Genotypic Alterations Research Articles

Association of single nucleotide polymorphisms of tissue factor and tissue factor pathway inhibitor with venous thromboembolism in patients with lung cancer

Objective: s To investigate the distributions of single nucleotide polymorphisms (SNPs) of tissue factor (TF) and its inhibitor tissue factor pathway inhibitor (TFPI) and analyze the association of the SNPs with venous thromboembolism (VTE) in lung cancer patients. Methods: Between October 2009 and August 2013, a total of 152 hospitalized patients with newly diagnosed primary non-small cell lung cancer were enrolled from Beijing Chao Yang Hospital. Among them [male 105 cases, female 47 cases, with an age of (62.4±13.2) years old], 40 cases were lung cancer patients with VTE, 112 cases were lung cancer patients without VTE. In the same period, 79 healthy controls were included from the physical examination center. All patients' blood specimens were collected and their DNA was isolated. The selected SNPs were TF+ 5466A/G, TFPI-287T/C and TFPI-33T/C and they were investigated by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) followed by validation of DNA sequence analysis. Results: Allelic frequencies of TF+ 5466G, TFPI-287C and TFPI-33C were 2.5%, 33.8% and 8.8%, respectively. There was no significant difference among the three groups in genotype or allele frequency distributions of TF+ 5466A/G, TFPI-287T/C and TFPI-33T/C polymorphisms (all P>0.05). There was no difference from different genders and ages in allele or genotype frequency distributions of TF+ 5466A/G, TFPI-287T/C and TFPI-33T/C polymorphisms among the three groups (all P>0.05). Meanwhile, the frequency distributions of genotype and allele of the three SNPs were not associated with lung cancer patients with VTE (all P>0.05). Still, no relationship was found between genotype or allele frequency distributions of the three SNPs with prognosis of lung cancer patients with VTE. Conclusion: Genotype alterations in TF+ 5466A/G, TFPI-287T/C and TFPI-33T/C may be unrelated to the occurrence of VTE and the prognosis of lung cancer patients with VTE.

Differential expression of photosynthesis-related genes in pentaploid interspecific hybrid and its decaploid of Fragaria spp.

Polyploidization always induces a series of changes in genome, transcriptome and epigenetics, of which changes in gene expression are the immediate causes of genotype alterations of polyploid plants. In our previous study on strawberry polyploidization, genes related to photosynthesis were found to undergo changes in gene expression and DNA methylation. Therefore, we chose 11 genes that were closely related to plant photosynthesis and analysed their expression during strawberry hybridization and chromosome doubling. Most genes of pentaploids showed expression levels between parents and were more similar to F. × ananassa. Gene expression levels of decaploids were higher than those of pentaploids and F. × ananassa. Different types of photosynthesis-related genes responded differently to hybridization and chromosome doubling. Chloroplast genes and regulatory genes showed complex responses. Structural genes of the photosynthetic system were expressed at a constant level and displayed a clear dosage effect. The methylation levels of one CG site on SIGE, which regulates expression of chloroplast genes, were negatively correlated with gene expression. In pentaploids and decaploids, more transcripts were from F. × ananassa than from F. viridis. The ratio of transcripts from from F. × ananassa to those from F. viridis was close to the ratio (4:1) of the genome of F. × ananassa to that of F. viridis in pentaploids and decaploids, but there were also some exceptions with obvious deviation.

Radiomics in precision medicine for lung cancer.

With the improvement of external radiotherapy delivery accuracy, such as intensity-modulated and stereotactic body radiation therapy, radiation oncology has recently entered in the era of precision medicine. Despite these precise irradiation modalities, lung cancers remain one of the most aggressive human cancers worldwide, possibly because of diverse genotypic alterations that drive and maintain lung tumorigenesis. It has been long recognized that imaging could aid in the diagnosis, tumor delineation, and monitoring of lung cancer. Moreover, accumulating evidence suggests that imaging information could be further used to tailor treatment type and intensity, as well as predict treatment outcomes in radiotherapy. However, these imaging tasks have been carried out either qualitatively or using simplistic metrics that doesn't take advantage of the full scale of imaging knowledge. Radiomics, which is a recent field of research that aims to provide a more quantitative representation of imaging information relating tumor phenotypes to clinical and genotypic endpoints by embedding extracted image features into predictive mathematical models. These predictive models can be a key component in the clinician decision making and treatment personalization. This review provides an overview of the radiomics application and its methodology for radiation oncology studies in lung cancer.

