Search

Regulatory T cells (Tregs) play a key role in suppressing systemic effector immune responses, thereby preventing autoimmune diseases but also potentially contributing to tumor progression. Thus, there is great interest in clinically manipulating Tregs, but the precise mechanisms governing in vitro-induced Treg (iTreg) differentiation are not yet fully understood. Here, we used multiparametric mass cytometry to phenotypically profile human iTregs during the early stages of in vitro differentiation at single-cell level. A panel of 25 metal-conjugated antibodies specific to markers associated with human Tregs was used to characterize these immunomodulatory cells. We found that iTregs highly express the transcription factor FOXP3, as well as characteristic Treg-associated surface markers (e.g. CD25, PD1, CD137, CCR4, CCR7, CXCR3, and CD103). Expression of co-inhibitory factors (e.g. TIM3, LAG3, and TIGIT) increased slightly at late stages of iTreg differentiation. Further, CD103 was upregulated on a subpopulation of iTregs with greater suppressive capacity than their CD103 - counterparts. Using mass-spectrometry-based proteomics, we showed that sorted CD103 + iTregs express factors associated with immunosuppression. Overall, our study highlights that during early stages of differentiation, iTregs resemble memory-like Treg features with immunosuppressive activity, and provides opportunities for further investigation into the molecular mechanisms underlying Treg function., (© 2024. The Author(s).)

Previous studies have revealed heterogeneity in the progression to clinical type 1 diabetes in children who develop islet-specific antibodies either to insulin (IAA) or glutamic acid decarboxylase (GADA) as the first autoantibodies. Here, we test the hypothesis that children who later develop clinical disease have different early immune responses, depending on the type of the first autoantibody to appear (GADA-first or IAA-first). We use mass cytometry for deep immune profiling of peripheral blood mononuclear cell samples longitudinally collected from children who later progressed to clinical disease (IAA-first, GADA-first, ≥2 autoantibodies first groups) and matched for age, sex, and HLA controls who did not, as part of the Type 1 Diabetes Prediction and Prevention study. We identify differences in immune cell composition of children who later develop disease depending on the type of autoantibodies that appear first. Notably, we observe an increase in CD161 expression in natural killer cells of children with ≥2 autoantibodies and validate this in an independent cohort. The results highlight the importance of endotype-specific analyses and are likely to contribute to our understanding of pathogenic mechanisms underlying type 1 diabetes development., (© 2024. The Author(s).)

Background: Although prostate cancer (PCa) is the most common cancer in men in Western countries, there is significant variability in geographical incidence. This might result from genetic factors, discrepancies in screening policies, or differences in lifestyle. Gut microbiota has recently been associated with cancer progression, but its role in PCa is unclear., Objective: Characterization of the gut microbiota and its functions associated with PCa., Design Setting and Participants: In a prospective multicenter clinical trial (NCT02241122), the gut microbiota profiles of 181 men with a clinical suspicion of PCa were assessed utilizing 16S rRNA sequencing., Outcome Measurements and Statistical Analysis: Sequences were assigned to operational taxonomic units, differential abundance analysis, and α- and β-diversities, and predictive functional analyses were performed. Plasma steroid hormone levels corresponding to the predicted microbiota steroid hormone biosynthesis profiles were investigated., Results and Limitations: Of 364 patients, 181 were analyzed, 60% of whom were diagnosed with PCa. Microbiota composition and diversity were significantly different in PCa, partially affected by Prevotella 9 , the most abundant genus of the cohort, and significantly higher in PCa patients. Predictive functional analyses revealed higher 5-α-reductase, copper absorption, and retinol metabolism in the PCa-associated microbiome. Plasma testosterone was associated negatively with the predicted microbial 5-α-reductase level., Conclusions: Gut microbiota of the PCa patients differed significantly compared with benign individuals. Microbial 5-α-reductase, copper absorption, and retinol metabolism are potential mechanisms of action. These findings support the observed association of lifestyle, geography, and PCa incidence., Patient Summary: In this report, we found that several microbes and potential functions of the gut microbiota are altered in prostate cancer compared with benign cases. These findings suggest that gut microbiota could be the link between environmental factors and prostate cancer., (© 2024 The Author(s).)

