Transcriptome classification reveals molecular subtypes in psoriasis

ABSTRACT: BACKGROUND: Psoriasis is an immune-mediated disease characterised by chronically elevated pro-inflammatory cytokine levels, leading to aberrant keratinocyte proliferation and differentiation. Although certain clinical phenotypes, such as plaque psoriasis, are well defined, it is currently unclear whether there are molecular subtypes that might impact on prognosis or treatment outcomes. RESULTS: We present a pipeline for patient stratification through a comprehensive analysis of gene expression in paired lesional and non-lesional psoriatic tissue samples, compared with controls, to establish differences in RNA expression patterns across all tissue types. Ensembles of decision tree predictors were employed to cluster psoriatic samples on the basis of gene expression patterns and reveal gene expression signatures that best discriminate molecular disease subtypes. This multi-stage procedure was applied to several published psoriasis studies and a comparison of gene expression patterns across datasets was performed. CONCLUSION: Overall, classification of psoriasis gene expression patterns revealed distinct molecular sub-groups within the clinical phenotype of plaque psoriasis. Enrichment for TGFb and ErbB signaling pathways, noted in one of the two psoriasis subgroups, suggested that this group may be more amenable to therapies targeting these pathways. Our study highlights the potential biological relevance of using ensemble decision tree predictors to determine molecular disease subtypes, in what may initially appear to be a homogenous clinical group. The R code used in this paper is available upon request.     

BECN1/Beclin 1 sorts cell-surface APP/amyloid β precursor protein for lysosomal degradation

The regulation of plasma membrane (PM)-localized transmembrane protein/receptor trafficking has critical implications for cell signaling, metabolism and survival. In this study, we investigated the role of BECN1 (Beclin 1) in the degradative trafficking of PM-associated APP (amyloid β precursor protein), whose metabolism to amyloid-β, an essential event in Alzheimer disease, is dependent on divergent PM trafficking pathways. We report a novel interaction between PM-associated APP and BECN1 that recruits macroautophagy/endosomal regulatory proteins PIK3C3 and UVRAG. We found that BECN1 promotes surface APP internalization and sorting predominantly to endosomes and endolysosomes. BECN1 also promotes the targeting of a smaller fraction of internalized APP to LC3-positive phagophores, suggesting a role for BECN1-dependent PM macroautophagy in APP degradation. Furthermore, BECN1 facilitates lysosomal degradation of surface APP and reduces the secretion of APP metabolites (soluble ectodomains, sAPP). The association between APP and BECN1 is dependent on the evolutionarily conserved domain (ECD) of BECN1 (amino acids 267–337). Deletion of a BECN1 ECD subregion (amino acids 285–299) did not impair BECN1- PIK3C3 interaction, PtdIns3K function or macroautophagy, but was sufficient to impair the APP-BECN1 interaction and BECN1's effects on surface APP internalization and degradation, resulting in increased secretion of sAPPs. Interestingly, both the BECN1-APP association and BECN1-dependent APP endocytosis and degradative trafficking were negatively regulated by active AKT. Our results further implicate phosphorylation of the BECN1 Ser295 residue in the inhibition of APP degradation by AKT. Our studies reveal a novel function for BECN1 in the sorting of a plasma membrane protein for endolysosomal and macroautophagic degradation.     

Preliminary studies on the toxicity and mutagenicity of 1-amino-2-naphthol-4-sulphonic acid inDrosophila melanogaster

The toxicity and mutagenicity of 1-amino-2-naphtho-4-sulphonic acid were analysed inDrosphila melanogaster. Rate of development and viability were the two parameters employed to study the toxicity. The frequency of dominant lethals was scored to evaluate the mutagenic effect of the chemical on male and female germ cells. Concentrations of 250 mg and above/100 ml wheat cream agar medium were found to be significantly toxic. Significant number of dominant lethals was induced even by a concentration as low as 50 mg/100 ml medium. Male germ cells were more sensitive than female germ cells.     

Adaptive and cross resistance to cadmium (II) and zinc (II) by Pseudomonas aeruginosa BC15

Cadmium and zinc appear in the combined forms and they are co-pollutants. Cd is the most hazardous metal ion for human beings and causes renal dysfunction, liver and lungs damage, bone degeneration and blood damage. Though Zn is an essential nutrient, excess of Zn is toxic. Biological process was more important because conventional methods fail to remediate these pollutants due to high costs and less affordability. The screening and understanding of the functioning of microorganism plays an important role in removal and recovery of metals from heavy-metal-polluted water and soil. In our study, the strain Pseudomonas aeruginosa BC15 was isolated from oil-mill-treated waste water and it showed to be highly resistant to 6 mM Cd and 20 mM Zn in the solid and liquid media. The growth studies of BC15 strain in the medium without induction exhibited high tolerable capacity when compared to other microbes. Pretreatment of P. aeruginosa BC15 with sub-lethal concentrations of Cd induced adaptive resistance to lethal doses of Cd. Cadmium-induced cells also showed cross resistance to lethal concentration of zinc. The organism had high resistance against Cd and Zn. This has been clearly proven through biosorption studies: Cd was absorbed up to 62% and Zn about 60% in single solution, whereas in binary solution Cd was biosorbed up to 82% and Zn 85%. In conclusion, this study reveals the significance of using the strain P. aeruginosa BC15 in the bioremediation of Cd and Zn from industrial waste water and contaminated soil.     

