Enhancers predominantly regulate gene expression during differentiation via transcription initiation

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Laboratory diagnosis of invasive aspergillosis

Invasive aspergillosis is major cause of morbility and mortality in immunosuppressed patients, in part due to the inability to identify infected patients at an early stage of the disease. Diagnosis is based on a combination of imaging (high-resolution computed tomography) and a number of laboratory techniques including direct examination, culture and circulating markers (galactomannan and Aspergillus DNA) which can be detected at early stages of the infection.     

Protein expression profiles distinguish between experimental invasive pulmonary aspergillosis and Pseudomonas pneumonia

We hypothesized that invasive pulmonary aspergillosis (IPA) may generate a distinctive proteomic signature in plasma and bronchoalveolar lavage (BAL). Proteins in plasma and BAL from two neutropenic rabbit models of IPA and Pseudomonas pneumonia were analyzed by SELDI-TOF MS. Hierarchical clustering analysis of plasma time course spectra demonstrated two clusters of peaks that were differentially regulated between IPA and Pseudomonas pneumonia (57 and 34 peaks, respectively, p<0.001). PCA of plasma proteins demonstrated a time-dependent separation of the two infections. A random forest analysis that ranked the top 30 spectral points distinguished between late Aspergillus and Pseudomonas pneumonias with 100% sensitivity and specificity. Based on spectral data analysis, three proteins were identified using SDS-PAGE and LC/MS and quantified using reverse phase arrays. Differences in the temporal sequence of plasma haptoglobin (p<0.001), apolipoprotein A1 (p<0.001) and transthyretin (p<0.038) were observed between IPA and Pseudomonas pneumonia, as was C-reactive protein (p<0.001). In summary, proteomic analysis of plasma and BAL proteins of experimental Aspergillus and Pseudomonas pneumonias demonstrates unique protein profiles with principal components and spectral regions that are shared in early infection and diverge at later stages of infection. Haptoglobin, apolipoprotein A1, transthyretin, and C-reactive protein are differentially expressed in these infections suggesting important contributions to host defense against IPA.     

Stromal and epithelial networks: Temporal gene expression profiling during invasive neoplasia

The interaction between tumor cells and the stromal microenvironment is a critical factor in cancer development and progression. A recent study from the Khavari group profiled the expression changes during progression to invasion in a Ras-inducible model of human epithelial neoplasia and used network modeling to analyze the molecular interactions. Human dermis was seeded with H-Ras- and IκBα-expressing keratinocytes then grafted on to immune-deficient mice. The epithelial and stromal gene expression profiles were captured during progression from quiescent epithelial tissue to in situ neoplasia to invasive neoplasia. A subset of these altered genes was compiled into a “core tumor progression signature” (CTPS), which was shown to have clinical relevance in several cancer types. Network modeling of the CTPS revealed highly interconnected “hubs”, which was dominated by extracellular matrix-related genes, including β₁ integrin. Targeting integrin β₁ functionality reduced Ras-driven tumorigenesis in vivo and validated the network modeling strategy for predicting genes essential to neoplasia. By integrating temporal analysis of both the epithelial and stromal compartments with network modeling of molecular interactions, this work has described an effective strategy for identifying highly interconnected targets essential to tumor development.Key words: skin model, tumor invasion, microarray, network modelling, molecular interactions     

Stromal and epithelial networks: Temporal gene expression profiling during invasive neoplasia

The interaction between tumor cells and the stromal microenvironment is a critical factor in cancer development and progression. A recent study from the Khavari group profiled the expression changes during progression to invasion in a Ras-inducible model of human epithelial neoplasia and used network modeling to analyze the molecular interactions. Human dermis was seeded with H-Ras- and IκBα-expressing keratinocytes then grafted on to immune-deficient mice. The epithelial and stromal gene expression profiles were captured during progression from quiescent epithelial tissue to in situ neoplasia to invasive neoplasia. A subset of these altered genes was compiled into a "core tumor progression signature" (CTPS), which was shown to have clinical relevance in several cancer types. Network modeling of the CTPS revealed highly interconnected "hubs", which was dominated by extracellular matrix-related genes, including β₁ integrin. Targeting integrin β₁ functionality reduced Ras-driven tumorigenesis in vivo and validated the network modeling strategy for predicting genes essential to neoplasia. By integrating temporal analysis of both the epithelial and stromal compartments with network modeling of molecular interactions, this work has described an effective strategy for identifying highly interconnected targets essential to tumor development.     