Induced drought and salinity tolerance in the variants of Brassica campestris (L.).

The variants obtained from M2 generation of gamma irradiated toria varieties, T-9 and PT303 of Brassica campestris (L.) were evaluated for drought and salt tolerance. Among them, variant TV4 of var. T-9 and the variants PD3 and PD4 of PT303 showed significantly higher antioxidant enzyme activities, proline content, relative water content percentage and yield per plant under these stress conditions. These variants appear more adaptive which may be assigned to their induced favorable genotypic alterations, and could be utilized for developing drought and salinity tolerant Brassicas.

Cancer bronchique à petites cellules : traitements de première ligne et maintenance

Among all kind of lung cancer, small-cell lung cancer (SCLC) has a particular role. Nowadays, SCLC is epidemiologically declining and the idea that this cancer would disappear while remaining undefeated may be read everywhere in the medical literature. Yet, there are still progress made to optimize the initial therapy and the next chapters aims at summarizing them.First, we present the main arguments that led to the algorithm used nowadays. If there is something for sure, the first steps of SCLC care are critical in terms of prognostic. As a result, the initial care of SCLC is crucial, and has to be quick and optimal, even more than in non-small cell lung cancer. Whatever the stage, a sub-optimal first-line chemotherapy seriously compromises the chances of survival at 2 years. Concerning limited stage, thoracic radiotherapy begun within thirty days after the first administration of chemotherapy has better results than irradiation delivered later (also than sequential radiotherapy).Finally, this article describes new perspectives: clinicians expect a lot from the analysis of genotypic alterations in SCLC. A few steps have been made and a new target is already known: DLL3 (Delta Like Protein 3), which is NOTCH ligand. If anti-angiogenic therapies’ influence is too weak to go on trying in this direction, immunotherapies, using modern immuno-oncologic treatment, are still giving some hope. But let’s remain careful because these therapies are still on development and studies are going on.

AML-induced osteogenic differentiation in mesenchymal stromal cells supports leukemia growth.

Genotypic and phenotypic alterations in the bone marrow (BM) microenvironment, in particular in osteoprogenitor cells, have been shown to support leukemogenesis. However, it is unclear how leukemia cells alter the BM microenvironment to create a hospitable niche. Here, we report that acute myeloid leukemia (AML) cells, but not normal CD34+ or CD33+ cells, induce osteogenic differentiation in mesenchymal stromal cells (MSCs). In addition, AML cells inhibited adipogenic differentiation of MSCs. Mechanistic studies identified that AML-derived BMPs activate Smad1/5 signaling to induce osteogenic differentiation in MSCs. Gene expression array analysis revealed that AML cells induce connective tissue growth factor (CTGF) expression in BM-MSCs irrespective of AML type. Overexpression of CTGF in a transgenic mouse model greatly enhanced leukemia engraftment in vivo. Together, our data suggest that AML cells induce a preosteoblast-rich niche in the BM that in turn enhances AML expansion.

Abstract 2420: Integrative analyses of gene expression, DNA methylation, genotype and copy number alterations characterize X-chromosome inactivation in ovarian cancer

