Prognostic and predictive value of common mutations for treatment response and survival in patients with metastatic colorectal cancer.

BACKGROUND: We address the prognostic and predictive value of KRAS, PIK3CA and BRAF mutations for clinical outcomes in response to active agents in the treatment of metastatic colorectal cancer (mCRC). METHODS: We determined KRAS, BRAF and PIK3CA mutations in tumours from 168 patients treated for mCRC at two institutions. All patients received 5-FU-based first-line chemotherapy and treatment outcome was analysed retrospectively. RESULTS: KRAS, BRAF and PIK3CA mutations were present in 62 (37%), 13 (8%) and 26 (15%) cases, respectively. Multivariate analysis uncovered BRAF mutation as an independent prognostic factor for decreased survival (hazard ratio (HR) 4.0, 95% confidence interval (CI) 2.1-7.6). In addition, patients with BRAF-mutant tumours had significantly lower progression-free survival (PFS: HR 4.0, 95% CI 2.2-7.4) than those whose tumors that carried wild-type BRAF. Among 92 patients treated using chemotherapy and cetuximab as salvage therapy, KRAS mutation was associated with lack of response (P=0.002) and shorter PFS (P=0.09). BRAF (P=0.0005) and PIK3CA (P=0.01) mutations also predicted reduced PFS in response to cetuximab salvage therapy. CONCLUSIONS: These results underscore the potential of mutational profiling to identify CRCs with different natural histories or treatment responses. The adverse significance of BRAF mutation should inform patient selection and stratification in clinical trials.

The lore of the RINGs: substrate recognition and catalysis by ubiquitin ligases.

Recently, many new examples of E3 ubiquitin ligases or E3 enzymes have been found to regulate a host of cellular processes. These E3 enzymes direct the formation of multiubiquitin chains on specific protein substrates, and - typically - the subsequent destruction of those proteins. We discuss how the modular architecture of E3 enzymes connects one of two distinct classes of catalytic domains to a wide range of substrate-binding domains. In one catalytic class, a HECT domain transfers ubiquitin directly to substrate bound to a non-catalytic domain. Members of the other catalytic class, found in the SCF, VBC and APC complexes, use a RING finger domain to facilitate ubiquitylation. The separable substrate-recognition domains of E3 enzymes provides a flexible means of linking a conserved ubiquitylation function to potentially thousands of ubiquitylated substrates in eukaryotic cells.

Binding of 14-3-3 proteins to the protein kinase Raf and effects on its activation.

To identify proteins that may participate in the activation of the protein kinase Raf, proteins that interact with Raf were selected in a two-hybrid screen. Two members of the 14-3-3 protein family were isolated that interacted with both the amino terminal regulatory regions of Raf and the kinase domain of Raf, but did not compete with the guanine nucleotide-binding protein Ras for binding to Raf. 14-3-3 proteins associated with Raf in mammalian cells and accompanied Raf to the membrane in the presence of activated Ras. In yeast cells expressing Raf and MEK, mammalian 14-3-3 beta or 14-3-3 zeta activated Raf to a similar extent as did expression of Ras. Therefore, 14-3-3 proteins may participate in or be required for the regulation of Raf function. These findings suggest a role for 14-3-3 proteins in Raf-mediated signal transduction.

Synthetic chimeric nucleases function for efficient genome editing.

CRISPR-Cas systems have revolutionized genome editing across a broad range of biotechnological endeavors. Many CRISPR-Cas nucleases have been identified and engineered for improved capabilities. Given the modular structure of such enzymes, we hypothesized that engineering chimeric sequences would generate non-natural variants that span the kinetic parameter landscape, and thus provide for the rapid selection of nucleases fit for a particular editing system. Here, we design a chimeric Cas12a-type library with approximately 560 synthetic chimeras, and select several functional variants. We demonstrate that certain nuclease domains can be recombined across distantly related nuclease templates to produce variants that function in bacteria, yeast, and human cell lines. We further characterize selected chimeric nucleases and find that they have different protospacer adjacent motif (PAM) preferences and the M44 chimera has higher specificity relative to wild-type (WT) sequences. This demonstration opens up the possibility of generating nuclease sequences with implications across biotechnology.

