Male-Pattern Vertex Baldness Trajectories, Chest Hair Patterns, and Odds of Overall and Aggressive Prostate Cancer

BACKGROUND

The link between hormones and hair growth is well established. Inconsistent associations have been found between hair patterns and cancer of the prostate, a hormone-dependent organ. We assessed vertex baldness trajectories, chest hair amount, and their relationships with the odds of developing prostate cancer in a large case-control study in Montreal, Canada.

METHODS

In-person interviews were conducted with 1,931 incident prostate cancer cases and 1,994 population-based age-matched (±5 years) controls. Participants reported their hair patterns using the validated Hamilton-Norwood scale of baldness for 10-year increments starting at age 30, and their current amount of chest hair. Group-based trajectories were used to identify men sharing similar patterns of vertex baldness severity over adulthood. Multivariable logistic regression assessed associations between indicators of baldness (frontal, vertex, age at onset, severity, and trajectories), chest hair, and odds of prostate cancer.

RESULTS

Vertex balding onset at age 30 was associated with increased odds of overall prostate cancer [Odds ratio (OR), 1.30; 95% confidence interval (CI), 1.03-1.64]. Men in the trajectory characterized by early moderate vertex baldness and developing severe baldness had increased odds of overall (OR, 1.42; 95% CI, 1.03-1.96) and especially aggressive prostate cancer (OR, 1.98; 95% CI, 1.21-3.22) compared with men without baldness. Men with little chest hair had higher odds of aggressive tumors than those with a moderate amount/a lot of chest hair.

CONCLUSIONS

Early-onset moderate vertex baldness that progresses and having little chest hair may be useful biomarkers of aggressive prostate cancer.

IMPACT

Integration of early-onset vertex balding patterns into risk prediction models of aggressive prostate cancer should be envisaged.

Dicer-dependent heterochromatic small RNAs in the model diatom species Phaeodactylum tricornutum

Diatoms are eukaryotic microalgae responsible for nearly half of the marine productivity. RNA interference (RNAi) is a mechanism of regulation of gene expression mediated by small RNAs (sRNAs) processed by the endoribonuclease Dicer (DCR). To date, the mechanism and physiological role of RNAi in diatoms are unknown. We mined diatom genomes and transcriptomes for key RNAi effectors and retraced their phylogenetic history. We generated DCR knockout lines in the model diatom species Phaeodactylum tricornutum and analyzed their mRNA and sRNA populations, repression-associated histone marks, and acclimatory response to nitrogen starvation. Diatoms presented a diversification of key RNAi effectors whose distribution across species suggests the presence of distinct RNAi pathways. P. tricornutum DCR was found to process 26-31-nt-long double-stranded sRNAs originating mostly from transposons covered by repression-associated epigenetic marks. In parallel, P. tricornutum DCR was necessary for the maintenance of the repression-associated histone marks H3K9me2/3 and H3K27me3. Finally, PtDCR-KO lines presented a compromised recovery post nitrogen starvation suggesting a role for P. tricornutum DCR in the acclimation to nutrient stress. Our study characterized the molecular function of the single DCR homolog of P. tricornutum suggesting an association between RNAi and heterochromatin maintenance in this model diatom species.

aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative controls, and therefore have limited use cases. We present a reference-free decontamination tool tailored for the removal of contaminant DNA of ancient oral sample called aKmerBroom. Our tool builds a Bloom filter of known ancient and modern oral k-mers, then scans an input set of ancient metagenomic reads using multiple passes to iteratively retain reads likely to be of oral origin. On synthetic data, aKmerBroom achieves over 89.53 % sensitivity and 94.00 % specificity. On real datasets, aKmerBroom shows higher read retainment (+ 60 % on average) than other methods. We anticipate aKmerBroom will be a valuable tool for the processing of ancient oral samples as it will prevent contaminated datasets from being completely discarded in downstream analyses.

decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods

BACKGROUND

The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices.

RESULTS

We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker.

CONCLUSIONS

decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. Video Abstract.

Computing Geographical Networks Generated by Air-Mass Movement

As air masses move within the troposphere, they transport a multitude of components including gases and particles such as pollen and microorganisms. These movements generate atmospheric highways that connect geographic areas at distant, local, and global scales that particles can ride depending on their aerodynamic properties and their reaction to environmental conditions. In this article we present an approach and an accompanying web application called tropolink for measuring the extent to which distant locations are potentially connected by air-mass movement. This approach is based on the computation of trajectories of air masses with the HYSPLIT atmospheric transport and dispersion model, and on the computation of connection frequencies, called connectivities, in the purpose of building trajectory-based geographical networks. It is illustrated for different spatial and temporal scales with three case studies related to plant epidemiology. The web application that we designed allows the user to easily perform intensive computation and mobilize massive archived gridded meteorological data to build weighted directed networks. The analysis of such networks allowed us for example, to describe the potential of invasion of a migratory pest beyond its actual distribution. Our approach could also be used to compute geographical networks generated by air-mass movement for diverse application domains, for example, to assess long-term risk of spread from persistent or recurrent sources of pollutants, including wildfire smoke.

Building alternative splicing and evolution-aware sequence-structure maps for protein repeats

Alternative splicing of repeats in proteins provides a mechanism for rewiring and fine-tuning protein interaction networks. In this work, we developed a robust and versatile method, ASPRING, to identify alternatively spliced protein repeats from gene annotations. ASPRING leverages evolutionary meaningful alternative splicing-aware hierarchical graphs to provide maps between protein repeats sequences and 3D structures. We re-think the definition of repeats by explicitly accounting for transcript diversity across several genes/species. Using a stringent sequence-based similarity criterion, we detected over 5,000 evolutionary conserved repeats by screening virtually all human protein-coding genes and their orthologs across a dozen species. Through a joint analysis of their sequences and structures, we extracted specificity-determining sequence signatures and assessed their implication in experimentally resolved and modelled protein interactions. Our findings demonstrate the widespread alternative usage of protein repeats in modulating protein interactions and open avenues for targeting repeat-mediated interactions.