Abstract Introduction: In females, X-chromosome inactivation (XCI) epigenetically silences transcription of one copy of the X chromosome. Which chromosome is silenced is randomly selected, and is tissue- and cell-specific. While some genes are known to escape XCI under normal conditions, aberrant XCI patterns are thought to occur in female-specific cancers, although the role of XCI in ovarian tumorigenesis and progression is largely unknown. The process of XCI is complex, and integration of gene expression, DNA methylation, and copy number data can inform the XCI status of individual genes and chromosome-wide XCI patterns for individual patients. Methods: We evaluated gene- and chromosome-level patterns of XCI by integrating RNA sequence, copy number alteration, genotype, and DNA methylation data to study XCI escape patterns in tumor samples from 99 ovarian cancer patients. We measured allele-specific expression (ASE) for 397 X-linked genes to identify the active alleles for each tumor. Combining ASE data with knowledge of copy number status, we used a Bayesian beta-binomial mixture model to estimate which genes escaped XCI for each patient, and validated our findings using DNA methylation data. To assess global XCI patterns, we performed cluster analyses on the ASE and methylation data, after adjusting for loss of heterozygosity. We examined the relationship between the clusters and clinical factors, including overall survival and time to recurrence. Results: DNA promoter methylation demonstrated inverse regional correlations with ASE. Cluster analyses using ASE and methylation data demonstrated evidence of two tumor clusters, representing normal XCI and global XCI dysregulation. The dysregulated XCI cluster (N=52) was associated with lower X-inactive specific transcript expression as expected (p<0.01). Patients with XCI dysregulated tumors were higher grade, stage, serous histology and were sub-optimally debulked (p<0.05). These patients also had shorter overall survival time (HR=1.87, p=0.02) and time to recurrence (HR=2.34, p<0.01), although associations were attenuated after covariate adjustment. In 45 tumor samples with sufficient data, we observed escape patterns largely consistent with previous reports of multiple tissue types. When comparing tumor to normal ovarian tissue, eight genes (CXorf23, CXorf36, BRWD3, ELF4, SLITRK4, GABRE, CLCN4, SH3BGRL) showed putative escape in the tumor and two genes (RBBP7, OFD1) showed discrepant tumor inactivation. Conclusions: We identified discrepant gene-level XCI tumor classifications compared to normal tissue and identified a group of patients with chromosome-wide XCI dysregulation associated with worse clinical prognosis. This provides evidence of the role of XCI in ovarian cancer and highlights the need to integrate multiple genomic data types to study XCI. Citation Format: Stacey J. Winham, Nicholas B. Larson, Sebastian M. Armasu, Zachary C. Fogarty, Melissa C. Larson, Kimberly R. Kalli, Kate Lawrenson, Simon Gayther, Brooke L. Fridley, Ellen L. Goode. Integrative analyses of gene expression, DNA methylation, genotype and copy number alterations characterize X-chromosome inactivation in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2420. doi:10.1158/1538-7445.AM2017-2420

Reduction in Migratory Phenotype in a Metastasized Breast Cancer Cell Line via Downregulation of S100A4 and GRM3

To investigate phenotypic and genotypic alterations before and after bone metastasis, we conducted genome-wide mRNA profiling and DNA exon sequencing of two cell lines (TMD and BMD) derived from a mouse xenograft model. TMD cells were harvested from the mammary fat pad after transfecting MDA-MB-231 breast cancer cells, while BMD cells were isolated from the metastasized bone. Compared to BMD cells, TMD cells exhibited higher cellular motility. In contrast, BMD cells formed a spheroid with a smoother and more circular surface when co-cultured with osteoblasts. In characterizing mRNA expression using principal component analysis, S100 calcium-binding protein A4 (S100A4) was aligned to a principal axis associated with metastasis. Partial silencing of S100A4 suppressed migratory capabilities of TMD cells, while Paclitaxel decreased the S100A4 level and reduced TMD’s cellular motility. DNA mutation analysis revealed that the glutamate metabotropic receptor 3 (GRM3) gene gained a premature stop codon in BMD cells, and silencing GRM3 in TMD cells altered their spheroid shape closer to that of BMD cells. Collectively, this study demonstrates that metastasized cells are less migratory due in part to the post-metastatic downregulation of S100A4 and GRM3. Targeting S100A4 and GRM3 may help prevent bone metastasis.

* Synthesis and Characterization of Electroactive Gellan Gum Spongy-Like Hydrogels for Skeletal Muscle Tissue Engineering Applications.