The randomized controlled Special Turku Coronary Risk Factor Intervention Project (STRIP) has completed a 20-year infancy-onset dietary counselling intervention to reduce exposure to atherosclerotic cardiovascular disease risk factors via promotion of a heart-healthy diet. The counselling on, e.g., low intake of saturated fat and cholesterol and promotion of fruit, vegetable, and whole-grain consumption has affected the dietary characteristics of the intervention participants. By leveraging this unique cohort, we further investigated whether this long-term dietary intervention affected the gut microbiota bacterial profile six years after the intervention ceased. Our sub-study comprised 357 individuals aged 26 years (intervention n = 174, control n = 183), whose gut microbiota were profiled using 16S rRNA amplicon sequencing. We observed no differences in microbiota profiles between the intervention and control groups. However, out of the 77 detected microbial genera, the Veillonella genus was more abundant in the intervention group compared to the controls (log2 fold-change 1.58, p < 0.001) after adjusting for multiple comparison. In addition, an association between the study group and overall gut microbiota profile was found only in males. The subtle differences in gut microbiota abundances observed in this unique intervention setting suggest that long-term dietary counselling reflecting dietary guidelines may be associated with alterations in gut microbiota.

Large-scale phosphoproteome profiling using mass spectrometry (MS) provides functional insight that is crucial for disease biology and drug discovery. However, extracting biological understanding from these data is an arduous task requiring multiple analysis platforms that are not adapted for automated high-dimensional data analysis. Here, we introduce an integrated pipeline that combines several R packages to extract high-level biological understanding from large-scale phosphoproteomic data by seamless integration with existing databases and knowledge resources. In a single run, PhosPiR provides data clean-up, fast data overview, multiple statistical testing, differential expression analysis, phosphosite annotation and translation across species, multilevel enrichment analyses, proteome-wide kinase activity and substrate mapping and network hub analysis. Data output includes graphical formats such as heatmap, box-, volcano- and circos-plots. This resource is designed to assist proteome-wide data mining of pathophysiological mechanism without a need for programming knowledge., (© The Author(s) 2021. Published by Oxford University Press.)

Objective: Gut microbiota and diet are known to contribute to human metabolism. We investigated whether the metagenomic gut microbiota composition and function changes over pregnancy are related to gestational diabetes mellitus (GDM) and can be modified by dietary supplements, fish oil and/or probiotics., Design: The gut microbiota of 270 overweight/obese women participating in a mother-infant clinical study were analysed with metagenomics approach in early (mean gestational weeks 13.9) and late (gestational weeks 35.2) pregnancy. GDM was diagnosed with a 2 hour 75 g oral glucose tolerance test., Results: Unlike women with GDM, women without GDM manifested changes in relative abundance of bacterial species over the pregnancy, particularly those receiving the fish oil + probiotics combination. The specific bacterial species or function did not predict the onset of GDM nor did it differ according to GDM status, except for the higher abundance of Ruminococcus obeum in late pregnancy in the combination group in women with GDM compared with women without GDM. In the combination group, weak decreases over the pregnancy were observed in basic bacterial housekeeping functions., Conclusions: The specific gut microbiota species do not contribute to GDM in overweight/obese women. Nevertheless, the GDM status may disturb maternal gut microbiota flexibility and thus limit the capacity of women with GDM to respond to diet, as evidenced by alterations in gut microbiota observed only in women without GDM. These findings may be important when considering the metabolic complications during pregnancy, but further studies with larger populations are called for to verify the findings., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. No commercial re-use. See rights and permissions. Published by BMJ.)

Gut microbiota participates in diverse metabolic and homeostatic functions related to health and well-being. Its composition varies between individuals, and depends on factors related to host and microbial communities, which need to adapt to utilize various nutrients present in gut environment. We profiled fecal microbiota in 63 healthy adult individuals using metaproteomics, and focused on microbial CAZy (carbohydrate-active) enzymes involved in glycan foraging. We identified two distinct CAZy profiles, one with many Bacteroides-derived CAZy in more than one-third of subjects (n = 25), and it associated with high abundance of Bacteroides in most subjects. In a smaller subset of donors (n = 8) with dietary parameters similar to others, microbiota showed intense expression of Prevotella-derived CAZy including exo-beta-(1,4)-xylanase, xylan-1,4-beta-xylosidase, alpha-L-arabinofuranosidase and several other CAZy belonging to glycosyl hydrolase families involved in digestion of complex plant-derived polysaccharides. This associated invariably with high abundance of Prevotella in gut microbiota, while in subjects with lower abundance of Prevotella, microbiota showed no Prevotella-derived CAZy. Identification of Bacteroides- and Prevotella-derived CAZy in microbiota proteome and their association with differences in microbiota composition are in evidence of individual variation in metabolic specialization of gut microbes affecting their colonizing competence.

