Deletion of the signalling molecule synthase ScbA has pleiotropic effects on secondary metabolite biosynthesis, morphological differentiation and primary metabolism in Streptomyces coelicolor A3(2)

Streptomycetes have high biotechnological relevance as producers of diverse metabolites widely used in medical and agricultural applications. The biosynthesis of these metabolites is controlled by signalling molecules, γ-butyrolactones, that act as bacterial hormones. In Streptomyces coelicolor, a group of signalling molecules called SCBs (S. coelicolorbutanolides) regulates production of the pigmented antibiotics coelicolor polyketide (CPK), actinorhodin and undecylprodigiosin. The γ-butyrolactone synthase ScbA is responsible for the biosynthesis of SCBs. Here we show the results of a genome-wide transcriptome analysis of a scbA deletion mutant prior to and during the transition to antibiotic production. We report a strong perturbation in the expression of three pigmented antibiotic clusters in the mutant throughout the growth curve, thus providing a molecular explanation for the antibiotic phenotype observed previously. Our study also revealed, for the first time, that the secondary metabolite cluster responsible for synthesis of the siderophore desferrioxamine is under the control of SCB signalling. Moreover, expression of the genes encoding enzymes for primary metabolism pathways, which supply antibiotic precursors and genes for morphological differentiation, was found shifted earlier in time in the mutant. In conclusion, our time series analysis demonstrates new details of the regulatory effects of the γ-butyrolactone system in Streptomyces.

Interleukin 6/interleukin 6 receptor interaction and its role as a therapeutic target for treatment of cachexia and cancer

Interleukin 6 (IL6) mediates pleiotropic physiological functions through its interaction with the IL6 receptor (IL6R). Signal transduction can occur via cis- and trans-signaling. The role of IL6/IL6R interaction via autocrine and paracrine loops in tumor proliferation and progression is discussed. The potential role of IL6/IL6R interaction in different experimental systems and tumor entities is summarized while the focus is on inhibition of IL6 signaling with monoclonal antibodies directed against IL6 or IL6R and their potential impact for treatment of tumor-associated cachexia and as antitumoral agents as monotherapy and in combination with small molecule compounds.

ALCAM/CD166: cancer-related issues

Activated leucocyte adhesion molecule (ALCAM) was originally identified as a transmembrane receptor which is involved in T-cell activation and has other still unresolved functions in hematopoiesis, development, inflammation and transendothelial migration of neutrophils. ALCAM is a member of a subfamily of immunoglobulin receptors with five immunoglobulin-like domains (VVC2C2C2) in the extracellular domain and is expressed in many types of tumors. The tumor-type-dependent impact of its expression level with respect to prognosis points to a possible context-dependent function. Most functional investigations have focused on malignant melanoma, in which high ALCAM expression at the protein level correlates with a poor prognosis. ALCAM mediates low-affinity homophilic interactions and much stronger interactions with CD6. Modulation of ALCAM function with agents such as transfected dominant negative ALCAM and ligand-binding secreted ALCAM both lead to inhibition of matrix metalloproteinase-2 activation, but their impact with respect to invasion in vitro and metastasis in vivo are different. Single-chain Fv fragments directed against ALCAM are efficiently internalized, paving the way for exploration of immunoconjugates as therapeutic agents. Validation experiments of the target with modulatory agents for possible therapeutic application in oncology are discussed.

The Roche Cancer Genome Database (RCGDB)

Sequence variations are being studied for a better understanding of the mechanism and development of cancer as a mutation-driven disease. The systematic sequencing of genes in tumors and technological advances in high-throughput techniques combined with efficient data acquisition methods have resulted in an explosion of available cancer genome-related data. Despite the technological progress and increase of data, improvements in the application area, for example, drug target discovery, have failed to keep pace with increased research and development spending. One reason for this discrepancy is the ever increasing number of databases and the absence of a unified access to the mutation data. Currently, researchers typically have to browse several, often highly specialized databases to obtain the required information. A more complete understanding of relations and dependencies between mutations and cancer, however, requires the availability of an efficient integrative cancer genome information system. To facilitate this, we developed the Roche Cancer Genome Database (RCGDB), a freely available biological information system integrating different kinds of mutation data. The database is the first comprehensive integration of disparate cancer genome data like single nucleotide variants, single nucleotide polymorphisms, and chromosomal aberrations (CGH and FISH). RCGDB is freely accessible via a Google-like Web interface at http://rcgdb.bioinf.uni-sb.de/MutomeWeb/.

