Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database

<p>Abstract</p> <p>Background</p> <p><it>Porphyromonas gingivalis </it>is a Gram-negative intracellular pathogen associated with periodontal disease. We have previously reported on whole-cell quantitative proteomic analyses to investigate the differential expression of virulence factors as the organism transitions from an extracellular to intracellular lifestyle. The original results with the invasive strain <it>P. gingivalis </it>ATCC 33277 were obtained using the genome sequence available at the time, strain W83 [GenBank: <ext-link ext-link-id="AE015924" ext-link-type="gen">AE015924</ext-link>]. We present here a re-processed dataset using the recently published genome annotation specific for strain ATCC 33277 [GenBank: <ext-link ext-link-id="AP009380" ext-link-type="gen">AP009380</ext-link>] and an analysis of differential abundance based on metabolic pathways rather than individual proteins.</p> <p>Results</p> <p>Qualitative detection was observed for 1266 proteins using the strain ATCC 33277 annotation for 18 hour internalized <it>P. gingivalis </it>within human gingival epithelial cells and controls exposed to gingival cell culture medium, an improvement of 7% over the W83 annotation. Internalized cells showed increased abundance of proteins in the energy pathway from asparagine/aspartate amino acids to ATP. The pathway producing one short chain fatty acid, propionate, showed increased abundance, while that of another, butyrate, trended towards decreased abundance. The translational machinery, including ribosomal proteins and tRNA synthetases, showed a significant increase in protein relative abundance, as did proteins responsible for transcription.</p> <p>Conclusion</p> <p>Use of the ATCC 33277 specific genome annotation resulted in improved proteome coverage with respect to the number of proteins observed both qualitatively in terms of protein identifications and quantitatively in terms of the number of calculated abundance ratios. Pathway analysis showed a significant increase in overall protein synthetic and transcriptional machinery in the absence of significant growth. These results suggest that the interior of host cells provides a more energy rich environment compared to the extracellular milieu. Shifts in the production of cytotoxic fatty acids by intracellular <it>P. gingivalis </it>may play a role in virulence. Moreover, despite extensive genomic re-arrangements between strains W83 and 33277, there is sufficient sequence similarity at the peptide level for proteomic abundance trends to be largely accurate when using the heterologous strain annotated genome as the reference for database searching.</p

Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis

<p>Abstract</p> <p>Background</p> <p>Methanogenic Archaea play key metabolic roles in anaerobic ecosystems, where they use H₂and other substrates to produce methane. <it>Methanococcus maripaludis </it>is a model for studies of the global response to nutrient limitations.</p> <p>Results</p> <p>We used high-coverage quantitative proteomics to determine the response of <it>M. maripaludis </it>to growth-limiting levels of H₂, nitrogen, and phosphate. Six to ten percent of the proteome changed significantly with each nutrient limitation. H₂limitation increased the abundance of a wide variety of proteins involved in methanogenesis. However, one protein involved in methanogenesis decreased: a low-affinity [Fe] hydrogenase, which may dominate over a higher-affinity mechanism when H₂is abundant. Nitrogen limitation increased known nitrogen assimilation proteins. In addition, the increased abundance of molybdate transport proteins suggested they function for nitrogen fixation. An apparent regulon governed by the euryarchaeal nitrogen regulator NrpR is discussed. Phosphate limitation increased the abundance of three different sets of proteins, suggesting that all three function in phosphate transport.</p> <p>Conclusion</p> <p>The global proteomic response of <it>M. maripaludis </it>to each nutrient limitation suggests a wider response than previously appreciated. The results give new insight into the function of several proteins, as well as providing information that should contribute to the formulation of a regulatory network model.</p

Radiogenomics analysis reveals the associations of dynamic contrast-enhanced–MRI features with gene expression characteristics, PAM50 subtypes, and prognosis of breast cancer

BackgroundTo investigate reliable associations between dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) features and gene expression characteristics in breast cancer (BC) and to develop and validate classifiers for predicting PAM50 subtypes and prognosis from DCE-MRI non-invasively.MethodsTwo radiogenomics cohorts with paired DCE-MRI and RNA-sequencing (RNA-seq) data were collected from local and public databases and divided into discovery (n = 174) and validation cohorts (n = 72). Six external datasets (n = 1,443) were used for prognostic validation. Spatial–temporal features of DCE-MRI were extracted, normalized properly, and associated with gene expression to identify the imaging features that can indicate subtypes and prognosis.ResultsExpression of genes including RBP4, MYBL2, and LINC00993 correlated significantly with DCE-MRI features (q-value &lt; 0.05). Importantly, genes in the cell cycle pathway exhibited a significant association with imaging features (p-value &lt; 0.001). With eight imaging-associated genes (CHEK1, TTK, CDC45, BUB1B, PLK1, E2F1, CDC20, and CDC25A), we developed a radiogenomics prognostic signature that can distinguish BC outcomes in multiple datasets well. High expression of the signature indicated a poor prognosis (p-values &lt; 0.01). Based on DCE-MRI features, we established classifiers to predict BC clinical receptors, PAM50 subtypes, and prognostic gene sets. The imaging-based machine learning classifiers performed well in the independent dataset (areas under the receiver operating characteristic curve (AUCs) of 0.8361, 0.809, 0.7742, and 0.7277 for estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2)-enriched, basal-like, and obtained radiogenomics signature). Furthermore, we developed a prognostic model directly using DCE-MRI features (p-value &lt; 0.0001).ConclusionsOur results identified the DCE-MRI features that are robust and associated with the gene expression in BC and displayed the possibility of using the features to predict clinical receptors and PAM50 subtypes and to indicate BC prognosis

