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Arthrospira platensis, a blue‐green alga, is a popular nutraceutical substance having potent antioxidant properties with potential anti‐carcinogenic activities. The aim of our study was to assess the possible anti‐angiogenic effects of A platensis in an experimental model of pancreatic cancer. The effects of an A platensis extract were investigated on human pancreatic cancer cells (PA‐TU‐8902) and immortalized endothelial‐like cells (Ea.hy926). PA‐TU‐8902 pancreatic tumours xenografted to athymic mice were also examined. In vitro migration and invasiveness assays were performed on the tested cells. Multiple angiogenic factors and signalling pathways were analysed in the epithelial, endothelial and cancer cells, and tumour tissue. The A platensis extract exerted inhibitory effects on both migration and invasion of pancreatic cancer as well as endothelial‐like cells. Tumours of mice treated with A platensis exhibited much lesser degrees of vascularization as measured by CD31 immunostaining (P = .004). Surprisingly, the VEGF‐A mRNA and protein expressions were up‐regulated in pancreatic cancer cells. A platensis inhibited ERK activation upstream of Raf and suppressed the expression of ERK‐regulated proteins. Treatment of pancreatic cancer with A platensis was associated with suppressive effects on migration and invasiveness with various anti‐angiogenic features, which might account for the anticancer effects of this blue‐green alga.

Background/Aim: Pancreatic ductal adenocarcinoma (PDAC) still represents one of the most aggressive cancers. Understanding of the epithelial–mesenchymal crosstalk as a crucial part of the tumor microenvironment should pave the way for therapies to improve patient survival rates. Well-established cell lines present a useful and reproducible model to study PDAC biology. However, the tumor–stromal interactions between cancer cells and cancer–associated fibroblasts (CAFs) are still poorly understood. Materials and Methods: We studied interactions between four PDAC cell lines (Panc-1, CAPAN-2, MIAPaCa-2, and PaTu-8902) and conditioned media derived from primary cultures of normal fibroblasts/PDAC–derived CAFs (PANFs). Results: When the tested PDAC cell lines were stimulated by PANF–derived conditioned media, the most aggressive behavior was acquired by the Panc-1 cell line (increased number and size of colonies, remaining expression of vimentin and keratin 8 as well as increase of epithelial-to-mesenchymal polarization markers), whereas PaTu-8902 cells were rather inhibited. Of note, administration of the conditioned media to MIAPaCa-2 cells resulted in an inverse effect on the size and number of colonies, whereas CAPAN-2 cells were rather stimulated. To explain the heterogeneous pattern of the observed PDAC crosstalk at the in vitro level, we further compared the phenotype of primary cultures of cells derived from ascitic fluid with that of the tested PDAC cell lines, analyzed tumor samples of PDAC patients, and performed gene expression profiling of PANFs. Immuno-cyto/histo-chemical analysis found specific phenotype differences within the group of examined patients and tested PDAC cell lines, whereas the genomic approach in PANFs found the key molecules (IL6, IL8, MFGE8 and periostin) that may contribute to the cancer aggressive behavior. Conclusion: The desmoplastic patient-specific regulation of cancer cells by CAFs (also demonstrated by the heterogeneous response of PDAC cell lines to fibroblasts) precludes simple targeting and development of an effective treatment strategy and rather requires establishment of an individualized tumor–specific treatment protocol.