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

BACKGROUND

Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres.

METHODS

This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low-middle-income countries.

RESULTS

In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of 'single-use' consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low-middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia.

CONCLUSION

This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high- and low-middle-income countries.

Combination of whole genome sequencing and supervised machine learning provides unambiguous identification of eae-positive Shiga toxin-producing Escherichia coli

Introduction

The objective of this study was to develop, using a genome wide machine learning approach, an unambiguous model to predict the presence of highly pathogenic STEC in E. coli reads assemblies derived from complex samples containing potentially multiple E. coli strains. Our approach has taken into account the high genomic plasticity of E. coli and utilized the stratification of STEC and E. coli pathogroups classification based on the serotype and virulence factors to identify specific combinations of biomarkers for improved characterization of eae-positive STEC (also named EHEC for enterohemorrhagic E.coli) which are associated with bloody diarrhea and hemolytic uremic syndrome (HUS) in human.

Methods

The Machine Learning (ML) approach was used in this study on a large curated dataset composed of 1,493 E. coli genome sequences and 1,178 Coding Sequences (CDS). Feature selection has been performed using eight classification algorithms, resulting in a reduction of the number of CDS to six. From this reduced dataset, the eight ML models were trained with hyper-parameter tuning and cross-validation steps.

Results and discussion

It is remarkable that only using these six genes, EHEC can be clearly identified from E. coli read assemblies obtained from in silico mixtures and complex samples such as milk metagenomes. These various combinations of discriminative biomarkers can be implemented as novel marker genes for the unambiguous EHEC characterization from different E. coli strains mixtures as well as from raw milk metagenomes.

1358. Establishing Genomic SARS-CoV-2 Surveillance at the National Level: Germany, 2021

Background

The COVID-19 pandemic has demonstrated the importance of pathogen genomic surveillance. At RKI, the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance.

Methods

SARS-CoV-2 positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. This surveillance instrument enables (i) almost-real-time monitoring of SARS-CoV-2 genomic diversity and evolution, (ii) in vitro assessment of vaccine coverage against emerging variants and (iii) genome-based estimates of SARS-CoV-2-incidences.

Results

We report the results of our analyses of 3623 SARS-CoV-2 genomes collected between 12/1/2020 and 12/31/2021. All variants of concern were identified, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Lineage distributions fluctuated over time, covering the rise of the Alpha and Delta, as well as the emergence of Omicron. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modelled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave.

Conclusion

This example illustrates that pathogen genomics enables a proactive approach to controlling a pandemic as the virus evolves. Molecular and genomic SARS-CoV-2 surveillance will be crucial during the post-pandemic future, informing public health policies including vaccination strategies. Of note, the IMS-SC2 infrastructure can be adapted to many other pathogens, serving as a blueprint for future efforts to increase genomic pathogen surveillance.

Disclosures

All Authors: No reported disclosures.

CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance

SUMMARY

The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand the evolution of the virus, to monitor the viral population, and plan epidemiological responses. Detailed analysis, easy visualization and intuitive filtering of the latest viral sequences are powerful for this purpose. We present CovRadar, a tool for genomic surveillance of the SARS-CoV-2 Spike protein. CovRadar consists of an analytical pipeline and a web application that enable the analysis and visualization of hundreds of thousand sequences. First, CovRadar extracts the regions of interest using local alignment, then builds a multiple sequence alignment, infers variants and consensus and finally presents the results in an interactive app, making accessing and reporting simple, flexible and fast.

AVAILABILITY AND IMPLEMENTATION

CovRadar is freely accessible at https://covradar.net, its open-source code is available at https://gitlab.com/dacs-hpi/covradar.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021

BACKGROUND

Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern led to an expansion of genomic sequencing activities in Germany.

METHODS

At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2-positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI.

RESULTS

We report analyses of 3623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modeled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave.

CONCLUSIONS

SARS-CoV-2 molecular and genomic surveillance may inform public health policies including vaccination strategies and enable a proactive approach to controlling coronavirus disease 2019 spread as the virus evolves.

Early life Bacillus Calmette-Guerin vaccination and incidence of type 1, type 2, and latent autoimmune diabetes in adulthood

AIMS

Bacillus Calmette-Guerin (BCG) vaccination limits blood sugar elevations and autoimmunity. Previous studies focused on type 1 diabetes among children, despite possible effects on other phenotypes later in life. We studied associations between BCG vaccination and type 1, type 2 and latent autoimmune diabetes (LADA) in adulthood.

METHODS

A 1970-1974 birth cohort was linked with the BCG vaccination registry and administrative health data of Quebec. 396,118 people aged 22-44 years were followed-up for diabetes mellitus (DM) onset. Incident DM cases were subjects with ≥1 hospitalization or ≥2 physician claims related to DM over a 2-year period. Type 1 diabetes, type 2 diabetes, and LADA cases were individuals with ≥1 reimbursement of insulin, oral antidiabetic agent, or both. Cox proportional regressions were used to estimate hazard ratios (HR), adjusting for potential confounders.

RESULTS

Forty-four percent of subjects were BCG vaccinated, 88% of these before age 1. For type 1 diabetes, no association was found before 30 years old, but vaccinated subjects had a lower risk of this phenotype after age 30 (HRadj= 0.65, 95% CI: 0.44-0.95). BCG vaccination was associated with a lower risk of type 2 diabetes (HRadj=0.85, 95% CI: 0.79-0.92), whereas no association was observed for LADA (HRadj=1.30, 95% CI: 0.71-2.38). Results did not differ by sex.

CONCLUSIONS

Early life BCG vaccination was associated with lower risks of both type 1 and type 2 diabetes from early to middle adulthood, but not of LADA. Future studies should explore these long-term associations, while distinguishing diabetes phenotypes.