Phenformin Induces Cell Cycle Change, Apoptosis, and Mesenchymal-Epithelial Transition and Regulates the AMPK/mTOR/p70s6k and MAPK/ERK Pathways in Breast Cancer Cells.

Breast cancer remains a world-wide challenge, and additional anti-cancer therapies are still urgently needed. Emerging evidence has demonstrated the potent anti-tumor effect of biguanides, among which phenformin was reported to potentially be a more active anti-cancer agent than metformin. However, little attention has been given to the role of phenformin in breast cancer. In this study, we reveal the role of phenformin in cell death of the MCF7, ZR-75-1, MDA-MB-231 and SUM1315 breast cancer cell lines. The respective IC50 values of phenformin in MCF7, ZR-75-1, MDA-MB-231 and SUM1315 cells were 1.184±0.045 mM, 0.665±0.007 mM, 2.347±0.010 mM and 1.885±0.015 mM (mean± standard error). Phenformin induced cell cycle change and apoptosis in breast cancer cells via the AMPK/mTOR/p70s6k and MAPK/ERK pathways. Interestingly, phenformin induced MET (mesenchymal-epithelial transition) and decreased the migration rate in breast cancer cell lines. Furthermore, our results suggest that phenformin inhibits breast cancer cell metastasis after intracardiac injection into nude mice. Taken together, our study further confirms the potential benefit of phenformin in breast cancer treatment and provides novel mechanistic insight into its anti-cancer activity in breast cancer

Percutaneous microwave coagulation for eradication of VX2 tumors subcutaneously in rabbits

Abstract Background Percutaneous microwave coagulation (PMC) has been accepted as a promising modality in the treatment of tumors in well-vascularized tissues such as liver tumors and hysteromyoma. However, PMC for treatment of tumors in low blood-flow tissues has been seldom reported. The aim of this study was to determine the feasibility and safety of PMC for the treatment of tumors in low blood-flow tissues in a rabbit model. Methods Fifteen rabbits with VX2 tumors implanted subcutaneously underneath the right second nipple were divided into a PMC group (n = 9) and a control group (n = 6). PMC was performed with output power of 40 W for one to two minutes. The therapeutic efficacy was evaluated by magnetic resonance imaging (MRI), physical examinations, survival rate, and histology. The cosmetic outcome after PMC was also assessed. Results In the PMC group, tumor eradication was achieved in six rabbits (66.7%) without any evidence of tumor recurrence and metastasis as proven by MRI and histological examinations. The mean greatest and shortest tumor diameters of these six rabbits were 1.83 and 1.33 cm, respectively. Slight epidermal burns, which proved reversible, were found in seven rabbits (77.8%). The PMC group had a significantly longer survival than those in the control group (P = 0.0097). The four rabbits with coagulated tumors survived more than three months with their tumors becoming nonpalpable and undetectable by MRI and histological examinations. Conclusions PMC is feasible and safe in the treatment of tumors in low blood-flow tissues in a rabbit model. Attention should be paid to avoid skin burns with PMC.</p

Phenformin inhibits the metastasis of MDA-MB-231 cells in nude mice.

<p>(A) The luciferase-tagged MDA-MB-231 cells were inoculated intracardially into female nude mice. After the injections, the mice were separated into the control and phenformin groups (10 mice per group). The control group’s drinking water was replaced with 5% sucrose. The phenformin group’s drinking water was replaced with 5% sucrose containing phenformin (300 mgkg^-1). The development of metastasis was monitored using whole mouse fluorescence and bioluminescence imaging(negative control: mice did not receive an intracardiac injection of luciferase-expressing cells). (B)Four weeks after the intracardiac injections, the total flux signals in the control group were significantly higher than those in the phenformin group (p = 0.0065). The data are presented as the mean±SEM and the Wilcoxon rank sum test was used to identify significant differences in total flux between the control and phenformin- treated animals.</p