Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Generation of induced pluripotent stem cells (iPSCs) and converting one cell type to another (transdifferentiation) by manipulating the expression of a small number of genes highlight the progress of cellular reprogramming, which holds great promise for regenerative medicine. A key challenge is to find the recipes of perturbing genes to achieve successful reprogramming such that the reprogrammed cells function in the same way as the natural cells.</p> <p>Results</p> <p>We present here a systems biology approach that allows systematic search for effective reprogramming recipes and monitoring the reprogramming progress to uncover the underlying mechanisms. Using budding yeast as a model system, we have curated a genetic network regulating cell cycle and sporulation. Phenotypic consequences of perturbations can be predicted from the network without any prior knowledge, which makes it possible to computationally reprogram cell fate. As the heterogeneity of natural cells is important in many biological processes, we find that the extent of this heterogeneity restored by the reprogrammed cells varies significantly upon reprogramming recipes. The heterogeneity difference between the reprogrammed and natural cells may have functional consequences.</p> <p>Conclusions</p> <p>Our study reveals that cellular reprogramming can be achieved by many different perturbations and the reprogrammability of a cell depends on the heterogeneity of the original cell state. We provide a general framework that can help discover new recipes for cellular reprogramming in human.</p

Impact of Aspergillus fumigatus in allergic airway diseases

For decades, fungi have been recognized as associated with asthma and other reactive airway diseases. In contrast to type I-mediated allergies caused by pollen, fungi cause a large number of allergic diseases such as allergic bronchopulmonary mycoses, rhinitis, allergic sinusitis and hypersensitivity pneumonitis. Amongst the fungi, Aspergillus fumigatus is the most prevalent cause of severe pulmonary allergic disease, including allergic bronchopulmonary aspergillosis (ABPA), known to be associated with chronic lung injury and deterioration in pulmonary function in people with chronic asthma and cystic fibrosis (CF). The goal of this review is to discuss new understandings of host-pathogen interactions in the genesis of allergic airway diseases caused by A. fumigatus. Host and pathogen related factors that participate in triggering the inflammatory cycle leading to pulmonary exacerbations in ABPA are discussed

Comparative Oncogenomic Analysis of Copy Number Alterations in Human and Zebrafish Tumors Enables Cancer Driver Discovery

The identification of cancer drivers is a major goal of current cancer research. Finding driver genes within large chromosomal events is especially challenging because such alterations encompass many genes. Previously, we demonstrated that zebrafish malignant peripheral nerve sheath tumors (MPNSTs) are highly aneuploid, much like human tumors. In this study, we examined 147 zebrafish MPNSTs by massively parallel sequencing and identified both large and focal copy number alterations (CNAs). Given the low degree of conserved synteny between fish and mammals, we reasoned that comparative analyses of CNAs from fish versus human MPNSTs would enable elimination of a large proportion of passenger mutations, especially on large CNAs. We established a list of orthologous genes between human and zebrafish, which includes approximately two-thirds of human protein-coding genes. For the subset of these genes found in human MPNST CNAs, only one quarter of their orthologues were co-gained or co-lost in zebrafish, dramatically narrowing the list of candidate cancer drivers for both focal and large CNAs. We conclude that zebrafish-human comparative analysis represents a powerful, and broadly applicable, tool to enrich for evolutionarily conserved cancer drivers.Kathy and Curt Marble Cancer Research FundArthur C. MerrillNational Institutes of Health (U.S.) (Grant CA106416)National Institutes of Health (U.S.) (Grant ROI RR020833)National Institutes of Health (U.S.) (Grant 1F32GM095213-01

DEFECT IN POTENTIATION OF ADENYLYL-CYCLASE CORRELATES WITH BRONCHIAL HYPERREACTIVITY

Background: Adenylyl cyclase is a transmembrane signaling system involved in the inhibition of cellular responses. Recently, we showed that the activity of adenylyl cyclase may be potentiated by stimuli that induce an increase of cellular responses but that do not activate adenylyl cyclase. This is probably an important physiologic feedback mechanism that prevents cells from becoming ''overstimulated.'' Objective: Because increased cellular activities are frequently observed in persons with asthma, we hypothesized that a defect in potentiation of adenylyl cyclase might be involved. Methods: Potentiation of isoprenaline-induced adenosine cyclic monophosphate (cAMP) production with the mitogen phytohemagglutinin (PHA; 45 mu g/ml) or the calcium ionophore A23187 (1 mu mol/L) was studied in peripheral blood mononuclear cells taken from patients with asthma (n = 8) and healthy control subjects (n = 11). Results: Isoprenaline-induced cAMP production was potentiated significantly in the healthy control subjects (PHA, 110% +/- 15%; A23187, 92% +/- 25%). In contrast, potentiation was not seen with PHA ol A23187 in the total group of patients with asthma. However; some patients showed weak potentiation, whereas in others PHA decreased isoprenaline-induced CAMP production. Moreover, the effect of PHA isoprenaline-induced cAMP production correlated significantly with the degree of bronchial hyperreactivity in patients with asthma (r = 0.96; p = 0.0001). Conclusions: The observed defect in signal transduction could play an important part in bronchial hyperresponsiveness

Resistance of activated human T(h)2 cells to NO-induced apoptosis is mediated by gamma-glutamyltranspeptidase

Activation-induced death of inflammatory cells (AICD) has an important function in immune maintenance, Type 1 T-h cells are known to be more susceptible to AICD than T(h)2 cells. In the current study we examined whether NO-induced apoptosis also preferentially eliminates T(h)1 cells over Th2 cells. Naive human Th lymphocytes (CD4(+)CD45RO(-)) were activated in vitro for 1 week in the presence of IL-12 plus anti-IL-4 or IL-4 plus anti-IL-12 to generate T(h)1- and T(h)2-polarized cultures respectively, Cultures were exposed to the NO donors Spermine-nonoate (Sper) and DPTA-nonoate to study NO-induced apoptosis. We found that NO preferentially induced apoptosis in T(h)1-polarized cells as demonstrated by Annexin staining in the presence of 10 muM Sper(70 +/- 16 versus 23 +/- 4.4% in T(h)2 cells P <0.01) and by DioC(6) staining (38 10 versus 11 +/- 5% in T(h)2 cells, P <0.01), The mechanism of NO-induced apoptosis in T(h)1/T(h)2-polarized cells was distinct from AICD and Pas-induced apoptosis, Differential sensitivity between T(h)1- and T(h)2-polarized cultures originated at the level of intracellular glutathione (GSH) metabolism. GSH levels were higher in T(h)2 cells (1.6 0.2-fold T(h)1, P <0,01). High intracellular GSH in T(h)2-polarized cells did not account for reduced susceptibility to NO per se, since the inhibition of -glutamyltranspeptidase (gamma -GT), which is involved in GSH import, sensitized T(h)2 cells to NO-induced apoptosis without GSH depletion. Therefore, higher activity of gamma -GT in Th2 cells (2.1 +/- 0.4-fold T(h)1, P <0.001) specifically protects T(h)2 cells against NO-induced apoptosis, Preferential NO-induced elimination of human T(h)1 cells at sites of inflammation may thus select Th2 cells and contribute to immune deviation