Statistical inference for simultaneous clustering of gene expression data

Current methods for analysis of gene expression data are mostly based on clustering and classification of either genes or samples. We offer support for the idea that more complex patterns can be identified in the data if genes and samples are considered simultaneously. We formalize the approach and propose a statistical framework for two-way clustering. A simultaneous clustering parameter is defined as a function theta=Phi(P) of the true data generating distribution P, and an estimate is obtained by applying this function to the empirical distribution P(n). We illustrate that a wide range of clustering procedures, including generalized hierarchical methods, can be defined as parameters which are compositions of individual mappings for clustering patients and genes. This framework allows one to assess classical properties of clustering methods, such as consistency, and to formally study statistical inference regarding the clustering parameter. We present results of simulations designed to assess the asymptotic validity of different bootstrap methods for estimating the distribution of Phi(P(n)). The method is illustrated on a publicly available data set.     

Signalling shortcuts: cell-surface receptors in the nucleus?

Do cell-surface growth-factor receptors and their ligands accumulate in the nucleoplasm under physiological conditions? And, if so, how do they get there and what function do they serve in this location? Recent advances have provided tantalizing hints to the answers to these questions, and hold the key to identifying a new mode of signal transduction.     

Stimulation of glucose transport by semicarbazide-sensitive amine oxidase activity in adipocytes from diabetic rats

Semicarbazide-sensitive amine oxidase (SSAO) is highly expressed in adipose cells, and substrates of SSAO such as benzylamine in combination with low concentrations of vanadate strongly stimulate glucose transport and GLUT4 recruitment in mouse 3T3-L1 adipocytes and in isolated rat adipocytes. Here we examined whether this combination of molecules also stimulates glucose transport in adipocytes from streptozotocin-induced diabetic rats and from Goto-Kakizaki diabetic rats. As previously reported, adipocytes obtained from streptozotocin-induced diabetic rats, showed a reduced stimulation of glucose transport in response to insulin. Under these conditions, the combination of benzylamine and vanadate caused a marked stimulation of glucose transport that was similar to the stimulation detected in control adipocytes. Adipocytes isolated from Goto-Kakizaki diabetic rats also showed a defective response to insulin; however, acute incubation in the presence of benzylamine and vanadate stimulated glucose transport in these cells to the same extent than in adipocytes from non-diabetic rats. These data indicate that adipocytes obtained from two different models of animal diabetes do not show resistance to the activation of glucose transport by SSAO activity, which is in contrast to the well reported resistance to insulin action. It seems to suggest that SSAO activity in combination with vanadate triggers a glucose transport-activating intracellular pathway that remains intact in the diabetic state. Further, our data support the view that the combination of benzylamine and vanadate could be an effective therapy in diabetes.     

Effects of a β3-adrenergic agonist on the immune response in diet-induced (cafeteria) obese animals

Molecules with affinity for beta3-adrenoceptors are not only effective anti-obesity agents in rodent models, but may play a role in the regulation of the immune response. The aim of the current investigation was to analyse the effects of trecadrine on the immune response in diet-induced (cafeteria) obese rats. Male Wistar rats were divided into 2 groups, the control group (C, n=9) was fed with the standard pelleted chow laboratory diet, while the other group was fed with a high-fat (cafeteria) diet. Cafeteria-fed rats were divided into two new subgroups (n=9 each), which received either i.p. saline (obese, O) or trecadrine (1mg/kg/day) (obese+trecadrine, O+T) daily for 5 weeks. Lymphocyte subpopulations and the proliferative response were determined by validated procedures. The administration of trecadrine was able to prevent the onset of obesity in cafeteria-fed rats. Trecadrine-treatment to obese animals appeared to improve the number of lymphocyte subpopulations (CD4+ and CD8+) as compared to those animals only receiving the high-fat diet, being the values of the trecadrine-treated animals on the high-fat diet similar to the control rats. However, the lymphoproliferative response when stimulated with several mitogens was markedly reduced by the cafeteria intake and was further decreased by the beta3-adrenergic administration. The spleen mRNA expression level of UCP2, PPARgamma and Ob-Rb were not affected by the trecadrine treatment. Summing up, at the immune system level, trecadrine administration increased the proportion of CD4+ spleen lymphocytes, although it was not able to restore the lymphocyte proliferative response which was depressed.     

Isolation,structural characterization,and antiviral activity of positional isomers of monopegylated interferon alpha-2a (PEGASYS)

Interferon alpha-2a plays an essential role in the treatment of chronic hepatitis C, but it is limited in its efficacy by the short in vivo half-life. To improve the half-life and efficacy, interferon alpha-2a is conjugated with a 40-kDa branched polyethylene glycol moiety (PEG-IFN, PEGASYS). From this preparation the positional PEG-IFN isomers were isolated and characterized by different analytical methods and antiviral assay. Two chromatographic steps were used to separate and purify nine isomers. The analytical methods IE-HPLC, RP-HPLC, SE-HPLC, SDS-PAGE, and MALDI-TOF MS indicated that each of these nine isomers is conjugated to the branched polyethylene glycol chain at a specific lysine. No isomer with a modification at the amino terminus was observed. All positional isomers induced viral protection of MDBK cells in the antiviral assay. When comparing the quantitative potency of the individual isomers with the whole mixture of PEG-IFN, significant differences in the specific activities were observed: PEG-Lys(31) and PEG-Lys(134) showed higher activities than the mixture, PEG-Lys(164) was equal to the mixture, whereas the activities of PEG-Lys(49), PEG-Lys(70), PEG-Lys(83), PEG-Lys(112), PEG-Lys(121), and PEG-Lys(131) were lower.     

Basal fat oxidation and after a peak oxygen consumption test in obese women with a beta2 adrenoceptor gene polymorphism

The Glu27Glu genotype in the beta2-adrenergic receptor (ADRB2) has been linked to a higher fat deposition and obesity in females. Also, in our population, it has been described that physically active women carrying the Glu allele had a higher BMI as compared to non-carriers performing the same level of activity. Since exercise may counterbalance a gene predisposition to obesity, we tested the hypothesis of a potential different metabolic response among ADRB2 Gln27Gln versus Glu27Glu obese women when submitted to a peak oxygen consumption test on a treadmill. In our study, 10 obese women with the Gln27Gln genotype were compared to 9 matched obese women bearing the Glu27Glu genotype. The ADRB2 polymorphism was identified by PCR-RFLP, fat oxidation was determined by indirect calorimetry and blood measurements were carried out following conventional procedures. The ADRB2 Glu27Glu subjects had lower plasma glycerol levels (P = 0.026), while plasma triglycerides (P <0.001) and the insulin:glucose ratio were higher (P = 0.046) as compared to the Gln27Gln group along the peak oxygen consumption trial intervention. There was a significantly lower fat oxidation (P = 0.024) in the Glu27Glu obese women during the recovery compared to Gln27Gln obese individuals. These data suggest that exercise would not benefit equally the two ADRB2 polymorphism homozygous groups, since both lipolysis and fat oxidation promoted by a peak oxygen consumption test appear to be blunted in the polymorphic Glu27Glu obese group.