Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although the MYC oncogene has been implicated in cancer, a systematic assessment of alterations of MYC, related transcription factors, and co-regulatory proteins, forming the proximal MYC network (PMN), across human cancers is lacking. Using computational approaches, we define genomic and proteomic features associated with MYC and the PMN across the 33 cancers of The Cancer Genome Atlas. Pan-cancer, 28% of all samples had at least one of the MYC paralogs amplified. In contrast, the MYC antagonists MGA and MNT were the most frequently mutated or deleted members, proposing a role as tumor suppressors. MYC alterations were mutually exclusive with PIK3CA, PTEN, APC, or BRAF alterations, suggesting that MYC is a distinct oncogenic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such as immune response and growth factor signaling; chromatin, translation, and DNA replication/repair were conserved pan-cancer. This analysis reveals insights into MYC biology and is a reference for biomarkers and therapeutics for cancers with alterations of MYC or the PMN. We present a computational study determining the frequency and extent of alterations of the MYC network across the 33 human cancers of TCGA. These data, together with MYC, positively correlated pathways as well as mutually exclusive cancer genes, will be a resource for understanding MYC-driven cancers and designing of therapeutics

Pistachio

Within the Anacardiaceae family, the genus Pistacia L. consists of 11 or more species of which one, P. vera L. or pistachio, is commercially grown for its edible nut. Other Pistacia species are used as rootstocks or used in agroforestry. The cultivated pistachio is native to the Middle East and Central Asia. The center of diversity for wild P. vera is in Northern Iran and Southern Turkmenistan as well as parts of Afghanistan. Iran, the USA, Turkey, and Syria are the main pistachio producing countries, contributing over 90% of the world production. Pistacia species are dioecious with several isolated reports of monoecious individuals. Extensive collections of pistachio cultivars and germplasm resources were assembled at several experimental stations in the middle-southern former Soviet republics during the 1950s and 1960s. Selections of native cultivars in Iran, Italy, Greece, Syria, Turkey, and Tunisia were made and are now conserved. The number of described male and female pistachio cultivars is rather limited, and they are conserved in a few gene banks. The California pistachio industry was started with the introduction of the Kerman cultivar. California pistachios are grown primarily on three rootstocks, two species and one interspecific hybrid from the Pistacia genus. Beside the Californian breeding program, the only organized breeding programs at present are located in Spain, Turkey, and Israel. The California breeding program was formerly focused on -precocity (early bearing), nut size, yield, split percentage, and early season harvest. Early season maturity is important to avoid navel orangeworm damage and to maximize the efficiency of harvest and processing facilities. Disease resistance, especially resistance to Alternaria alternata, has been a secondary objective in the program. Molecular markers have been used for genetic studies and determination of the origin of cultivars. While a number of molecular marker studies have been conducted, a molecular genetic marker map has not been constructed yet. © Springer Science+Business Media, LLC 2012. All rights reserved