Computational and Experimental Evaluation of the Immune Response of Neoantigens for Personalized Vaccine Design.

In the last few years, the importance of neoantigens in the development of personalized antitumor vaccines has increased remarkably. In order to study whether bioinformatic tools are effective in detecting neoantigens that generate an immune response, DNA samples from patients with cutaneous melanoma in different stages were obtained, resulting in a total of 6048 potential neoantigens gathered. Thereafter, the immunological responses generated by some of those neoantigens ex vivo were tested, using a vaccine designed by a new optimization approach and encapsulated in nanoparticles. Our bioinformatic analysis indicated that no differences were found between the number of neoantigens and that of non-mutated sequences detected as potential binders by IEDB tools. However, those tools were able to highlight neoantigens over non-mutated peptides in HLA-II recognition (p-value 0.03). However, neither HLA-I binding affinity (p-value 0.08) nor Class I immunogenicity values (p-value 0.96) indicated significant differences for the latter parameters. Subsequently, the new vaccine, using aggregative functions and combinatorial optimization, was designed. The six best neoantigens were selected and formulated into two nanoparticles, with which the immune response ex vivo was evaluated, demonstrating a specific activation of the immune response. This study reinforces the use of bioinformatic tools in vaccine development, as their usefulness is proven both in silico and ex vivo.

Prevention of diabetes in overweight/obese children through a family based intervention program including supervised exercise (PREDIKID project): study protocol for a randomized controlled trial.

BACKGROUND: The global pandemic of obesity has led to an increased risk for prediabetes and type-2 diabetes (T2D). The aims of the current project are: (1) to evaluate the effect of a 22-week family based intervention program, including supervised exercise, on insulin resistance syndrome (IRS) risk in children with a high risk of developing T2D and (2) to identify the profile of microRNA in circulating exosomes and in peripheral blood mononuclear cells in children with a high risk of developing T2D and its response to a multidisciplinary intervention program including exercise. METHODS: A total of 84 children, aged 8-12 years, with a high risk of T2D will be included and randomly assigned to control (N = 42) or intervention (N = 42) groups. The control group will receive a family based lifestyle education and psycho-educational program (2 days/month), while the intervention group will attend the same lifestyle education and psycho-educational program plus the exercise program (3 days/week, 90 min per session including warm-up, moderate to vigorous aerobic activities, and strength exercises). The following measurements will be evaluated at baseline prior to randomization and after the intervention: fasting insulin, glucose and hemoglobin A1c; body composition (dual-energy X-ray absorptiometry); ectopic fat (magnetic resonance imaging); microRNA expression in circulating exosomes and in peripheral blood mononuclear cells (MiSeq; Illumina); cardiorespiratory fitness (cardiopulmonary exercise testing); dietary habits and physical activity (accelerometry). DISCUSSION: Prevention and identification of children with a high risk of developing T2D could help to improve their cardiovascular health and to reduce the comorbidities associated with obesity. TRIAL REGISTRATION: ClinicalTrials.gov, ID: NCT03027726 . Registered on 16 January 2017.

Independent and combined influence of the FTO rs9939609 and MC4Rrs17782313 polymorphisms on hypocaloric diet induced changes in body mass and composition and energy metabolism in non-morbid obese premenopausal women.

PURPOSE: To examine the independent and combined influence of the FTOrs9939609 and the MC4Rrs17782313 polymorphisms on changes in fat mass (FM), resting energy expenditure (REE), leptin, and thyrotropin (TSH) levels, after a 12-week energy-restricted diet intervention in non-morbid premenopausal obese women. METHODS: Fat mass (dual X-ray absorptiometry), REE (indirect calorimetry) and plasma leptin and thyrotropin levels were measured (before and after the intervention) in 77 obese (BMI: 33.9 ± 2.8 kg/m(2)) women (age: 36.8 ± 7.0y). RESULTS: There were no significant differences across FTOrs9939609 genotype groups (TT vs. A allele carriers, Ps>0.1) on changes in body mass (-8.6 ± 3.2% vs. -8.7 ± 3.3 %), FM (12.8 ± 4.7% vs. -12.9 ± 6.3%), REE (-11.3 ± 4.7 vs. -9.4 ± 8.1%), leptin (-34.1 ± 25.1% vs. -43.5 ± 24.1%) or TSH (5.2 ± 34.5% vs. -1.7 ± 27.1%) levels. Moreover, it was not observed any significant difference on changes in body mass (-8.6 ± 3.6% vs. -8.9 ± 2.6%), FM (-12.7 ± 6.1% vs. -13.4 ± 5.3%), REE (-9.8 ± 7.4% -9.4 ± 9.4%), leptin (-39.0 ± 26.9% vs. -44.8 ± 18.4%) or TSH (-1.0 ± 30.0% vs. 1.5 ± 26.5%) levels between non-C allele carriers and C allele carriers of the MC4Rrs17782313 (Ps>0.3). Finally, there were no significant difference on changes in body mass and composition, REE, leptin or TSH levels among non-risk allele carriers, carriers of the C allele risk of the MC4Rrs17782313, carriers of the A allele of the FTOrs9939609 and carriers of both risk alleles after the 12-week energy-restricted diet intervention (Ps>0.1). CONCLUSION: Carrying the A risk allele of the FTOrs9939609 and/or the C risk allele of the MC4Rrs17782313 did not influence body mass and FM loss, or REE decrease in obese women after a 12-week energy-restricted diet intervention.