Metagenomic approaches focus on taxonomy or gene annotation but lack power in defining functionality of gut microbiota. Therefore, metaproteomics approaches have been introduced to overcome this limitation. However, the common metaproteomics approach uses data-dependent acquisition mass spectrometry, which is known to have limited reproducibility when analyzing samples with complex microbial composition. In this work, we provide a proof of concept for data-independent acquisition (DIA) metaproteomics. To this end, we analyze metaproteomes using DIA mass spectrometry and introduce an open-source data analysis software package, diatools, which enables accurate and consistent quantification of DIA metaproteomics data. We demonstrate the feasibility of our approach in gut microbiota metaproteomics using laboratory-assembled microbial mixtures as well as human fecal samples.

Fragile X syndrome (FXS) and associated disorders are caused by expansion of the cytosine-guanine-guanine (CGG) trinucleotide repeat in the 5' untranslated region (UTR) of the Fragile X mental retardation-1 (FMR1) gene promoter. Conventionally, capillary electrophoresis fragment analysis on a genetic analyzer is used for the sizing of the CGG repeats of FMR1, but additional Southern blot analysis is required for exact measurement when the repeat number is higher than 200. Here, we present an accurate and robust polymerase chain reaction (PCR)-based method for quantification of the CGG repeats of FMR1. The first step of this test is PCR amplification of the repeat sequences in the 5'UTR of the FMR1 promoter using a Fragile X PCR kit, followed by purification of the PCR products and fragment sizing on a microfluidic capillary electrophoresis instrument, and subsequent interpretation of the number of CGG repeats by referencing standards with known repeats using the analysis software. This PCR-based assay is reproducible and capable of identifying the full range of CGG repeats of FMR1 promoters, including those with a repeat number of more than 200 (classified as full mutation), 55 to 200 (premutation), 46 to 54 (intermediate), and 10 to 45 (normal). It is a cost-effective method that facilitates classification of the FXS and Fragile X-associated disorders with robustness and rapid reporting time.

Background: One of the key behavioral phenotypes in infancy are different temperament traits, and certain early life temperament traits have been shown to precede later mental health problems. Differences in the gut microbiota composition (GMC) have been suggested to link with neurodevelopment. For example, toddler temperament traits have been found to associate with differences in GMC; however, studies in infants are lacking although infancy is a rapid period of neurodevelopment as well as GM development. Thus, we aimed to investigate association between infant GMC and temperament., Methods: The study population (n = 301, 53% boys) was drawn from the FinnBrain Birth Cohort Study. Stool samples were collected from the 2.5-month-old infants and sequenced with 16S Illumina MiSeq platform. GMC taxonomic composition (at Genus and OTU level), observed sample clusters, diversity and richness were investigated in relation to the maternal reports of Infant Behavior Questionnaire -Revised (IBQ-R) at the age of 6 months., Results: Three sample clusters (Bifidobacterium/Enterobacteriaceae, Bacteroides, V. Dispar) based on GMC were identified, of which Bifidobacterium/Enterobacteriaceae-cluster presented with higher scores on the IBQ-R main dimension regulation and its subscale duration of orienting compared to Bacteroides-cluster. The clusters associated with temperament in a sex-dependent manner. The IBQ-R main dimension surgency (positive emotionality) was associated positively both with genus Bifidobacterium and Streptococcus. Alpha diversity had a negative association with negative emotionality and fear reactivity., Conclusion: This is the first study demonstrating associations, but not causal connections, between GMC and temperament in young infants in a prospective design., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)

Objectives: To investigate dietary effects on the gut microbiota composition in a rat model of nonbacterial chronic prostate inflammation (CPI)., Materials and Methods: Nonbacterial CPI was induced in the Wistar rat strain with subcutaneous testosterone and 17β-oestradiol (E 2 ) hormone pellets for 18 weeks. Rats with placebo pellets served as healthy controls. Rats with CPI were stratified into two groups, which drank either plain tap water (control group) or tap water supplemented with 2% galactoglucomannan-rich hemicellulose extract (GGM group) from Norway spruce (Picea abies) for 5 weeks. Faecal samples were collected at the end of the study, total DNA was extracted, and the bacterial composition was analysed by 16S rRNA gene sequencing. In addition, faecal samples were assayed for short-chain fatty acid (SCFA) concentrations using gas chromatography. Lipopolysaccharide-binding protein (LBP) was measured in serum samples, as an indirect indicator for bacterial lipopolysaccharide (LPS) load in blood., Results: The microbial biodiversity was significantly different between the treatment groups. In the rats with CPI, there was a significant increase in gut microbial populations Rikenellaceae, Odoribacter, Clostridiaceae, Allobaculum and Peptococcaceae compared with healthy rats. Conversely, levels of Bacteroides uniformis, Lactobacillus and Lachnospiraceae were decreased in rats with CPI. SCFA butyric-, valeric- and caproic-acid concentrations were also decreased in the faecal samples of the rats with CPI. In contrast, acetic acid concentrations and serum LBP were significantly elevated in CPI rats compared with healthy ones. Amongst rats with CPI, treatment with the GGM extract significantly reduced the abundance of Odoribacter and Clostridiaceae levels, and increased the B. uniformis levels compared with CPI rats drinking tap water only. In addition, GGM significantly increased the levels of butyric acid and caproic acid, and reduced the levels of LBP in serum., Conclusions: Hormone-induced nonbacterial CPI in rats is associated with specific changes in gut microbiota and secondary changes in SCFAs and LPS due to gut microbiota alteration. Our results further suggest that fermentable compounds may have a beneficial effect on CPI., (© 2018 The Authors BJU International © 2018 BJU International Published by John Wiley & Sons Ltd.)