Bacillus Calmette-Guerin vaccination and multiple sclerosis: a population-based birth cohort study in Quebec, Canada

BACKGROUND

The Bacillus Calmette-Guerin (BCG) vaccine could reduce the incidence of multiple sclerosis (MS) through immunomodulation. Previous studies, presenting some limitations, reported no association. We re-examined this association in a large cohort focusing on relapsing-remitting MS (RRMS).

METHODS

The cohort included 400,563 individuals, and was linked with the Quebec provincial BCG vaccination registry and administrative health data. Individuals were followed-up from 1983 to 2014 and then within period 1 (1983-1996) and period 2 (1997-2014), for the occurrence of MS. Incident MS cases were defined as those with ≥3 hospital or physician claims for MS. Subjects with ≥1 drug reimbursement for MS disease-modifying therapies were classified as RRMS. Cox proportional hazards regression was used to estimate hazard ratios (HR) over the follow-ups, adjusting for potential confounders. Possible effect modification due to sex was assessed.

RESULTS

A total of 178,335 (46%) individuals were BCG vaccinated. There were 274 (0.06%) incident MS cases identified in 1983-1996, and 1,433 (0.4%) in 1997-2014. No association was found with RRMS, either in period 1 (adjusted HRs= 0.96, 95% confidence interval: 0.63-1.45; 96 cases) or in period 2 (HRadj= 1.02, 0.85-1.23; 480 cases). The remaining MS cases, for whom the phenotype was unknown, were positively associated with BCG over the entire follow-up (HRadj= 1.25, 1.10-1.41; 1,131 cases) and in period 2 (HRadj=1.33, 1.17-1.52; 953 cases). No interaction with sex was found.

CONCLUSION

Findings suggest that BCG vaccination does not decrease the risk of RRMS, and that future studies should consider phenotypes of MS.

Association between Bacillus Calmette-Guerin vaccination and type 1 diabetes in adolescence: A population-based birth cohort study in Quebec, Canada

The Bacillus Calmette-Guerin (BCG) vaccine could reduce the incidence of type 1 diabetes through non-specific immunomodulation. Previous epidemiological studies, presenting some limitations, report no association. We examined this association of early life BCG vaccination and age at vaccination with type 1 diabetes incidence in adolescence in a large representative cohort in Quebec. The cohort included 387,704 individuals born in Quebec between 1970 and 1974 whose BCG vaccination status was determined from a provincial registry. Individuals were followed up from 1985 to their 19th birthday (maximum to 1993) for their use of physician services. Individuals were defined as type 1 diabetes cases if they had ≥4 related physician claims over a 2-year period, with at least 30 days between two claims. Cox proportional hazards regression was used to estimate the association of BCG vaccination and age at vaccination with type 1 diabetes. Covariates were selected based on a directed acyclic graph. Interaction according to sex was evaluated. A total of 178,133 (45.9%) individuals were vaccinated and 442 (0.11%) incident cases of type 1 diabetes were identified. The risk of type 1 diabetes was similar in vaccinated compared with unvaccinated individuals (adjusted hazard ratio = 1.06 [95% CI: 0.88-1.29]). There was no association with age at vaccination, and results did not differ by sex (Interaction, p = 0.60). Our results suggest that BCG vaccination does not prevent type 1 diabetes in adolescence.

Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants

In Staphylococcus aureus, resistance to β-lactamase stable β-lactam antibiotics is mediated by the penicillinbinding protein 2a, encoded by mecA or by its homologues mecB or mecC. However, a substantial number of meticillin-resistant isolates lack known mec genes and, thus, are called meticillin resistant lacking mec (MRLM). This study aims to identify the genetic mechanisms underlying the MRLM phenotype. A total of 141 MRLM isolates and 142 meticillin-susceptible controls were included in this study. Oxacillin and cefoxitin minimum inhibitory concentrations were determined by broth microdilution and the presence of mec genes was excluded by PCR. Comparative genomics and a genome-wide association study (GWAS) approach were applied to identify genetic polymorphisms associated with the MRLM phenotype. The potential impact of such mutations on the expression of PBP4, as well as on cell morphology and biofilm formation, was investigated. GWAS revealed that mutations in gdpP were significantly associated with the MRLM phenotype. GdpP is a phosphodiesterase enzyme involved in the degradation of the second messenger cyclic-di-AMP in S. aureus. A total of 131 MRLM isolates carried truncations, insertions or deletions as well as amino acid substitutions, mainly located in the functional DHH-domain of GdpP. We experimentally verified the contribution of these gdpP mutations to the MRLM phenotype by heterologous complementation experiments. The mutations in gdpP had no effect on transcription levels of pbp4; however, cell sizes of MRLM strains were reduced. The impact on biofilm formation was highly strain dependent. We report mutations in gdpP as a clinically relevant mechanism for β-lactam resistance in MRLM isolates. This observation is of particular clinical relevance, since MRLM are easily misclassified as MSSA (meticillin-susceptible S. aureus), which may lead to unnoticed spread of β-lactam-resistant isolates and subsequent treatment failure.

Assessing conservation of alternative splicing with evolutionary splicing graphs

Understanding how protein function has evolved and diversified is of great importance for human genetics and medicine. Here, we tackle the problem of describing the whole transcript variability observed in several species by generalizing the definition of splicing graph. We provide a practical solution to construct parsimonious evolutionary splicing graphs where each node is a minimal transcript building block defined across species. We show a clear link between the functional relevance, tissue regulation, and conservation of alternative transcripts on a set of 50 genes. By scaling up to the whole human protein-coding genome, we identify a few thousand genes where alternative splicing modulates the number and composition of pseudorepeats. We have implemented our approach in ThorAxe, an efficient, versatile, robust, and freely available computational tool.

Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany

Here, we report on the increasing frequency of the SARS-CoV-2 lineage A.27 in Germany during the first months of 2021. Genomic surveillance identified 710 A.27 genomes in Germany as of 2 May 2021, with a vast majority identified in laboratories from a single German state (Baden-Wuerttemberg, n = 572; 80.5%). Baden-Wuerttemberg is located near the border with France, from where most A.27 sequences were entered into public databases until May 2021. The first appearance of this lineage based on sequencing in a laboratory in Baden-Wuerttemberg can be dated to early January '21. From then on, the relative abundance of A.27 increased until the end of February but has since declined-meanwhile, the abundance of B.1.1.7 increased in the region. The A.27 lineage shows a mutational pattern typical of VOIs/VOCs, including an accumulation of amino acid substitutions in the Spike glycoprotein. Among those, L18F, L452R and N501Y are located in the epitope regions of the N-terminal- (NTD) or receptor binding domain (RBD) and have been suggested to result in immune escape and higher transmissibility. In addition, A.27 does not show the D614G mutation typical for all VOIs/VOCs from the B lineage. Overall, A.27 should continue to be monitored nationally and internationally, even though the observed trend in Germany was initially displaced by B.1.1.7 (Alpha), while now B.1.617.2 (Delta) is on the rise.

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

General and abdominal obesity trajectories across adulthood, and risk of prostate cancer: results from the PROtEuS study, Montreal, Canada

PURPOSE

Greater body fatness is a probable cause of advanced prostate cancer (PCa). Body fat distribution and timing of exposure may be relevant. We investigated associations between body size trajectories and PCa incidence in a population-based case-control study in Montreal, Canada.

METHODS

Cases (n = 1,931), aged ≤ 75 years, were diagnosed with PCa in 2005-2009; 1,994 controls were selected from the electoral list. Interviews were conducted to assess body mass index (BMI) and Stunkard's silhouette at ages 20, 40, 50, 60 years, and before interview. Current waist and hip circumferences were measured, and a predictive model estimated waist circumference in the past. BMI and waist circumference trajectories were determined to identify subgroups. Logistic regression estimated odds ratios (OR) and 95% confidence intervals (CI) for the association between anthropometric indicators and PCa.

RESULTS

Subjects with a current BMI ≥ 30 kg/m² had a lower risk of overall PCa (OR 0.71, 95% CI 0.59-0.85). Associations with adult BMI followed similar trends for less and more aggressive tumors, with stronger inverse relationships in early adulthood. Contrastingly, current waist circumference ≥ 102 cm was associated with elevated risk of high-grade PCa (OR 1.33, 95% CI 1.03-1.71). Men with increasing BMI or waist circumference adult trajectories had a lower risk of PCa, especially low-grade, than those in the normal-stable range. This was especially evident among men in the obese-increase group for BMI and waist circumference.

CONCLUSION

Abdominal obesity increased the risk of aggressive PCa. The inverse relationship between body size trajectories and PCa may reflect PSA hemodilution, lower detection, and/or a true etiological effect.

Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A

Motivation

The understanding of the ever-increasing number of metagenomic sequences accumulating in our databases demands for approaches that rapidly ‘explore’ the content of multiple and/or large metagenomic datasets with respect to specific domain targets, avoiding full domain annotation and full assembly.

Results

S3A is a fast and accurate domain-targeted assembler designed for a rapid functional profiling. It is based on a novel construction and a fast traversal of the Overlap-Layout-Consensus graph, designed to reconstruct coding regions from domain annotated metagenomic sequence reads. S3A relies on high-quality domain annotation to efficiently assemble metagenomic sequences and on the design of a new confidence measure for a fast evaluation of overlapping reads. Its implementation is highly generic and can be applied to any arbitrary type of annotation. On simulated data, S3A achieves a level of accuracy similar to that of classical metagenomics assembly tools while permitting to conduct a faster and sensitive profiling on domains of interest. When studying a few dozens of functional domains—a typical scenario—S3A is up to an order of magnitude faster than general purpose metagenomic assemblers, thus enabling the analysis of a larger number of datasets in the same amount of time. S3A opens new avenues to the fast exploration of the rapidly increasing number of metagenomic datasets displaying an ever-increasing size.

Availability and implementation

S3A is available at http://www.lcqb.upmc.fr/S3A_ASSEMBLER/.

Supplementary information

Supplementary data are available at Bioinformatics online.

Characterizing Short-Term Jobs in a Population-Based Study

BACKGROUND

Work histories generally cover all jobs held for ≥1 year. However, it may be time and cost prohibitive to conduct a detailed exposure assessment for each such job. While disregarding short-term jobs can reduce the assessment burden, this can be problematic if those jobs contribute important exposure information towards understanding disease aetiology.

OBJECTIVE

To characterize short-term jobs, defined as lasting more than 1 year, but less than 2 years, in a population-based study conducted in Montreal, Canada.

METHODS

In 2005-2012, we collected work histories for some 4000 participants in a case-control study of prostate cancer. Overall, subjects had held 19 462 paid jobs lasting ≥1 year, including 3655 short-term jobs. Using information from interviews and from the Canadian Classification and Dictionary of Occupations, we characterized short-term jobs and compared them to jobs held ≥2 years.

RESULTS

Short-term jobs represented <4% of subjects' work years on average. Forty-five per cent of subjects had at least one short-term job; of these, 49% had one, 24% had two, and 27% had at least three. Half of all short-term jobs had been held before the age of 24. Short-term jobs entailed more often exposure to fumes, odours, dust, and/or poor ventilation than longer jobs (17 versus 13%), as well as outdoor work (10 versus 5%) and heavy physical activity (16 versus 12%).

CONCLUSIONS

Short-term jobs occurred often in early careers and more frequently entailed potentially hazardous exposures than longer-held jobs. However, as they represented a small proportion of work years, excluding them should have a marginal impact on lifetime exposure assessment.

