Foods, nutrients and the risk of oral and pharyngeal cancer.

Background:Besides tobacco and alcohol, dietary habits may have a relevant role in oral cavity and pharyngeal (OCP) cancer.Methods:We analysed the role of selected food groups and nutrients on OCP cancer in a case-control study carried out between 1997 and 2009 in Italy and Switzerland. This included 768 incident, histologically confirmed squamous cell carcinoma cases and 2078 hospital controls. Odds ratios (ORs) were estimated using logistic regression models including terms for tobacco, alcohol and other relevant covariates.Results:Significant inverse trends in risk were observed for all vegetables (OR=0.19, for the highest vs the lowest consumption) and all fruits (OR=0.39), whereas significant direct associations were found for milk and dairy products (OR=1.50), eggs (OR=1.71), red meat (OR=1.55), potatoes (OR=1.85) and desserts (OR=1.68), although trends in risk were significant only for potatoes and desserts. With reference to nutrients, significant inverse relations were observed for vegetable protein (OR=0.45, for the highest vs the lowest quintile), vegetable fat (OR=0.54), polyunsaturated fatty acids (OR=0.53), α-carotene (OR=0.51), β-carotene (OR=0.28), β-cryptoxanthin (OR=0.37), lutein and zeazanthin (OR=0.34), vitamin E (OR=0.26), vitamin C (OR=0.40) and total folate (OR=0.34), whereas direct ones were observed for animal protein (OR=1.57), animal fat (OR=2.47), saturated fatty acids (OR=2.18), cholesterol (OR=2.29) and retinol (OR=1.88). Combinations of low consumption of fruits and vegetables, and high consumption of meat with high tobacco and alcohol, led to 10- to over 20-fold excess risk of OCP cancer.Conclusion:Our study confirms and further quantifies that a diet rich in fruits and vegetables and poor in meat and products of animal origin has a favourable role against OCP cancer.

GSVA: gene set variation analysis for microarray and RNA-seq data

Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets. To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments. GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at http://www.bioconductor.org.

Hospital outbreak of methicillin-resistant Staphylococcus aureus caused by a new, possibly hyperepidemic variant from a previously sporadic strain.

Objective: To describe an ongoing outbreak that tripled the annual detection of methicillin-resistant Staphylococcus aureus (MRSA) carriage in a tertiary care hospital. Methods: Active surveillance of MRSA is performed since 20 years in our hospital. Our protocol includes screening of patients transferred from high-incidence health-care institutions or countries, roommates of new MRSA cases, and wards where _2 patients acquired MRSA during the same week. Contact precautions are used for known carriers. PFGE was used for molecular typing until 2004, and was then replaced by Double-Locus Sequence Typing (DLST). Results: A median yearly incidence of 173 new carriers of MRSA was observed from 2002 to 2007. Since September 2008, an increasing number of new cases were observed, mainly as successive clusters limited to distinct wards, reaching a total of 398 until October 2009. The yearly incidence of new cases rose to 275 in 2008 and 613 in 2009. 60% of the cases were due to one strain: DLST 4−4, ST 228, SCCmecI. The incidence of new cases due to the previously predominant strains remained unchanged. The epidemic strain corresponded to a new variant of a clone responsible for a previous outbreak in 2001, and only sporadically isolated (mean of 20 cases/year) since then. A case- control study documented a significant association between acquisition of the epidemic strain and a stay in intensive and intermediary care units, a highest number of internal transfers, but did not identify a point source of transmission. Infection control practices and antibiotic policy had remained unchanged for several years. Compliance with handhygiene as monitored yearly was on the rise. Screening of 313 healthcare workers only found one carrier of the epidemic strain lately in the outbreak. Additional infection control measures were enforced, including screening at ICU admission and discharge with PCR-based rapid test, routine screening for all patients leaving epidemic wards, introduction of PCR-based rapid test for contact tracing, additional working forces for environmental disinfection, and hospital-wide education of healthcare workers. However, the outbreak was still ongoing after 5 months. Conclusions: Factors linked to the dissemination of this new variant in our institution remain undetermined. This unresolved outbreak suggests that this new variant acquired hyperepidemic properties, which calls for further investigations.