Aim: Chromosome analysis of prenatal samples and products of conception (POC) has conventionally been done by karyotyping (KT). Shortcomings of KT like high turnaround time and culture failure led to technology innovations, such as the bacterial artificial chromosomes (BAC)s-on-Beads (BoBs)-based tests, Prenatal BoBs (prenatal samples) and KaryoLite BoBs (POC samples). In the present study, we validated and evaluated the utility of each test on prenatal, POC and blood samples., Methods: Study A (n = 305; 259 prenatal + 46 blood/POC) and Study B (n = 176; 146 POC/chorionic vill + 30 blood/amniotic fluid) samples were analyzed using Prenatal and KaryoLite BoBs kits, respectively. KT, array-based Comparative Genomic Hybridization (arrayCGH) and fluorescence in situ hybridization (FISH) were used for comparison of results. Ability of KaryoLite BoBs to identify ring chromosomes was tested., Results: Prenatal BoBs had zero test failure rate and results of all samples were concordant with KT results. Totally four microdeletions were identified by Prenatal BoBs but not by KT. In Study B, all but two POC samples (one triploid and one tetraploid) were concordant with KT and arrayCGH. Partial chromosomal imbalance detection rate was ~64% and KaryoLite BoBs indicated the presence of a ring chromosome in all four cases. The failure rate of KaryoLite BoBs was 3%., Conclusion: We conclude that Prenatal BoBs (common aneuploidies and nine microdeletions) together with KT constitutes more comprehensive prenatal testing compared to FISH and KT. KaryoLite BoBs for aneuploidies of all chromosomes is highly successful in POC analysis and the ability to indicate presence of ring chromosomes improves its clinical sensitivity. Both tests are robust and could also be used for different specimens., (© 2019 Japan Society of Obstetrics and Gynecology.)

Data-independent acquisition (DIA) mode of mass spectrometry, such as the SWATH-MS technology, enables accurate and consistent measurement of proteins, which is crucial for comparative proteomics studies. However, there is lack of free and easy to implement data analysis protocols that can handle the different data processing steps from raw spectrum files to peptide intensity matrix and its downstream analysis. Here, we provide a data analysis protocol, named diatools, covering all these steps from spectral library building to differential expression analysis of DIA proteomics data. The data analysis tools used in this protocol are open source and the protocol is distributed at Docker Hub as a complete software environment that supports Linux, Windows, and macOS operating systems.

Background: Pregnancy is a time of numerous hormonal, metabolic, and immunological changes for both the mother and the fetus. Furthermore, maternal gut microbiota composition (GMC) is altered during pregnancy. One major factor affecting GMC in pregnant and nonpregnant populations is obesity. The aim was to analyze associations between maternal overweight/obesity, as well as gestational weight gain (GWG) and GMC. Moreover, the modifying effect of depression and anxiety symptom scores on weight and GMC were investigated., Methods: Study included 46 women from the FinnBrain Birth Cohort study, of which 36 were normal weight, and 11 overweight or obese according to their prepregnancy body mass index (BMI). Stool samples were collected in gestational week 24, and the GMC was sequenced with Illumina MiSeq approach. Hierarchical clustering was executed to illuminate group formation according to the GMC. The population was divided according to Firmicutes and Bacteroidetes dominance. Symptoms of depression, general anxiety, and pregnancy-related anxiety were measured by using standardized questionnaires., Results: Excessive GWG was associated with distinct GMC in mid-pregnancy as measured by hierarchical clustering and grouping according to Firmicutes or Bacteroidetes dominance, with Bacteroidetes being prominent and Firmicutes being less prominent in the GMC among those with increased GWG. Reduced alpha diversity was observed among the Bacteroidetes-dominated subjects. There were no zero-order effects between the abundances of bacterial genera or phyla, alpha or beta diversity, and prepregnancy BMI or GWG., Conclusion: Bacteroidetes-dominated GMC in mid-pregnancy is associated with increased GWG and reduced alpha diversity.