Objetivo: Examinar la influencia individual y combinada de los polimorfismos genéticos FTO rs9939609 y MC4R rs17782313 en los cambios en la masa grasa (MG), gasto energético en reposo (GER), leptina y tirotropina (TSH) tras una intervención de 12 semanas de duración con dieta hipocalórica en mujeres pre-menopáusicas con obesidad no mórbida. Métodos: Se evaluaron al inicio y al final de la intervención la MG (absorciometría dual de rayos X), el GER (calorimetría indirecta) y los niveles de leptina y TSH en sangre en 77 mujeres (edad: 36.8±7.0 años) obesas (IMC: 33.9±2.8kg/m2). Resultados: No se observaron diferencias estadísticamente significativas (Ps>0.1) entre las portadores y las no portadoras del alelo A del FTOrs9939609 (TT vs. portadores del alelo) en los cambios en la masa corporal (-8.6±3.2% vs. -8.7±3.3 %), MG (12.8±4.7% vs. ­12.9±6.3%), GER (-11.3±4.7 vs. -9.4±8.1%), leptina (-34.1±25.1% vs. -43.5±24.1%) y TSH (5.2±34.5% vs. -1.7±27.1%). Tampoco se observaron diferencias estadísticamente significativas en los cambios en la masa corporal (-8.6±3.6% vs. -8.9±2.6%), MG (-12.7±6.1% vs. -13.4±5.3%), GER (-9.8±7.4% -9.4±9.4%), leptina (-39.0±26.9% vs. -44.8±18.4%) y TSH (-1.0±30.0% vs. 1.5±26.5%) entre las participantes portadoras y no portadoras del alelo C del MC4Rrs17782313 (Ps>0.3). Finalmente, no se encontraron diferencias estadísticamente significativas en los cambios en la masa y composición corporal, el GER, o los niveles de leptina y TSH entre mujeres no portadoras de alelos de riesgo, portadoras del alelo C del MC4Rrs17782313, portadoras del alelo A del FTOrs9939609 y portadoras de los dos alelos de riesgo (A y C) al final de las 12 semanas de intervención con dieta hipocalórica (Ps>0.1). Conclusión: Ser portador del alelo de riesgo A del FTOrs9939609 y/o del alelo de riesgo C del MC4Rrs17782313 no influye en la pérdida de masa grasa o en el descenso del GER en mujeres obesas tras 12 semanas de intervención con dieta hipocalórica.

Independent and combined influence of the FTO rs9939609 and MC4R rs17782313 polymorphisms on hypocaloric diet induced changes in body mass and composition and energy metabolism in non-morbid obese premenopausal women / Influencia individual y combinada de los polimorfismos genéticos FTO rs9939609 y mc4r rs17782313 sobre los cambios en la masa y composición corporal y el metabolismo energético inducidos por un tratamiento con dieta hipocalórica en mujeres pre-menopáusicas con obesidad no mórbida

Purpose: To examine the independent and combined influence of the FTOrs9939609 and the MC4Rrs17782313 polymorphisms on changes in fat mass (FM), resting energy expenditure (REE), leptin, and thyrotropin (TSH) levels, after a 12-week energy-restricted diet intervention in non-morbid premenopausal obese women. Methods: Fat mass (dual X-ray absorptiometry), REE (indirect calorimetry) and plasma leptin and thyrotropin levels were measured (before and after the intervention) in 77 obese (BMI: 33.9±2.8kg/m2 ) women (age: 36.8±7.0y). Results: There were no significant differences across FTOrs9939609 genotype groups (TT vs. A allele carriers, Ps>0.1) on changes in body mass (-8.6±3.2% vs. -8.7±3.3 %), FM (12.8±4.7% vs. –12.9±6.3%), REE (-11.3±4.7 vs. -9.4±8.1%), leptin (-34.1±25.1% vs. -43.5±24.1%) or TSH (5.2±34.5% vs. -1.7±27.1%) levels. Moreover, it was not observed any significant difference on changes in body mass (-8.6±3.6% vs. -8.9±2.6%), FM (-12.7±6.1% vs. -13.4±5.3%), REE (-9.8±7.4% -9.4±9.4%), leptin (-39.0±26.9% vs. -44.8±18.4%) or TSH (-1.0±30.0% vs. 1.5±26.5%) levels between non-C allele carriers and C allele carriers of the MC4Rrs17782313 (Ps>0.3). Finally, there were no significant difference on changes in body mass and composition, REE, leptin or TSH levels among non-risk allele carriers, carriers of the C allele risk of the MC4Rrs17782313, carriers of the A allele of the FTOrs9939609 and carriers of both risk alleles after the 12-week energy-restricted diet intervention (Ps>0.1). Conclusion: Carrying the A risk allele of the FTOrs9939609 and/or the C risk allele of the MC4Rrs17782313 did not influence body mass and FM loss, or REE decrease in obese women after a 12-week energy-restricted diet intervention (AU)