Human variation databases

More than 100 000 human genetic variations have been described in various genes that are associated with a wide variety of diseases. Such data provides invaluable information for both clinical medicine and basic science. A number of locus-specific databases have been developed to exploit this huge amount of data. However, the scope, format and content of these databases differ strongly and as no standard for variation databases has yet been adopted, the way data is presented varies enormously. This review aims to give an overview of current resources for human variation data in public and commercial resources.

Cancer-related issues of CD147

CD147 is involved in many physiological functions, such as lymphocyte responsiveness, spermatogenesis, implantation, fertilization and neurological functions at early stages of development. Here we specifically review the role of CD147 in cancer. We focus on the following aspects: expression of CD147 in malignant versus normal tissues and its possible impact on prognosis, interaction of tumor cell-expressed CD147 with stroma cells and induction of matrix metalloproteinases, as well as the role of CD147 in tumor angiogenesis. The function of CD147 in supercomplexes with monocarboxylate transporters (MCT) and amino acid transporters such as CD98hc and large neutral amino acid transporter 1 (LAT1), as well as the functional contribution of CD147 in complexes with caveolin-1 and integrins, is discussed. Target validation experiments making use of CD147-directed RNAi and monoclonal antibodies are summarized. Finally, the relevance of CD147 as a target for therapeutic intervention in cancer patients is discussed.

Bead array-based microrna expression profiling of peripheral blood and the impact of different RNA isolation approaches

Blood-based mRNA expression profiling has already become an important issue in clinical applications. More recently, the characterization of the small RNA transcriptome offers additional avenues for diagnostic approaches. However, when applying miRNA expression profiling in routine clinical settings, the method of RNA preservation and the manner of RNA extraction as well as the reliability of the miRNA profiling procedure have to be carefully considered. Here we evaluate a recently introduced bead array-based technology as a robust method for the generation of blood-based human miRNA expression profiles. Importantly the comparison of different RNA extraction strategies resulted in dissimilar profiles depending on the RNA extraction method as well as on the underlying source. Expression profiles obtained from peripheral mononuclear cells (PBMCs) substantially differed from those of whole blood samples, whereby both sources per se yielded reproducible and reliable results. Expression profiles were also distinct when using either fresh or frozen PBMCs. Moreover RNA size fractioning resulted in discriminative miRNA expression profiles compared with total RNA based profiles. This study outlines important steps toward the establishment of a robust strategy for blood-based miRNA profiling and provides a reliable strategy for its implementation in routine handling for diagnostic purposes.

Virally infected mouse liver endothelial cells trigger CD8+ T-cell immunity

BACKGROUND & AIMS

Dendritic cell activation through ligation of pattern recognition receptors leading to full functional maturation causes induction of CD8(+) T-cell immunity through increased delivery of costimulatory signals instead of tolerance. Here we investigate whether organ-resident antigen-presenting cells, such as liver sinusoidal endothelial cells (LSECs), also switch from tolerogenic to immunogenic CD8(+) T-cell activation upon such stimulation.

METHODS

Murine LSECs were isolated by immunomagnetic separation and analyzed for functional maturation upon triggering pattern recognition receptors or viral infection employing gene expression analysis and T cell coculture assays. In vivo relevance of the findings was confirmed with bone-marrow chimeric animals.

RESULTS

LSECs expressed numerous pattern recognition receptors that allowed for sentinel function, but ligand-induced activation of these receptors was not sufficient to overcome tolerance induction of CD8(+) T cells. Importantly, viral infection with murine cytomegalovirus caused functional maturation of antigen-presenting LSECs and was sufficient to promote antigen-specific differentiation into effector CD8(+) T cells in the absence of dendritic cells and independent of CD80/86.

CONCLUSIONS

These results shed new light on the generation of organ-specific immunity and may contribute to overcoming tolerance in relevant situations, such as cancer.