Objectives: Several studies have reported that the intestinal microbiota composition of celiac disease (CD) patients differs from healthy individuals. The possible role of gut microbiota in the pathogenesis of the disease is, however, not known. Here, we aimed to assess the possible differences in early fecal microbiota composition between children that later developed CD and healthy controls matched for age, sex and HLA risk genotype., Materials and Methods: We used 16S rRNA gene sequencing to examine the fecal microbiota of 27 children with high genetic risk of developing CD. Nine of these children developed the disease by the age of 4 years. Stool samples were collected at the age of 9 and 12 months, before any of the children had developed CD. The fecal microbiota composition of children who later developed the disease was compared with the microbiota of the children who did not have CD or associated autoantibodies at the age of 4 years. Delivery mode, early nutrition, and use of antibiotics were taken into account in the analyses., Results: No statistically significant differences in the fecal microbiota composition were found between children who later developed CD (n = 9) and the control children without disease or associated autoantibodies (n = 18)., Conclusions: Based on our results, the fecal microbiota composition at the age of 9 and 12 months is not associated with the development of CD. Our results, however, do not exclude the possibility of duodenal microbiota changes or a later microbiota-related trigger for the disease.

Aim: Childhood brain tumour survivors have a high risk of endocrine morbidity. This study evaluated the growth, pubertal development and gonadal function in survivors of childhood brain tumours and identified factors associated with the problems we observed., Methods: The 52 subjects (52% male) were diagnosed in 1983-1997 and treated for brain tumours at Tampere University Hospital, Finland. They were followed up at a mean age of 14.2 (3.8-28.7) years, a mean of 7.5 (1.5-15.1) years after diagnosis., Results: We found that 30 (58%) participants had a lower height standard deviation score at follow-up than at diagnosis and short stature at follow-up was associated with tumour malignancy (p = 0.005), radiotherapy (p = 0.004), chemotherapy (p = 0.024), growth hormone deficiency (p < 0.001), hypogonadism (p = 0.044) and delayed puberty (p = 0.021). We found that five needed sex hormones to induce puberty, one had precocious puberty, 12 (23%) had growth hormone deficiency and eight (22%) of the 36 pubertal or postpubertal patients had hypogonadism. Testicular volume was low in 83% of late or postpubertal male survivors., Conclusion: Growth impairment, growth hormone deficiency and hypogonadism were common in childhood brain tumour survivors and low testicular volume was also common in male survivors. Lifelong annual follow-up checks are indicated for survivors., (©2017 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.)

Next-generation sequencing (NGS) is currently the method of choice for analyzing gut microbiota composition. As gut microbiota composition is a potential future target for clinical diagnostics, it is of utmost importance to enhance and optimize the NGS analysis procedures. Here, we have analyzed the impact of DNA extraction and selected 16S rDNA primers on the gut microbiota NGS results. Bacterial DNA from frozen stool specimens was extracted with 5 commercially available DNA extraction kits. Special attention was paid to the semiautomated DNA extraction methods that could expedite the analysis procedure, thus being especially suitable for clinical settings. The microbial composition was analyzed with 2 distinct protocols: 1 targeting the V3-V4 and the other targeting the V4-V5 area of the bacterial 16S rRNA gene. The overall effect of DNA extraction on the gut microbiota 16S rDNA profile was relatively small, whereas the 16S rRNA gene target region had an immense impact on the results. Furthermore, semiautomated DNA extraction methods clearly appeared suitable for NGS procedures, proposing that application of these methods could importantly reduce hands-on time and human errors without compromising the validity of results.

