Causal mediation for uncausally related mediators in the context of survival analysis.

Objective: The study of the potential intermediate effect of several variables on the association between an exposure and a time-to-event outcome is a question of interest in epidemiologic research. However, to our knowledge, no tools have been developed for the evaluation of multiple correlated mediators in a survival setting. Methods: In this work, we extended the multimediate algorithm, which conducts mediation analysis in the context of multiple uncausally correlated mediators, to a time-to-event setting using the semiparametric additive hazards model. We theoretically demonstrated that, under certain assumptions, indirect, direct and total effects can be calculated using the counterfactual framework with collapsible survival models. We also adapted the algorithm to accommodate exposure-mediator interactions. Results and conclusions: Using simulations, we demonstrated that our algorithm performs better than the product of coefficients method, even for uncorrelated mediators. The additive hazards model quantifies the effects as rate differences, which constitute a measure of impact, with applications that can be highly informative for public health. Our algorithm can be found in the R package multimediate, which is available in Github.

Omics feature selection with the extended SIS R package: identification of a body mass index epigenetic multi-marker in the Strong Heart Study.

The statistical analysis of omics data poses a great computational challenge given its ultra-high dimensional nature and frequent between-features correlation. In this work, we extended the Iterative Sure Independence Screening (ISIS) algorithm by pairing ISIS with elastic-net (Enet) and two versions of adaptive Enet (AEnet and MSAEnet) to efficiently improve feature selection and effect estimation in omics research. We subsequently used genome-wide human blood DNA methylation data from American Indians of the Strong Heart Study (N=2,235 participants), measured in 1989-1991, to compare the performance (predictive accuracy, coefficient estimation and computational efficiency) of SIS-paired regularization methods to Bayesian shrinkage and traditional linear regression to identify epigenomic multi-marker of body mass index. ISIS-AEnet outperformed the other methods in prediction. In biological pathway enrichment analysis of genes annotated to BMI-related differentially methylated positions, ISIS-AEnet captured most of the enriched pathways in common for at least two of all the evaluated methods. ISIS-AEnet can favor biological discovery because it identifies the most robust biological pathways while achieving an optimal balance between bias and efficient feature selection. In the extended SIS R package, we also implemented ISIS paired with Cox and logistic regression for time-to-event and binary endpoints, respectively, and bootstrap confidence intervals for the estimated regression coefficients.

Smoking, blood DNA methylation sites and lung cancer risk.

Altered DNA methylation (DNAm) might be a biological intermediary in the pathway from smoking to lung cancer. In this study, we investigated the contribution of differential blood DNAm to explain the association between smoking and lung cancer incidence. Blood DNAm was measured in 2321 Strong Heart Study (SHS) participants. Incident lung cancer was assessed as time to event diagnoses. We conducted mediation analysis, including validation with DNAm and paired gene expression data from the Framingham Heart Study (FHS). In the SHS, current versus never smoking and pack-years single-mediator models showed, respectively, 29 and 21 differentially methylated positions (DMPs) for lung cancer with statistically significant mediated effects (14 of 20 available, and five of 14 available, positions, replicated, respectively, in FHS). In FHS, replicated DMPs showed gene expression downregulation largely in trans, and were related to biological pathways in cancer. The multimediator model identified that DMPs annotated to the genes AHRR and IER3 jointly explained a substantial proportion of lung cancer. Thus, the association of smoking with lung cancer was partly explained by differences in baseline blood DNAm at few relevant sites. Experimental studies are needed to confirm the biological role of identified eQTMs and to evaluate potential implications for early detection and control of lung cancer.

Suprarenal Masses in Very Young Infants: Is It Safe to Watch and Wait? Report of a SIOPEN Observational Study Results.

Background: To assess whether expectant observation of infants ≤ 90 days old with small suprarenal masses (sSRMs) could avoid unnecessary surgery without impacting outcome. Methods: Infants ≤ 90 days with a ≤ 5 cm mass, without midline extension or lymph node or distant spread were registered (ClinicalTrials.org:NCT01728155). Once staging was completed, they were followed with ultrasound, MRI and urinary catecholamines. Surgical resection was only planned if there was a ≥40% mass volume increase or for a mass persisting after 48 weeks of the planned observation. Results: Over a 5-year period, 128 infants were registered. No infant had detectable MYCN amplification in the peripheral blood. Surgery was performed in 39 (30.5%) patients, in 18 during and in 21 after the planned 48-week observation, and 74% were confirmed to be neuroblastomas. Non-life-threatening surgical complications occurred in two cases. The 3-year overall survival and event-free survival were 100% and 87.1%, respectively. The 16 events observed were volume increase (N = 11) and progression to neuroblastoma stage MS (N = 5). Patients with solid masses or MIBG-positive masses had lower EFS. Conclusions: Expectant observation for infants with sSRMs with clinical follow-up and timely imaging (including MRI scan) is safe and effective, allowing surgery to be avoided in the majority of them.