Plasminogen alleles influence susceptibility to invasive aspergillosis

Invasive aspergillosis (IA) is a common and life-threatening infection in immunocompromised individuals. A number of environmental and epidemiologic risk factors for developing IA have been identified. However, genetic factors that affect risk for developing IA have not been clearly identified. We report that host genetic differences influence outcome following establishment of pulmonary aspergillosis in an exogenously immune suppressed mouse model. Computational haplotype-based genetic analysis indicated that genetic variation within the biologically plausible positional candidate gene plasminogen (Plg; Gene ID 18855) correlated with murine outcome. There was a single nonsynonymous coding change (Gly110Ser) where the minor allele was found in all of the susceptible strains, but not in the resistant strains. A nonsynonymous single nucleotide polymorphism (Asp472Asn) was also identified in the human homolog (PLG; Gene ID 5340). An association study within a cohort of 236 allogeneic hematopoietic stem cell transplant (HSCT) recipients revealed that alleles at this SNP significantly affected the risk of developing IA after HSCT. Furthermore, we demonstrated that plasminogen directly binds to Aspergillus fumigatus. We propose that genetic variation within the plasminogen pathway influences the pathogenesis of this invasive fungal infection.     

Comparative analysis of binary expression systems for directed gene expression in transgenic insects

Binary expression systems are of key interest to functional gene analysis by over- or misexpression. The application of such systems in diverse organisms would allow the study of many biological problems not addressable in model organisms. Here we report a set of constructs and an effective kinetic approach to quantitatively compare a series of diverse binary expression systems based on GAL4/UAS, LexA/(LL)(4) and tetracycline-controlled tTA/TRE. By the use of these constructs, we could show that in Drosophila melanogaster the yeast-derived GAL4/UAS systems are more effective in activating responder gene expression than the bacterial-derived LexA/(LL)(4) and tTA/TRE systems. The constructs are embedded in broad-range piggyBac-based transposon vectors and the transactivators are driven by the widely applicable 3xP3 promoter. These constructs should therefore be transferable to evaluate the functionality of binary expression systems in non-model insect species.     

Cell-cycle regulation of hydroxyproline-rich glycoprotein HRGPnt3 gene expression during the initiation of lateral root meristems

Analysis of transgenic tobacco plants containing a tobacco hydroxyproline-rich glycoprotein HRGPnt3 gene promoter-β-glucuronidase (GUS) gene fusion (HRGPnt3-uidA) showed that this promoter is active not only in the early stages of initiation of lateral roots as previously described, but also in the initiation of adventitious roots, with similar selective expression in a subset of pericycle cells. HRGPnt3 is also induced during initiation of hairy roots following transformation by Agrobacterium rhizogenes. The auxin indole acetic acid (IAA) induces an increase in the number of characteristic discrete sites of HRGP-nt3 expression. It is shown that these sites are destined to form new root primordia from pericycle cells of both adventitious and main roots. Dose-dependent induction of root meristems by auxin overcomes the limitations of this naturally stochastic process and makes lateral root initiation amenable to biochemical analysis. Quiescent pericycle cells, which are developmentally arrested in the G₂ phase of the cell cycle, rapidly progress into M phase upon mitogenic stimulation. Colchicine and nocodazole, which block completion of mitosis, inhibited the activation of the HRGPnt3 promoter but did not block auxin induction of parA, a marker for de-differentiation in leaf mesophyll cell-derived protoplasts. Hydroxyurea, which inhibits cell-cycle progression at the G₁/S-phase transition and also blocks lateral root initiation, did not inhibit HRGPnt3 induction. Thus, HRGPnt3 induction precedes completion of the first cell division during primordium formation, and is one of the initial steps in a sequential program of gene expression activated upon stimulation of cell division for the development of a new meristem during lateral root initiation.