Background: Prenatal metformin exposure has been shown to improve the metabolic outcome in the offspring of high fat diet fed dams. However, if this is evident also in a genetic model of obesity and whether gut microbiota has a role, is not known., Methods: The metabolic effects of prenatal metformin exposure were investigated in a genetic model of obesity, mice overexpressing neuropeptide Y in the sympathetic nervous system and in brain noradrenergic neurons (OE-NPYDβH). Metformin was given for 18 days to the mated female mice. Body weight, body composition, glucose tolerance and serum parameters of the offspring were investigated on regular diet from weaning and sequentially on western diet (at the age of 5-7 months). Gut microbiota composition was analysed by 16S rRNA sequencing at 10-11 weeks., Results: In the male offspring, metformin exposure inhibited weight gain. Moreover, weight of white fat depots and serum insulin and lipids tended to be lower at 7 months. In contrast, in the female offspring, metformin exposure impaired glucose tolerance at 3 months, and subsequently increased body weight gain, fat mass and serum cholesterol. In the gut microbiota, a decline in Erysipelotrichaceae and Odoribacter was detected in the metformin exposed offspring. Furthermore, the abundance of Sutterella tended to be decreased and Parabacteroides increased. Gut microbiota composition of the metformin exposed male offspring correlated to their metabolic phenotype., Conclusion: Prenatal metformin exposure caused divergent metabolic phenotypes in the female and male offspring. Nevertheless, gut microbiota of metformin exposed offspring was similarly modified in both genders., Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: Author UP is employed 80% by Orion Corporation/Orion Pharma, Turku, Finland. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Background: Increased intestinal permeability may precede adverse metabolic conditions. The extent to which the composition of the gut microbiota and diet contribute to intestinal permeability during pregnancy is unknown., Objective: The aim was to investigate whether the gut microbiota and diet differ according to serum zonulin concentration, a marker of intestinal permeability, in overweight pregnant women., Methods: This cross-sectional study included 100 overweight women [mean age: 29 y; median body mass index (in kg/m(2)): 30] in early pregnancy (<17 wk of gestation; median: 13 wk). Serum zonulin (primary outcome) was determined by using ELISA, gut microbiota by 16S ribosomal RNA sequencing, and dietary intake of macro- and micronutrients from 3-d food diaries. The Mann-Whitney U test was used for pairwise comparisons and linear regression and Spearman's nonparametric correlations for relations between serum zonulin and other outcome variables., Results: Women were divided into "low" (<46.4 ng/mL) and "high" (≥46.4 ng/mL) serum zonulin groups on the basis of the median concentration of zonulin (46.4 ng/mL). The richness of the gut microbiota (Chao 1, observed species and phylogenetic diversity) was higher in the low zonulin group than in the high zonulin group (P = 0.01). The abundances of Bacteroidaceae and Veillonellaceae, Bacteroides and Blautia, and Blautia sp. were lower and of Faecalibacterium and Faecalibacterium prausnitzii higher (P < 0.05) in the low zonulin group than in the high zonulin group. Dietary quantitative intakes of n-3 (ω-3) polyunsaturated fatty acids (PUFAs), fiber, and a range of vitamins and minerals were higher (P < 0.05) in women in the low zonulin group than those in the high zonulin group., Conclusions: The richness and composition of the gut microbiota and the intake of n-3 PUFAs, fiber, and a range of vitamins and minerals in overweight pregnant women are associated with serum zonulin concentration. Modification of the gut microbiota and diet may beneficially affect intestinal permeability, leading to improved metabolic health of both the mother and fetus. This trial was registered at clinicaltrials.gov as NCT01922791., (© 2016 American Society for Nutrition.)

This population-based cross-sectional study evaluates the clinical value of electroretinography and visual evoked potentials in childhood brain tumor survivors. A flash electroretinography and a checkerboard reversal pattern visual evoked potential (or alternatively a flash visual evoked potential) were done for 51 survivors (age 3.8-28.7 years) after a mean follow-up time of 7.6 (1.5-15.1) years. Abnormal electroretinography was obtained in 1 case, bilaterally delayed abnormal visual evoked potentials in 22/51 (43%) cases. Nine of 25 patients with infratentorial tumor location, and altogether 12 out of 31 (39%) patients who did not have tumors involving the visual pathways, had abnormal visual evoked potentials. Abnormal electroretinographies are rarely observed, but abnormal visual evoked potentials are common even without evident anatomic lesions in the visual pathway. Bilateral changes suggest a general and possibly multifactorial toxic/adverse effect on the visual pathway. Electroretinography and visual evoked potential may have clinical and scientific value while evaluating long-term effects of childhood brain tumors and tumor treatment., (© The Author(s) 2016.)

A number of supervised machine learning models have recently been introduced for the prediction of drug-target interactions based on chemical structure and genomic sequence information. Although these models could offer improved means for many network pharmacology applications, such as repositioning of drugs for new therapeutic uses, the prediction models are often being constructed and evaluated under overly simplified settings that do not reflect the real-life problem in practical applications. Using quantitative drug-target bioactivity assays for kinase inhibitors, as well as a popular benchmarking data set of binary drug-target interactions for enzyme, ion channel, nuclear receptor and G protein-coupled receptor targets, we illustrate here the effects of four factors that may lead to dramatic differences in the prediction results: (i) problem formulation (standard binary classification or more realistic regression formulation), (ii) evaluation data set (drug and target families in the application use case), (iii) evaluation procedure (simple or nested cross-validation) and (iv) experimental setting (whether training and test sets share common drugs and targets, only drugs or targets or neither). Each of these factors should be taken into consideration to avoid reporting overoptimistic drug-target interaction prediction results. We also suggest guidelines on how to make the supervised drug-target interaction prediction studies more realistic in terms of such model formulations and evaluation setups that better address the inherent complexity of the prediction task in the practical applications, as well as novel benchmarking data sets that capture the continuous nature of the drug-target interactions for kinase inhibitors., (© The Author 2014. Published by Oxford University Press.)