Objetivo: Examinar la influencia individual y combinada de los polimorfismos genéticos FTO rs9939609 y MC4R rs17782313 en los cambios en la masa grasa (MG), gasto energético en reposo (GER), leptina y tirotropina (TSH) tras una intervención de 12 semanas de duración con dieta hipocalórica en mujeres pre-menopáusicas con obesidad no mórbida. Métodos: Se evaluaron al inicio y al final de la intervención la MG (absorciometría dual de rayos X), el GER (calorimetría indirecta) y los niveles de leptina y TSH en sangre en 77 mujeres (edad: 36.8±7.0 años) obesas (IMC: 33.9±2.8kg/m2 ). Resultados: No se observaron diferencias estadísticamente significativas (Ps>0.1) entre las portadores y las no portadoras del alelo A del FTOrs9939609 (TT vs. portadores del alelo) en los cambios en la masa corporal (-8.6±3.2% vs. -8.7±3.3 %), MG (12.8±4.7% vs. –12.9±6.3%), GER (-11.3±4.7 vs. -9.4±8.1%), leptina (-34.1±25.1% vs. -43.5±24.1%) y TSH (5.2±34.5% vs. -1.7±27.1%). Tampoco se observaron diferencias estadísticamente significativas en los cambios en la masa corporal (-8.6±3.6% vs. -8.9±2.6%), MG (-12.7±6.1% vs. -13.4±5.3%), GER (-9.8±7.4% -9.4±9.4%), leptina (-39.0±26.9% vs. -44.8±18.4%) y TSH (-1.0±30.0% vs. 1.5±26.5%) entre las participantes portadoras y no portadoras del alelo C del MC4Rrs17782313 (Ps>0.3). Finalmente, no se encontraron diferencias estadísticamente significativas en los cambios en la masa y composición corporal, el GER, o los niveles de leptina y TSH entre mujeres no portadoras de alelos de riesgo, portadoras del alelo C del MC4Rrs17782313, portadoras del alelo A del FTOrs9939609 y portadoras de los dos alelos de riesgo (A y C) al final de las 12 semanas de intervención con dieta hipocalórica (Ps>0.1). Conclusión: Ser portador del alelo de riesgo A del FTOrs9939609 y/o del alelo de riesgo C del MC4Rrs17782313 no influye en la pérdida de masa grasa o en el descenso del GER en mujeres obesas tras 12 semanas de intervención con dieta hipocalórica (AU)

Aspergillus fumigatus transcriptome response to a higher temperature during the earliest steps of germination monitored using a new customized expression microarray.

Aspergillus fumigatus is considered to be the most prevalent airborne pathogenic fungus and can cause invasive diseases in immunocompromised patients. It is known that its virulence is multifactorial, although the mechanisms of pathogenicity remain unclear. With the aim of improving our understanding of these mechanisms, we designed a new expression microarray covering the entire genome of A. fumigatus. In this first study, we analysed the transcriptomes of this fungus at the first steps of germination after being grown at 24 and 37 °C. The microarray data revealed that 1249 genes were differentially expressed during growth at these two temperatures. According to our results, A. fumigatus modified significantly the expression of genes related to metabolism to adapt to new conditions. The high percentages of genes that encoded hypothetical or unclassified proteins differentially expressed implied that many as yet unknown genes were involved in the establishment of A. fumigatus infection. Furthermore, amongst the genes implicated in virulence upregulated at 37 °C on the microarray, we found those that encoded proteins mainly related to allergens (Asp F1, Asp F2 and MnSOD), gliotoxin biosynthesis (GliP and GliZ), nitrogen (NiiA and NiaD) or iron (HapX, SreA, SidD and SidC) metabolism. However, gene expression in iron and nitrogen metabolism might be influenced not only by heat shock, but also by the availability of nutrients in the medium, as shown by the addition of fresh medium.

Preliminary findings on the influence of FTO rs9939609 and MC4R rs17782313 polymorphisms on resting energy expenditure, leptin and thyrotropin levels in obese non-morbid premenopausal women

Given that leptin, ghrelin and thyrotropin play a major role in the regulation of resting energy expenditure (REE) and that the FTO rs9939609 and the MC4R rs17782313 polymorphisms have been proposed to affect energy homeostasis, we hypothesized that both polymorphisms are associated with REE and that these relationships can be mediated by leptin, ghrelin and thyrotropin in obesity. Therefore, the present study aimed to examine the relationships between FTO rs9939609 and the MC4R rs17782313 with REE, leptin, ghrelin and thyrotropin levels in obese women. The study comprised 77 obese (body mass index 34.0 ± 2.8 kg/m2) women (age 36.7 ± 7 years). We measured body composition by dual-energy X-ray absorptiometry and REE by indirect calorimetry. We analysed fasting leptin, ghrelin and thyrotropin levels and the ratio of leptin to fat mass was calculated. Genotype distributions of the polymorphisms did not deviate from Hardy-Weinberg expectations (P values >0.2). Women carrying the A allele of the FTO rs9939609 had lower REE (1,580 ± 22 vs. 1,739 ± 35 kcal/day, P < 0.001) and higher leptin to fat mass ratio (1.33 ± 0.05 vs. 1.13 ± 0.08 ng/ml kg, P < 0.05) and thyrotropin levels (1.93 ± 0.10 vs. 1.53 ± 0.16 ìU/ml, P < 0.05) regardless of age and body mass index. We found no significant influence of the MC4R rs17782313 on energy metabolism or biochemical variables. Our findings confirm that the A allele of the FTOrs9939609 is associated with lower REE and increased plasma leptin levels. We also found an association between the FTO rs9939609 and thyrotropin, suggesting the possible influence of FTOin the hypothalamic-pituitary-thyroid axis as a potential mechanism of the increased adiposity

Preliminary findings on the influence of FTO rs9939609 and MC4R rs17782313 polymorphisms on resting energy expenditure, leptin and thyrotropin levels in obese non-morbid premenopausal women.

Given that leptin, ghrelin and thyrotropin play a major role in the regulation of resting energy expenditure (REE) and that the FTO rs9939609 and the MC4R rs17782313 polymorphisms have been proposed to affect energy homeostasis, we hypothesized that both polymorphisms are associated with REE and that these relationships can be mediated by leptin, ghrelin and thyrotropin in obesity. Therefore, the present study aimed to examine the relationships between FTO rs9939609 and the MC4R rs17782313 with REE, leptin, ghrelin and thyrotropin levels in obese women. The study comprised 77 obese (body mass index 34.0 ± 2.8 kg/m(2)) women (age 36.7 ± 7 years). We measured body composition by dual-energy X-ray absorptiometry and REE by indirect calorimetry. We analysed fasting leptin, ghrelin and thyrotropin levels and the ratio of leptin to fat mass was calculated. Genotype distributions of the polymorphisms did not deviate from Hardy-Weinberg expectations (P values >0.2). Women carrying the A allele of the FTO rs9939609 had lower REE (1,580 ± 22 vs. 1,739 ± 35 kcal/day, P < 0.001) and higher leptin to fat mass ratio (1.33 ± 0.05 vs. 1.13 ± 0.08 ng/ml kg, P < 0.05) and thyrotropin levels (1.93 ± 0.10 vs. 1.53 ± 0.16 µU/ml, P < 0.05) regardless of age and body mass index. We found no significant influence of the MC4R rs17782313 on energy metabolism or biochemical variables. Our findings confirm that the A allele of the FTO rs9939609 is associated with lower REE and increased plasma leptin levels. We also found an association between the FTO rs9939609 and thyrotropin, suggesting the possible influence of FTO in the hypothalamic-pituitary-thyroid axis as a potential mechanism of the increased adiposity.

