A Multi-Skilled Mathematical Model of Bacterial Attachment in Initiation of Biofilms.

The initial step of biofilm formation is bacteria attachment to biotic or abiotic surfaces and other bacteria through intra or interspecies interactions. Adhesion can be influenced by physicochemical conditions of the environment, such as iron. There is no available mathematical model of bacterial attachment giving realistic initiation rather than random adhesion. We describe a simple stochastic attachment model, from the simplest case in two dimensions with one bacterial species attaching on a homogeneous flat surface to more complex situations, with either several bacterial species, inhomogeneous or non-flat surfaces, or in three dimensions. The model depends on attachment probabilities (on the surface, laterally, or vertically on bacteria). Effects of each of these parameters were analyzed. This mathematical model is then applied to experimental oral microcolonies of Porphyromonas gingivalis, Streptococcus gordonii, and Treponema denticola, either as mono-, two, or three species, under different iron concentrations. The model allows to characterize the adhesion of three bacterial species and explore the effect of iron on attachment. This model appears as a powerful tool for initial attachment analysis of bacterial species. It will enable further modeling of biofilm formation in later steps with biofilm initialization more relevant to real-life subgingival biofilms.

Method for screening antimicrobial gels against multi-species oral biofilms.

We described a microtiter plate-based method that was effectively tailored for testing gel formulations against oral multispecies biofilms established on peg-lids. This method lifts the limitations imposed mainly by the anaerobic nature of the targeted bacterial species and the viscous properties of the targeted treatments.

The events that may contribute to subgingival dysbiosis: a focus on the interplay between iron, sulfide and oxygen.

This minireview considers the disruption of the host-microbiota harmless symbiosis in the subgingival niche. The establishment of a chronic infection by subversion of a commensal microbiota results from a complex and multiparametric sequence of events. This review narrows down to the interplay between oxygen, iron and sulfide that can result in a vicious cycle that would favor peroxygenic and glutathione producing streptococci as well as sulfidogenic anaerobic pathogens in the subgingival niche. We propose hypothesis and discuss strategies for the therapeutic modulation of the microbiota to prevent periodontitis and promote oral health.

Periodontal pathogens and clinical parameters in chronic periodontitis.

The use of next generation sequencing and bioinformatics has revealed the complexity and richness of the human oral microbiota. While some species are well known for their periodontal pathogenicity, the molecular-based approaches for bacterial identification have raised awareness about new putative periodontal pathogens. Although they are found increased in case of periodontitis, there is currently a lack of data on their interrelationship with the periodontal measures. We processed the sequencing data of the subgingival microbiota of 75 patients with hemochromatosis and chronic periodontitis in order to characterize the well-described and newly identified subgingival periodontal pathogens. We used correlation tests and statistical models to assess the association between the periodontal pathogens and mean pocket depth, and to determine the most relevant bacterial biomarkers of periodontitis severity. Based on correlation test results, nine taxa were selected and included in the statistical models. The multiple linear regression models adjusted for systemic and periodontal clinical variables showed that mean pocket depth was negatively associated with Aggregatibacter and Rothia, and positively associated with Porphyromonas. Furthermore, a bacterial ratio that was previously described as a signature of dysbiosis in periodontitis (%Porphyromonas+%Treponema+%Tannerella)/(%Rothia+%Corynebacterium) was the most significant predictor. In this specific population, we found that the best model in predicting the mean pocket depth was microbial dysbiosis using the dysbiosis ratio taxa formula. While further studies are needed to assess the validity of these results on the general population, such a dysbiosis ratio could be used in the future to monitor the subgingival microbiota.

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis.

Genetic haemochromatosis (GH) is responsible for iron overload. Increased transferrin saturation (TSAT) has been associated with severe periodontitis, which is a chronic inflammatory disease affecting tissues surrounding the teeth and is related to dysbiosis of the subgingival microbiota. Because iron is essential for bacterial pathogens, alterations in iron homeostasis can drive dysbiosis. To unravel the relationships between serum iron biomarkers and the subgingival microbiota, we analysed samples from 66 GH patients. The co-occurrence analysis of the microbiota showed very different patterns according to TSAT. Healthy and periopathogenic bacterial clusters were found to compete in patients with normal TSAT (≤45%). However, significant correlations were found between TSAT and the proportions of Porphyromonas and Treponema, which are two genera that contain well-known periopathogenic species. In patients with high TSAT, the bacterial clusters exhibited no mutual exclusion. Increased iron bioavailability worsened periodontitis and promoted periopathogenic bacteria, such as Treponema. The radical changes in host-bacteria relationships and bacterial co-occurrence patterns according to the TSAT level also suggested a shift in the bacterial iron supply from transferrin to NTBI when TSAT exceeded 45%. Taken together, these results indicate that iron bioavailability in biological fluids is part of the equilibrium between the host and its microbiota.