Mendelian Randomization and the Environmental Epigenetics of Health: a Systematic Review.

PURPOSE OF REVIEW: Epigenetic modifications are environmentally responsive and may play a mechanistic role in the development of disease. Mendelian randomization uses genetic variation to assess the causal effect of modifiable exposures on health outcomes. We conducted a systematic review of Mendelian randomization studies evaluating the causal role of DNA methylation (DNAm) changes on the development of health states, emphasizing on studies that formally evaluate exposure-DNAm, in addition to DNAm-outcome, causal associations. RECENT FINDINGS: We identified 15 articles, 4 of them including an environmental determinant of DNAm, including self-reported tobacco smoke exposure, in utero tobacco smoke exposure, measured vitamin B12, and glycemia. Selected articles suggest a causal association of DNAm with some cardiometabolic endpoints. DNAm seemed to partly explain the association of postnatal and prenatal exposure to tobacco smoke and vitamin B12 with inflammation biomarkers, birth weight, and cognitive outcomes, respectively. However, the current evidence is not sufficient to infer causality. Additional Mendelian randomization studies from large epidemiologic samples are needed to support the causal role of environmental factors as determinants of health-related epigenetic modifications.

Impact of colonic fermentation on sterols after the intake of a plant sterol-enriched beverage: A randomized, double-blind crossover trial.

BACKGROUND: Cholesterol microbial transformation has been widely studied using in vitro fermentation assays, but less information is available on the biotransformation of plant sterols (PS). The excretion percentage of animal sterols (AS) (67-73%) is considerably greater than that of PS (27-33%) in feces from healthy humans following a Western diet. However, a lower content of AS in feces from subjects following a vegetarian, vegan or low-fat animal diet has been seen when compared to omnivorous subjects. Although only one human study has reported fecal sterol excretion after the consumption of PS-enriched food (8.6 g PS/day), it was found that the target group showed an increase in the excretion of cholesterol and a 57% decrease in its metabolites compared to the control group. OBJECTIVE: Evaluation of the impact of a PS-enriched milk based fruit beverage intake on fecal sterol excretion and the microbial conversion of sterols in postmenopausal women with mild hypercholesterolemia. METHODS: Forty postmenopausal women participated in a randomized, double-blind, crossover study with two beverages, with a PS-enriched (2 g PS/day) or without. The women were divided in two groups: 20 women consumed the PS-enriched beverage and the other 20 women consumed a placebo (without PS) beverage for 6 weeks. After a four-week washout period, the type of beverage was exchanged and consumed for another 6 weeks. Feces were collected at the start (0 and 10 weeks) and end of each intervention period (6 and 16 weeks), and fecal sterols were determined by capillary gas chromatography with mass spectrometry. RESULTS: The intake of the PS-enriched beverage modified the fecal sterol excretion profile. A significant increase mainly in PS and their metabolites versus the placebo intervention period was observed. Although the same effect was not observed in the case of AS, a tendency towards increased cholesterol and decreased coprostanol (the main metabolite of cholesterol) was recorded after PS-enriched beverage intake versus placebo. Furthermore, the PS-enriched beverage also modified the microbial conversion of sterols. In this context, an important decrease in the conversion percentage of cholesterol in 16 women (between 11% and 50%) and of sitosterol in 24 women (between 15% and 61%) was observed. CONCLUSIONS: The results obtained suggest that the microbiota could preferably use PS as a substrate, when present in a greater proportion compared with cholesterol. Besides, a lower sitosterol and cholesterol conversion trend would mean that intake of the PS-enriched beverage could modulate the metabolic activity of the gut microbiota. Therefore, further studies on the impact of PS-enriched foods upon gut microbiota modulation are needed. Clinical Trial Registry Number: NCT02065024 listed on the NIH website: ClinicalTrials.gov. Clinical Trial Registry Name: Food Matrix and Genetic Variability as Determinants of Bioavailability and Biological Effects of Beta-cryptoxanthin and Phytosterols (foodmagenpol). The full trial protocol is available upon request to the corresponding author.

Sterols in human milk during lactation: bioaccessibility and estimated intakes.