Effects of dietary supplementation with epigallocatechin-3-gallate on weight loss, energy homeostasis, cardiometabolic risk factors and liver function in obese women: randomised, double-blind, placebo-controlled clinical trial.

The aim of the present study was to examine the effects of green tea epigallocatechin-3-gallate (EGCG) on changes in body composition, energy and substrate metabolism, cardiometabolic risk factors and liver function enzymes after an energy-restricted diet intervention in obese women. In the present randomised, double-blind, placebo-controlled study, eighty-three obese (30 kg/m² > BMI < 40 kg/m²) pre-menopausal women consumed 300 mg/d of EGCG or placebo (lactose). We measured body weight and adiposity (dual-energy X-ray absorptiometry), energy expenditure and fat oxidation rates (indirect calorimetry), blood lipid levels (TAG, total cholesterol, LDL-cholesterol and HDL-cholesterol), insulin resistance, C-reactive protein and liver function markers (aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, γ-glutamyltransferase, urea, bilirubin and 2-keto[1-¹³C]isocaproate oxidation) before and after the intervention in the EGCG and control groups. We did not find any significant difference in the changes in body weight (-0.3 kg, 95% CI -5.0, 4.3), fat mass (-0.7 kg, 95% CI -3.5, 2.1), energy (0.3 kJ/kg per d, 95% CI -3.1, 2.7) and fat (-0.1 g/min, 95% CI -0.03, 0.01) metabolism, homeostasis assessment model for insulin resistance (0.2, 95% CI -0.2, 0.7), total cholesterol (-0.21 mmol/l, 95% CI -0.55, 0.13), LDL-cholesterol (-0.15 mmol/l, 95% CI -0.50, 0.20), TAG (-0.4 mmol/l, 95% CI -0.56, 0.29) and liver function markers between the EGCG and control groups. In conclusion, the present results suggest that dietary supplementation with 300 mg/d of EGCG for 12 weeks did not enhance energy-restricted diet-induced adiposity reductions, and did not improve weight-loss-induced changes in cardiometabolic risk factors in obese Caucasian women. The intake of 300 mg/d of EGCG for 12 weeks did not cause any adverse effect on liver function biomarkers.

Influence of menopause on adipose tissue clock gene genotype and its relationship with metabolic syndrome in morbidly obese women.

Menopausal women exhibit a loss of circadian coordination, a process that runs parallel with a redistribution of adipose tissue. However, the specific genetic mechanisms underlying these alterations have not been studied. Thus, the aim of the present study was to determine whether the development of menopause induces an alteration of the genes that control biological rhythms in human subcutaneous (SAT) and visceral (VAT) adipose tissue, and whether changes in clock gene expression are involved in the increased risk of developing metabolic syndrome (MetS), which is frequently associated with menopause. To this end, VAT and SAT biopsies were taken in pre- (n = 7) and postmenopausal (n = 7) women at similar hours in the morning. RNA was extracted, and a microarray analysis was made. Data were confirmed by quantitative real-time polymerase chain reaction. Western blot and immunohistochemical analysis were also performed. When clock gene expression was compared between both groups of women, data in SAT showed that expression of the core clock gene period3 was significantly higher in postmenopausal women, while casein kinase-1δ, E1A-binding protein and cAMP-responsive element were preferentially expressed in the premenopausal group. In VAT, period2 (PER2) and v-myc myelocytomatosis viral oncogene expressions were significantly higher in the postmenopausal group. Western blot analysis indicated that PER2 and PER3 protein expression was also increased in postmenopausal women. In addition, several genes, including PER2, were differentially expressed depending on whether or not the patient met the MetS criteria. We conclude that menopause transition induces several changes in the genotype of the adipose tissue chronobiological machinery related to an increased risk of developing MetS.

Role of baseline leptin and ghrelin levels on body weight and fat mass changes after an energy-restricted diet intervention in obese women: effects on energy metabolism.

CONTEXT: Hormones related to energy balance control may play an important role on weight loss resistance after low-caloric diet (LCD) intervention. OBJECTIVE: To investigate the predictive value of baseline leptin and ghrelin on body fat mass (FM) loss after 12 wk of LCD intervention and to study whether these associations could be related to changes in resting metabolic rate (RMR). DESIGN: The study comprised a total of 78 obese women (age 36.7 ± 7 yr). We measured, before and after the LCD intervention, FM (dual-energy x-ray absorptiometry) and RMR (kilojoules per kilogram body weight per day, indirect calorimetry). We also analyzed fasting serum leptin and ghrelin, and leptin to ghrelin ratio was calculated. MAIN OUTCOME MEASURES: FM and RMR changes (data at baseline - data after the intervention) were assessed. RESULTS: Baseline serum leptin (r = -0.301; age- and baseline FM-adjusted P = 0.009) and ghrelin (r = 0.314, adjusted P = 0.014) levels as well as leptin to ghrelin levels (r = -0.331; adjusted P = 0.009) were significantly correlated with FM changes. Leptin to ghrelin ratio was significantly correlated with RMR at baseline and after the LCD (both P < 0.010). Baseline leptin to ghrelin ratio significantly predicted changes in RMR after the LCD (r = 0.298; P = 0.019) regardless of age, baseline RMR, and total body weight (r = 0.307; P = 0.016) or FM loss (r = 0.312; P = 0.015). CONCLUSIONS: Obese women with higher leptin and lower ghrelin levels at baseline seem to be more resistant to FM loss. The leptin to ghrelin ratio could be proposed as a biomarker for predicting metabolic adaptations to energy restriction treatment and, if confirmed in future studies, as a predictor of treatment success/failure.

