Identification of Druggable Cancer Driver Genes Amplified across TCGA Datasets

Abstract

The Cancer Genome Atlas (TCGA) projects have advanced our understanding of the driver mutations, genetic backgrounds, and key pathways activated across cancer types. Analysis of TCGA datasets have mostly focused on somatic mutations and translocations, with less emphasis placed on gene amplifications. Here we describe a bioinformatics screening strategy to identify putative cancer driver genes amplified across TCGA datasets. We carried out GISTIC2 analysis of TCGA datasets spanning 14 cancer subtypes and identified 461 genes that were amplified in two or more datasets. The list was narrowed to 73 cancer-associated genes with potential “druggable” properties. The majority of the genes were localized to 14 amplicons spread across the genome. To identify potential cancer driver genes, we analyzed gene copy number and mRNA expression data from individual patient samples and identified 40 putative cancer driver genes linked to diverse oncogenic processes. Oncogenic activity was further validated by siRNA/shRNA knockdown and by referencing the Project Achilles datasets. The amplified genes represented a number of gene families, including epigenetic regulators, cell cycle-associated genes, DNA damage response/repair genes, metabolic regulators, and genes linked to the Wnt, Notch, Hedgehog, JAK/STAT, NF-KB and MAPK signaling pathways. Among the 40 putative driver genes were known driver genes, such as EGFR, ERBB2 and PIK3CA. Wild-type KRAS was amplified in several cancer types, and KRAS-amplified cancer cell lines were most sensitive to KRAS shRNA, suggesting that KRAS amplification was an independent oncogenic event. A number of MAP kinase adapters were co-amplified with their receptor tyrosine kinases, such as the FGFR adapter FRS2 and the EGFR family adapter GRB7. The ubiquitin-like ligase DCUN1D1 and the histone methyltransferase NSD3 were also identified as novel putative cancer driver genes. We discuss the patient tailoring implications for existing cancer drug targets and we further discuss potential novel opportunities for drug discovery efforts.

The Ubiquitin-associated (UBA) Domain of SCCRO/DCUN1D1 Protein Serves as a Feedback Regulator of Biochemical and Oncogenic Activity

“…We have shown previously that increased neddylation activity resulting from overexpression of SCCRO promotes oncogenesis in vitro and in vivo (30). In primary tumors, the oncogenic activity of SCCRO is promoted by amplification that is present in many types of cancers, including lung, ovarian, head and neck, and esophageal cancers (35)(36)(37). Interestingly, we found that transgenic expression of UBA domain mutants of SCCRO was more oncogenic than that of wild-type SCCRO.…”

Mutation and Transcriptional Profiling of Formalin-Fixed Paraffin Embedded Specimens as Companion Methods to Immunohistochemistry for Determining Therapeutic Targets in Oropharyngeal Squamous Cell Carcinoma (OPSCC): A Pilot of Proof of Principle

“…However, these technologies have had little impact on standard methods for diagnosis and treatment of HNSCC and many other types of cancer with one or more known mutational or copy number drivers. Despite extensive literature of differential gene expression profiles, mutations and copy number abnormalities in head and neck tumors that could potentially impact future clinical applications, little other than HPV status is done routinely upon diagnosis [7,10,11,13,15,24,32,[35][36][37][38][39][40][41][42][43][44][45][46][47]. A main factor contributing to this lack of progress is that no clear directives or actionable guidelines have been adopted for molecularly profiling HNSCCs.…”

“…All SNVs were assessed for likelihood of clinical relevance based on published literature and public databases including dbSNP, 1000 genome, TCGA and COSMIC [22][23][24]. There were a combined 170 variants (162 HPV-, (purple bars) in the HPV-negative specimens.…”

H3K36 Methyltransferases as Cancer Drug Targets: Rationale and Perspectives for Inhibitor Development

“…In prostate cancer for example, the EZH2/NSD2 axis confers increased cell proliferation, migration, invasion, stem cell-like properties and tumor growth in a mouse xenograft model [66]. Further studies in prostate cancer have shown that NSD2 acts as a co-activator with NF-κB and androgen receptor [67,68], and regulates the epithelial to mesenchymal transition by dimethylating H3K36 at the TWIST1 locus and activating TWIST1 expression [69].NSD3: frequently overexpressed in diverse tumor types NSD3, also known as WHSC1L1, is overexpressed in cancer [70] and catalyzes mono-and di-methylation at H3K36 in vitro [71]. In cells NSD3 functions as a transcriptional activator, but NSD3's KMTase activity may contribute only partially to its geneactivating role.…”

“…NSD3 undergoes copy number amplification in 21% of lung squamous cell carcinomas and 15% of breast invasive carcinomas, with a high correlation between copy number and mRNA expression, suggesting that NSD3 may function as an oncogenic driver [70]. Indeed, RNAi knockdown of NSD3 in non-small-cell lung cancer, colorectal cancer, bladder cancer and breast cancer cell lines with NSD3 overexpression causes reduced cell proliferation due to increased apoptosis or cell cycle arrest in the various cancer cell lines [70,75,76]. The breast epithelial cell line MCF10A is normally highly dependent on growth factors and forms small acinar-like structures in 3D Matrigel culture, but these cells can be transformed by expression of NSD3, which confers growth factor-independent proliferation, colony-forming ability in soft agar and expanded and disorganized growth in 3D culture [76].…”