Personalized medicine and proteomics: lessons from non-small cell lung cancer

Personalized medicine allows the selection of treatments best suited to an individual patient and disease phenotype. To implement personalized medicine, effective tests predictive of response to treatment or susceptibility to adverse events are needed, and to develop a personalized medicine test, both high quality samples and reliable data are required. We review key features of state-of-the-art proteomic profiling and introduce further analytic developments to build a proteomic toolkit for use in personalized medicine approaches. The combination of novel analytical approaches in proteomic data generation, alignment and comparison permit translation of identified biomarkers into practical assays. We further propose an expanded statistical analysis to understand the sources of variability between individuals in terms of both protein expression and clinical variables and utilize this understanding in a predictive test.     

5'-upstream structure of the gene coding for chicken riboflavin-binding protein and its relation to estrogen induction

To elucidate the mechanism of the estrogen-dependent induction of chicken riboflavin-binding protein (RfBP), we analyzed the 5'-upstream structure of its gene. A noncoding exon exists there, and around this sequence, 9 widely spaced half-palindromic estrogen-response element (ERE) motifs (5'-GGTCA or 5'-TGACC) were found. Furthermore, an imperfect ERE-like palindromic sequence (5'-ATGTCANNNTGACAT-3') was also found at the 2.25 kb upstream region. No consensus palindromic ERE was observed. By luciferase reporter assay, the regions containing the half ERE motifs and the imperfect ERE showed estrogen-dependent enhancer activities, suggesting that these two characteristic sequences might confer estrogen-inducibility upon the chicken RfBP gene. However the activities were lower than that of a consensus ERE. It remains uncertain whether these sequences act cooperatively.     

Substrate specificity classes and the recognition signal for Salmonella type III flagellar export

Most flagellar proteins of Salmonella are exported to their assembly destination via a specialized apparatus. This apparatus is a member of the type III superfamily, which is widely used for secretion of virulence factors by pathogenic bacteria. Extensive studies have been carried out on the export of several of the flagellar proteins, most notably the hook protein (FlgE), the hook-capping protein (FlgD), and the filament protein flagellin (FliC). This has led to the concept of two export specificity classes, the rod/hook type and the filament type. However, little direct experimental evidence has been available on the export properties of the basal-body rod proteins (FlgB, FlgC, FlgF, and FlgG), the putative MS ring-rod junction protein (FliE), or the muramidase and putative rod-capping protein (FlgJ). In this study, we have measured the amounts of these proteins exported before and after hook completion. Their amounts in the culture supernatant from a flgE mutant (which is still at the hook-type specificity stage) were much higher than those from a flgK mutant (which has advanced to the filament-type specificity stage), placing them in the same class as the hook-type proteins. Overproduction of FliE, FlgB, FlgC, FlgF, FlgG, or FlgJ caused inhibition of the motility of wild-type cells and inhibition of the export of the hook-capping protein FlgD. We also examined the question of whether export and translation are linked and found that all substrates tested could be exported after protein synthesis had been blocked by spectinomycin or chloramphenicol. We conclude that the amino acid sequence of these proteins suffices to mediate their recognition and export.     

Electron microscopic and pharmacological studies on the rat median eminence

Summary The rat median eminence contains at least three kinds of granules or vesicles: 1. large electron-dense granules (perhaps carriers of neurohypophysial hormones), 2. small electron-dense granules with or without haloes (perhaps carriers of catecholamines) and 3. synaptic vesicle-like structures (perhaps carriers of acetylcholine). The former two electrondense granules exist in separate axons but they coexist with the latter vesicles in the same axons.The pars nervosa shows basically a similar structure to the median eminence. However, the axons containing the small electron-dense granules are very few. In the pars tuberalis, there are at least two types of cells: the cells of one type contain much cytoplasm with large round nuclei and those of the other type contain a small amount of cytoplasm with polymorphic nuclei. The cells of the former include multivesicular bodies and secretory granules, but those of the latter do not. Some of capillaries of the primary plexus are surrounded by the cells of the pars tuberalis on one side and by neurosecretory axon endings on the other side.The median eminence contains high concentration of acetylcholine or an acetylcholine-like substance and shows neurohypophysial hormone activity.Aided by Grant A-3678 from the United States National Institute of Arthritis and Metabolic Diseases. The authors are indebted to Dr. Welsh, Harvard University, for the kind gift of Mytolon.     