CD28-negative cytolytic effector T cells frequently express NK receptors and are present at variable proportions in circulating lymphocytes from healthy donors and melanoma patients.

In humans, NK receptors are expressed by natural killer cells and some T cells, the latter of which are preferentially alphabetaTCR+ CD8+ cytolytic T lymphocytes (CTL). In this study we analyzed the expression of nine NK receptors (p58.1, p58.2, p70, p140, ILT2, NKRP1A, ZIN176, CD94 and CD94/NKG2A) in PBL from both healthy donors and melanoma patients. The percentages of NK receptor-positive T cells (NKT cells) varied strongly, and this variation was more important between individual patients than between individual healthy donors. In all the individuals, the NKT cells were preferentially CD28-, and a significant correlation was found between the percentage of CD28- T cells and the percentage of NK receptor+ T cells. Based on these data and the known activated phenotype of CD28- T cells, we propose that the CD28- CD8+ T cell pool represents or contains the currently active CTL population, and that the frequent expression of NK receptors reflects regulatory mechanisms modulating the extent of CTL effector function. Preliminary results indicate that some tumor antigen-specific T cells may indeed be CD28- and express NK receptors in vivo.

Susceptibilitat genètica al càncer gàstric: caracterització de les interaccions de segon ordre entre gens i variants identificades en l’estudi EPIC‐EURGAST

En aquest Treball de Final de Grau s’exposen els resultats de l’anàlisi de les dades genètiques del projecte EurGast2 "Genetic susceptibility, environmental exposure and gastric cancer risk in an European population”, estudi cas‐control niat a la cohort europea EPIC “European Prospective lnvestigation into Cancer and Nutrition”, que té per objectiu l’estudi dels factors genètics i ambientals associats amb el risc de desenvolupar càncer gàstric (CG). A partir de les dades resultants de l’estudi EurGast2, en el què es van analitzar 1.294 SNPs en 365 casos de càncer gàstric i 1.284 controls en l’anàlisi Single SNP previ, la hipòtesi de partida del present Treball de Final de Grau és que algunes variants amb un efecte marginal molt feble, però que conjuntament amb altres variants estarien associades al risc de CG, podrien no haver‐se detectat. Així doncs, l’objectiu principal del projecte és la identificació d’interaccions de segon ordre entre variants genètiques de gens candidats implicades en la carcinogènesi de càncer gàstric. L’anàlisi de les interaccions s’ha dut a terme aplicant el mètode estadístic Model‐based Multifactor Dimensionality Reduction Method (MB‐MDR), desenvolupat per Calle et al. l’any 2008 i s’han aplicat dues metodologies de filtratge per seleccionar les interaccions que s’exploraran: 1) filtratge d’interaccions amb un SNP significatiu en el Single SNP analysis i 2) filtratge d’interaccions segons la mesura Sinèrgia. Els resultats del projecte han identificat 5 interaccions de segon ordre entre SNPs associades significativament amb un major risc de desenvolupar càncer gàstric, amb p‐valor inferior a 10‐4. Les interaccions identificades corresponen a interaccions entre els gens MPO i CDH1, XRCC1 i GAS6, ADH1B i NR5A2 i IL4R i IL1RN (que s’ha validat en les dues metodologies de filtratge). Excepte CDH1, cap altre d’aquests gens s’havia associat significativament amb el CG o prioritzat en les anàlisis prèvies, el que confirma l’interès d’analitzar les interaccions genètiques de segon ordre. Aquestes poden ser un punt de partida per altres anàlisis destinades a confirmar gens putatius i a estudiar a nivell biològic i molecular els mecanismes de carcinogènesi, i orientades a la recerca de noves dianes terapèutiques i mètodes de diagnosi i pronòstic més eficients.

