SUMMARY Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole exome sequencing and DNA copy number analyses, and 196 HCC also by DNA methylation, RNA, miRNA, and proteomic expression. DNA sequencing and mutation analysis identified significantly mutated genes including LZTR1, EEF1A1, SF3B1, and SMARCA4. Significant alterations by mutation or down-regulation by hypermethylation in genes likely to result in HCC metabolic reprogramming (ALB, APOB, and CPS1) were observed. Integrative molecular HCC subtyping incorporating unsupervised clustering of five data platforms identified three subtypes, one of which was associated with poorer prognosis in three HCC cohorts. Integrated analyses enabled development of a p53 target gene expression signature correlating with poor survival. Potential therapeutic targets for which inhibitors exist include WNT signaling, MDM4, MET, VEGFA, MCL1, IDH1, TERT, and immune checkpoint proteins CTLA-4, PD-1, and PD-L1.

X-ray or NMR structures of proteins are often derived without their 1 Departments of Cellular and ligands, and even when the structure of a full complex is available, the area Molecular Pharmacology and of contact that is functionally and energetically significant may be a Medicine and 2Department of specialized subset of the geometric interface deduced from the spatial Pharmaceutical Chemistry University of California proximity between ligands. Thus, even after a structure is solved, it remains a major theoretical and experimental goal to localize protein San Francisco functional interfaces and understand the role of their constituent residues. CA 94143-0450, USAThe evolutionary trace method is a systematic, transparent and novel predictive technique that identifies active sites and functional interfaces in proteins with known structure. It is based on the extraction of functionally important residues from sequence conservation patterns in homologous proteins, and on their mapping onto the protein surface to generate clusters identifying functional interfaces. The SH2 and SH3 modular signaling domains and the DNA binding domain of the nuclear hormone receptors provide tests for the accuracy and validity of our method. In each case, the evolutionary trace delineates the functional epitope and identifies residues critical to binding specificity. Based on mutational evolutionary analysis and on the structural homology of protein families, this simple and versatile approach should help focus site-directed mutagenesis studies of structure-function relationships in macromolecules, as well as studies of specificity in molecular recognition. More generally, it provides an evolutionary perspective for judging the functional or structural role of each residue in a protein structure.

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based Critical Assessment of protein Function Annotation (CAFA) experiment. Fifty-four methods representing the state-of-the-art for protein function prediction were evaluated on a target set of 866 proteins from eleven organisms. Two findings stand out: (i) today’s best protein function prediction algorithms significantly outperformed widely-used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is significant need for improvement of currently available tools.

Physiological effects of ␤ adrenergic receptor (␤2AR) stimulation have been classically shown to result from G s -dependent adenylyl cyclase activation. Here we demonstrate a novel signaling mechanism wherein ␤-arrestins mediate ␤2AR signaling to extracellularsignal regulated kinases 1/2 (ERK 1/2) independent of G protein activation. Activation of ERK1/2 by the ␤2AR expressed in HEK-293 cells was resolved into two components dependent, respectively, on G s -G i /protein kinase A (PKA) or ␤-arrestins. G proteindependent activity was rapid, peaking within 2-5 min, was quite transient, was blocked by pertussis toxin (G i inhibitor) and H-89 (PKA inhibitor), and was insensitive to depletion of endogenous ␤-arrestins by siRNA. ␤-Arrestin-dependent activation was slower in onset (peak 5-10 min), less robust, but more sustained and showed little decrement over 30 min. It was insensitive to pertussis toxin and H-89 and sensitive to depletion of either ␤-arrestin1 or -2 by small interfering RNA. In G s knock-out mouse embryonic fibroblasts, wild-type ␤2AR recruited ␤-arrestin2-green fluorescent protein and activated pertussis toxin-insensitive ERK1/2. Furthermore, a novel ␤2AR mutant (␤2AR T68F,Y132G,Y219A or ␤2AR TYY ), rationally designed based on Evolutionary Trace analysis, was incapable of G protein activation but could recruit ␤-arrestins, undergo ␤-arrestin-dependent internalization, and activate ␤-arrestin-dependent ERK. Interestingly, overexpression of GRK5 or -6 increased mutant receptor phosphorylation and ␤-arrestin recruitment, led to the formation of stable receptor-␤-arrestin complexes on endosomes, and increased agonist-stimulated phospho-ERK1/2. In contrast, GRK2, membrane translocation of which requires G␤␥ release upon G protein activation, was ineffective unless it was constitutively targeted to the plasma membrane by a prenylation signal (CAAX). These findings demonstrate that the ␤2AR can signal to ERK via a GRK5/6-␤-arrestin-dependent pathway, which is independent of G protein coupling.The ␤2-adrenergic receptor (␤2AR) 4 is a well studied member of the large and diverse group of seven transmembrane receptors (7TMRs), which have been shown classically to exert their intracellular effects through G protein activation (1-3). Agonist stimulation of the ␤2AR leads to G s -mediated activation of adenylyl cyclase, resulting in the production of cAMP and subsequent downstream signaling events. Moreover, additional studies both in cultured cell lines and in vitro have demonstrated that, in response to agonist, the ␤2AR can undergo PKAdependent phosphorylation leading to activation of G i (a process referred to as G protein "switching"), thereby effectively changing the signaling specificity of the receptor (4).Cessation of agonist-activated ␤2AR-G s -mediated signaling occurs via recruitment of modulatory proteins, ␤-arrestins, to the cytoplasmic surface of the receptor, a process that is enhanced by receptor phosphorylation by G protein-coupled receptor kinases (GRKs) (5). ␤-arrestin binding physically pre...

The lysosomal degradation pathway of autophagy has a crucial role in defence against infection, neurodegenerative disorders, cancer and ageing. Accordingly, agents that induce autophagy may have broad therapeutic applications. One approach to developing such agents is to exploit autophagy manipulation strategies used by microbial virulence factors. Here we show that a peptide, Tat–beclin 1—derived from a region of the autophagy protein, beclin 1, which binds human immunodeficiency virus (HIV)-1 Nef—is a potent inducer of autophagy, and interacts with a newly identified negative regulator of autophagy, GAPR-1 (also called GLIPR2). Tat–beclin 1 decreases the accumulation of polyglutamine expansion protein aggregates and the replication of several pathogens (including HIV-1) in vitro, and reduces mortality in mice infected with chikungunya or West Nile virus. Thus, through the characterization of a domain of beclin 1 that interacts with HIV-1 Nef, we have developed an autophagy-inducing peptide that has potential efficacy in the treatment of human diseases.