New growth media for oral bacteria.

New growth media have been designed for the iron-controlled co-cultures of three oral bacteria. These media share a common core composition enabling the switch from mono- to co-cultures, and efficiently promote both planktonic and biofilm cultures of Porphyromonas gingivalis, Treponema denticola and Streptococcus gordonii.

Signature of Microbial Dysbiosis in Periodontitis.

Periodontitis is driven by disproportionate host inflammatory immune responses induced by an imbalance in the composition of oral bacteria; this instigates microbial dysbiosis, along with failed resolution of the chronic destructive inflammation. The objectives of this study were to identify microbial signatures for health and chronic periodontitis at the genus level and to propose a model of dysbiosis, including the calculation of bacterial ratios. Published sequencing data obtained from several different studies (196 subgingival samples from patients with chronic periodontitis and 422 subgingival samples from healthy subjects) were pooled and subjected to a new microbiota analysis using the same Visualization and Analysis of Microbial Population Structures (VAMPS) pipeline, to identify microbiota specific to health and disease. Microbiota were visualized using CoNet and Cytoscape. Dysbiosis ratios, defined as the percentage of genera associated with disease relative to the percentage of genera associated with health, were calculated to distinguish disease from health. Correlations between the proposed dysbiosis ratio and the periodontal pocket depth were tested with a different set of data obtained from a recent study, to confirm the relevance of the ratio as a potential indicator of dysbiosis. Beta diversity showed significant clustering of periodontitis-associated microbiota, at the genus level, according to the clinical status and independent of the methods used. Specific genera (Veillonella, Neisseria, Rothia, Corynebacterium, and Actinomyces) were highly prevalent (>95%) in health, while other genera (Eubacterium, Campylobacter, Treponema, and Tannerella) were associated with chronic periodontitis. The calculation of dysbiosis ratios based on the relative abundance of the genera found in health versus periodontitis was tested. Nonperiodontitis samples were significantly identifiable by low ratios, compared to chronic periodontitis samples. When applied to a subgingival sample set with well-defined clinical data, the method showed a strong correlation between the dysbiosis ratio, as well as a simplified ratio (Porphyromonas, Treponema, and Tannerella to Rothia and Corynebacterium), and pocket depth. Microbial analysis of chronic periodontitis can be correlated with the pocket depth through specific signatures for microbial dysbiosis.IMPORTANCE Defining microbiota typical of oral health or chronic periodontitis is difficult. The evaluation of periodontal disease is currently based on probing of the periodontal pocket. However, the status of pockets "on the mend" or sulci at risk of periodontitis cannot be addressed solely through pocket depth measurements or current microbiological tests available for practitioners. Thus, a more specific microbiological measure of dysbiosis could help in future diagnoses of periodontitis. In this work, data from different studies were pooled, to improve the accuracy of the results. However, analysis of multiple species from different studies intensified the bacterial network and complicated the search for reproducible microbial signatures. Despite the use of different methods in each study, investigation of the microbiota at the genus level showed that some genera were prevalent (up to 95% of the samples) in health or disease, allowing the calculation of bacterial ratios (i.e., dysbiosis ratios). The correlation between the proposed ratios and the periodontal pocket depth was tested, which confirmed the link between dysbiosis ratios and the severity of the disease. The results of this work are promising, but longitudinal studies will be required to improve the ratios and to define the microbial signatures of the disease, which will allow monitoring of periodontal pocket recovery and, conceivably, determination of the potential risk of periodontitis among healthy patients.

A new mathematical model of bacterial interactions in two-species oral biofilms.