A 41-kilodalton protein is a potential substrate for the p210bcr-abl protein-tyrosine kinase in chronic myelogenous leukemia cells.

Chronic myelogenous leukemia (CML) is characterized by a translocation involving the c-abl protein-tyrosine kinase gene. A chimeric mRNA is formed containing sequences from a chromosome 22 gene (bcr) at its 5' end and all but the variable exon 1 of c-abl sequence. The product of this mRNA, p210bcr-abl, has constitutively high protein-tyrosine kinase activity. We examined K562 cells and other lines established from CML patients for the presence of phosphotyrosine (P-Tyr)-containing proteins which might be p210bcr-abl substrates. Two-dimensional gel separation of 32P-labeled proteins followed by phosphoamino acid analysis of 25 phosphoproteins, which comprised the major alkali-stable phosphoproteins, indicated that three related proteins of 41 kDa are the most prominent P-Tyr-containing proteins detected by this method. The 41-kDa phosphoproteins are found in two other CML lines that we examined but not in lines of similar lineage isolated from patients with distinct leukemic disease. A protein that comigrates with the major form of pp41 (pp41A) and contains P-Tyr is also found in murine fibroblasts and B-lymphoid cells transformed by Abelson murine leukemia virus, which encodes the v-abl protein, and in platelet-derived growth factor-treated fibroblasts, in which it has been described previously. We analyzed three pairs of Epstein-Barr virus-immortalized B-cell lines from individual CML patients and found that only the lines in which active p210bcr-abl was present contained detectable pp41. We also performed immunoblotting with anti-P-Tyr antibodies on the same CML cell lines and detected at least four other putative substrates of p210bcr-abl, which were undetected with use of the two-dimensional gel technique.

Transformation of NIH 3T3 cells by cotransfection with c-src and nuclear oncogenes.

pp60c-src, the cellular homolog of the Rous sarcoma virus transforming protein, does not completely transform cells even when present at high levels, but has been shown to be involved in polyomavirus-induced transformation when activated by polyomavirus middle T (pmt)-antigen binding. Here we show that cotransfection, but not solo transfection, of expression plasmids for c-src and either adenovirus E1A, v-myc, c-myc, or the 5' half of polyomavirus large T (pltN) antigen into NIH 3T3 cells induces anchorage-independent growth, enhanced focus formation, and, for pltN cotransfection, tumorigenicity in adult NFS mice. Enhancement of transformation was not observed with polyomavirus small t (pst) antigen. Cotransfection of c-src with pltN induced modification of pp60c-src that altered its electrophoretic mobility and in vivo phosphorylation state and stimulated its in vitro kinase activity. Similar alterations were not seen after c-src-E1A cotransfection, suggesting that at least two different mechanisms of enhancement are involved.

A Consensus View of ESCRT-Mediated Human Immunodeficiency Virus Type 1 Abscission.

The strong dependence of retroviruses, such as human immunodeficiency virus type 1 (HIV-1), on host cell factors is no more apparent than when the endosomal sorting complex required for transport (ESCRT) machinery is purposely disengaged. The resulting potent inhibition of retrovirus release underscores the importance of understanding fundamental structure-function relationships at the ESCRT-HIV-1 interface. Recent studies utilizing advanced imaging technologies have helped clarify these relationships, overcoming hurdles to provide a range of potential models for ESCRT-mediated virus abscission. Here, we discuss these models in the context of prior work detailing ESCRT machinery and the HIV-1 release process. To provide a template for further refinement, we propose a new working model for ESCRT-mediated HIV-1 release that reconciles disparate and seemingly conflicting studies.

Cells induced to express a human immunodeficiency virus type 1 envelope gene mutant inhibit the spread of wild-type virus.

The feasibility of using a trans-dominant interfering human immunodeficiency virus type 1 (HIV-1) envelope mutant for inducible gene therapy of HIV infection was investigated. Genes encoding wild-type or mutant glycoproteins were introduced into CD4+ cells, where they were stably maintained but not expressed until induced. Envelope (env) gene expression was dependent upon the viral regulatory protein Tat. Induction of the mutant env resulted in resistance to cytopathic effects mediated by wild-type envelope and decreased infectious vector virus production. When cells containing the mutant env gene were infected with wild-type virus, viral spread was inhibited. The fact that maintenance of the env gene was stable over time suggests that inducible gene therapy using the dominantly interfering env mutant may be a feasible approach to slowing the progression of HIV-1 disease.