Profile of adipose tissue gene expression in premenopausal and postmenopausal women: site-specific differences.

OBJECTIVES: Menopause increases the risk of several pathologies, probably due to enlarged levels of visceral fat. Apart from morphological and endocrine changes, a cluster of genes, still not fully defined, may be involved in these alterations. The objectives of the present study, therefore, were to analyze differences in adipose tissue gene expression between premenopausal and postmenopausal women and to ascertain whether any differences were depot specific. METHODS: Visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) biopsies were taken from 7 premenopausal and 7 postmenopausal women undergoing surgery because of morbid obesity. RNA was extracted, and the overall gene expression profile was analyzed by microarray analysis. RESULTS: In general, SAT genes were overexpressed, whereas VAT genes were down-regulated in premenopausal compared with postmenopausal women. We found 724 differentially expressed genes in SAT and 327 in VAT. These differences suggest that several biological processes, such as the immune system and other metabolic processes, were altered based on menopause status. Regarding individual genes, neurexin 3, metallothionein 1E, and keratyn 7 showed the most pronounced differences. Interestingly, the expression of these genes was related to body fat distribution. CONCLUSIONS: Our results reveal that menopause influences the adipose tissue expression of many genes, especially of neurexin 3, metallothionein 1E, and keratyn 7, which are associated with the alteration of several key biological processes, such as the immune system and cell metabolism. Gene expression in adipose tissue could be used for diagnosis and the development of new therapeutic strategies against obesity and related alterations, depending on menopause status.

Role of ß2-adrenergic receptor polymorphisms on body weight and body composition response to energy restriction in obese women: preliminary results.

We investigated the role of common ß2-adrenergic receptor (ADRB2) rs1042714 (Gln27Glu) and rs1042713 (Arg16Gly) polymorphisms on body weight and body composition response to 12-week energy-restricted diet in women. The study comprised 78 Spanish obese (BMI: 34.0 ± 2.8 kg/m²) women (age: 36.7 ± 7 years). We measured (before and after the dietary intervention) weight and height, and BMI calculated. Moreover, body fat mass and lean mass (LM) were measured by dual energy X-ray absorptiometry. We observed an interaction effect between the Gln27Glu polymorphism and diet-induced changes on body weight (P = 0.006), BMI (P = 0.004), and LM (P = 0.001). Women carrying the Glu allele had a greater reduction in body weight than non-Glu allele carriers (9.5 ± 2.9 vs. 7.0 ± 3.5%, respectively, P = 0.002). Moreover, women with the Glu allele lost more LM than the Gln27Gln group (5.9 ± 2.7 vs. 4.0 ± 2.7%, respectively, P = 0.001). We did not find any significant interaction effect between the Arg16Gly polymorphism and diet-induced changes on the outcome variables (all P > 0.1). The results suggest that the ADRB2 Gln27Glu polymorphism has a modulating effect on diet-induced changes on body weight and body composition, and should be considered in future obesity treatments. These findings should be taken as preliminary and be replicated in further energy restriction studies with larger sample sizes.

Klebsiella pneumoniae subverts the activation of inflammatory responses in a NOD1-dependent manner.

Klebsiella pneumoniae is an important cause of community-acquired and nosocomial pneumonia. Subversion of inflammation is essential for pathogen survival during infection. Evidence indicates that K. pneumoniae infections are characterized by lacking an early inflammatory response although the molecular bases are currently unknown. Here we unveil a novel strategy employed by a pathogen to counteract the activation of inflammatory responses. K. pneumoniae attenuates pro-inflammatory mediators-induced IL-8 secretion. Klebsiella antagonizes the activation of NF-κB via the deubiquitinase CYLD and blocks the phosphorylation of mitogen-activated protein kinases (MAPKs) via the MAPK phosphatase MKP-1. Our studies demonstrate that K. pneumoniae has evolved the capacity to manipulate host systems dedicated to control the immune balance. To exert this anti-inflammatory effect, Klebsiella engages NOD1. In NOD1 knock-down cells, Klebsiella neither induces the expression of CYLD and MKP-1 nor blocks the activation of NF-κB and MAPKs. Klebsiella inhibits Rac1 activation; and inhibition of Rac1 activity triggers a NOD1-mediated CYLD and MKP-1 expression which in turn attenuates IL-1ß-induced IL-8 secretion. A capsule (CPS) mutant does not attenuate the inflammatory response. However, purified CPS neither reduces IL-1ß-induced IL-8 secretion nor induces the expression of CYLD and MKP-1 thereby indicating that CPS is necessary but not sufficient to attenuate inflammation.