Aims/hypothesis: Gut microbiota (GM) and diet both appear to be important in the pathogenesis of type 1 diabetes. Fermentable fibres (FFs), of which there is an ample supply in natural, diabetes-promoting diets, are used by GM as a source of energy. Our aim was to determine whether FFs modify GM and diabetes incidence in the NOD mouse., Methods: Female NOD mice were weaned to a semisynthetic diet and the effects of FF supplementation on diabetes incidence and insulitis were evaluated. Real-time quantitative PCR was employed to determine the effects imposed to gene transcripts in the colon and lymph nodes. Changes to GM were analysed by next-generation sequencing., Results: NOD mice fed semisynthetic diets free from FFs were largely protected from diabetes while semisynthetic diets supplemented with the FFs pectin and xylan (PX) resulted in higher diabetes incidence. Semisynthetic diet free from FFs altered GM composition significantly; addition of PX changed the composition of the GM towards that found in natural-diet-fed mice and increased production of FF-derived short-chain fatty acid metabolites in the colon. The highly diabetogenic natural diet was associated with expression of proinflammatory and stress-related genes in the colon, while the semisynthetic diet free from FFs promoted Il4, Il22, Tgfβ and Foxp3 transcripts in the colon and/or pancreatic lymph node. PX in the same diet counteracted these effects and promoted stress-related IL-18 activation in gut epithelial cells. 16S RNA sequencing revealed each diet to give rise to its particular GM composition, with different Firmicutes to Bacteroidetes ratios, and enrichment of mucin-degrading Ruminococcaceae following diabetes-protective FF-free diet., Conclusions/interpretation: FFs condition microbiota, affect colon homeostasis and are important components of natural, diabetes-promoting diets in NOD mice.

We have explored how older twins experience and describe themselves in relation to their co-twin. The life stories of 20 older twins were analyzed with narrative analysis. Results showed that the twins described themselves from the point of differences in relation to the co-twin. This was based on experiences of how other people viewed them as alike, as well as on life events along the life course, which contributed to the perception of oneself as an individual in relation to the co-twin. The emphasis on unlikeness was therefore interpreted as a way of trying to establish a position as an individual within the co-twin relationship and to assert ones individuality to the rest of the social environment. To claim oneself as an individual was an ongoing identity work along the life course., (© 2013.)

We assessed neurological and neurocognitive outcome in childhood brain tumor survivors. Altogether, 75 out of 80 brain tumor survivors diagnosed below 17 years between 1983 and 1997; and treated in Tampere University Hospital, Finland, were invited to participate in this population-based cross-sectional study. Fifty-two (69%) participated [mean age 14.2 (3.8-28.7) years, mean follow-up 7.5 (1.5-15.1) years]. Neurological status was abnormal in 69% cases. All were ambulatory, but only 50% showed normal motor function. Twenty-nine percent showed clumsiness/mild asymmetry and 21% hemiparesis. One suffered from intractable epilepsy. According to structured interview, 87% coped normally in daily living. Median full-scale IQ was 85 (39-110) in 21 6-16 year olds (70%); in 29% IQ was <70. Thirty of the 44 school-aged subjects attended school with normal syllabus and 32% needed special education. Six of the 16 patients over 18 years of age were working. Regarding quality of life, 38% were active without disability, 33% active with mild disability, 21% were partially disabled, but capable of self-care, and 8% had severe disability, being incapable of self-care. Supratentorial/hemispheric tumor location, tumor reoperations, shunt revisions and chemotherapy were associated with neurological, cognitive and social disabilities. In conclusion, of the 52 survivors, neurological status was abnormal in 69%; 71% lived an active life with minor disabilities, 29% had major neurological, cognitive and social disabilities, and 8% of them were incapable of self-care. Predictors of these disabilities included supratentorial/hemispheric tumor location, tumor reoperations, shunt revisions and chemotherapy. Survivors need life-long, tailor-made multiprofessional support and follow-up.