Transcripts' Evolutionary History and Structural Dynamics Give Mechanistic Insights into the Functional Diversity of the JNK Family

Alternative splicing and alternative initiation/termination transcription sites have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms. We reconstruct phylogenetic forests relating 60 protein-coding transcripts from the c-Jun N-terminal kinase (JNK) family observed in seven species. We identify two alternative splicing events of ancient origin and show that they induce subtle changes in the protein's structural dynamics. We highlight a previously uncharacterized transcript whose predicted structure seems stable in solution. We further demonstrate that orphan transcripts, for which no phylogeny could be reconstructed, display peculiar sequence and structural properties. Our approach is implemented in PhyloSofS (Phylogenies of Splicing Isoforms Structures), a fully automated computational tool freely available at https://github.com/PhyloSofS-Team/PhyloSofS.

Night-Shift Work and Risk of Prostate Cancer: Results From a Canadian Case-Control Study, the Prostate Cancer and Environment Study

Night-shift work involving disruption of circadian rhythms has been associated with breast cancer risk. A role in prostate cancer is also suspected, but evidence is limited. We investigated the association between night-shift work and prostate cancer incidence in the Prostate Cancer and Environment Study (PROtEuS), a population-based case-control study conducted in 2005-2012 in Montreal, Quebec, Canada. Participants were 1,904 prostate cancer cases (432 high-grade cancers) and 1,965 population controls. Detailed work schedules for each job held for at least 2 years (n = 15,724) were elicited in face-to-face interviews. Night-shift work was defined as having ever worked ≥3 hours between midnight and 5:00 am ≥3 nights/month for ≥1 year. Unconditional logistic regression was used to estimate odds ratios and 95% confidence intervals for the association between night-shift work and prostate cancer, adjusting for age, ancestry, and education. No association was found between overall prostate cancer and night-shift work metrics, including ever exposure, duration, intensity, cumulative exposure, rotating shifts, and early-morning shifts. For none of the exposure indices was there evidence of heterogeneity in odds ratios between low- and high-grade cancers. Sensitivity analyses restricting exposures to ≥7 nights/month or considering screening history yielded similar results. Our findings lend no support for a major role of night-shift work in prostate cancer development.

Short link N acts as a disease modifying osteoarthritis drug

Osteoarthritis (OA) is a degenerative joint disease characterised by a progressive degradation of articular cartilage and underlaying bone and is associated with pain and disability. Currently, there is no medical treatment to reverse or even retard OA. Based on our previous reports, where we establish the repair potential of short Link N (sLN) in the intervertebral disc, a cartilage-like tissue, we hypothesise that sLN may hold similar promises in the repair of articular cartilage. This study aimed to determine if sLN, could prevent OA disease progression. Skeletally mature New Zealand white rabbits underwent unilateral anterior cruciate ligament transection (ACLT) of their left femorotibial joints to induce joint degeneration typical of OA. Beginning 3 weeks post-operatively, and every three weeks thereafter for 12 weeks, either saline (1 mL) or sLN (100 μg in 1 mL saline) was injected intraarticularly into the operated knee. Six additional rabbits underwent sham surgery but without ACLT or post-operative injections. The effects on gross joint morphology and cartilage histologic changes were evaluated. In the Saline group, prominent erosion of articular cartilage occurred in both femoral condyle compartments and the lateral compartment of the tibial plateau while, sLN treatment reduced the severity of the cartilage damage in these compartments of the knee showing erosion. Furthermore, statistically significant differences were detected between the joint OA score of the saline and sLN treated groups (p = 0.0118). Therefore, periodic intraarticular injection of sLN is a promising nonsurgical treatment for preventing or retarding OA progression, by reducing cartilage degradation.

A hybrid expert approach for retrospective assessment of occupational exposures in a population-based case-control study of cancer

BACKGROUND

While the expert-based occupational exposure assessment approach has been considered the reference method for retrospective population-based studies, its implementation in large study samples has become prohibitive. To facilitate its application and improve upon it we developed, in the context of a Montreal population-based study of prostate cancer (PROtEuS), a hybrid approach combining job-exposure profiles (JEPs) summarizing expert evaluations from previous studies and expert review. We aim to describe the hybrid expert method and its impacts on the exposures assigned in PROtEuS compared to those from a previous study coded using the traditional expert method.

METHODS

Applying the hybrid approach, experts evaluated semi-quantitative levels of confidence, concentration and frequency of exposure to 313 agents for 16,065 jobs held by 4005 subjects in PROtEuS. These assessments were compared to those from a different set of jobs coded in an earlier study of lung cancer, conducted on the same study base, for 90 blue-collar occupations and 203 agents. Endpoints evaluated included differences in the number of exposures and in the distribution of ratings across jobs, and the within-occupation variability in exposure.

RESULTS

Compared to jobs from the lung cancer study, jobs in PROtEuS had on average 0.3 more exposures. PROtEuS exposures were more often assigned definite confidence ratings, but concentration and frequency levels tended to be lower. The within-occupation variability in ratings assigned to jobs were lower in PROtEuS jobs for all metrics. This was particularly evident for concentration, although considerable variability remained with over 40% of occupation/agent cells in PROtEuS exposed at different levels. The hybrid approach reduced coding time by half, compared to the traditional expert assessment.

CONCLUSIONS

The new hybrid expert approach improved on efficiency and transparency, and resulted in greater confidence in assessments, compared to the traditional expert method applied in an earlier study involving a similar set of jobs. Assigned ratings were more homogeneous with the hybrid approach, possibly reflecting clearer guidelines for coding, greater coherence between experts and/or reliance on summaries of past assessments. Nevertheless, significant within-occupation variability remained with the hybrid approach, suggesting that experts took into account job-specific factors in their assessments.