Periodontitis are bacterial inflammatory diseases, where the bacterial biofilms present on the tooth-supporting tissues switch from a healthy state towards a pathogenic state. Among bacterial species involved in the disease, Porphyromonas gingivalis has been shown to induce dysbiosis, and to induce virulence of otherwise healthy bacteria like Streptococcus gordonii. During biofilm development, primary colonizers such as S. gordonii first attach to the surface and allow the subsequent adhesion of periodontal pathogens such as P. gingivalis. Interactions between those two bacteria have been extensively studied during the adhesion step of the biofilm. The aim of the study was to understand interactions of both species during the growing phase of the biofilm, for which little knowledge is available, using a mathematical model. This two-species biofilm model was based on a substrate-dependent growth, implemented with damage parameters, and validated thanks to data obtained on experimental biofilms. Three different hypothesis of interactions were proposed and assayed using this model: independence, competition between both bacteria species, or induction of toxicity by one species for the other species. Adequacy between experimental and simulated biofilms were found with the last hypothetic mathematical model. This new mathematical model of two species bacteria biofilms, dependent on different substrates for growing, can be applied to any bacteria species, environmental conditions, or steps of biofilm development. It will be of great interest for exploring bacterial interactions in biofilm conditions.

The Cytochrome bd Oxidase of Porphyromonas gingivalis Contributes to Oxidative Stress Resistance and Dioxygen Tolerance.

Porphyromonas gingivalis is an etiologic agent of periodontal disease in humans. The disease is associated with the formation of a mixed oral biofilm which is exposed to oxygen and environmental stress, such as oxidative stress. To investigate possible roles for cytochrome bd oxidase in the growth and persistence of this anaerobic bacterium inside the oral biofilm, mutant strains deficient in cytochrome bd oxidase activity were characterized. This study demonstrated that the cytochrome bd oxidase of Porphyromonas gingivalis, encoded by cydAB, was able to catalyse O2 consumption and was involved in peroxide and superoxide resistance, and dioxygen tolerance.

Identification of pVHL as a novel substrate for Aurora-A in clear cell renal cell carcinoma (ccRCC).

Clear cell renal cell carcinoma (ccRCC) is the most common histological subtype of kidney cancer and is often characterized by mutations or deletions of the Von Hippel Lindau (VHL) tumour suppressor gene. Aurora gene family members are implicated in proper mitotic progression and spindle checkpoint function and play a crucial role in cancer progression. In the present study, we assessed the expression of Aurora-A in a cohort of 30 ccRCC with fully characterized VHL status (wt/wt or mut/del) and Fuhrman grade. Aurora-A transcript and protein levels were significantly increased in high Fuhrman grade tumours and in VHLwt/wt tumours. These results suggest that Aurora-A and VHL interact in the ccRCC. We demonstrated that the two proteins interact in vivo and identified the Ser72 on the sequence of VHL as the unique site phosphorylated by Aurora-A.

Combination of Temsirolimus and tyrosine kinase inhibitors in renal carcinoma and endothelial cell lines.

PURPOSE: Multitargeted tyrosine kinase inhibitors (TKIs) (such as Sunitinib and Sorafenib) and mTOR inhibitors (such as Temsirolimus) are effective in treating metastatic clear-cell renal cell carcinoma (CCRCC), by acting on different pathways in both tumour and endothelial cells. A study of their combined effect could be of major interest. METHODS: We studied endothelial and CCRCC cell lines treated with Sunitinib, Sorafenib, Temsirolimus and 2 drug combinations: Sunitinib-Temsirolimus and Sorafenib-Temsirolimus. We studied inhibition of proliferation with an MTT assay under normoxia and hypoxia, VEGF expression by quantitative RT-PCR and ELISA, and angiogenesis with a Matrigel assay. RESULTS: TKIs and Temsirolimus inhibited proliferation of endothelial and tumour cell lines and inhibited angiogenesis. Anti-proliferative effects were more significant on cell lines with VHL gene inactivation and under hypoxic conditions. VEGF expression was induced by TKIs, but inhibited by Temsirolimus. The Sunitinib/Temsirolimus combination had synergistic or additive effects on the proliferation of tumour and endothelial cell lines. The Sorafenib-Temsirolimus combination had additive effects on the proliferation of most tumour cell lines, but not endothelial cell lines. Both combinations had additive effects on the inhibition of angiogenesis. CONCLUSION: In our model, Sunitinib, Sorafenib and Temsirolimus had anti-tumour and anti-angiogenic effects. The combinations of Sunitinib or Sorafenib with Temsirolimus had additive or synergistic effects on the inhibition of tumour and endothelial cell proliferation, and on the inhibition of angiogenesis. This work could lead to new trials with lower-dose combinations to prevent side effects and enhance efficacy.

Colocalization of Porphyromonas gingivalis with CD4+ T cells in periodontal disease.