Advances on materials' research for tissue engineering (TE) applications have shown that animal cells respond directly to the material physical, chemical, mechanical, and electrical stimuli altering a variety of cell signaling cascades, which consequently result in phenotypic and genotypic alterations. Gellan gum (GG) spongy-like hydrogels (SLH) with open microstructure, mechanical properties, and cell performance have shown promising results for soft TE applications. Taking advantage of intrinsic properties of GG-SLH and polypyrrole (PPy) electroactivity, we developed electroactive PPy-GG-SLH envisaging their potential use for skeletal muscle TE. Three different methods of in situ chemical oxidative polymerization were developed based on the availability of pyrrole: freely dissolved in solution (method I and III) or immobilized into GG hydrogels (method II). PPy was homogeneously distributed within (method I and III) and on the surface (method II) of GG-SLH, as also confirmed by Fourier Transform infrared spectra. PPy-GG-SLH showed higher conductivity than GG-SLH (p < 0.05) whereas PPy-GG-SLH (method I and II) showed the best conductivity among the 3 methods (∼1 to 2 × 10-4 S/cm). The microarchitecture of PPy-GG-SLH (method I) was similar to GG-SLH but PPy-GG-SLH (method II and III) presented smaller pore sizes and lower porosity. PPy-GG-SLH (method I and II) compressive modulus (∼450-500 KPa) and recovering capacity (∼75-90%) was higher than GG-SLH, nevertheless the mechanical properties of PPy-GG-SLH (method III) were lower. The water uptake of PPy-GG-SLH was rapidly up to 2500% and were stable along 60 days of degradation being the maximum weight loss 20%. Mechanically stable and electroactive PPy-GG-SLH (method I and II) were analyzed regarding cellular performance. PPy-GG-SLH were not cytotoxic for L929 cells. In addition, L929 and C2C12 myoblast cells were able to adhere and spread within PPy-GG-SLH, showing improved spreading in comparison to GG-SLH performance. Overall, PPy-GG-SLH show promising features as an alternative electroactive platform to analyze the influence of electrical stimulation on skeletal muscle cells.

Abstract P3-03-06: Characterization of HER2-positive breast cancer (BC) cells selected for tolerance to trastuzumab-induced antibody-dependent cell-mediated cytotoxicity (ADCC)

Abstract Cellular mechanisms of trastuzumab resistance include alteration(s) in cell signaling pathways (PTEN loss, activation of PI3K/Akt signaling), steric hindrance of antibody binding (by Muc-1/Muc-3), over-activation of alternate receptor kinases (HER3/c-Met/IGF-1R), and proteolysis of HER2 extracellular domain harboring target epitopes for antibody-based therapeutics. Prior studies of trastuzumab resistance have focused largely on cells selected ex vivo with the antibody in absence of human immune effector cells. We developed a selection model, wherein human HER2 positive BC cells (BT474, SKBR3) were subjected to acute ADCC (&amp;gt;90% cell death), trastuzumab concentration 100ug/mL, effector-target ratio 100:1, using human peripheral blood mononuclear cells (PBMCs) as effectors. Surviving cells were allowed to recover to confluence over 8-10 weeks, for 10 total rounds of ADCC selection ex vivo. Mock-treated parent, IgG1 isotype control, trastuzumab, and PBMCs alone were used as controls. ADCC assays based on calcein fluorescent labeling of live target cells, revealed significant reduction (maximum 20%, p&amp;lt;0.005) in cell lysis in immune-selected BT474 cell lines compared to parental controls (immune-selected SKBR3 cells exhibited a non-significant trend towards reduced ADCC). Transcriptome-wide next-generation RNA sequencing (Illumina NextSeq 500, 2 x 75 bp paired-end, median of 46 million paired-end reads/sample), coupled with pathway enrichment analysis (Reactome), followed by q-PCR validation, confirmed significant changes in expression in immune-selected cells (compared to parent control) for genes including: ALDH1, ANK1, TMPRSS3, HINT1, DNM2, TNNC1, COL4A4 in BT474; and ALDH1, ANK1, CAMP1, CPE, IDO1 in SKBR3 cells. Whole-genome sequencing (Illumina HiSeq X, 150 bp paired end, 30x coverage) elucidated 180 genes with single nucleotide variations (SNVs) in immune-selected cells compared to parent in BT474 cells, and 215 genes in SKBR3 cells. Thirty-four SNVs were shared in both cell lines. Further screening and validation confirm genes with SNVs demonstrating significant transcript up-regulation. These include: COL4A3, LEP, SOX-9 in BT474; and HLA-B, TNFRSF10B, HLA-B, PSMA6 in SKBR3. In further phenotypic analysis, ADCC-conditioned BT474 cells exhibit an elongated fibroblast-like morphology with multiple processes, in contrast to control. Immune-selected SKBR3 cells (and not BT474 cells) demonstrate significantly increased motility compared to control in transwell migration assays (p&amp;lt;0.001), and demonstrated increased cell proliferation (MTT assay, 10-15%, 48h; p=0.0242) as compared to parent controls. Our data indicate immune-selection by effector cells contributes to ADCC tolerance in vitro, and is associated with distinct genotypic and phenotypic alterations. Future investigation will determine whether Fc-engineered MAbs (afucosylated), antibody drug conjugates (T-DM1), or potentiation of ADCC by co-stimulatory agonist CD137 antibodies will re-sensitize ADCC-tolerance. This investigation will help to elucidate potentially targetable pathways that emerge from immune-selection with trastuzumab. Citation Format: Biswas T, Fritzemeier R, Mark A, Meißner T, Young B, Jones BL, Pegram M. Characterization of HER2-positive breast cancer (BC) cells selected for tolerance to trastuzumab-induced antibody-dependent cell-mediated cytotoxicity (ADCC) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-03-06.