Disadvantageous Socioeconomic Position at Specific Life Periods May Contribute to Prostate Cancer Risk and Aggressiveness

Background: Previous studies on socioeconomic position (SEP) and risk of prostate cancer (PCa) have produced contradictory results. Most measured SEP only once during the individuals' life span. The aim of the study was to identify life course models that describe best the relationship between SEP measured during childhood/adolescence, early- and late-adulthood, and risk of PCa overall as well as according to tumor aggressiveness at diagnosis. Methods: We used data from a population-based case-control study of PCa conducted in the predominantly French-speaking population in Montreal, Canada. Cases (n = 1,930) with new, histologically-confirmed PCa were ascertained across hospitals deserving the French-speaking population in 2005-2009. Controls (n = 1,991), selected from Quebec's list of French-speaking electors, were frequency-matched to cases (±5 years). In-person interviews collected information on socio-demographic and lifestyle characteristics, and a complete occupational history. Measures of SEP during childhood/adolescence included parents' ownership of a car and father's longest occupation, while the subject's first and longest occupations were used to indicate early- and late-adulthood SEP, respectively. We used the Bayesian relevant life course exposure model to investigate the relationship between lifelong SEP and PCa risk. Results: Cumulative exposure to disadvantageous SEP was associated with about a 50% increase in odds of developing PCa. Late-adulthood SEP was identified as a sensitive period for aggressive PCa. Childhood/adolescence SEP based on parents' ownership of a car was associated with non-aggressive PCa. Associations were independent from PCa screening. Conclusion: Disadvantageous SEP over the life course was associated with higher PCa incidence, with consistent evidence of sensitive time periods for cancer aggressiveness. The mechanisms through which disadvantageous SEP relates to PCa risk need to be further elucidated.

Synovial nerve fiber density decreases with naturally-occurring osteoarthritis in horses

OBJECTIVE

To measure the nerve fiber density in synovial membranes from healthy and OA equine joints and to investigate the relationship between synovial innervation and OA severity, synovial vascularity and synovitis.

DESIGN

Twenty-five equine metacarpophalangeal joints were collected post-mortem. The joints were dissected and the macroscopic lesions of the articular cartilage were scored. Synovial membrane specimens (n = 50) were harvested, fixed, sectioned and scored histologically. Immunohistochemical staining and immunofluorescence with S-100 protein, that identifies nerve fibers, and ⍺-actin, that stains vascular smooth muscle, were also performed on site-matched specimens and the relationships between these tissues was interrogated.

RESULTS

The nerve fiber density was higher in the superficial layer (≤200 μm) of the synovium when compared to the deeper layer in control equine joints (mean difference (95% C.I.): 0.054% (0.018%, 0.11%)). In osteoarthritic joints, synovial innervation decreased in the superficial layer with increasing macroscopic OA score (β (SEM), 95% C.I.: -0.0061 (0.00021), -0.0011, -0.00017). The blood vessel density was also higher in the superficial layer of the synovium compared to the deep layer in the control (mean difference (95% C.I.): 1.1% (0.36%, 2.3%)) and OA (mean difference (95% C.I.): 0.60% (0.22%, 1.2%)) equine joints. Moreover, considering all synovial specimens, higher nerve fiber density in the deep layer positively correlated with blood vessel density (β (SEM), 95% C.I.: 0.11 (0.036), 0.035, 0.18).

CONCLUSION

The reduction in nerve fiber density with advanced cartilage degeneration suggests that peripheral neuropathy is associated with equine OA. Whether this link is associated with neuropathic pain, requires further investigation.

Vitamin C Intake and Risk of Prostate Cancer: The Montreal PROtEuS Study

Background: Vitamin C is a reducing agent and free radical scavenger, acting as antioxidant in plasma membranes and within cells. Based on these properties, a role for vitamin C in cancer incidence has been suspected. There are as yet few large population-based studies focusing on prostate cancer, with the preponderant evidence leaning toward the absence of an association. Nevertheless, many previous studies overlooked prostate cancer aggressiveness, as well as screening and detection issues, which could bias potential associations.

Methods: The Prostate Cancer and Environment Study (PROtEuS) is a population-based case-control study conducted in Montreal, Canada. In-person interviews, conducted with 1,916 histologically confirmed prostate cancer cases and 1,985 population controls, elicited information on a wide range of socio-demographic, lifestyle, and medical factors, including PSA screening. Usual frequency of consumption of 63 food items two years prior to diagnosis/interview was collected, along with use of dietary supplements. Odds ratios (OR) and 95% confidence intervals (CI) between vitamin C intake and prostate cancer were estimated using logistic or polytomous regression, adjusting for potential confounders.

Results: We observed no association between dietary intakes of vitamin C (OR for upper vs. lower tertile: 0.95, 95%CI 0.77, 1.18), estimated using the residual method to account for energy intake, or between regular use of vitamin C supplements and/or multivitamins (OR 0.90, 95%CI 0.76–1.05), and overall prostate cancer. Analyses considering disease aggressiveness, or restricted to subjects recently screened with PSA, thereby limiting the potential for undiagnosed cancers in non-cases, generated results consistent with those from the main analyses.

Conclusion: Our findings document the absence of an association between recent dietary vitamin C intake, or supplementation, and prostate cancer incidence overall or prostate cancer grade at diagnosis. Based on this, and other available evidence, vitamin C intake does not seem to hold promises with regard to prostate cancer prevention.

DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data

Background

Discovering over-represented approximate motifs in DNA sequences is an essential part of bioinformatics. This topic has been studied extensively because of the increasing number of potential applications. However, it remains a difficult challenge, especially with the huge quantity of data generated by high throughput sequencing technologies. To overcome this problem, existing tools use greedy algorithms and probabilistic approaches to find motifs in reasonable time. Nevertheless these approaches lack sensitivity and have difficulties coping with rare and subtle motifs.

Results

We developed DiNAMO (for DNA MOtif), a new software based on an exhaustive and efficient algorithm for IUPAC motif discovery. We evaluated DiNAMO on synthetic and real datasets with two different applications, namely ChIP-seq peaks and Systematic Sequencing Error analysis. DiNAMO proves to compare favorably with other existing methods and is robust to noise.

Conclusions

We shown that DiNAMO software can serve as a tool to search for degenerate motifs in an exact manner using IUPAC models. DiNAMO can be used in scanning mode with sliding windows or in fixed position mode, which makes it suitable for numerous potential applications.

