations on thrombospondin-1 (TSP-1), because it has been previously shown to be important in the regulation of tumor angiogenesis and metastasis and is present in abundance in tumor stroma. Knockdown of B-Raf V600E resulted in TSP-1 downregulation and a reduction of adhesion and migration/invasion of human thyroid cancer cells. Knockdown of TSP-1 resulted in a similar phenotype. B-Raf V600E cells in which either B-Raf V600E or TSP-1 were knocked down were implanted orthotopically into the thyroids of immunocompromised mice, resulting in significant reduction in tumor size and fewer pulmonary metastases from the primary carcinoma as compared with the control cells. Treatment of orthotopic thyroid tumors, initiated 1 week after tumor cell implantation with PLX4720, an orally available selective inhibitor of B-Raf V600E , caused a significant tumor growth delay and decreased distant metastases, without evidence of toxicity. In conclusion, B-Raf V600E plays an important role in PTC progression through genes (i.e., TSP-1) important in tumor invasion and metastasis. Testing of a patient's thyroid cancer for B-Raf V600E will yield important information about potential tumor aggressiveness and also allow for future use of targeted therapies with selective B-Raf V600E inhibitors, such as PLX4720. extracellular matrix | metastasis | papillary thyroid cancer | tumor microenvironment | cell invasion P apillary thyroid cancer (PTC), with its incidence increasing by almost 5% each year, currently ranks as the eighth most common malignancy diagnosed in women (1). Neck recurrences alone are responsible for a third of thyroid cancer-related deaths. There is no effective treatment for radioiodine-resistant metastatic disease; the 10-year survival rate in these cases is only 10% (2). Molecular understanding of the aggressive clinical behavior of this subset of patients is needed to develop new therapeutic options.

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