The Complex Relationship between Virulence and Antibiotic Resistance.

Antibiotic resistance, prompted by the overuse of antimicrobial agents, may arise from a variety of mechanisms, particularly horizontal gene transfer of virulence and antibiotic resistance genes, which is often facilitated by biofilm formation. The importance of phenotypic changes seen in a biofilm, which lead to genotypic alterations, cannot be overstated. Irrespective of if the biofilm is single microbe or polymicrobial, bacteria, protected within a biofilm from the external environment, communicate through signal transduction pathways (e.g., quorum sensing or two-component systems), leading to global changes in gene expression, enhancing virulence, and expediting the acquisition of antibiotic resistance. Thus, one must examine a genetic change in virulence and resistance not only in the context of the biofilm but also as inextricably linked pathologies. Observationally, it is clear that increased virulence and the advent of antibiotic resistance often arise almost simultaneously; however, their genetic connection has been relatively ignored. Although the complexities of genetic regulation in a multispecies community may obscure a causative relationship, uncovering key genetic interactions between virulence and resistance in biofilm bacteria is essential to identifying new druggable targets, ultimately providing a drug discovery and development pathway to improve treatment options for chronic and recurring infection.

P3.01-042 Lung Cancer Cells Can Stimulate Functional and Genotypic Modifications in Normal Bronchial Epithelial Cells: Topic: Functional Biology in Lung Cancer

Normal lung epithelium cells may act in concert with tumor cells, given that bystander effects may exist between the two. This interaction may lead to inappropriate activation of pro-oncogenic signaling pathways, which may result in high mutational load and tumor heterogeneity. The aim of this project is to evaluate the effects of non-small cell lung cancer (NSCLC) cells on an immortalized normal bronchial epithelial cell line. A normal bronchial epithelial cell line (HBEC4) was exposed to A549 (adenocarcinoma), H460 (large cell carcinoma) and SK-MES-1 (squamous cell carcinoma) NSCLC cell lines in a trans-well co-culture system. Cellular characteristics were examined using a Cytell Cell Imaging System (cell number, viability, apoptosis, cell cycle). The gene expression profile was also determined in terms of inflammatory mediators, stem cell markers (RT-PCR) and miRNA profiling (Nanostring). The proliferative effect of NSCLC cancer exosomes was also examined (BrdU ELISA) on the HBEC4 cell line. A number of functional and gene modifications were observed in the HBEC4 cell line after seven days of co-culture. While patterns were similar amongst all NSCLC subtypes, SK-MES-1 elicited the most significant effects in terms of cell number, viability, cell cycle progression and proliferative potential of isolated cancer exosome fraction. Promotion of both inflammatory mediators and stem cell marker expression was evident at the mRNA level. There was no apparent consensus between NSCLC subtypes and miRNA expression, as exposure to each cell line resulted in distinct profiles of miRNAs in HBEC4 cells. Bioinformatic analysis of miRNA target genes, demonstrated that pathways such as p53, MAPK, VEGF, TLR and Wnt were amongst those altered. Cancer cells may promote significant genotypic and phenotypic alterations within the normal lung epithelium though multiple mechanisms. These modifications may, in part, contribute to the heterogeneity of lung cancer tumors and influence response to both chemotherapeutics and targeted agents.

Genetic impairments in folate enzymes increase dependence on dietary choline for phosphatidylcholine production at the expense of betaine synthesis.