Porphyromonas gingivalis, an anaerobic, asaccharolytic gram-negative bacterium, is a causative agent in chronic periodontitis. It has many virulence factors that facilitate infection of the gingiva, but little is known about the local immune cells that respond to this bacterium. The aims of this study were to quantify P. gingivalis in gingival biopsies from patients with periodontitis using laser capture microdissection (LCM) plus qRT-PCR and to determine the phenotype of immune cells associated with the bacteria using immunofluorescence. The presence of P. gingivalis was confirmed in periodontitis gingival tissue from 10 patients, and differences in bacterial distribution in the epithelium and connective tissue with or without inflammatory infiltrates were observed. Immune cells found in the biopsy tissues, including CD20+ mature B cells and CD138+ plasma cells, were associated with the Th2-type immune response. Most P. gingivalis was in direct contact with CD4+ T cells. This study revealed for the first time the colocalization of P. gingivalis with immune cells. Use of LCM combined with qRT-PCR enabled quantitative analysis of bacteria in a selected area of a biopsy sample without any tissue degradation. Observation of the immune cells associated with these bacteria was also performed by immunofluorescence.

A SUMOylation Motif in Aurora-A: Implications for Spindle Dynamics and Oncogenesis.

Aurora-A is a serine/threonine kinase that plays critical roles in centrosome maturation, spindle dynamics, and chromosome orientation and it is frequently over-expressed in human cancers. In this work, we show that Aurora-A interacts with the SUMO-conjugating enzyme UBC9 and co-localizes with SUMO1 in mitotic cells. Aurora-A can be SUMOylated in vitro and in vivo. Mutation of the highly conserved SUMOylation residue lysine 249 significantly disrupts Aurora-A SUMOylation and mitotic defects characterized by defective and multipolar spindles ensue. The Aurora-A(K249R) mutant has normal kinase activity but displays altered dynamics at the mitotic spindle. In addition, ectopic expression of the Aurora-A(K249R) mutant results in a significant increase in susceptibility to malignant transformation induced by the Ras oncogene. These data suggest that modification by SUMO residues may control Aurora-A function at the spindle and that deficiency of SUMOylation of this kinase may have important implications for tumor development.

Targeting the polyamine transport system with benzazepine- and azepine-polyamine conjugates.

The polyamine transport system (PTS) whose activity is up-regulated in cancer cells is an attractive target for drug design. Two heterocyclic (azepine and benzazepine) systems were conjugated to various polyamine moieties through an amidine bound to afford 18 compounds which were evaluated for their affinity for the PTS and their ability to use the PTS for cell delivery. Structure-activity relationship studies and lead optimization afforded two attractive PTS targeting compounds. The azepine-spermidine conjugate 14 is a very selective substrate of the PTS that may serve as a vector for radioelements used for diagnoses or therapeutics in nuclear medicine. The nitrobenzazepine-spermine conjugate 28 is a very powerful PTS inhibitor with very low intrinsic cytotoxicity, able to prevent the growth of polyamine depleted cells in presence of exogenous polyamines.

Effects of the Aurora kinase inhibitor VX-680 on anaplastic thyroid cancer-derived cell lines.

Anaplastic thyroid cancers (ATC) are aggressive tumors, which exhibit cell cycle misregulations leading to uncontrolled cellular proliferation and genomic instability. They fail to respond to chemotherapeutic agents and radiation therapy, and most patients die within a few months of diagnosis. In the present study, we evaluated the in vitro effects on ATC cells of VX-680, an inhibitor of the Aurora serine/threonine kinases involved in the regulation of multiple aspects of chromosome segregation and cytokinesis. The effects of VX-680 on proliferation, apoptosis, soft agar colony formation, cell cycle, and ploidy were tested on the ATC-derived cell lines CAL-62, 8305C, 8505C, and BHT-101. Treatment of the different ATC cells with VX-680 inhibited proliferation in a time- and dose-dependent manner, with the IC50 between 25 and 150 nM. The VX-680 significantly impaired the ability of the different cell lines to form colonies in soft agar. Analysis of caspase-3 activity showed that VX-680 induced apoptosis in the different cell lines. CAL-62 cells exposed for 12 h to VX-680 showed an accumulation of cells with > or =4N DNA content. Time-lapse analysis demonstrated that VX-680-treated CAL-62 cells exit metaphase without dividing. Moreover, histone H3 phosphorylation was abrogated following VX-680 treatment. In conclusion, our data demonstrated that VX-680 is effective in reducing cell growth of different ATC-derived cell lines and warrant further investigation to exploit its potential therapeutic value for ATC treatment.