What makes Aspergillus fumigatus a successful pathogen? Genes and molecules involved in invasive aspergillosis

Dos secciones incluyen los genes y moléculas relacionadas con la absorción de nutrientes, la señalización y las regulaciones metabólicas implicadas en la virulencia, incluyendo enzimas, como las serin-proteasas (alp/asp f 13, alp2 y asp f 18), metaloproteasas (mep/asp f 5, mepB y mep20), aspártico-proteasas (pep/asp f 10, pep2 y ctsD), dipeptidilpeptidasas (dppIV y dppV) y fosfolipasas (plb1-3 y fosfolipasa C); sideróforos y la adquisición de hierro (sidA-G sreA, ftrA, fetC, mirB-C y amcA); adquisición de zinc (zrfA-H, zafA, y pacC); biosíntesis de aminoácidos, absorción de nitrógeno, y regulación por Cross-pathway Control (areA, rhbA, mcsA, lysF, cpcA/gcn4p y cpcC/gcn2p); vías de biosíntesis generales (pyrG, hcsA, y pabaA) y biosíntesis de trehalosa (tpsA y tpsB); otras vías de regulación, como MAP quinasas (sakA/hogA, mpkA-C, ste7, pbs2, mkk2, steC/ste11, bck1, ssk2 y sho1), proteínas G (gpaA, sfaD y cpgA), AMPc-PKA (acyA, gpaB, pkaC1 y pkaR), histidin-quinasas (fos1 y tcsB), señalización de Ca2+(calA/cnaA, crzA, gprC y gprD), familia Ras (rasA, rasB y rhbA), y otros (ace2, medA, y srbA). Por último, también se comentan los efectos de los alérgenos de A. fumigatus (Asp f 1 a Asp f 34) en la AI. Los datos obtenidos generan un complejo rompecabezas, cuyas piezas serían factores de virulencia o diferentes actividades del hongo, que se deben reunir para obtener una visión conjunta de la virulencia de A. fumigatus. Los estudios de expresión mediante microarrays de ADN podrían ser útiles para entender esta compleja virulencia, y para detectar dianas para desarrollar métodos rápidos de diagnóstico y nuevos agentes antifúngicos. Aspergillus fumigatus es un patógeno oportunista que causa el 90% de las aspergilosis invasoras (AI) con un 50–95% de mortalidad. Se ha postulado la existencia de factores de virulencia característicos, pero en A. fumigatus existe una gran variabilidad de factores de virulencia «no clásicos». Todos los estudios han demostrado que la virulencia de este hongo es multifactorial, asociada a su estructura, su capacidad de crecimiento y adaptación a condiciones de estrés, sus mecanismos de evasión del sistema inmune y su capacidad de causar daños en un huésped. En esta revisión se pretende dar una visión general de los genes y moléculas que intervienen en el desarrollo de la AI. La sección de termotolerancia incluye cinco genes relacionados con la capacidad de que el hongo crezca a más de 30°C (thtA, cgrA, afpmt1, kre2/afmnt1 y hsp1/asp f 12). En las siguientes secciones se discuten las moléculas y los genes relacionados con la interacción con el huésped y con la respuesta inmune. Estas secciones incluyen el β-glucano, el α-glucano, la quitina, el galactomanano, galactomanoproteinas (afmp1/asp f 17 y afmp2), hidrofobinas (rodA/hyp1 y rodB), la DHN-melanina, sus respectivas enzimas sintasas (fks1, rho1-4, ags1-3, chsA-G, och1-4, mnn9, van1, anp1, glfA, pksP/alb1, arp1, arp2, abr1, abr2 y ayg1) y enzimas modificantes (gel1-7, bgt1, eng1, ecm33, afpigA, afpmt1-2, afpmt4, kre2/afmnt1, afmnt2-3, afcwh41 y pmi), varias enzimas relacionadas con la protección del estrés oxidativo como catalasas (catA, cat1/catB, cat2/katG, catC y catE), superóxido dismutasas (sod1-2, sod3/asp f 6 y sod4), oxigenasas de ácidos grasos (ppoA-C), glutatión transferasas (gstA-E) y otros (afyap1, skn7 y pes1), y los transportadores de moléculas (mdr1-4, atrF, abcA-E y msfA-E)...(AU)

Two sections cover genes and molecules related with nutrient uptake, signaling and metabolic regulations involved in virulence, including enzymes, such as serine proteases (alp/asp f 13, alp2, and asp f 18), metalloproteases (mep/asp f 5, mepB, and mep20), aspartic proteases (pep/asp f 10, pep2, and ctsD), dipeptidylpeptidases (dppIV and dppV), and phospholipases (plb1–3 and phospholipase C); siderophores and iron acquisition (sidA–G, sreA, ftrA, fetC, mirB–C, and amcA); zinc acquisition (zrfA–H, zafA, and pacC); amino acid biosynthesis, nitrogen uptake, and cross-pathways control (areA, rhbA, mcsA, lysF, cpcA/gcn4p, and cpcC/gcn2p); general biosynthetic pathway (pyrG, hcsA, and pabaA), trehalose biosynthesis (tpsA and tpsB), and other regulation pathways such as those of the MAP kinases (sakA/hogA, mpkA–C, ste7, pbs2, mkk2, steC/ste11, bck1, ssk2, and sho1), G-proteins (gpaA, sfaD, and cpgA), cAMP-PKA signaling (acyA, gpaB, pkaC1, and pkaR), His kinases (fos1 and tcsB), Ca2+ signaling (calA/cnaA, crzA, gprC and gprD), and Ras family (rasA, rasB, and rhbA), and others (ace2, medA, and srbA). Finally, we also comment on the effect of A. fumigatus allergens (Asp f 1–Asp f 34) on IA. The data gathered generate a complex puzzle, the pieces representing virulence factors or the different activities of the fungus, and these need to be arranged to obtain a comprehensive vision of the virulence of A. fumigatus. The most recent gene expression studies using DNA-microarrays may be help us to understand this complex virulence, and to detect targets to develop rapid diagnostic methods and new antifungal agents. Aspergillus fumigatus is an opportunistic pathogen that causes 90% of invasive aspergillosis (IA) due to Aspergillus genus, with a 50–95% mortality rate. It has been postulated that certain virulence factors are characteristic of A. fumigatus, but the “non-classical” virulence factors seem to be highly variable. Overall, published studies have demonstrated that the virulence of this fungus is multifactorial, associated with its structure, its capacity for growth and adaptation to stress conditions, its mechanisms for evading the immune system and its ability to cause damage to the host. In this review we intend to give a general overview of the genes and molecules involved in the development of IA. The thermotolerance section focuses on five genes related with the capacity of the fungus to grow at temperatures above 30°C (thtA, cgrA, afpmt1, kre2/afmnt1, and hsp1/asp f 12)... (AU)

What makes Aspergillus fumigatus a successful pathogen? Genes and molecules involved in invasive aspergillosis.

