The molecular pathogenesis of renal cell carcinoma (RCC) is poorly understood. Whole-genome and exome sequencing followed by innovative tumorgraft analyses (to accurately determine mutant allele ratios) identified several putative two-hit tumor suppressor genes including BAP1. BAP1, a nuclear deubiquitinase, is inactivated in 15% of clear-cell RCCs. BAP1 cofractionates with and binds to HCF-1 in tumorgrafts. Mutations disrupting the HCF-1 binding motif impair BAP1-mediated suppression of cell proliferation, but not H2AK119ub1 deubiquitination. BAP1 loss sensitizes RCC cells in vitro to genotoxic stress. Interestingly, BAP1 and PBRM1 mutations anticorrelate in tumors (P=3×10−5), and combined loss of BAP1 and PBRM1 in a few RCCs was associated with rhabdoid features (q=0.0007). BAP1 and PBRM1 regulate seemingly different gene expression programs, and BAP1 loss was associated with high tumor grade (q=0.0005). Our results establish the foundation for an integrated pathological and molecular genetic classification of RCC, paving the way for subtype-specific treatments exploiting genetic vulnerabilities.

SUMMARY Background Clear cell renal cell carcinoma (ccRCC) displays a variety of clinical behaviors. However, the molecular genetic events driving these behaviors are unknown. We discovered that BAP1 is mutated in approximately 15% of ccRCC and that BAP1 and PBRM1 mutations are largely mutually exclusive. The aim of this study was to investigate the clinicopathological significance of these molecular subtypes and to determine whether patients with BAP1-mutant and PBRM1-mutant tumors had different overall survival. Methods In this retrospective analysis, we assessed 145 patients with primary clear-cell renal-cell carcinoma and defined PBRM1 and BAP1 mutation status from the University of Texas Southwestern Medical Center (UTSW), TX, USA, between 1998 and 2011. We classified patients into those with BAP1-mutant tumors and those with tumors exclusively mutated for PBRM1 (PBRM1-mutant). We used a second independent cohort (n=327) from The Cancer Genome Atlas (TCGA) for validation. In both cohorts, more than 80% of patients had localized or locoregional disease at presentation. Overall both cohorts were similar, although the TCGA had more patients with metastatic and higher-grade disease, and more TCGA patients presented before molecularly targeted therapies became available. Findings The median overall survival in the UTSW cohort was significantly shorter for patients with BAP1-mutant tumors (4.6 years; 95% CI 2.1-7.2), than for patients with PBRM1-mutant tumors (10.6 years; 9.8-11.5), corresponding to a HR of 2.7 (95% CI 0.99-7.6, p=0.044). Median overall survival in the TCGA cohort was 1.9 years (95% CI 0.6-3.3) for patients with BAP1-mutant tumors and 5.4 years (4.0-6.8) for those with PBRM1-mutant tumors. A HR similar to the UTSW cohort was noted in the TCGA cohort (2.8; 95% CI 1.4-5.9; p=0.004). Patients with mutations in both BAP1 and PBRM1, although a minority (three in UTSW cohort and four in TCGA cohort), had the worst overall survival (median 2.1 years, 95% CI 0.3-3.8, for the UTSW cohort, and 0.2 years, 0.0-1.2, for the TCGA cohort). Interpretation Our findings identify mutation-defined subtypes of ccRCC with distinct clinical outcomes, a high-risk BAP1-mutant group and a favorable PBRM1-mutant group. These data establish the basis for a molecular genetic classification of ccRCC that could influence treatment decisions in the future. The existence of different molecular subtypes with disparate outcomes should be considered in the design and evaluation of clinical studies. Funding Cancer Prevention and Research Institution of Texas and NCI.

Regulation of TFEB and V-ATPases by mTORC1TORC1 is a key regulator of cell growth in response to nutrients and acts at the surface of the late endosome. This study identifies V-ATPase genes as transcriptional targets of TORC1 and implicates the transcription factor TFEB as an important mediator of TORC1-dependent gene expression and TORC1-regulated endocytosis.

The pharmacological inhibition of general transcriptional regulators has the potential to block growth through targeting multiple tumorigenic signaling pathways simultaneously. Here, using an innovative cell-based screen, we identify a structurally unique small molecule (named JIB-04) which specifically inhibits the activity of the Jumonji family of histone demethylases in vitro, in cancer cells, and in tumors in vivo. Unlike known inhibitors, JIB-04 is not a competitive inhibitor of α-ketoglutarate. In cancer but not in patient-matched normal cells, JIB-04 alters a subset of transcriptional pathways and blocks viability. In mice, JIB-04 reduces tumor burden and prolongs survival. Importantly, we find that patients with breast tumors that overexpress Jumonji demethylases have significantly lower survival. Thus JIB-04, a novel inhibitor of Jumonji demethylases in vitro and in vivo, constitutes a unique potential therapeutic and research tool against cancer, and validates the use of unbiased cellular screens to discover chemical modulators with disease relevance.

Partial or total replacement of fish meal by a mixture of plant protein (PP) sources (corn gluten, wheat gluten, extruded peas, rapeseed meal and sweet white lupin) balanced with indispensable amino acids was examined in juvenile gilthead sea bream over the course of a 6-month growth trial. A diet with fish meal (FM) as the sole protein source was compared to diets with 50%, 75% and 100% of replacement (PP50, PP75, and PP100). The possible influence of diets on growth performance, plasma metabolites, gut integrity, liver structure, anti-oxidant and immune status was evaluated. Final body weight was progressively decreased with PP inclusion, but in PP50 and PP75-fed fish, feed efficiency (FE) was significantly improved and specific growth rates remained unchanged or slightly reduced in comparison to fish fed the FM diet. In fish fed PP100 diet, FE remained unchanged and feed intake and growth decreased dramatically. In this group of fish, liver fat deposition was also largely increased, enterocytes showed an increased number of lipidic vacuoles and/or deposition of protein droplets, and the submucosa of intestine was dilated/hypertrophied and infiltrated with eosinophilic granular cells. Plasma glucose levels did not differ among the four groups, but a significant and progressive decrease of plasma cholesterol and plasma protein levels was found with FM replacement. The glutathione redox status in blood and liver increased with the increase of PP content and this increment was statistically significant in the liver of the three PP-fed groups. Glutathione reductase and γ-glutamyl transferase were also enhanced by PP inclusion. Plasma lysozyme levels were not altered by the dietary treatment, but respiratory burst of head kidney leucocytes and plasma myeloperoxidase values were significantly increased in PP75 and PP100 fish, respectively. Complement (ACH50) was significantly increased in PP50 fed fish and decreased in PP75 and PP100 groups. As a general conclusion, substitution of FM by a mixture of PP sources exerted an anti-oxidative effect, compromised growth performance only at the 100% level, and decreased one of the immune defence mechanisms at above 75% level.