Availability

https://github.com/bonsai-team/DiNAMO.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2215-1) contains supplementary material, which is available to authorized users.

Meet-U: Educating through research immersion

We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master’s students in bioinformatics and modeling, with protein–protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.

Jointly aligning a group of DNA reads improves accuracy of identifying large deletions

Performing sequence alignment to identify structural variants, such as large deletions, from genome sequencing data is a fundamental task, but current methods are far from perfect. The current practice is to independently align each DNA read to a reference genome. We show that the propensity of genomic rearrangements to accumulate in repeat-rich regions imposes severe ambiguities in these alignments, and consequently on the variant calls-with current read lengths, this affects more than one third of known large deletions in the C. Venter genome. We present a method to jointly align reads to a genome, whereby alignment ambiguity of one read can be disambiguated by other reads. We show this leads to a significant improvement in the accuracy of identifying large deletions (≥20 bases), while imposing minimal computational overhead and maintaining an overall running time that is at par with current tools. A software implementation is available as an open-source Python program called JRA at https://bitbucket.org/jointreadalignment/jra-src.

PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data

The iCLIP and eCLIP techniques facilitate the detection of protein–RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP (https://github.com/skrakau/PureCLIP), a hidden Markov model based approach, which simultaneously performs peak-calling and individual crosslink site detection. It explicitly incorporates a non-specific background signal and, for the first time, non-specific sequence biases. On both simulated and real data, PureCLIP is more accurate in calling crosslink sites than other state-of-the-art methods and has a higher agreement across replicates.

C2K77 ELISA detects cleavage of type II collagen by cathepsin K in equine articular cartilage

OBJECTIVES

Develop a species-specific ELISA for a neo-epitope generated by cathepsin K cleavage of equine type II collagen to: (1) measure cartilage type II collagen degradation by cathepsin K in vitro, (2) identify cytokines that upregulate cathepsin K expression and (3) compare cathepsin K with matrix metalloproteinase (MMP) collagenase activity in stimulated cartilage explants and freshly isolated normal and osteoarthritic (OA) articular cartilages.

DESIGN

A new ELISA (C2K77) was developed and tested by measuring the activity of exogenous cathepsin K on equine articular cartilage explants. The ELISA was then employed to measure endogenous cathepsin K activity in cultured cartilage explants with or without stimulation by interleukin-1 beta (IL-1β), tumour necrosis-alpha (TNF-α), oncostatin M (OSM) and lipopolysaccharide (LPS). Cathepsin K activity in cartilage explants (control and osteoarthritic-OA) and freshly harvested cartilage (control and OA) was compared to that of MMPs employing C2K77 and C1,2C immunoassays.

RESULTS

The addition of Cathepsin K to normal cartilage caused a significant increase (P < 0.01) in the C2K77 epitope release. Whereas the content of C1,2C, that reflects MMP collagenase activity, was increased in media by the addition to cartilage explants of TNF-α and OSM (P < 0.0001) or IL-1β and OSM (P = 0.002), no change was observed in C2K77 which also unchanged in OA cartilages compared to normal.

CONCLUSIONS

The ELISA C2K77 measured the activity of cathepsin K in equine cartilage which was unchanged in OA cartilage. Cytokines that upregulate MMP collagenase activity had no effect on endogenous cathepsin K activity, suggesting a different activation mechanism that requires further study.

Lifetime occupational exposure to metals and welding fumes, and risk of glioma: a 7-country population-based case-control study

BACKGROUND

Brain tumor etiology is poorly understood. Based on their ability to pass through the blood-brain barrier, it has been hypothesized that exposure to metals may increase the risk of brain cancer. Results from the few epidemiological studies on this issue are limited and inconsistent.

METHODS

We investigated the relationship between glioma risk and occupational exposure to five metals - lead, cadmium, nickel, chromium and iron- as well as to welding fumes, using data from the seven-country INTEROCC study. A total of 1800 incident glioma cases and 5160 controls aged 30-69 years were included in the analysis. Lifetime occupational exposure to the agents was assessed using the INTEROCC JEM, a modified version of the Finnish job exposure matrix FINJEM.

RESULTS

In general, cases had a slightly higher prevalence of exposure to the various metals and welding fumes than did controls, with the prevalence among ever exposed ranging between 1.7 and 2.2% for cadmium to 10.2 and 13.6% for iron among controls and cases, respectively. However, in multivariable logistic regression analyses, there was no association between ever exposure to any of the agents and risk of glioma with odds ratios (95% confidence intervals) ranging from 0.8 (0.7-1.0) for lead to 1.1 (0.7-1.6) for cadmium. Results were consistent across models considering cumulative exposure or duration, as well as in all sensitivity analyses conducted.

CONCLUSIONS

Findings from this large-scale international study provide no evidence for an association between occupational exposure to any of the metals under scrutiny or welding fumes, and risk of glioma.

Equine meniscal degeneration is associated with medial femorotibial osteoarthritis

BACKGROUND

There is limited information available concerning normal equine meniscal morphology, its degeneration and role in osteoarthritis (OA).

OBJECTIVES

To characterise normal equine meniscal morphology and lesions and to explore the relationship between equine meniscal degeneration and femorotibial OA.

STUDY DESIGN

Ex vivo cadaveric study.

METHODS

Menisci were harvested from 7 normal joints (n = 14 menisci) and 15 joints with OA (n = 30 menisci). A macroscopic femorotibial OA score (cartilage degeneration and osteophytosis) was employed to measure disease severity in each compartment. The femoral and tibial meniscal surfaces were scored for macroscopic fibrillation and tears (1-4). Histological sections (regions: cranial and caudal horn; body) were also scored for microscopic fibrillation and tears (0-3) and inner border degeneration (0-3).