L1-CAM as a target for treatment of cancer with monoclonal antibodies

L1 cell adhesion molecule (L1-CAM) is a neuronal adhesion molecule which is expressed in many tumor entities. L1-CAM was shown to be involved in proliferation, invasion and metastasis both in vitro and in vivo. L1-CAM is engaged in homophilic interactions and complexes with many other ligands in a context-dependent manner. Activation and modulation of the extracellular signal-related kinase pathway by L1-CAM has been documented. In normal tissues, L1-CAM expression is restricted to nerve bundles and kidney tubules; however, L1-CAM is expressed in many tumor entities and, with the exception of neuroblastoma, L1-CAM expression correlates with poor prognosis. L1-CAM occurs in two isoforms, full-length L1-CAM and a variant in which exons 2 and 27 have been deleted. Preclinical experiments with available monoclonal antibodies are summarized and L1-CAM is analysed as a target for treatment of cancer with monoclonal antibodies.

The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays

Background

The MAQC project demonstrated that microarrays with comparable content show inter- and intra-platform reproducibility. However, since the content of gene databases still increases, the development of new generations of microarrays covering new content is mandatory. To better understand the potential challenges updated microarray content might pose on clinical and biological projects we developed a methodology consisting of in silico analyses combined with performance analysis using real biological samples.

Results

Here we clearly demonstrate that not only oligonucleotide design but also database content and annotation strongly influence comparability and performance of subsequent generations of microarrays. Additionally, using human blood samples and purified T lymphocyte subsets as two independent examples, we show that a performance analysis using biological samples is crucial for the assessment of consistency and differences.

Conclusion

This study provides an important resource assisting investigators in comparing microarrays of updated content especially when working in a clinical or regulatory setting.

Cancer vaccine enhanced, non-tumor-reactive CD8(+) T cells exhibit a distinct molecular program associated with "division arrest anergy"

Immune-mediated tumor rejection relies on fully functional T-cell responses and neutralization of an adverse tumor microenvironment. In clinical trials, we detected peptide-specific but non-tumor-reactive and therefore not fully functional CD8(+) T cells post-vaccination against tumor antigens. Understanding the molecular mechanisms behind nontumor reactivity will be a prerequisite to overcome this CD8(+) T-cell deviation. We report that these non-tumor-reactive CD8(+) T cells are characterized by a molecular program associated with hallmarks of "division arrest anergy." Non-tumor-reactive CD8(+) T cells are characterized by coexpression of CD7, CD25, and CD69 as well as elevated levels of lck(p505) and p27(kip1). In vivo quantification revealed high prevalence of non-tumor-reactive CD8(+) T cells with increased levels during cancer vaccination. Furthermore, their presence was associated with a trend toward shorter survival. Dynamics and frequencies of non-target-reactive CD8(+) T cells need to be further addressed in context of therapeutic vaccine development in cancer, chronic infections, and autoimmune diseases.

RNA fingerprints provide direct evidence for the inhibitory role of TGFβ and PD-1 on CD4+ T cells in Hodgkin lymphoma

A hallmark of various human malignancies is the expression of immunoinhibitory factors within the tumor microenvironment. There is indirect evidence based on in vitro experiments that tumor-infiltrating T cells in human malignancies are suppressed by such factors. Still, direct evidence of the influence of individual inhibitory factors on immune cells in human cancer in vivo is lacking. To address this question, we used Hodgkin lymphoma (HL) as a model because histopathological characteristics of HL are thought to be due mostly to the effects of a wide variety of cytokines, including TGFβ or membrane-bound receptors such as PD-1 that are suspected to contribute to immune evasion of tumor cells. Using a genome-wide transcriptional approach, we established specific RNA fingerprints of TGFβ and PD-1 signaling in human T cells in vitro. Applying these specific fingerprints, we directly demonstrate that CD4+ T cells in HL—but not in follicular lymphoma (FL)—are under the inhibitory influence of both TGFβ and PD-1 in vivo. This approach can be easily generalized to provide direct evidence of the impact of any given soluble or cell-bound factor on any cell type within diseased tissue.