Aspergillus fumigatus is an opportunistic pathogen that causes 90% of invasive aspergillosis (IA) due to Aspergillus genus, with a 50-95% mortality rate. It has been postulated that certain virulence factors are characteristic of A. fumigatus, but the "non-classical" virulence factors seem to be highly variable. Overall, published studies have demonstrated that the virulence of this fungus is multifactorial, associated with its structure, its capacity for growth and adaptation to stress conditions, its mechanisms for evading the immune system and its ability to cause damage to the host. In this review we intend to give a general overview of the genes and molecules involved in the development of IA. The thermotolerance section focuses on five genes related with the capacity of the fungus to grow at temperatures above 30°C (thtA, cgrA, afpmt1, kre2/afmnt1, and hsp1/asp f 12). The following sections discuss molecules and genes related to interaction with the host and with the immune responses. These sections include ß-glucan, α-glucan, chitin, galactomannan, galactomannoproteins (afmp1/asp f 17 and afmp2), hydrophobins (rodA/hyp1 and rodB), DHN-melanin, their respective synthases (fks1, rho1-4, ags1-3, chsA-G, och1-4, mnn9, van1, anp1, glfA, pksP/alb1, arp1, arp2, abr1, abr2, and ayg1), and modifying enzymes (gel1-7, bgt1, eng1, ecm33, afpigA, afpmt1-2, afpmt4, kre2/afmnt1, afmnt2-3, afcwh41 and pmi); several enzymes related to oxidative stress protection such as catalases (catA, cat1/catB, cat2/katG, catC, and catE), superoxide dismutases (sod1, sod2, sod3/asp f 6, and sod4), fatty acid oxygenases (ppoA-C), glutathione tranferases (gstA-E), and others (afyap1, skn7, and pes1); and efflux transporters (mdr1-4, atrF, abcA-E, and msfA-E). In addition, this review considers toxins and related genes, such as a diffusible toxic substance from conidia, gliotoxin (gliP and gliZ), mitogillin (res/mitF/asp f 1), hemolysin (aspHS), festuclavine and fumigaclavine A-C, fumitremorgin A-C, verruculogen, fumagillin, helvolic acid, aflatoxin B1 and G1, and laeA. Two sections cover genes and molecules related with nutrient uptake, signaling and metabolic regulations involved in virulence, including enzymes, such as serine proteases (alp/asp f 13, alp2, and asp f 18), metalloproteases (mep/asp f 5, mepB, and mep20), aspartic proteases (pep/asp f 10, pep2, and ctsD), dipeptidylpeptidases (dppIV and dppV), and phospholipases (plb1-3 and phospholipase C); siderophores and iron acquisition (sidA-G, sreA, ftrA, fetC, mirB-C, and amcA); zinc acquisition (zrfA-H, zafA, and pacC); amino acid biosynthesis, nitrogen uptake, and cross-pathways control (areA, rhbA, mcsA, lysF, cpcA/gcn4p, and cpcC/gcn2p); general biosynthetic pathway (pyrG, hcsA, and pabaA), trehalose biosynthesis (tpsA and tpsB), and other regulation pathways such as those of the MAP kinases (sakA/hogA, mpkA-C, ste7, pbs2, mkk2, steC/ste11, bck1, ssk2, and sho1), G-proteins (gpaA, sfaD, and cpgA), cAMP-PKA signaling (acyA, gpaB, pkaC1, and pkaR), His kinases (fos1 and tcsB), Ca(2+) signaling (calA/cnaA, crzA, gprC and gprD), and Ras family (rasA, rasB, and rhbA), and others (ace2, medA, and srbA). Finally, we also comment on the effect of A. fumigatus allergens (Asp f 1-Asp f 34) on IA. The data gathered generate a complex puzzle, the pieces representing virulence factors or the different activities of the fungus, and these need to be arranged to obtain a comprehensive vision of the virulence of A. fumigatus. The most recent gene expression studies using DNA-microarrays may be help us to understand this complex virulence, and to detect targets to develop rapid diagnostic methods and new antifungal agents.

Klebsiella pneumoniae capsule polysaccharide impedes the expression of beta-defensins by airway epithelial cells.