Designing the polyamine pharmacophore: influence of N-substituents on the transport behavior of polyamine conjugates.

N-Ethylated N-arylmethyl polyamine conjugates were synthesized and evaluated for their ability to target the polyamine transporter (PAT). To understand the effect of N-ethylation upon PAT selectivity, ethyl groups were appended onto a PAT-selective N (1)-anthracenenylmethyl homospermidine derivative, 1b. Bioevaluation in L1210 murine leukemia cells and in two Chinese hamster ovary cell lines (PAT-active CHO and PAT-deficient CHO-MG) revealed a dramatic decrease in PAT targeting ability upon N (1) or N (5) ethylation of the pharmacophore 1b. Experiments using the amine oxidase inhibitor, aminoguanidine (AG, 2 mM), revealed that the N (9)-ethyl and N (9)-methyl analogues were able to retain their PAT selectivity and cytotoxicity properties in the presence or absence of AG. In contrast, the lead compound 1b (containing a terminal NH 2 group) revealed a dramatic reduction in both its PAT-targeting ability and cytotoxicity in the absence of AG. An improved balance between these three properties of PAT-targeting, cytotoxicity and metabolic stability can be attained via N-methylation at the N (9)-position.

A comparison of chloroambucil- and xylene-containing polyamines leads to improved ligands for accessing the polyamine transport system.

Several disubstituted arylene- and chloroambucil-polyamine conjugates were synthesized and evaluated for their ability to target cells via their polyamine transport system (PAT). As compared to the monosubstituted analogues, the disubstituted arylene systems were superior PAT targeting agents. Using a Chinese hamster ovary (CHO) cell line (PAT active) and its CHO-MG mutant (PAT inactive), the series was screened for their PAT targeting ability. The data were expressed as a CHOMG/CHO IC 50 ratio. Indeed, the disubstituted systems gave high IC 50 ratios (e.g., ratio > 2000), which indicated high selectivity for the PAT. The chloroambucil adducts were less toxic than the corresponding arylmethyl compounds. In this regard, having the proper recognition element (i.e., homospermidine) and cytotoxic "cargo" were deemed paramount for successful drug delivery via the PAT.

Modeling the preferred shapes of polyamine transporter ligands and dihydromotuporamine-C mimics: shovel versus hoe.

Preferred conformers generated from motuporamine and anthracene-polyamine derivatives provided insight into the shapes associated with polyamine transporter (PAT) recognition and potentially dihydromotuporamine C (4a) bioactivity. Molecular modeling revealed that N(1)-(anthracen-9-ylmethyl)-3,3-triamine (6a), N(1)-(anthracen-9-ylmethyl)-4,4-triamine (6b), N(1)-(anthracen-9-ylmethyl)-N(1)-ethyl-3,3-triamine (7a), N(1)-(anthracen-9-ylmethyl)-N(1)-ethyl-4,4-triamine (7b), and 4a all preferred a hoe motif. This hoe shape was defined by the all-anti polyamine shaft extending above the relatively flat, appended ring system. The hoe geometry was also inferred by the (1)H NMR spectrum of the free amine of 7a (CDCl(3)), which showed a strong shielding effect of the anthracene ring on the chemical shifts associated with the appended polyamine chain. This shielding effect was found to be independent over a broad concentration range of 7a, which also supported an intramolecular phenomenon. The degree of substitution at the N(1)-position seems to be an important determinant of both the molecular shape preferences and biological activity of anthracenylmethyl-polyamine conjugates.

Effect of polyamine homologation on the transport and biological properties of heterocyclic amidines.

Five sets of heterocyclic derivatives of various sizes and complexities coupled by an amidine function to putrescine, spermidine, or spermine were prepared. They were essentially tested to determine the influence of the polyamine chain on their cellular transport. To comment on affinity and on selective transport via the polyamine transport system (PTS), K(i) values for polyamine uptake were determined in L1210 cells, and the cytotoxicity and accumulation of the conjugates were determined in CHO and polyamine transport-deficient mutant CHO-MG cells, as well as in L1210 and alpha-difluoromethylornithine- (DFMO-) treated L1210 cells. Unlike spermine, putrescine and spermidine were clearly identified as selective motifs that enable cellular entry via the PTS. However, this property was clearly limited by the size of substituents: these polyamines were able to ferry a dihydroquinoline system via the PTS but did not impart any selectivity to bulkier substituents.