In this study, following its isolation from contaminated soil, the genomic sequence of Pseudomonas alcaliphila strain JAB1 (=DSM 26533), a biphenyl-degrading bacterium, is reported and analyzed in relation to its extensive degradative capabilities. The P. alcaliphila JAB1 genome (GenBank accession no. CP016162) consists of a single 5.34 Mbp-long chromosome with a GC content of 62.5%. Gene function was assigned to 3816 of the 4908 predicted genes. The genome harbors a bph gene cluster, permitting degradation of biphenyl and many congeners of polychlorinated biphenyls (PCBs), a ben gene cluster, enabling benzoate and its derivatives to be degraded, and phe gene cluster, which permits phenol degradation. In addition, P. alcaliphila JAB1 is capable of cometabolically degrading cis-1,2-dichloroethylene (cDCE) when grown on phenol. The strain carries both catechol and protocatechuate branches of the β-ketoadipate pathway, which is used to funnel the pollutants to the central metabolism. Furthermore, we propose that clustering of MALDI-TOF MS spectra with closest phylogenetic relatives should be used when taxonomically classifying the isolated bacterium; this, together with 16S rRNA gene sequence and chemotaxonomic data analyses, enables more precise identification of the culture at the species level. Electronic supplementary material The online version of this article (10.1186/s40793-017-0306-7) contains supplementary material, which is available to authorized users.

Neoplastic growth is frequently associated with genomic DNA methylation that causes transcriptional silencing of tumor suppressor genes. We used a collection of colorectal polyps and carcinomas in combination with bioinformatics analysis of large datasets to study the expression and methylation of Hypermethylated in cancer 1 (HIC1), a tumor suppressor gene inactivated in many neoplasms. In premalignant stages, HIC1 expression was decreased, and the decrease was linked to methylation of a specific region in the HIC1 locus. However, in carcinomas, the HIC1 expression was variable and, in some specimens, comparable to healthy tissue. Importantly, high HIC1 production distinguished a specific type of chemotherapy-responsive tumors.

Description of five regions harboring genes for aromatic compound degradation pathways were identified in the JAB1 genome. (DOCX 34 kb)

List of primers used for quantitative real-time PCR analyses. Table S4. Quantitative RT PCR analysis of selected genes. (DOCX 18 kb)

List of primers used for quantitative real-time PCR analyses. Table S4. Quantitative RT PCR analysis of selected genes. (DOCX 18 kb)

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

Term enrichment analysis of GO biological process terms for comparisons among four genome-wide transcription studies of D. melanogaster. 3wD, three weeks diapause (whole animals) our study; 1wD, abdomens sampled after one week diapause [140]; cold intolerance [141] and starvation [143]. Comparison based on genes in the Venn diagram in Fig. 10b. Term analysis of Groups A – H are shown separately. (PDF 1267 kb)

GSEA of KEGG pathway analysis. (A) The set of KEGG pathways enriched for upregulated genes encompass mostly carbohydrate metabolic pathways, drug metabolism and circadian rhythm pathway. (B) The set of KEGG pathways enriched for downregulated genes covers mostly RNA and DNA metabolism and protein degradation. Genes with |log2FC| ≥ 0.04 and q ≤ 0.05 were considered significantly regulated. Pathways highlighted in italics were defined only on the basis of experiments performed in mammalian systems. (PDF 45 kb)

SPIA of KEGG pathways. Significantly inhibited pathways are highlighted in blue and significantly activated ones in orange. Genes with |log2FC| ≥ 0.1 and q ≤ 0.05 were considered significantly regulated. Pathways highlighted in italics were defined only on the basis of experiments performed in mammalian systems. (PDF 42 kb)

Supplementary figures S1 to S3

Results of overrepresentation test of GO biological process terms for comparisons between our genome-wide transcription study of D. melanogaster dormancy and aging studies. 3wD, three weeks diapause (whole animals) our study; Aging, aging response genes [136] and candidate lifespan extending genes [135]. Comparison based on genes in the Venn diagram in Fig. 10a. Term enrichment analysis of Groups A – D are shown separately. (PDF 405 kb)

SPIA of KEGG pathways. Significantly inhibited pathways are highlighted in blue and significantly activated ones in orange. Genes with |log2FC| ≥ 0.1 and q ≤ 0.05 were considered significantly regulated. Pathways highlighted in italics were defined only on the basis of experiments performed in mammalian systems. (PDF 42 kb)