Human beta-defensins (hBDs) contribute to the protection of the respiratory tract against pathogens. It is reasonable to postulate that pathogens have developed countermeasures to resist them. Klebsiella pneumoniae capsule polysaccharide (CPS), but not the lipopolysaccharide O antigen, mediated resistance against hBD1 and hBD2. hBD3 was the most potent hBD against Klebsiella. We investigated the possibility that as a strategy for survival in the lung, K. pneumoniae may not activate the expression of hBDs. Infection of A549 and normal human bronchial cells with 52145-Deltawca(K2), a CPS mutant, increased the expression of hBD2 and hBD3. Neither the wild type nor the lipopolysaccharide O antigen mutant increased the expression of hBDs. In vivo, 52145-Deltawca(K2) induced higher levels of mBD4 and mBD14, possible mouse orthologues of hBD2 and hBD3, respectively, than the wild type. 52145-Deltawca(K2)-dependent upregulation of hBD2 occurred via NF-kappaB and mitogen-activated protein kinases (MAPKs) p44/42, Jun N-terminal protein kinase (JNK)-dependent pathways. The increase in hBD3 expression was dependent on the MAPK JNK. 52145-Deltawca(K2) engaged Toll-like receptors 2 and 4 (TLR2 and TLR4) to activate hBD2, whereas hBD3 expression was dependent on NOD1. K. pneumoniae induced the expression of CYLD and MKP-1, which act as negative regulators for 52145-Deltawca(K2)-induced expression of hBDs. Bacterial engagement of pattern recognition receptors induced CYLD and MKP-1, which may initiate the attenuation of proinflammatory pathways. The results of this study indicate that K. pneumoniae CPS not only protects the pathogen from the bactericidal action of defensins but also impedes their expression. These features of K. pneumoniae CPS may facilitate pathogen survival in the hostile environment of the lung.

DNA copy number variation and gene expression analyses reveal the implication of specific oncogenes and genes in GBM.

To understand the pathogenesis of glioblastoma multiforme (GBM) we used high-resolution comparative genomic hybridization arrays and gene expression microarrays to identify DNA copy number alterations and gene expression changes in comparable sets of GBM samples. Gains were detected at chromosomes 1, 2, 7, 9, 12, 19, and 20 and losses at 6, 9, and 10. Gene expression analyses identified specific genes overexpressed in GBM mapping at amplified chromosomal regions. Among these genes we found genes involved in angiogenesis, extracellular matrix remodeling and several oncogenes. DNA copy number analysis along with gene expression profiles provides a powerful strategy to understand tumor progression and identification of genes involved in GBM pathogenesis.

Klebsiella pneumoniae increases the levels of Toll-like receptors 2 and 4 in human airway epithelial cells.

Airway epithelial cells act as the first barrier against pathogens. These cells recognize conserved structural motifs expressed by microbial pathogens via Toll-like receptors (TLRs) expressed on the surface. In contrast to the level of expression in lymphoid cells, the level of expression of TLR2 and TLR4 in airway epithelial cells is low under physiological conditions. Here we explored whether Klebsiella pneumoniae upregulates the expression of TLRs in human airway epithelial cells. We found that the expression of TLR2 and TLR4 by A549 cells and human primary airway cells was upregulated upon infection with K. pneumoniae. The increased expression of TLRs resulted in enhancement of the cellular response upon stimulation with Pam3CSK4 and lipopolysaccharide, which are TLR2 and TLR4 agonists, respectively. Klebsiella-dependent upregulation of TLR expression occurred via a positive IkappaBalpha-dependent NF-kappaBeta pathway and via negative p38 and p44/42 mitogen-activated protein kinase-dependent pathways. We showed that Klebsiella-induced TLR2 and TLR4 upregulation was dependent on TLR activation. An isogenic capsule polysaccharide (CPS) mutant did not increase TLR2 and TLR4 expression. Purified CPS upregulated TLR2 and TLR4 expression, and polymyxin B did not abrogate CPS-induced TLR upregulation. Although no proteins were detected in the CPS preparation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and colloidal gold staining, we could not rule out the possibility that traces of protein in our CPS preparation could have been responsible, at least in part, for the TLR upregulation.

Differential expression of oxidative stress and inflammation related genes in peripheral blood mononuclear cells in response to a low-calorie diet: a nutrigenomics study.

Nutrigenomics is a new application of omics technologies in nutritional science. Nutrigenomics aims to identify molecular markers of diet-related diseases and mechanisms of interindividual variability in response to food. The aim of this study was to evaluate peripheral blood mononuclear cells (PBMC) as a model system and readily available source of RNA to discern gene expression signatures in relation to personalized therapy of obesity. PBMC were collected from obese men before and after an 8-week low-calorie diet (LCD) to lose weight. Changes in gene expression before and after the LCD were initially screened using a DNA-microarray platform and validated by qRT-PCR. Global gene expression analysis identified 385 differentially expressed transcripts after the LCD. Further analyses showed a decrease in some specific oxidative stress and inflammation genes. Interestingly, expression of these genes was directly related to body weight, while a lower IL8 gene expression was associated with higher fat mass decrease. Collectively, these observations suggest that PBMCs are a suitable RNA source and model system to perform nutrigenomics studies related to obesity and development of personalized dietary treatments. IL8 gene expression warrant further research as a putative novel biomarker of changes in body fat percentage in response to an LCD.

Gene expression profiling of human gliomas reveals differences between GBM and LGA related to energy metabolism and notch signaling pathways.

Human malignant astrocytic tumors are the most common primary brain malignancies. Human gliomas are classified according to the extent of anaplasia or 'de-differentiation' appearance. Although this type of histological classification is widely accepted, the extensive heterogeneity of astrocytic tumors has made their pathological classification rather difficult. New genome-scale high throughput technologies for gene expression profiling, such as DNA microarrays, are emerging as new tools to allow a more accurate identification and characterization of different tumor degrees by discovering new specific markers and pathways of each stage. Present work reports interesting results that might be useful to differentiate between tumor grades. Data presented here provides new evidences about the molecular basis underlying different tumor stages. In this sense, we identified key metabolic pathways, crucial for tumor progression, as being differentially regulated in different tumor stages. On the other hand, remarkable findings regarding Notch pathway are reported, as some members of this receptor family were found to be differentially expressed depending on the malignancy degree. Our results clearly point out important molecular differences between different tumor stages and suggest that more studies are needed to understand specific molecular events characteristic of each stage. These types of studies represent a first step to deepen into the tumor physiology, which may potentially help for better and a more precise diagnosis of gliomas.