Detection of gene pathways with predictive power for breast cancer prognosis

<p>Abstract</p> <p>Background</p> <p>Prognosis is of critical interest in breast cancer research. Biomedical studies suggest that genomic measurements may have independent predictive power for prognosis. Gene profiling studies have been conducted to search for predictive genomic measurements. Genes have the inherent pathway structure, where pathways are composed of multiple genes with coordinated functions. The goal of this study is to identify gene pathways with predictive power for breast cancer prognosis. Since our goal is fundamentally different from that of existing studies, a new pathway analysis method is proposed.</p> <p>Results</p> <p>The new method advances beyond existing alternatives along the following aspects. First, it can assess the predictive power of gene pathways, whereas existing methods tend to focus on model fitting accuracy only. Second, it can account for the joint effects of multiple genes in a pathway, whereas existing methods tend to focus on the marginal effects of genes. Third, it can accommodate multiple heterogeneous datasets, whereas existing methods analyze a single dataset only. We analyze four breast cancer prognosis studies and identify 97 pathways with significant predictive power for prognosis. Important pathways missed by alternative methods are identified.</p> <p>Conclusions</p> <p>The proposed method provides a useful alternative to existing pathway analysis methods. Identified pathways can provide further insights into breast cancer prognosis.</p

Phone and e-mail counselling are effective for weight management in an overweight working population: a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>The work setting provides an opportunity to introduce overweight (i.e., Body Mass Index ≥ 25 kg/m²) adults to a weight management programme, but new approaches are needed in this setting. The main purpose of this study was to investigate the effectiveness of lifestyle counselling by phone or e-mail on body weight, in an overweight working population. Secondary purposes were to establish effects on waist circumference and lifestyle behaviours, and to assess which communication method is the most effective.</p> <p>Methods</p> <p>A randomized controlled trial with three treatments: intervention materials with phone counselling (phone group); a web-based intervention with e-mail counselling (internet group); and usual care, i.e. lifestyle brochures (control group). The interventions used lifestyle modification and lasted a maximum of six months. Subjects were 1386 employees, recruited from seven companies (67% male; mean age 43 (SD 8.6) y; mean BMI 29.6 (SD 3.5) kg/m²). Body weight was measured by research personnel and by questionnaire. Secondary outcomes fat, fruit and vegetable intake, physical activity and waist circumference were assessed by questionnaire. Measurements were done at baseline and after six months. Missing body weight was multiply imputed.</p> <p>Results</p> <p>Body weight reduced 1.5 kg (95% CI -2.2;-0.8, p < 0.001) in the phone group and 0.6 kg (95% CI -1.3; -0.01, p = 0.045) in the internet group, compared with controls. In completers analyses, weight and waist circumference in the phone group were reduced with 1.6 kg (95% CI -2.2;-1.0, p < 0.001) and 1.9 cm (95% CI -2.7;-1.0, p < 0.001) respectively, fat intake decreased with 1 fatpoint (1 to 4 grams)/day (95% CI -1.7;-0.2, p = 0.01) and physical activity increased with 866 METminutes/week (95% CI 203;1530, p = 0.01), compared with controls. The internet intervention resulted in a weight loss of 1.1 kg (95% CI -1.7;-0.5, p < 0.001) and a reduction in waist circumference of 1.2 cm (95% CI -2.1;-0.4, p = 0.01), in comparison with usual care. The phone group appeared to have more and larger changes than the internet group, but comparisons revealed no significant differences.</p> <p>Conclusion</p> <p>Lifestyle counselling by phone and e-mail is effective for weight management in overweight employees and shows potential for use in the work setting.</p> <p>Trial registration</p> <p>ISCRTN04265725.</p

The Minimal Proteome in the Reduced Mitochondrion of the Parasitic Protist Giardia intestinalis

The mitosomes of Giardia intestinalis are thought to be mitochondria highly-reduced in response to the oxygen-poor niche. We performed a quantitative proteomic assessment of Giardia mitosomes to increase understanding of the function and evolutionary origin of these enigmatic organelles. Mitosome-enriched fractions were obtained from cell homogenate using Optiprep gradient centrifugation. To distinguish mitosomal proteins from contamination, we used a quantitative shot-gun strategy based on isobaric tagging of peptides with iTRAQ and tandem mass spectrometry. Altogether, 638 proteins were identified in mitosome-enriched fractions. Of these, 139 proteins had iTRAQ ratio similar to that of the six known mitosomal markers. Proteins were selected for expression in Giardia to verify their cellular localizations and the mitosomal localization of 20 proteins was confirmed. These proteins include nine components of the FeS cluster assembly machinery, a novel diflavo-protein with NADPH reductase activity, a novel VAMP-associated protein, and a key component of the outer membrane protein translocase. None of the novel mitosomal proteins was predicted by previous genome analyses. The small proteome of the Giardia mitosome reflects the reduction in mitochondrial metabolism, which is limited to the FeS cluster assembly pathway, and a simplicity in the protein import pathway required for organelle biogenesis

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Alterations in adult rat heart after neonatal dexamethasone therapy

Glucocorticoid treatment in preterm babies to prevent chronic lung disease causes myocardial hypertrophy and increased myocardial protein content. Although these changes are thought to be transient, there is evidence that dexamethasone (DEX) induces permanent myocardial abnormalities as well. We investigated whether a therapeutic course of neonatal DEX in rat pups produces anatomic and biochemical alterations in rat hearts during adult life. Twenty-four rat pups were treated with DEX on d 1, 2, and 3 (0.5, 0.3, and 0.1 mug/g) of life, with doses proportional to those used in preterm babies. Twenty-four control pups were treated with saline. At d 7, wk 8, or wk 45 (n = 8 per group) rats were killed. The anatomic parameters measured were body weight (Bw, in grams), heart (myocardial) weight (Hw, in milligrams), and the Hw:Bw ratio. Myocardial total protein (Prot) and DNA content were determined, and the Prot:DNA ratio was calculated. Histopathology and morphometry were performed on 45-wk-old rat hearts. In DEX-treated rat pups, at d 7, Bw and Hw were lower and the Hw:Bw ratio was increased. DNA content was lower, Prot higher, and Prot:DNA ratio was increased. In 8-wk-old rats Bw, Hw, DNA content, Prot content or Prot:DNA ratio did not differ between groups, but the Prot:DNA ratio still tended to be higher in DEX-treated rats. In 45-wk-old rats Hw and Hw:Bw ratio were significantly lower and Prot:DNA ratio higher in DEX-treated rats. Histopathologic analysis showed larger cardiomyocyte volume, length, and width, indicating hypertrophy, and increased collagen, indicating early degeneration of individual myocytes. In conclusion, neonatal DEX treatment in rat pups causes a permanent decrease in heart weight, as well as hypertrophy and early degeneration of cardiomyocytes during adulthood