Dissecting the genetic heterogeneity of depression through age at onset.

Genome-wide studies in major depression have identified few replicated associations, potentially due to heterogeneity within the disorder. Several studies have suggested that age at onset (AAO) can distinguish sub-types of depression with specific heritable components. This paper investigates the role of AAO in the genetic susceptibility for depression using genome-wide association data on 2,746 cases and 1,594 screened controls from the RADIANT studies, with replication performed in 1,471 cases and 1,403 controls from two Munich studies. Three methods were used to analyze AAO: First a time-to-event analysis with controls censored, secondly comparing controls to case-subsets defined using AAO cut-offs, and lastly analyzing AAO as a quantitative trait. In the time-to-event analysis three SNPs reached suggestive significance (P < 5E-06), overlapping with the original case-control analysis of this study. In a case-control analysis using AAO thresholds, SNPs in 10 genomic regions showed suggestive association though again none reached genome-wide significance. Lastly, case-only analysis of AAO as a quantitative trait resulted in 5 SNPs reaching suggestive significance. Sex specific analysis was performed as a secondary analysis, yielding one SNP reaching genome-wide significance in early-onset males. No SNPs achieved significance in the replication study after correction for multiple testing. Analysis of AAO as a quantitative trait did suggest that, across all SNPs, common genetic variants explained a large proportion of the variance (51%, P = 0.04). This study provides the first focussed analysis of the genetic contribution to AAO in depression, and establishes a statistical framework that can be applied to a quantitative trait underlying any disorder. © 2012 Wiley Periodicals, Inc.

The value of intraoperative ultrasound in oblique corpectomy for cervical spondylotic myelopathy and ossified posterior longitudinal ligament.

Intraoperative ultrasound (IOUS) has been described to be useful during central corpectomy for compressive cervical myelopathy. This study aimed at documenting the utility of IOUS in oblique cervical corpectomy (OCC). Prospective data from 24 patients undergoing OCC for cervical spondylotic myelopathy and ossified posterior longitudinal ligament (OPLL) were collected. Patients had a preoperative cervical spine magnetic resonance (MR) image, IOUS and a postoperative cervical CT scan. Retrospective data from 16 historical controls that underwent OCC without IOUS were analysed to compare the incidence of residual compression between the two groups. IOUS identified the vertebral artery in all cases, detected residual cord compression in six (27%) and missed compression in two cases (9%). In another two cases with OPLL, IOUS was sub-optimal due to shadowing. IOUS measurement of the corpectomy width correlated well with these measurements on the postoperative CT. The extent of cord expansion noted on IOUS after decompression showed no correlation with immediate or 6-month postoperative neurological recovery. No significant difference in residual compression was noted in the retrospective and prospective groups of the study. Craniocaudal spinal cord motion was noted after the completion of the corpectomy. IOUS is an inexpensive and simple real-time imaging modality that may be used during OCC for cervical spondylotic myelopathy. It is helpful in identifying the vertebral artery and determining the trajectory of approach, however, it has limited utility in patients with OPLL due to artifacts from residual ossification.

Early pregnancy sex steroids and maternal risk of epithelial ovarian cancer.