Although single nucleotide polymorphisms (SNPs) in folate-mediated pathways predict susceptibility to choline deficiency during severe choline deprivation, it is unknown if effects persist at recommended intakes. Thus, we used stable isotope liquid chromatography-mass spectrometry (LC-MS) methodology to examine the impact of candidate SNPs on choline metabolism in a long-term, randomized, controlled feeding trial among pregnant, lactating, and nonpregnant (NP) women consuming 480 or 930 mg/d choline (22% as choline-d9, with d9 indicating a deuterated trimethyl amine group) and meeting folate-intake recommendations. Variants impairing folate metabolism, methylenetetrahydrofolate reductase (MTHFR) rs1801133, methionine synthase (MTR) rs1805087 [wild-type (WT)], MTR reductase (MTRR) rs1801394, and methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase-formyltetrahydrofolate synthetase (MTHFD1) rs2236225, influenced choline dynamics, frequently through interactions with reproductive state and choline intake, with fewer genotypic alterations observed among pregnant women. Women with these variants partitioned more dietary choline toward phosphatidylcholine (PC) biosynthesis via the cytidine diphosphate (CDP)-choline pathway at the expense of betaine synthesis even when use of betaine as a methyl donor was increased. Choline intakes of 930 mg/d restored partitioning of dietary choline between betaine and CDP-PC among NP (MTHFR rs1801133 and MTR rs1805087 WT) and lactating (MTHFD1 rs2236225) women with risk genotypes. Overall, our findings indicate that loss-of-function variants in folate-metabolizing enzymes strain cellular PC production, possibly via impaired folate-dependent phosphatidylethanolamine-N-methyltransferase (PEMT)-PC synthesis, and suggest that women with these risk genotypes may benefit from choline intakes exceeding current recommendations.-Ganz, A. B., Shields, K., Fomin, V. G., Lopez, Y. S., Mohan, S., Lovesky, J., Chuang, J. C., Ganti, A., Carrier, B., Yan, J., Taeswuan, S., Cohen, V. V., Swersky, C. C., Stover, J. A., Vitiello, G. A., Malysheva, O. V., Mudrak, E., Caudill, M. A. Genetic impairments in folate enzymes increase dependence on dietary choline for phosphatidylcholine production at the expense of betaine synthesis.

Association of IL28B SNPs rs12979860 and rs8099917 on Hepatitis C Virus-RNA Status in Donors/Recipients of Living Donor Liver Transplantation.

To investigate the effect of IL28B single nucleotide polymorphisms (SNPs) (rs8099917 and rs12979860) in the donors and recipients on the outcome of Hepatitis C virus-RNA clearance after living donor liver transplantation (LDLT). The rs8099917 and rs12979860 genotypes in 50 donor and recipients pairs were explored on the pre-operative day (POD) and post-operative day 30 (POD30). There was a significant difference in HCV-RNA clearance before (12%, 6/50) and after (48%, 24/50) liver transplantation (P < 0.001). The rs8099917 genotype TT was dominant in both the recipients (82%, 41/50) and donors (86%, 43/50), but had no significant effect on HCV-RNA clearance (87.5%, 21/24) and recurrence (76.9%, 20/26) after LDLT. One recipient was detected with genotype GG on POD, which changed to genotype GT on POD30. Prevalence of rs12979860 genotype CT was 98% (49/50 recipient) and 92% (46/50 donor) and prevalence of genotype CC was 2% (1/50 recipient) and 8% (4/50 donor) on POD and POD30, respectively. Of the 4 recipients with rs12979860 genotype CC on POD30, 3 recipients (12.5%, 3/24) exhibited HCV clearance and 1 experienced recurrence (3.9%, 1/26), however, this was not statistically significant. In conclusion, alterations in IL28B SNP genotype may occur after LDLT, leading to modifications in the host genome or donor proteome by HCV. This predicted mechanism will need to be investigated further.

Neil3-dependent base excision repair regulates lipid metabolism and prevents atherosclerosis in Apoe-deficient mice.