Novel GABA analogues as hypotensive agents.

The actions of four analogues of gamma-aminobutyric acid (GABA) on blood pressure and heart rate were measured in the cat after intracerebroventricular administration. These compounds were previously found to inhibit binding to GABAA receptors of neuronal membranes from the CNS of the rat. Each of the drugs, together with GABA, produced an average maximum reduction in blood pressure of 27.63% +/- 12.5. However, aminoethanethiosulfonic acid (AETS) was the most potent (ED50 = 2.24 X 10(-10) mol/kg) of the drugs, followed by 5-phenyl-2-pyrrole propionic acid (PPP), urocanic acid (UCA), m-aminobenzoic acid (MABA) and GABA. None of the compounds produced a significant effect on heart rate. The fact that these analogues mimicked the action of GABA on the cardiovascular system of the cat and that they were able to inhibit binding to GABAA receptors, indicates that they may be GABA agonists.

Identification of conserved residues in the human immunodeficiency virus type 1 principal neutralizing determinant that are involved in fusion.

The principal neutralizing determinant of the human immunodeficiency virus type 1 (HIV-1) is located within the V3 loop of the surface glycoprotein gp120. Recently a mutational approach was used to demonstrate that the tip of the V3 loop is involved in cell fusion mediated by the HIV-1 envelope glycoproteins. Here these results are extended by introducing seven additional single amino acid mutations in the V3 loop. Mutations at highly conserved amino acids in the left stem, tip, and right stem of the V3 loop blocked or greatly reduced cell fusion without affecting envelope glycoprotein processing, transport, or binding to the CD4 receptor molecule. This study further characterizes the involvement of the V3 loop in cell fusion mediated by the HIV-1 envelope glycoproteins and identifies residues involved in the fusion reaction.

Studies on the role of the V3 loop in human immunodeficiency virus type 1 envelope glycoprotein function.

Mutations within the principal neutralizing determinant (the V3 loop) of the HIV-1 surface envelope glycoprotein gp120 block or greatly reduce the ability of the HIV-1 envelope glycoprotein to induce cell fusion in CD4+ HeLa T4 cells while keeping its CD4 binding ability. However, when either cysteine or both cysteines forming the V3 disulfide bridge were mutated, the resultant glycoprotein could not mediate cell fusion, undergo proteolytic processing, or bind CD4. To investigate the role that the V3 loop plays in gp160 processing and CD4 binding, we deleted the entire V3 loop region of the HIV-1 env gene. The resultant glycoprotein could not mediate cell fusion in the HeLa T4 cell line and no proteolytic processing of gp160 or CD4 binding could be detected. To test whether any domain of the V3 loop is involved in attaining the proper envelope glycoprotein conformation required for proteolytic processing and CD4 binding, we introduced a series of deletions into the coding region of the V3 loop. Most of the residues within the V3 loop could be removed while retaining gp160 processing and CD4 binding. Our results indicate that the cysteines that form the V3 loop or the disulfide bond itself are important for proper envelope glycoprotein folding and processing. Because many of the mutants constructed in this study do not contain the type-specific neutralizing determinant of HIV-1, they may be potential reagents to bind group-specific neutralizing antibodies or to elicit a group-specific neutralizing response against HIV-1.

Analysis of HIV-1 envelope mutants and pseudotyping of replication-defective HIV-1 vectors by genetic complementation.

Infectious HIV-1 particles containing replication-defective vectors that express the hygromycin B phosphotransferase gene were generated by transient complementation in COS-1 cells. A defective vector dependent only on trans-complementation with an env gene and a small vector containing a deletion of almost all of the trans region were used to examine pseudotyping of HIV-1 by an amphotropic murine retrovirus. Although pseudotyping by the heterologous envelope glycoprotein occurred with efficiency, no pseudotyping at the RNA level was observed. Genetic complementation was used to rapidly analyze the effect of env mutations in the V3, proteolytic processing site, fusion domain, and cytoplasmic tail on viral infectivity. Mutations decreasing syncytium formation usually also lowered infectivity. However, a mutation in the cytoplasmic tail and a separate mutation adjacent to the fusion domain dramatically decreased viral particle infectivity but did not appreciably decrease envelope glycoprotein-mediated cell-to-cell fusion. These results may indicate that these regions of the transmembrane peptide are necessary for acquisition of envelope glycoprotein by budding virus particles or for virus entry.