Human milk (HM) is the exclusive food during the first 4-6 months of an infant's life. Breastfeeding has been related to significant health benefits for infants, and hence it is of interest to study the bioactive compounds present in HM, such as sterols (cholesterol being the most abundant). The aim of this study was to determine the contents of sterols (cholesterol, desmosterol, lathosterol, lanosterol, campesterol, stigmasterol and ß-sitosterol) in 10 pools of colostrum, transitional milk, and 1, 3 and 6 month HM obtained from Spanish volunteers from two different geographical areas (coastal and central) and to estimate the intake and bioaccessibility (BA) of sterols in order to ascertain the fate of sterols after digestion. The results showed that the total sterol contents decreased to half the initial level during lactation (24-11 mg per 100 mL) and was significantly higher in samples from the coastal area. Total and animal sterol intakes were between 200 and 400 times higher than plant sterol intakes and were significantly higher in samples from the coastal area. However, no statistically significant differences were found in cholesterol and plant sterol intakes between areas. The BA of total sterols ranged from 45% to 69% and was higher in the first month, which coinciding with the highest fat content of milk. In conclusion, the sterol content varies depending on the lactation stage and the geographical area, and the BA of sterols can be positively affected by a higher lipid content. All these data may contribute to the development of infant formulas that are more similar to HM in terms of composition and behaviour after digestion, according to the lactation stage involved.

Arsenic exposure, diabetes-related genes and diabetes prevalence in a general population from Spain.

Inorganic arsenic exposure may be associated with diabetes, but the evidence at low-moderate levels is not sufficient. Polymorphisms in diabetes-related genes have been involved in diabetes risk. We evaluated the association of inorganic arsenic exposure on diabetes in the Hortega Study, a representative sample of a general population from Valladolid, Spain. Total urine arsenic was measured in 1451 adults. Urine arsenic speciation was available in 295 randomly selected participants. To account for the confounding introduced by non-toxic seafood arsenicals, we designed a multiple imputation model to predict the missing arsenobetaine levels. The prevalence of diabetes was 8.3%. The geometric mean of total arsenic was 66.0 µg/g. The adjusted odds ratios (95% confidence interval) for diabetes comparing the highest with the lowest tertile of total arsenic were 1.76 (1.01, 3.09) and 2.14 (1.47, 3.11) before and after arsenobetaine adjustment, respectively. Polymorphisms in several genes including IL8RA, TXN, NR3C2, COX5A and GCLC showed suggestive differential associations of urine total arsenic with diabetes. The findings support the role of arsenic on diabetes and the importance of controlling for seafood arsenicals in populations with high seafood intake. Suggestive arsenic-gene interactions require confirmation in larger studies.

Hypermethylation of apoptotic genes as independent prognostic factor in neuroblastoma disease.

Neuroblastoma (NB) is an embryonal tumour of neuroectodermal cells, and its prognosis is based on patient age at diagnosis, tumour stage and MYCN amplification, but it can also be classified according to their degree of methylation. Considering that epigenetic aberrations could influence patient survival, we studied the methylation status of a series of 17 genes functionally involved in different cellular pathways in patients with NB and their impact on survival. We studied 82 primary NB tumours and we used methylation-specific-PCR to perform the epigenetic analysis. We evaluated the putative association among the evidence of hypermethylation with the most important NB prognostic factors, as well as to determine the relationship among methylation, clinical classification and survival. CASP8 hypermethylation showed association with relapse susceptibility and, TMS1 and APAF1 hypermethylation are associated with bad prognosis and showed high influence on NB overall survival. Hypermethylation of apoptotic genes has been identified as a good candidate of prognostic factor. We propose the simultaneous analysis of hypermethylation of APAF1, TMS1 and CASP8 apoptotic genes on primary NB tumour as a good prognostic factor of disease progression.

Poor survival for infants with MYCN-amplified metastatic neuroblastoma despite intensified treatment: the International Society of Paediatric Oncology European Neuroblastoma Experience.

PURPOSE: To report the results of a prospective, nonrandomized European study on infants with neuroblastoma and MYCN gene amplification. PATIENTS AND METHODS: Infants with neuroblastoma (stage 2, 3, 4, and 4s) and MYCN gene amplification who were diagnosed between 1999 and 2004 were eligible for enrollment onto the study. After diagnosis, staging, and mandatory biologic studies, induction chemotherapy (IC) with conventional drugs was administered, followed by delayed surgery, megatherapy (busulfan-melphalan as a conditioning regimen), and local radiotherapy. RESULTS: Of the 46 infants enrolled onto the study, 35 infants were eligible; of these 35 infants, 97% had metastatic spread (24 infants had stage 4, and 10 infants had stage 4s). Two-year overall survival (OS) was 30% (SE, 0.08), with median survival time of 12 months, and 23 deaths due to disease. Two-year, event-free survival (EFS) was 29% (SE, 0.07). The treatment was well tolerated with no deaths as a result of toxicity or severe toxicity. Despite protocol adherence, 30% of the patients who were assessable for response to IC experienced disease progression or did not respond. Stage and high lactate dehydrogenase reached significance in the univariate analysis (P = .028 and .039, respectively for OS; and P = .05 and .031 respectively, for EFS). Ten of 16 patients who received megatherapy are still alive. CONCLUSION: Although treatment was well tolerated, survival was poor and our IC failed to achieve a satisfactory response in 30% of our patients. New therapeutic approaches and more intense world-wide collaboration are needed to achieve a cure in this population.