Increasing evidence suggests that oxidative DNA damage accumulates in atherosclerosis. Recently, we showed that a genetic variant in the human DNA repair enzyme NEIL3 was associated with increased risk of myocardial infarction. Here, we explored the role of Neil3/NEIL3 in atherogenesis by both clinical and experimental approaches. Human carotid plaques revealed increased NEIL3 mRNA expression which significantly correlated with mRNA levels of the macrophage marker CD68. Apoe−/−Neil3−/− mice on high-fat diet showed accelerated plaque formation as compared to Apoe−/− mice, reflecting an atherogenic lipid profile, increased hepatic triglyceride levels and attenuated macrophage cholesterol efflux capacity. Apoe−/−Neil3−/− mice showed marked alterations in several pathways affecting hepatic lipid metabolism, but no genotypic alterations in genome integrity or genome-wide accumulation of oxidative DNA damage. These results suggest a novel role for the DNA glycosylase Neil3 in atherogenesis in balancing lipid metabolism and macrophage function, potentially independently of genome-wide canonical base excision repair of oxidative DNA damage.

Phenotypic and Genotypic Alterations of Durancin GL-Resistant Enterococcus durans Strains.

The emergence and spread of bacteriocin-resistant bacteria threaten the efficiency of bacteriocin usage as food preservatives. In this experiment, 19 selected Enterococcus durans strains acquired resistance after exposure to durancin GL, and the mutants had similar intermediate levels of resistance. One wild-type E. durans KLDS 6.0603 and its two resistant mutants, E. durans KLDS 6.0603-2 and E. durans KLDS 6.0603-3, were used to characterize phenotypic and genotypic differences. Approximately 100 μg/mL of durancin GL can penetrate the cytoplasmic membrane of E. durans KLDS 6.0603, causing damage to bacterial cells, but cannot penetrate E. durans KLDS 6.0603-2 and KLDS 6.0603-3 membranes. Unsaturated fatty acid content in resistant strains was significantly increased compared with wild-type strains, indicating that the former has more fluidity of cell membrane than the latter. Decreased mannose phosphotransferase system gene expression (mptD) was observed in the two resistant strains. Results showed that the factors, including the increased unsaturated fatty acid and decreased mptD expression, could contribute to durancin GL resistance.

Impact of Cytochrome P450 2D6 Function on the Chiral Blood Plasma Pharmacokinetics of 3,4-Methylenedioxymethamphetamine (MDMA) and Its Phase I and II Metabolites in Humans.

3,4-methylenedioxymethamphetamine (MDMA; ecstasy) metabolism is known to be stereoselective, with preference for S-stereoisomers. Its major metabolic step involves CYP2D6-catalyzed demethylenation to 3,4-dihydroxymethamphetamine (DHMA), followed by methylation and conjugation. Alterations in CYP2D6 genotype and/or phenotype have been associated with higher toxicity. Therefore, the impact of CYP2D6 function on the plasma pharmacokinetics of MDMA and its phase I and II metabolites was tested by comparing extensive metabolizers (EMs), intermediate metabolizers (IMs), and EMs that were pretreated with bupropion as a metabolic inhibitor in a controlled MDMA administration study. Blood plasma samples were collected from 16 healthy participants (13 EMs and three IMs) up to 24 h after MDMA administration in a double-blind, placebo-controlled, four-period, cross-over design, with subjects receiving 1 week placebo or bupropion pretreatment followed by a single placebo or MDMA (125 mg) dose. Bupropion pretreatment increased the maximum plasma concentration (Cmax) and area under the plasma concentration-time curve from 0 to 24 h (AUC24) of R-MDMA (9% and 25%, respectively) and S-MDMA (16% and 38%, respectively). Bupropion reduced the Cmax and AUC24 of the CYP2D6-dependently formed metabolite stereoisomers of DHMA 3-sulfate, DHMA 4-sulfate, and 4-hydroxy-3-methoxymethamphetamine (HMMA sulfate and HMMA glucuronide) by approximately 40%. The changes that were observed in IMs were generally comparable to bupropion-pretreated EMs. Although changes in stereoselectivity based on CYP2D6 activity were observed, these likely have low clinical relevance. Bupropion and hydroxybupropion stereoisomer pharmacokinetics were unaltered by MDMA co-administration. The present data might aid further interpretations of toxicity based on CYP2D6-dependent MDMA metabolism.

