BackgroundNodular melanoma is one of the most life threatening tumors with still poor therapeutic outcome. Similarly to other tumors, permissive microenvironment is essential for melanoma progression. Features of this microenvironment are arising from molecular crosstalk between the melanoma cells (MC) and the surrounding cell populations in the context of skin tissue. Here, we study the effect of melanoma cells on human primary keratinocytes (HPK). Presence of MC is as an important modulator of the tumor microenvironment and we compare it to the effect of nonmalignant lowly differentiated cells also originating from neural crest (NCSC).MethodsComparative morphometrical and immunohistochemical analysis of epidermis surrounding nodular melanoma (n = 100) was performed. Data were compared to results of transcriptome profiling of in vitro models, in which HPK were co-cultured with MC, normal human melanocytes, and NCSC, respectively. Differentially expressed candidate genes were verified by RT-qPCR. Biological activity of candidate proteins was assessed on cultured HPK.ResultsEpidermis surrounding nodular melanoma exhibits hyperplastic features in 90% of cases. This hyperplastic region exhibits aberrant suprabasal expression of keratin 14 accompanied by loss of keratin 10. We observe that MC and NCSC are able to increase expression of keratins 8, 14, 19, and vimentin in the co-cultured HPK. This in vitro finding partially correlates with pseudoepitheliomatous hyperplasia observed in melanoma biopsies. We provide evidence of FGF-2, CXCL-1, IL-8, and VEGF-A participation in the activity of melanoma cells on keratinocytes.ConclusionWe conclude that the MC are able to influence locally the differentiation pattern of keratinocytes in vivo as well as in vitro. This interaction further highlights the role of intercellular interactions in melanoma. The reciprocal role of activated keratinocytes on biology of melanoma cells shall be verified in the future.Electronic supplementary materialThe online version of this article (doi:10.1186/1476-4598-14-1) contains supplementary material, which is available to authorized users.

Graphical Abstract Highlights d Tumorigenesis depends on functional OXPHOS d OXPHOS-derived ATP is not required for tumor formation d DHODH-driven pyrimidine biosynthesis requires CoQ redoxcycling d CoQ redox-cycling via OXPHOS drives tumorigenesis through pyrimidine biosynthesis

Animal eyes are morphologically diverse. Their assembly, however, always relies on the same basic principle, i.e., photoreceptors located in the vicinity of dark shielding pigment. Cnidaria as the likely sister group to the Bilateria are the earliest branching phylum with a well developed visual system. Here, we show that cameratype eyes of the cubozoan jellyfish, Tripedalia cystophora, use genetic building blocks typical of vertebrate eyes, namely, a ciliary phototransduction cascade and melanogenic pathway. Our findings indicative of parallelism provide an insight into eye evolution. Combined, the available data favor the possibility that vertebrate and cubozoan eyes arose by independent recruitment of orthologous genes during evolution.T he assembly of diverse animal eyes requires two fundamental building blocks, photoreceptors and dark shielding pigment. The function of photoreceptors is to convert light (stream of photons) into intracellular signaling. The photoreceptor cells (PRCs) are classified into two distinct types: rhabdomeric, characteristic of vision in invertebrate eyes; and ciliary, characteristic of vision in vertebrate eyes (1). In both ciliary and rhabdomeric PRCs, the seven-transmembrane receptor (opsin) associates with retinal to constitute a functional photosensitive pigment. Each photoreceptor type uses a separate phototransduction cascade. Rhabdomeric photoreceptors employ r-opsins and a phospholipase C cascade, whereas ciliary photoreceptors use c-opsins and a phosphodiesterase (PDE) cascade (2, 3). In general, the dark pigment reduces photon scatter and orients the direction optimally sensitive to light. The biochemical nature of the dark pigment appears more diverse than the phototransduction cascades used by the PRCs. Vertebrate eyes use melanin as their exclusive dark pigment. However, among invertebrates, pterins constitute the eye pigment in the polychaete Platynereis dumerilii (4), pterins and ommochromes are accumulated in eyes of Drosophila (5), and melanin is found rarely such as in the inverse cup-like eyes of the planarian, Dugesia (6).Cnidaria, the likely sister group to the Bilateria, constitute the earliest branching phylum containing a well developed visual system. For example, Cubozoa (known as ''box jellyfish'') have camera-type eyes with cornea, lens, and retina; unexpectedly, the cubozoan retina has ciliated PRCs that are typical for vertebrate eyes (7-9). Cubomedusae are active swimmers that are able to make directional changes in response to visual stimuli (10). The cubozoan jellyfish, Tripedalia cystophora (Fig. 1A), has four sensory structures called rhopalia that are equally spaced around the bell. In addition to two camera-type lens containing eyes at right angles to one another, each rhopalium has two pit-shaped and two slit-shaped pigment cup eyes (Fig. 1B). Thus, with six eyes located on each rhopalium, Tripedalia has 24 eyes altogether. Because the visual fields of individual eyes of the rhopalium partly overlap, Tripedalia (like other Cubomedusae) has an al...