Well-established associations between reproductive characteristics and epithelial ovarian cancer (EOC) support an involvement of sex steroid hormones in the etiology of EOC. Limited previous studies have evaluated circulating androgens and the risk of EOC, and estrogens and progesterone have been investigated in only one of the previous studies. Furthermore, there is little data on potential heterogeneity in the association between circulating hormones and EOC by histological subgroup. Therefore, we conducted a nested case-control study within the Finnish Maternity Cohort and the Northern Sweden Maternity Cohort to investigate the associations between circulating pre-diagnostic sex steroid concentrations and the histological subtypes of EOC. We identified 1052 EOC cases among cohort members diagnosed after recruitment (1975-2008) and before March 2011. Up to three controls were individually matched to each case (n=2694). Testosterone, androstenedione, 17-hydroxyprogesterone (17-OHP), progesterone, estradiol (E2), and sex hormone-binding globulin levels were measured in serum samples collected during the last pregnancy before EOC diagnosis. We used conditional logistic regression to estimate odds ratios (ORs) and 95% CIs. Associations between hormones and EOC differed with respect to tumor histology and invasiveness. Sex steroid concentrations were not associated with invasive serous tumors; however, doubling of testosterone and 17-OHP concentration was associated with approximately 40% increased risk of borderline serous tumors. A doubling of androgen concentrations was associated with a 50% increased risk of mucinous tumors. The risk of endometrioid tumors increased with higher E2 concentrations (OR: 1.89 (1.20-2.98)). This large prospective study in pregnant women supports a role of sex steroid hormones in the etiology of EOC arising in the ovaries.

The protective effect of the obesity-associated rs9939609 A variant in fat mass- and obesity-associated gene on depression.

Candidate gene and genome-wide association studies have not identified common variants, which are reliably associated with depression. The recent identification of obesity predisposing genes that are highly expressed in the brain raises the possibility of their genetic contribution to depression. As variation in the intron 1 of the fat mass- and obesity-associated (FTO) gene contributes to polygenic obesity, we assessed the possibility that FTO gene may contribute to depression in a cross-sectional multi-ethnic sample of 6561 depression cases and 21 932 controls selected from the EpiDREAM, INTERHEART, DeCC (depression case-control study) and Cohorte Lausannoise (CoLaus) studies. Major depression was defined according to DSM IV diagnostic criteria. Association analyses were performed under the additive genetic model. A meta-analysis of the four studies showed a significant inverse association between the obesity risk FTO rs9939609 A variant and depression (odds ratio=0.92 (0.89, 0.97), P=3 × 10(-4)) adjusted for age, sex, ethnicity/population structure and body-mass index (BMI) with no significant between-study heterogeneity (I(2)=0%, P=0.63). The FTO rs9939609 A variant was also associated with increased BMI in the four studies (β 0.30 (0.08, 0.51), P=0.0064) adjusted for age, sex and ethnicity/population structure. In conclusion, we provide the first evidence that the FTO rs9939609 A variant may be associated with a lower risk of depression independently of its effect on BMI. This study highlights the potential importance of obesity predisposing genes on depression.

The effect of obesity, age, puberty and gender on resting metabolic rate in children and adolescents.

During puberty fat-free mass (FFM) and fat mass (FM) change quickly and these changes are influenced by sex and obesity. Since it is not completely known how these changes affect resting metabolic rate (RMR), the aim of the present study was to investigate the effect of body composition, age, sex and pubertal development of postabsorptive RMR in 9.5- to 16.5- year-old obese and non-obese children. Postabsorptive RMR was measured in a sample of 371 pre- and postpubertal children comprising 193 males (116 non-obese and 77 obese) and 178 females (119 non-obese and 59 obese). RMR was assessed by indirect calorimetry using a ventilated hood system for 45 min after an overnight fast. Body composition (FFM and FM) was estimated from skinfold measurements. The mean (+/- SD) RMR was significantly (P < 0.001) lower in non-obese (males: 5600 +/- 972 kJ/24 h; females: 5112 +/- 632 kJ/24 h) than in obese (males: 7223 +/- 1220 kJ/24 h; females: 6665 +/- 1106 kJ/24 h) children. This difference became non-significant when RMR was adjusted for body composition (FFM+FM). However, the difference between the genders still remained significant (control male: 6118 +/- 507, control female: 5652 +/- 507, P < 0.001; obese male: 6256 +/- 507, obese female: 5818 +/- 507 kJ/24 h, P < 0.001). The main determinant of RMR was FFM. In the whole cohort. FFM explained 79.8% of the variation in RMR, followed by age, gender and FM adding further 3.8%, 1.1% and 0.8% to the predictability of RMR, respectively. No significant contribution for study group (obese, non-obese), pubertal stage, or fat distribution was found in the regression for RMR. The adjusted value of RMR (for FFM and FM) slightly, but significantly (P < 0.01) decreased between the age of 10-16 years, demonstrating the important effect of age on RMR. CONCLUSIONS: The resting metabolic rate of obese and control children is not different when adjusted for body composition. The main determinant of RMR is the fat-free mass, however, age, gender and fat mass are also significant factors. Pubertal development and fat distribution do not influence RMR independently from the changes in body composition.

Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.

Numerous genetic loci have been associated with systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Europeans. We now report genome-wide association studies of pulse pressure (PP) and mean arterial pressure (MAP). In discovery (N = 74,064) and follow-up studies (N = 48,607), we identified at genome-wide significance (P = 2.7 × 10(-8) to P = 2.3 × 10(-13)) four new PP loci (at 4q12 near CHIC2, 7q22.3 near PIK3CG, 8q24.12 in NOV and 11q24.3 near ADAMTS8), two new MAP loci (3p21.31 in MAP4 and 10q25.3 near ADRB1) and one locus associated with both of these traits (2q24.3 near FIGN) that has also recently been associated with SBP in east Asians. For three of the new PP loci, the estimated effect for SBP was opposite of that for DBP, in contrast to the majority of common SBP- and DBP-associated variants, which show concordant effects on both traits. These findings suggest new genetic pathways underlying blood pressure variation, some of which may differentially influence SBP and DBP.

Increased salt sensitivity of ambulatory blood pressure in women with a history of severe preeclampsia.

Cardiovascular diseases are the principal cause of death in women in developed countries and are importantly promoted by hypertension. The salt sensitivity of blood pressure (BP) is considered as an important cardiovascular risk factor at any BP level. Preeclampsia is a hypertensive disorder of pregnancy that arises as a risk factor for cardiovascular diseases. This study measured the salt sensitivity of BP in women with a severe preeclampsia compared with women with no pregnancy hypertensive complications. Forty premenopausal women were recruited 10 years after delivery in a case-control study. Salt sensitivity was defined as an increase of >4 mm Hg in 24-hour ambulatory BP on a high-sodium diet. The ambulatory BP response to salt was significantly increased in women with a history of preeclampsia compared with that of controls. The mean (95% confidence interval) daytime systolic/diastolic BP increased significantly from 115 (109-118)/79 (76-82) mm Hg on low-salt diet to 123 (116-130)/80 (76-84) on a high-salt diet in women with preeclampsia, but not in the control group (from 111 [104-119]/77 [72-82] to 111 [106-116]/75 [72-79], respectively, P<0.05). The sodium sensitivity index (SSI=Δmean arterial pressure/Δurinary Na excretion×1000) was 51.2 (19.1-66.2) in women with preeclampsia and 6.6 (5.8-18.1) mm Hg/mol per day in controls (P=0.015). The nocturnal dip was blunted on a high-salt diet in women with preeclampsia. Our study shows that women who have developed preeclampsia are salt sensitive before their menopause, a finding that may contribute to their increased cardiovascular risk. Women with a history of severe preeclampsia should be targeted at an early stage for preventive measures of cardiovascular diseases.

Mining the human phenome using allelic scores that index biological intermediates.