Cloning and tissue distribution of a carnitine palmitoyltransferase I gene in rainbow trout (Oncorhynchus mykiss)

The carnitine palmitoyltransferase I (EC.2.3.1.21; CPT I) mediates the transport of fatty acids across the outer mitochondrial membrane. In mammals, there are two different proteins CPT I in the skeletal muscle (M) and liver (L) encoded by two genes. The carnitine palmitoyltransferase system of lower vertebrates received little attention. With the aim of improving knowledge on the CPT family in fish, we examined CPT I cDNA and CPT activity in different tissues of rainbow trout (Oncorhynchus mykiss). Using RT-PCR, we successfully cloned a partial CPT I cDNA sequence (1650 bp). The predicted protein sequence revealed identities of 63% and 61% with human L-CPT I and M-CPT I, respectively. This mRNA is expressed in liver, white and red skeletal muscles, heart, intestine, kidney and adipose tissue of trout. This is in good agreement with the measurement of the CPT activity in the same tissues. The [IC(50)] that reflects the sensitivity to malonyl-CoA inhibition was 0.116+/-0.004 microM for the liver and 0.426+/-0.041 microM for the white muscle. These results demonstrate for the first time the existence of at least one gene encoding for CPT I present in both the liver and the muscle of rainbow trout.     

Effect of onion (Allium cepa Linn.) and garlic (Allium sativum Linn.) on plasma triglyceride content in Japanese quail (Coturnix coturnix japonicum)

Dietary onion and garlic caused an increase in the level of plasma triglyceride which could be due to insulin like activity of dietary alliums and other factors that promote lipogenesisi in growing stages. Changes in the plasma triglyceride level in the control group due to change in age and sex were also noted. The triglyceride level was more in female birds when compared to males of similar age group. The plasma trigelyceride level increased with age in both sex except for the level being similar in the 6 and 9-week old females and 3 and 6-week old male birds. The results suggest that the effects of alliums in growing and adult stages may be different which needs further study.     

Expression of the Kynurenine Pathway in Human Peripheral Blood Mononuclear Cells: Implications for Inflammatory and Neurodegenerative Disease

The kynurenine pathway is a fundamental mechanism of immunosuppression and peripheral tolerance. It is increasingly recognized as playing a major role in the pathogenesis of a wide variety of inflammatory, neurodegenerative and malignant disorders. However, the temporal dynamics of kynurenine pathway activation and metabolite production in human immune cells is currently unknown. Here we report the novel use of flow cytometry, combined with ultra high-performance liquid chromatography and gas chromatography-mass spectrometry, to sensitively quantify the intracellular expression of three key kynurenine pathway enzymes and the main kynurenine pathway metabolites in a time-course study. This is the first study to show that up-regulation of indoleamine 2,3-dioxygenase (IDO-1), kynurenine 3-monoxygenase (KMO) and quinolinate phosphoribosyltransferase (QPRT) is lacking in lymphocytes treated with interferon gamma. In contrast, peripheral monocytes showed a significant elevation of kynurenine pathway enzymes and metabolites when treated with interferon gamma. Expression of IDO-1, KMO and QPRT correlated significantly with activation of the kynurenine pathway (kynurenine:tryptophan ratio), quinolinic acid concentration and production of the monocyte derived, pro-inflammatory immune response marker: neopterin. Our results also describe an original and sensitive methodological approach to quantify kynurenine pathway enzyme expression in cells. This has revealed further insights into the potential role of these enzymes in disease processes.     

Analysis of the Global Architecture of Hemoglobin A2 by Heme Binding Studies and Molecular Modeling

The kinetics of CNProto- and CNDeutero-hemin binding to apohemoglobin A₂ was investigated in a stopped-flow device in 0.05 M potassium phosphate buffer, pH 7, at 10°C. The overall kinetic profile exhibited multiple phases: Phases I–IV corresponding with heme insertion (8.5–13 × 10⁷ M^–1 s^–1), local structural rearrangement (0.21–0.23 s^–1), global structural event (0.071–0.098 s^–1), and formation of the Fe–His bond (0.009–0.012 s^–1), respectively. Kinetic differences observed between apohemoglobin A₂ and apohemoglobin A (previously studied) prompted an analysis of the structures of and chains through molecular modeling. This revealed a structural repositioning of the residues not only at, but also distant from the site of the amino acid substitutions, specifically those involved in the heme contact and subunit interface. A significant global change was observed in the structure of the exon-coded 3 region and provided additional evidence for the designation of this as the subunit assembly domain.