AMPK and mTOR: sensors and regulators of immunometabolic changes during Salmonella infection in the chicken

Non-typhoidal Salmonella enterica induce an early pro-inflammatory response in chickens, but the response is short-lived, asymptomatic of clinical disease, results in a persistent colonization of the gastrointestinal (GI) tract, and can transmit infections to naïve hosts via fecal shedding of bacteria. The underlying mechanisms that facilitate this persistent colonization of the ceca of chickens by Salmonella are unknown. We have begun to concentrate on the convergence of metabolism and immune function as playing a major role in regulating the host responsiveness to infection. It is now recognized that the immune system monitors the metabolic state of tissues and responds by modulating metabolic function. The aim in this review is to summarize the literature that has defined a series of genotypic and phenotypic alterations in the regulatory host immune-metabolic signaling pathways in the local cecal microenvironment during the first 4 d following infection with Salmonella enterica serovar Enteritidis. Using chicken-specific kinomic immune-metabolism peptide arrays and quantitative real-time-PCR of cecal tissue during the early (4 to 48 h) and late stages (4 to 17 d) of a Salmonella infection in young broiler chickens, the local immunometabolic microenvironment has been ascertained. Distinct immune and metabolic pathways are altered between 2 to 4 d post-infection that dramatically changed the local immunometabolic environment. Thus, the tissue immunometabolic phenotype of the cecum plays a major role in the ability of the bacterium to establish a persistent cecal colonization. In general, our findings show that AMPK and mTOR are key players linking specific extracellular milieu and intracellular metabolism. Phenotypically, the early response (4 to 48 h) to Salmonella infection is pro-inflammatory, fueled by glycolysis and mTOR-mediated protein synthesis, whereas by the later phase (4 to 5 d), the local environment has undergone an immune-metabolic reprogramming to an anti-inflammatory state driven by AMPK-directed oxidative phosphorylation. Therefore, metabolism appears to provide a potential critical control point that can impact infection. Further understanding of metabolic control of immunity during infection should provide crucial information of the development of novel therapeutics based on metabolic modulators that enhance protection or inhibit infection.

Promotion of a cancer-like phenotype, through chronic exposure to inflammatory cytokines and hypoxia in a bronchial epithelial cell line model.

Globally, lung cancer accounts for approximately 20% of all cancer related deaths. Five-year survival is poor and rates have remained unchanged for the past four decades. There is an urgent need to identify markers of lung carcinogenesis and new targets for therapy. Given the recent successes of immune modulators in cancer therapy and the improved understanding of immune evasion by tumours, we sought to determine the carcinogenic impact of chronic TNF-α and IL-1β exposure in a normal bronchial epithelial cell line model. Following three months of culture in a chronic inflammatory environment under conditions of normoxia and hypoxia (0.5% oxygen), normal cells developed a number of key genotypic and phenotypic alterations. Important cellular features such as the proliferative, adhesive and invasive capacity of the normal cells were significantly amplified. In addition, gene expression profiles were altered in pathways associated with apoptosis, angiogenesis and invasion. The data generated in this study provides support that TNF-α, IL-1β and hypoxia promotes a neoplastic phenotype in normal bronchial epithelial cells. In turn these mediators may be of benefit for biomarker and/or immune-therapy target studies. This project provides an important inflammatory in vitro model for further immuno-oncology studies in the lung cancer setting.

Particular aspects in the cytogenetics and molecular biology of salivary gland tumours - current review of reports.

Salivary gland tumours are a group of lesions whose heterogeneity of biological and pathological features is widely reflected in the molecular aspect. This is demonstrated by an increasing number of studies in the field of genetics of these tumours.The aim of this study was to collect the most significant scientific reports on the cytogenetic and molecular data concerning these tumours, which might facilitate the identification of potential biomarkers and therapeutic targets. The analysis covered 71 papers included in the PubMed database. We focused on the most common tumours, such as pleomorphic adenoma, Warthin tumour, mucoepidermoid carcinoma, and others. The aim of this study is to present current knowledge about widely explored genotypic alterations (such as PLAG1 gene in pleomorphic adenoma or MECT1 gene in mucoepidermoid carcinoma), and also about rare markers, like Mena or SOX10 protein, which might also be associated with tumourigenesis and carcinogenesis of these tumours.