Cell Cycle Gene Networks Are Associated with Melanoma Prognosis

BACKGROUND: Our understanding of the molecular pathways that underlie melanoma remains incomplete. Although several published microarray studies of clinical melanomas have provided valuable information, we found only limited concordance between these studies. Therefore, we took an in vitro functional genomics approach to understand melanoma molecular pathways. METHODOLOGY/PRINCIPAL FINDINGS: Affymetrix microarray data were generated from A375 melanoma cells treated in vitro with siRNAs against 45 transcription factors and signaling molecules. Analysis of this data using unsupervised hierarchical clustering and Bayesian gene networks identified proliferation-association RNA clusters, which were co-ordinately expressed across the A375 cells and also across melanomas from patients. The abundance in metastatic melanomas of these cellular proliferation clusters and their putative upstream regulators was significantly associated with patient prognosis. An 8-gene classifier derived from gene network hub genes correctly classified the prognosis of 23/26 metastatic melanoma patients in a cross-validation study. Unlike the RNA clusters associated with cellular proliferation described above, co-ordinately expressed RNA clusters associated with immune response were clearly identified across melanoma tumours from patients but not across the siRNA-treated A375 cells, in which immune responses are not active. Three uncharacterised genes, which the gene networks predicted to be upstream of apoptosis- or cellular proliferation-associated RNAs, were found to significantly alter apoptosis and cell number when over-expressed in vitro. CONCLUSIONS/SIGNIFICANCE: This analysis identified co-expression of RNAs that encode functionally-related proteins, in particular, proliferation-associated RNA clusters that are linked to melanoma patient prognosis. Our analysis suggests that A375 cells in vitro may be valid models in which to study the gene expression modules that underlie some melanoma biological processes (e.g., proliferation) but not others (e.g., immune response). The gene expression modules identified here, and the RNAs predicted by Bayesian network inference to be upstream of these modules, are potential prognostic biomarkers and drug targets

Familial renal glycosuria: a genetic reappraisal of hexose transport by kidney and intestine

Renal glucose titration studies were carried out in 10 members of two pedigrees with familial renal glycosuria to test the accepted hypothesis of autosomal dominant inheritance and to investigate the genetic significance of “type A” and “type B” renal glycosuria. In one family, a brother and sister each had a moderately reduced threshold and tubular maximum for glucose (type A), but both of their parents reabsorbed glucose normally. In the second family, two brothers had severe type A renal glycosuria, their mother and one brother had a mild type A defect, and another brother demonstrated a reduced threshold, an exaggerated splay, and a normal tubular maximum, indicative of type B glycosuria. Hexose transport by intestinal mucosa was also investigated in controls and in the three brothers with the most severe renal glycosuria. D-glucose-(14)C and 3-O-methylglucose-(14)C were accumulated by jejunal mucosa from controls by processes which were saturable and concentrative. No differences in hexose transport were observed in the patients with renal glycosuria. We conclude that familial renal glycosuria can be inherited as an autosomal recessive trait; that mild and severe type A renal glycosuria and type B renal glycosuria can occur in the same pedigree; and that defective reabsorption of glucose by the kidney need not be accompanied by abnormalities in intestinal glucose transport. These findings indicate that glucose transport in the gut and kidney are not mediated by identical mechanisms, and that several different mutations are responsible for the phenotypic variability in familial renal glycosuria

Substrate specificity and stabilization by thiamine pyrophosphate of rat liver branched chain α-ketoacid dehydrogenase

Rat liver branched chain α-ketoacid dehydrogenase has been solubilized and used to investigate the substrate specificity, cofactor requirements, and stabilizing properties of thiamine pyrophosphate for this enzyme. Only the branched chain α-ketoacids are oxidatively decarboxylated with apparent K m values of 30, 32, and 35 μ m for α-ketoisovalerate, α-ketoisocaproate and α-keto-β-methylvalerate, respectively. Maximal CO 2 release requires the presence of CoASH, NAD +, Mg 2+ and thiamine pyrophosphate. The ketoacids competitively inhibit one another, activity for all three show identical pH optimum and heat lability which supports the concept of single enzyme complex acting on all three substrates. The activity can be stabilized by thiamine pyrophosphate which provides a rationale for treatment of maple syrup urine disease with pharmacologic doses of thiamine

Stabilization of mammalian liver branched-chain α-ketoacid dehydrogenase by thiamin pyrophosphate

Thiamin pyrophosphate, CoASH, and NAD + have been shown to reversibly bind to the purified bovine liver mitochondrial branched-chain α-ketoacid dehydrogenase complex. When saturated with thiamin pyrophosphate, the complex was more stable to heat and chymotrypsin inactivation. Under identical saturating conditions a conformational change in the complex was observed by circular dichroism spectroscopy. We postulate that thiamin pyrophosphate can increase the biological half-life of the in vivo, membrane-bound complex through conformational changes induced by the binding of this cofactor