GSEA of KEGG pathway analysis. (A) The set of KEGG pathways enriched for upregulated genes encompass mostly carbohydrate metabolic pathways, drug metabolism and circadian rhythm pathway. (B) The set of KEGG pathways enriched for downregulated genes covers mostly RNA and DNA metabolism and protein degradation. Genes with |log2FC| ≥ 0.04 and q ≤ 0.05 were considered significantly regulated. Pathways highlighted in italics were defined only on the basis of experiments performed in mammalian systems. (PDF 45 kb)

Primers used for quantitative real-time PCR. (PDF 55 kb)

Detailed data on genes in seven signal pathways. Description of genes shown in Figs. 4, 5, 7, 9 and Additional file 8: Figure S4 and discussed in the corresponding sections of the paper. References are also given for these genes. Note that the genes are listed as they are shown in the figures (from top to bottom in the pathways). (PDF 328 kb)

Acquisition of genes by plastid genomes (plastomes) via horizontal gene transfer (HGT) seems to be a rare phenomenon. Here, we report an interesting case of HGT revealed by sequencing the plastomes of the eustigmatophyte algae Monodopsis sp. MarTras21 and Vischeria sp. CAUP Q 202. These plastomes proved to harbour a unique cluster of six genes, most probably acquired from a bacterium of the phylum Bacteroidetes, with homologues in various bacteria, typically organized in a conserved uncharacterized putative operon. Sequence analyses of the six proteins encoded by the operon yielded the following annotation for them: (i) a novel family without discernible homologues; (ii) a new family within the superfamily of metallo-dependent hydrolases; (iii) a novel subgroup of the UbiA superfamily of prenyl transferases; (iv) a new clade within the sugar phosphate cyclase superfamily; (v) a new family within the xylose isomerase-like superfamily; and (vi) a hydrolase for a phosphate moiety-containing substrate. We suggest that the operon encodes enzymes of a pathway synthesizing an isoprenoid–cyclitol-derived compound, possibly an antimicrobial or other protective substance. To the best of our knowledge, this is the first report of an expansion of the metabolic capacity of a plastid mediated by HGT into the plastid genome.

Detailed data on genes in seven signal pathways. Description of genes shown in Figs. 4, 5, 7, 9 and Additional file 8: Figure S4 and discussed in the corresponding sections of the paper. References are also given for these genes. Note that the genes are listed as they are shown in the figures (from top to bottom in the pathways). (PDF 328 kb)

Background Statins (HMG-CoA reductase inhibitors) represent a major class of compounds for the treatment of hypercholesterolemia due to their ability to inhibit de novo cholesterol synthesis. In addition to their hypolipidemic effects, chemoprotective properties have been attributed to statins as well. These effects involve multiple mechanisms, which, however, are not known in detail. The aim of our study was to assess in non-malignant as well as cancer cells the impact of simvastatin on the amount of cytosolic lipid droplets (LDs) implicated in many biological processes including proliferation, inflammation, carcinogenesis, apoptosis, necrosis or growth arrest. Methods Human embryonic kidney cells HEK-293T and human pancreatic cancer cells MiaPaCa-2 were treated with simvastatin (6 and 12 μM) for 24 and 48 hours respectively. Neutral lipid probe Nile Red was used for detection of LDs by fluorescence microscopy. Cellular cholesterol content was determined by HPLC. Changes in expression of genes related to lipid metabolism in simvastatin-treated MiaPaCa-2 cells were examined by DNA microarray analysis. Validation of gene expression changes was performed using quantitative RT-PCR. Results The treatment of the cells with simvastatin increased their intracellular content of LDs in both non-malignant as well as cancer cells, partially due to the uptake of cholesterol and triacylglyceroles from medium; but in particular, due to enhanced synthesis of triacylglyceroles as proved by significant overexpression of genes related to de novo synthesis of triacylglyceroles and phospholipids. In addition, simvastatin also markedly influenced expression of genes directly affecting cell proliferation and signaling. Conclusions Simvastatin treatment led to accumulation of cytosolic LDs within the examined cells, a phenomenon which might contribute to the antiproliferative effects of statins.

Scientific reports 7, 15783 (2017). doi:10.1038/s41598-017-16132-8, Published by Nature Publishing Group, London