It is common practice in genome-wide association studies (GWAS) to focus on the relationship between disease risk and genetic variants one marker at a time. When relevant genes are identified it is often possible to implicate biological intermediates and pathways likely to be involved in disease aetiology. However, single genetic variants typically explain small amounts of disease risk. Our idea is to construct allelic scores that explain greater proportions of the variance in biological intermediates, and subsequently use these scores to data mine GWAS. To investigate the approach's properties, we indexed three biological intermediates where the results of large GWAS meta-analyses were available: body mass index, C-reactive protein and low density lipoprotein levels. We generated allelic scores in the Avon Longitudinal Study of Parents and Children, and in publicly available data from the first Wellcome Trust Case Control Consortium. We compared the explanatory ability of allelic scores in terms of their capacity to proxy for the intermediate of interest, and the extent to which they associated with disease. We found that allelic scores derived from known variants and allelic scores derived from hundreds of thousands of genetic markers explained significant portions of the variance in biological intermediates of interest, and many of these scores showed expected correlations with disease. Genome-wide allelic scores however tended to lack specificity suggesting that they should be used with caution and perhaps only to proxy biological intermediates for which there are no known individual variants. Power calculations confirm the feasibility of extending our strategy to the analysis of tens of thousands of molecular phenotypes in large genome-wide meta-analyses. We conclude that our method represents a simple way in which potentially tens of thousands of molecular phenotypes could be screened for causal relationships with disease without having to expensively measure these variables in individual disease collections.

Subclinical hypothyroidism and the risk of coronary heart disease: a meta-analysis.

PURPOSE: Subclinical hypothyroidism has been associated with elevated cholesterol and increased risk for atherosclerosis, but data on the risk of coronary heart disease (CHD) are conflicting. We performed a systematic review to determine whether subclinical hypothyroidism is associated with CHD in adults. METHODS: We searched MEDLINE from 1966 to April 2005, and the bibliographies of key articles to identify studies that provided risk estimates for CHD or cardiovascular mortality associated with subclinical hypothyroidism. Two authors independently reviewed each potential study for eligibility, assessed methodologic quality, and extracted the data. RESULTS: We identified 14 observational studies that met eligibility criteria. Subclinical hypothyroidism increased the risk of CHD (summary odds ratio [OR]: 1.65, 95% confidence interval [CI], 1.28-2.12). The summary OR for CHD was 1.81 (CI, 1.38-2.39) in 9 studies adjusted or matched for demographic characteristics, and 2.38 (CI, 1.53-3.69) after pooling the studies that adjusted for most cardiovascular risk factors. Sensitivity analyses including only population-based studies and those with formal outcome adjudication procedures yielded similar results. Subgroup analyses by type of study design showed a similar trend, but lower risk, in the 5 prospective cohort studies (OR 1.42, CI, 0.91-2.21), compared with the case-control and cross-sectional studies (OR 1.72, CI, 1.25-2.38). CONCLUSION: Our systematic review indicates that subclinical hypothyroidism is associated with an increased risk of CHD. Clinical trials are needed to assess whether thyroxine replacement reduces the risk of CHD in subjects with subclinical hypothyroidism.

Anti-HLA antibody repertoire after IVIg infusion in highly sensitized patients waiting for kidney transplantation.

Polyclonal intravenous immunoglobulin (IVIg) treatment reduces crossmatch positivity and increases rates of transplantation in highly sensitised patients (HS). We quantified the panel reactive antibody (PRA) by microlymphocytotoxicity (MLCC), and we analysed anti-HLA class I and class II IgG specific antibody repertoire by Luminex before and after IVIg infusion alone in HS patients awaiting kidney transplantation. Five patients received three monthly infusions of 1 g/kg of IVIg. Serum samples collected pre and post IVIg treatment were submitted for PRA analysis by MLCC. Anti-class I and anti-class II antibody specificities were then tested by Luminex. We focused on the anti-HLA class I and class II antibodies directed against HLA expressed by a previous graft. We also analysed the anti-HLA antibody repertoire in three patients who had not received IVIg infusion. The PRA level determined by MLCC decreased significantly in one of the five patients, dropping from 40% to 17%. The Luminex assay showed fluctuations of the anti-HLA antibody levels over time, but no significant longterm modifications of the anti-HLA antibody repertoire were observed, even in the patient with a strong and prolonged reduction of the PRA determined by MLCC. Our results show that IVIg at 1 g/kg is not sufficient to reduce PRA and does not modify the repertoire of specific anti-HLA antibody determined by Luminex.