Heterorhabditis bacteriophora is an entomopathogenic nematode (EPN) which infects its host by accessing the hemolymph where it releases endosymbiotic bacteria of the species Photorhabdus luminescens. We performed a genome-wide transcriptional analysis of the Drosophila response to EPN infection at the time point at which the nematodes reached the hemolymph either via the cuticle or the gut and the bacteria had started to multiply. Many of the most strongly induced genes have been implicated in immune responses in other infection models. Mapping of the complete set of differentially regulated genes showed the hallmarks of a wound response, but also identified a large fraction of EPN-specific transcripts. Several genes identified by transcriptome profiling or their homologues play protective roles during nematode infections. Genes that positively contribute to controlling nematobacterial infections encode: a homolog of thioester-containing complement protein 3, a basement membrane component (glutactin), a recognition protein (GNBP-like 3) and possibly several small peptides. Of note is that several of these genes have not previously been implicated in immune responses.

The purple nonsulfur photosynthetic bacterium Rhodobacter capsulatus has been extensively studied for its metabolic versatility as well as for production of a gene transfer agent called RcGTA. Production of RcGTA is highest in the stationary phase of growth and requires the response regulator protein CtrA. The CtrA protein in Caulobacter crescentus has been thoroughly studied for its role as an essential, master regulator of the cell cycle. Although the CtrA protein in R. capsulatus shares a high degree of sequence similarity with the C. crescentus protein, it is nonessential and clearly plays a different role in this bacterium. We have used transcriptomic and proteomic analyses of wild-type and ctrA mutant cultures to identify the genes dysregulated by the loss of CtrA in R. capsulatus. We have also characterized gene expression differences between the logarithmic and stationary phases of growth. Loss of CtrA has pleiotropic effects, with dysregulation of expression of ϳ6% of genes in the R. capsulatus genome. This includes all flagellar motility genes and a number of other putative regulatory proteins but does not appear to include any genes involved in the cell cycle. Quantitative proteomic data supported 88% of the CtrA transcriptome results. Phylogenetic analysis of CtrA sequences supports the hypothesis of an ancestral ctrA gene within the alphaproteobacteria, with subsequent diversification of function in the major alphaproteobacterial lineages.The purple nonsulfur bacterium Rhodobacter capsulatus is a model organism for various aspects of bacterial physiology, such as bioenergetics and N 2 fixation, and also engages in an unusual mechanism of genetic exchange, carried out by a bacteriophage-like element called the R. capsulatus gene transfer agent (RcGTA) (34, 56). The production of RcGTA is maximal in the stationary phase of growth of R. capsulatus cultures (49) and is regulated by at least 2 distinct signaling systems, one through quorum sensing of a long chain acyl-homoserine lactone (43) and the other involving the response regulator protein CtrA (30).The CtrA protein was first characterized for Caulobacter crescentus (41), where it is essential for viability and acts as a master regulator of the cell cycle (reviewed in reference 45), controlling at least 25% (144 of 553) of the genes involved in cell cycle progression (31). Despite sharing remarkable sequence identity (71%) with the CtrA protein from C. crescentus, the R. capsulatus protein has a very different role because it is not essential and does not appear to be involved in cell cycle processes. One function of CtrA in common to the two species is the regulation of expression of genes that encode the flagellum (29, 41). The ctrA genes of Sinorhizobium meliloti (3), Brucella abortus (6), and Ruegeria sp. strain TM1040 (36) have also been studied. Similarly to C. crescentus and R. capsulatus CtrA, Ruegeria CtrA controls motility (36). A search of the GenBank database reveals that convincing homologs which share Ͼ50% identity with the C. crescen...