Background: A population based cross-sectional study was used to examine the prevalence of metabolic syndrome and its components in childhood brain tumor survivors., Procedure: Fifty-two survivors were examined at a mean age of 14.4 years (range 3.8-28.7). Lipid and glucose metabolism, thyroid function, and plasma uric acid were evaluated. Fat mass and fat percentage were assessed by dual-energy X-ray absorptiometry (DXA). Metabolic syndrome was defined on International Diabetes Federation criteria., Results: Ten (19%) patients were overweight and four (8%) were obese. According to DXA, 16/46 (35%) patients were obese. Central obesity was found in 11 (21%) patients. Cranial irradiation, hypothalamic/hypophyseal damage, growth hormone (GH) deficiency and impaired mobility were associated with overweight/obesity and central obesity. Thirteen (25%) subjects had hypercholesterolemia, 14 (27%) had raised low-density lipoprotein cholesterol (LDL-C), 12 (23%) had raised blood pressure, four (8%) had metabolic syndrome, two (4%) had hyperinsulinemia and five (10%) had hyperuricemia. Cranial irradiation was associated with hypercholesterolemia (P = 0.019), raised LDL-C (P = 0.028), raised blood pressure (P = 0.040), and metabolic syndrome (P = 0.018). Impaired mobility was associated with hypercholesterolemia (P = 0.034). Hypothalamic/hypophyseal damage was associated with metabolic syndrome (P = 0.003) and hyperuricemia (P = 0.011) as was GH deficiency (P = 0.034 and P = 0.008). GH supplementation alleviated adverse metabolic outcomes among brain tumor survivors with GH deficiency., Conclusions: Obesity/overweight, dyslipidemia, hypertension, metabolic syndrome, and hyperuricemia were common in young childhood brain tumor survivors. Cranial irradiation, hypothalamic/hypophyseal damage, growth hormone deficiency, and/or impaired mobility were associated with higher risk for obesity and metabolic changes among these patients., ((c) 2009 Wiley-Liss, Inc.)

Aim: To determine the prevalence of low bone mineral density among children surviving brain tumours and to identify possible factors underlying impaired bone health., Methods: Cross-sectional study; total body bone mineral density (TBBMD), fat mass (FM) and lean body mass (LBM) were measured by dual-energy X-ray absorptiometry (DXA) in 46 brain tumour patients aged from 3.8 to 28.7 y (mean 14.9 y) treated in childhood 1.4-14.8 y (mean 6.4 y) after end of treatment for brain tumour. Low bone mineral density was defined as TBBMD z score < - 2.0., Results: Fifteen patients had TBBMD z scores < - 2.0, indicating a 33% prevalence of low bone density. The TBBMD z score ranged from -5.7 to 0.6 (mean -1.7). Out of several potential factors, only combined craniospinal irradiation was significantly associated with low z score (p=0.034, according to multiple regression analysis), while exclusive cranial irradiation showed a borderline statistical association (p=0.100, according to multiple regression analysis)., Conclusion: One third of brain tumour patients treated in childhood had reduced bone mineral density. The reasons for this condition are apparently multifactorial, including craniospinal irradiation.

Background: This study was designed to evaluate the renal consequences of the treatment of brain tumor patients diagnosed in childhood., Procedure: One hundred four primary brain tumor patients diagnosed before 17 years of age from 1983 to 1997 had been treated in Tampere University Hospital, Finland. Of the 80 survivors 52 (65.0%) were examined at a median age of 14.4 years (range 3.8-28.7) and median 6.0 years (range 1.2-14.8) after the last treatment. The main outcome measures were blood pressure (BP), renal function, and calcium metabolism., Results: Eight patients (15.4%) were hypertensive. Elevated BP was observed especially after exposure both to cisplatin and cranial irradiation. Spinal radiation did not increase the risk of elevated BP. Other adverse effects were observed only in patients treated with cisplatin. Five out of 14 patients treated with cisplatin evinced renal glomerular dysfunction (GFR < 87 mL/min/1.73 m2) immediately after treatment. They had a high cumulative dose of cisplatin (490-880 mg/m2). Recovery from renal glomerular dysfunction was observed in one patient. Nine of 14 patients were hypomagnesemic at the close of cisplatin treatment. Thereafter the magnesium level decreased in 10/14 cases (P = 0.006). During the study 10/14 were hypomagnesemic (P < 0.001); one evinced severe symptomatic hypomagnesemia. Low plasma phosphate (P = 0.016) and potassium levels (P = 0.026), tubular proteinuria (P = 0.055), metabolic alkalosis (P = 0.071), and hyperuricemia (P = 0.114) were also more common in patients on cisplatin treatment., Conclusions: Elevated BP is common among brain tumor patients treated in childhood. After cisplatin treatment renal glomerular dysfunction appears mostly to be permanent. Persistent and even progressive changes in renal tubular function are seen.