Human Resting CD4+ T Cells Are Constitutively Inhibited by TGFβ under Steady-State Conditions

Based on studies in knockout mice, several inhibitory factors such as TGFbeta, IL-10, or CTLA-4 have been implicated as gate keepers of adaptive immune responses. Lack of these inhibitory molecules leads to massive inflammatory responses mainly mediated by activated T cells. In humans, the integration of these inhibitory signals for keeping T cells at a resting state is less well understood. To elucidate this regulatory network, we assessed early genome-wide transcriptional changes during serum deprivation in human mature CD4(+) T cells. The most striking observation was a "TGFbeta loss signature" defined by down-regulation of many known TGFbeta target genes. Moreover, numerous novel TGFbeta target genes were identified that are under the suppressive control of TGFbeta. Expression of these genes was up-regulated once TGFbeta signaling was lost during serum deprivation and again suppressed upon TGFbeta reconstitution. Constitutive TGFbeta signaling was corroborated by demonstrating phosphorylated SMAD2/3 in resting human CD4(+) T cells in situ, which were dephosphorylated during serum deprivation and rephosphorylated by minute amounts of TGFbeta. Loss of TGFbeta signaling was particularly important for T cell proliferation induced by low-level TCR and costimulatory signals. We suggest TGFbeta to be the most prominent factor actively keeping human CD4(+) T cells at a resting state.

IlluminaGUI: graphical user interface for analyzing gene expression data generated on the Illumina platform

IlluminaGUI is a graphical user interface implemented for analyzing microarray data from the Illumina BeadChip platform. All key components of a microarray experiment, including quality control, normalization, inference and classification methods are provided in a 'point and click' approach. IlluminaGUI is implemented as a R package based on the R-Tcl/Tk interface and is available for platforms on which R runs including Windows, Mac and Unix-type machines.

AVAILABILITY

http://IlluminaGUI.dnsalias.org

Indoleamine 2,3-dioxygenase-expressing dendritic cells form suppurative granulomas following Listeria monocytogenes infection

Control of pathogens by formation of abscesses and granulomas is a major strategy of the innate immune system, especially when effector mechanisms of adaptive immunity are insufficient. We show in human listeriosis that DCs expressing indoleamine 2,3-dioxygenase (IDO), together with macrophages, are major cellular components of suppurative granulomas in vivo. Induction of IDO by DCs is a cell-autonomous response to Listeria monocytogenes infection and was also observed in other granulomatous infections with intracellular bacteria, such as Bartonella henselae. Reporting on our use of the clinically applied anti-TNF-alpha antibody infliximab, we further demonstrate in vitro that IDO induction is TNF-alpha dependent. Repression of IDO therefore might result in exacerbation of granulomatous diseases observed during anti-TNF-alpha therapy. These findings place IDO(+) DCs not only at the intersection of innate and adaptive immunity but also at the forefront of bacterial containment in granulomatous infections.

Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction

MOTIVATION

Wnt signaling is a very active area of research with highly relevant publications appearing at a rate of more than one per day. Building and maintaining databases describing signal transduction networks is a time-consuming and demanding task that requires careful literature analysis and extensive domain-specific knowledge. For instance, more than 50 factors involved in Wnt signal transduction have been identified as of late 2003. In this work we describe a natural language processing (NLP) system that is able to identify references to biological interaction networks in free text and automatically assembles a protein association and interaction map.

RESULTS

A 'gold standard' set of names and assertions was derived by manual scanning of the Wnt genes website (http://www.stanford.edu/~rnusse/wntwindow.html) including 53 interactions involved in Wnt signaling. This system was used to analyze a corpus of peer-reviewed articles related to Wnt signaling including 3369 Pubmed and 1230 full text papers. Names for key Wnt-pathway associated proteins and biological entities are identified using a chi-squared analysis of noun phrases over-represented in the Wnt literature as compared to the general signal transduction literature. Interestingly, we identified several instances where generic terms were used on the website when more specific terms occur in the literature, and one typographic error on the Wnt canonical pathway. Using the named entity list and performing an exhaustive assertion extraction of the corpus, 34 of the 53 interactions in the 'gold standard' Wnt signaling set were successfully identified (64% recall). In addition, the automated extraction found several interactions involving key Wnt-related molecules which were missing or different from those in the canonical diagram, and these were confirmed by manual review of the text. These results suggest that a combination of NLP techniques for information extraction can form a useful first-pass tool for assisting human annotation and maintenance of signal pathway databases.

AVAILABILITY

The pipeline software components are freely available on request to the authors.

CONTACT

dstates@umich.edu

SUPPLEMENTARY INFORMATION

http://stateslab.bioinformatics.med.umich.edu/software.html.