Differential tolerance to pentobarbital in rats bred for differences in alcohol sensitivity.

Two lines of rats bred for differences in motor impairment following alcohol treatment were also found to be differentially affected by sodium pentobarbital in three experiments. The most affected (MA) animals, bred for sensitivity to alcohol, showed a decrement in stabilimeter activity at doses of 8 mg and 16 mg pentobarbital per kg body weight. The least affected (LA) animals, bred for insensivity to alcohol, were affected only by the higher dose, at which the resulting impairment was still less than that of the MA group. This finding was partially replicated in a second study designed to test the possibility of an activating effect of pentobarbital on LA animals at 8 mg/kg. In a final study, MA animals were more likely to lose their righting reflex than LA animals at a dose of 18 mg/kg, and 'slept' longer following this dose. These results indicate that the differential sensitivity shown by these animals is not specific to alcohol, but can be generalized to another depressant.

Dose-response effects of alcohol upon rat strains bred for differences in reactivity to alcohol.

Two rat strains, designated LA and MA, selectively bred for differential impairment of motor activity following an injection of alcohol, were tested in stabilmeters and compared over a range of ethanol doses. As expected, increasing doses of ethanol produced progressively greater activity decrements in both strains; however, the same dose of ethanol induced a more pronounced decrement in the MA strain than in LA strain at all doses. At the highest alcohol dose (2.25 g/kg), the LA animals were twice as active as were the MA strain at the 1.5 g/kg dose. This strain difference in impairment was evident within 3 min postinjection and remained throughout the 30 min test session. The results are discussed in terms of differential neural and behavioral toelrance to ethanol in the two strains.

Alcoholism and the Rorschach test.

A review of studies in which the Rorschach Test was administered to alcoholics, and of studies of the effects of experimental intoxication upon Rorschach performances, reveals recurrent attempts to elucidate alcoholic "signs" and characteristic alcoholic perceptual style.

Alcoholism and schizophrenia: the search for perspectives. A review.

The historical search for meaningful relationships between alcoholism and schizophrenia is reviewed. The results are considered inconclusive and further lines of research are suggested.

Polydipsic and home-cage fluid choices: the effects of sweetening.

When rats were offered a choice of alcohol, butanediol and noncaloric saccharin solutions in a home-cage situation, consumption of saccharin dominated fluid choice, whether or not the animals were deprived of food.

Selective breeding of rats for differences in reactivity to alcohol. An approach to an animal model of alcoholism. I. General procedures.

Strains of rats are being developed which have distinct responses in spontaneous locomotor activity to a subhypnotic dose of alcohol. The purpose is to produce one strain in which the injection of a standard dose of alcohol will result in objectively measurable intoxication and a second in which an identical dose will result in virtually no effect.

Selective breeding of rats for differences in reactivity to alcohol. An approach to an animal model of alcoholism. II. Behavioral measures.

Two lines of rats have been bred which differ in sensitivity to alcohol over a range of doses, but the difference is not reflected in blood alcohol concentration, alcohol intake or selection. The two lines respond similarly on tests of emotionality; however, differences in running-wheel activity suggest differences in neural apparatus.

Selective breeding of rats for differences in reactivity to alcohol: an approach to an animal model of alcoholism. III. Some physical and behavioral measures.

The results of selective breeding for differential impairment of motor activity after alcohol injection is shown for the first 13 generations of the LA and MA rat strains. In F13 rats, the mean decrement of activity after 1.5 g ethanol per kg i/p. is 90% for MA rats and 42% for LA rats, the strain difference significant at a "p" of 1.8 x 10(-11). Blood alcohol levels, body weight, litter size, organ weights and induction of taste aversion to alcohol and lithium chloride are described for these strains in various of the generations. Although strain differences are apparent on some of these measures, none are of a degree or kind which offers more than a speculative explanation of the large difference between the strains in their central nervous system sensitivity to alcohol.