Quantitative determination of callose in tree roots

The formation of callose in tree roots has been suggested as a physiological indicator of aluminum (Al) toxicity. Quantifying callose in the roots in forest soils, however, is hampered by the presence of autofluorescent materials in the roots that disturb the measurement of callose by fluorescence spectrophotometry. Tannins in the roots cause these measurement problems. Here we report on the measurement of callose in the root apices of European chestnut (Castanea sativa) seedlings collected in an acidified forest soil. The callose was quantified with a modified protocol which included three washing steps with polyvinylpolypyrrolidone (PVPP) before the callose was extracted. This procedure reduced the autofluorescence by about 50%. With the use of water or ethanol alone, callose could be measured in only about 15% of the root samples, whereas with the use of PVPP callose could be determined in 95% of the samples. This improved method could help to evaluate the effects of Al toxicity on tree roots grown in forest soils, where callose is detected as a physiological indicator.     

Immunohistochemical localization of Na+-dependent glucose transporter in rat jejunum

Summary Glucose is actively absorbed via a Na⁺-dependent active glucose transporter (Na-GT) in the small intestine. We raised a polyclonal antibody against the peptide corresponding to amino acids 564–575 of rabbit intestinal Na-GT, and localized it immunohistochemically in the rat jejunum. By means of immunofluorescence staining, Na-GT was located at the brush border of the absorptive epithelial cells of the intestinal villi. Electron-microscopic examination showed that Na-GT was localized at the plasma membrane of the apical microvilli of these cells. Little Na-GT was found at the basolateral plasma membrane. Along the crypt-villus axis, all of the absorptive epithelial cells in the villus were positive for Na-GT. In addition to the brush border staining, the supranuclear positive staining, which was shown to be the Golgi apparatus by use of electron microscopy, was seen in cells located between the base to the middle of the villus. Cells in crypts exhibited little or no staining for Na-GT. Goblet cells scattered in the intestinal epithelium were negative for Na-GT staining. These observations show that Na-GT is specific to the apical plasma membrane of the absorptive epithelial cells, and that the onset of Na-GT synthesis may occur near the crypt-villus junction.     

Physiologically high concentrations of 17beta-estradiol enhance NF-kappaB activity in human T cells

Estrogen has diverse effects on inflammation and immune responses. That pregnancy is associated with remission of some autoimmune diseases and exacerbation of others suggests that physiological fluctuation in estrogen levels could affect the immune responses in humans. However, the molecular basis for these phenomena is poorly understood. We hypothesized that fluctuations of estrogen levels modulate intracellular signaling for immune responses via estrogen receptors (ERs). In reporter assays, 17beta-estradiol (E2) at a physiologically high concentration increased the activity of NF-kappaB in Jurkat cells stimulated by PMA/ionomycin or TNF-alpha. Overexpression and RNA interference experiments suggested that the effects were mediated through ERbeta. Immunoprecipitation assay showed that both ERalpha and ERbeta are directly associated with NF-kappaB in the cell nucleus. Using chromatin immunoprecipitation assay, we confirmed that ERalpha and ERbeta associated with NF-kappaB and steroid hormone coactivators at the promoter region of NF-kappaB regulated gene. Considering that NF-kappaB regulates the expression of various genes essential for cell growth and death, estrogen could regulate the fate of T cells by affecting the activity of NF-kappaB. To determine whether E2 alters the fate of T cells, we investigated E2 actions on T cell apoptosis, a well-known NF-kappaB-mediated phenomenon. E2 increased apoptosis of Jurkat cells and decreased that of human peripheral blood T cells. Our results indicate that E2 at a physiologically high concentration modulates NF-kappaB signaling in human T cells via ERbeta and affects T cell survival, suggesting that these actions may underlie the gender differences in autoimmune diseases.     

Elastin protein levels are a vital modifier affecting normal lung development and susceptibility to emphysema

Cigarette smoking is the strongest risk factor for emphysema. However, sensitivity to cigarette smoke-induced emphysema is highly variable, and numerous genetic and environmental factors are thought to mitigate lung response to injury. We report that the quantity of functional elastin in the lung is an important modifier of both lung development and response to injury. In mice with low levels of elastin, lung development is adversely affected, and mice manifest with congenital emphysema. Animals with intermediate elastin levels exhibit normal alveolar structure but develop worse emphysema than normal mice following cigarette smoke exposure. Mechanical testing demonstrates that lungs with low levels of elastin experience greater tissue strains for any given tissue stress compared with wild-type lungs, implying that force-mediated propagation of lung injury through alveolar wall failure may worsen the emphysema after an initial enzymatic insult. Our findings suggest that quantitative deficiencies in elastin predispose to smoke-induce emphysema in animal models and suggest that humans with altered levels of functional elastin could have relatively normal lung function while being more susceptible to smoke-induced lung injury.