T-cell factor/lymphoid enhancer-binding factor (TCF/LEF) proteins (TCFs) from the High Mobility Group (HMG) box family act as the main downstream effectors of the Wnt signaling pathway. The mammalian TCF/LEF family comprises four nuclear factors designated TCF7, LEF1, TCF7L1, and TCF7L2 (also known as TCF1, LEF1, TCF3, and TCF4, respectively). The proteins display common structural features and are often expressed in overlapping patterns implying their redundancy. Such redundancy was indeed observed in gene targeting studies; however, individual family members also exhibit unique features that are not recapitulated by the related proteins. In the present viewpoint, we summarized our current knowledge about the specific features of individual TCFs, namely structural-functional studies, posttranslational modifications, interacting partners, and phenotypes obtained upon gene targeting in the mouse. In addition, we employed several publicly available databases and web tools to evaluate the expression patterns and production of gene-specific isoforms of the TCF/LEF family members in human cells and tissues.

BackgroundIn models extensively used in studies of aging and extended lifespan, such as C. elegans and Drosophila, adult senescence is regulated by gene networks that are likely to be similar to ones that underlie lifespan extension during dormancy. These include the evolutionarily conserved insulin/IGF, TOR and germ line-signaling pathways. Dormancy, also known as dauer stage in the larval worm or adult diapause in the fly, is triggered by adverse environmental conditions, and results in drastically extended lifespan with negligible senescence. It is furthermore characterized by increased stress resistance and somatic maintenance, developmental arrest and reallocated energy resources. In the fly Drosophila melanogaster adult reproductive diapause is additionally manifested in arrested ovary development, improved immune defense and altered metabolism. However, the molecular mechanisms behind this adaptive lifespan extension are not well understood.ResultsA genome wide analysis of transcript changes in diapausing D. melanogaster revealed a differential regulation of more than 4600 genes. Gene ontology (GO) and KEGG pathway analysis reveal that many of these genes are part of signaling pathways that regulate metabolism, stress responses, detoxification, immunity, protein synthesis and processes during aging. More specifically, gene readouts and detailed mapping of the pathways indicate downregulation of insulin-IGF (IIS), target of rapamycin (TOR) and MAP kinase signaling, whereas Toll-dependent immune signaling, Jun-N-terminal kinase (JNK) and Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathways are upregulated during diapause. Furthermore, we detected transcriptional regulation of a large number of genes specifically associated with aging and longevity.ConclusionsWe find that many affected genes and signal pathways are shared between dormancy, aging and lifespan extension, including IIS, TOR, JAK/STAT and JNK. A substantial fraction of the genes affected by diapause have also been found to alter their expression in response to starvation and cold exposure in D. melanogaster, and the pathways overlap those reported in GO analysis of other invertebrates in dormancy or even hibernating mammals. Our study, thus, shows that D. melanogaster is a genetically tractable model for dormancy in other organisms and effects of dormancy on aging and lifespan.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2383-1) contains supplementary material, which is available to authorized users.

Animals sense light primarily by an opsin-based photopigment present in a photoreceptor cell. Cnidaria are arguably the most basal phylum containing a well-developed visual system. The evolutionary history of opsins in the animal kingdom has not yet been resolved. Here, we study the evolution of animal opsins by genome-wide analysis of the cubozoan jellyfish Tripedalia cystophora, a cnidarian possessing complex lens-containing eyes and minor photoreceptors. A large number of opsin genes with distinct tissue- and stage-specific expression were identified. Our phylogenetic analysis unequivocally classifies cubozoan opsins as a sister group to c-opsins and documents lineage-specific expansion of the opsin gene repertoire in the cubozoan genome. Functional analyses provided evidence for the use of the Gs-cAMP signaling pathway in a small set of cubozoan opsins, indicating the possibility that the majority of other cubozoan opsins signal via distinct pathways. Additionally, these tests uncovered subtle differences among individual opsins, suggesting possible fine-tuning for specific photoreceptor tasks. Based on phylogenetic, expression and biochemical analysis we propose that rapid lineage- and species-specific duplications of the intron-less opsin genes and their subsequent functional diversification promoted evolution of a large repertoire of both visual and extraocular photoreceptors in cubozoans.