RESULTS

Partial meniscal tears were present on both femoral and tibial surfaces in all 3 regions and most frequently identified on the femoral surface of the cranial horn of the medial meniscus and body of the lateral meniscus. There was a significantly positive correlation between the global medial meniscal macroscopic scores and osteophyte (r = 0.7, P = 0.002) or cartilage degeneration (r = 0.5, P = 0.03) scores within the medial femorotibial joint. The global medial meniscal macroscopic score was greater (P = 0.004) in the advanced OA joints compared with control joints.

MAIN LIMITATIONS

The menisci were principally from abattoir specimens without a known clinical history because of the challenge in obtaining a large number of specimens with a clinical diagnosis of femorotibial OA.

CONCLUSIONS

This study is the first to describe normal equine meniscal morphology and lesions. Meniscal lesions were identified in all segments and on both articular surfaces. Meniscal degeneration significantly correlated with OA severity in the equine medial femorotibial joint. The relationship between OA and meniscal pathology remains to be elucidated.

Residential greenness and risk of prostate cancer: A case-control study in Montreal, Canada

BACKGROUND

Recent studies suggest that exposure to greenness favors several health outcomes. We assessed whether living in the proximity of greener areas was related to prostate cancer incidence in a population-based case-control study in Montreal, Canada.

MATERIALS AND METHODS

Interviews eliciting lifetime addresses were conducted with 1933 prostate cancer cases diagnosed in 2005-2009 and 1994 population controls. Odds ratios (OR) and 95% confidence intervals (CI) estimated the association between residential greenness, both at recruitment (2005-2009) and about ten years prior (1996), defined by the normalized difference vegetation index (NDVI) around the home, and prostate cancer risk. Three models were developed adjusting for age, individual characteristics, and individual and ecological characteristics, estimating relative risk in relation to an interquartile range (IQR) increase of the NDVI.

RESULTS

We observed inverse associations between greenness measured within home buffers of 150m, 300m, 500m and 1000m, at both time points, and risk of prostate cancer, independently of individual and ecological characteristics. For instance, using a buffer of 300m, the OR for an IQR increase of 0.11 in NDVI at the time of recruitment was 0.82 (95%CI 0.74-0.92). The corresponding OR for an IQR increase of 0.15 in NDVI in 1996 was 0.86 (95%CI 0.74-1.00). There were little differences in risks according to buffer size, the time point of exposure, when considering prostate cancer aggressiveness, or when restricting controls to men recently screened for prostate cancer to reduce the likelihood of undiagnosed cancer among them.

CONCLUSION

Men living in greener areas, either recently or about a decade earlier, had lower risks of prostate cancer, independently of socio-demographic and lifestyle factors. These observations are novel and require confirmation.

Osteoclasts are recruited to the subchondral bone in naturally occurring post-traumatic equine carpal osteoarthritis and may contribute to cartilage degradation

The role of osteoclasts in osteochondral degeneration in osteoarthritis (OA) has rarely been investigated in spontaneous disease or animal models of OA.

OBJECTIVE

The objectives of the current study were to investigate osteoclast density and location in post-traumatic OA (PTOA) and control specimens from racehorses.

METHOD

Cores were harvested from a site in the equine third carpal bone, that undergoes repetitive, high intensity loading. Histological and immunohistochemical (Cathepsin K and Receptor-activator of Nuclear Factor kappa-β ligand (RANKL)) stained sections were scored (global and subregional) and the osteoclast density calculated. The cartilage histological scores were compared with osteoclast density and RANKL scores.

RESULTS

There was a greater density of osteoclasts in PTOA samples and they were preferentially located in the subchondral bone plate. RANKL scores positively correlated to the scores of cartilage degeneration and the osteoclast density. The relationship between hyaline articular cartilage RANKL score and osteoclast density was stronger than that of the subchondral bone RANKL score suggesting that cartilage RANKL may have a role in recruiting osteoclasts. The RANKL score in the articular calcified cartilage correlated with the number of microcracks also suggesting that osteoclasts recruited by RANKL may contribute to calcified cartilage degeneration in PTOA.

CONCLUSION

Our results support the hypothesis that osteoclasts are recruited during the progression of spontaneous equine carpal PTOA by cartilage RANKL, contributing to calcified cartilage microcracks and focal subchondral bone loss.

X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes

X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4(-/-) mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.

Fiona: a parallel and automatic strategy for read error correction

Motivation: Automatic error correction of high-throughput sequencing data can have a dramatic impact on the amount of usable base pairs and their quality. It has been shown that the performance of tasks such as de novo genome assembly and SNP calling can be dramatically improved after read error correction. While a large number of methods specialized for correcting substitution errors as found in Illumina data exist, few methods for the correction of indel errors, common to technologies like 454 or Ion Torrent, have been proposed.

Results: We present Fiona, a new stand-alone read error–correction method. Fiona provides a new statistical approach for sequencing error detection and optimal error correction and estimates its parameters automatically. Fiona is able to correct substitution, insertion and deletion errors and can be applied to any sequencing technology. It uses an efficient implementation of the partial suffix array to detect read overlaps with different seed lengths in parallel. We tested Fiona on several real datasets from a variety of organisms with different read lengths and compared its performance with state-of-the-art methods. Fiona shows a constantly higher correction accuracy over a broad range of datasets from 454 and Ion Torrent sequencers, without compromise in speed.

Conclusion: Fiona is an accurate parameter-free read error–correction method that can be run on inexpensive hardware and can make use of multicore parallelization whenever available. Fiona was implemented using the SeqAn library for sequence analysis and is publicly available for download at http://www.seqan.de/projects/fiona.

Contact: mschulz@mmci.uni-saarland.de or hugues.richard@upmc.fr

Supplementary information:Supplementary data are available at Bioinformatics online.

Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries

MOTIVATION

The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging.

RESULTS

Here, we present Ulysses, a tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high specificity over the complete spectrum of variants by assessing, in a principled manner, the statistical significance of each possible variant (duplications, deletions, translocations, insertions and inversions) against an explicit model for the generation of experimental noise. This statistical model proves particularly useful for the detection of low frequency variants. SV detection performed on a large insert Mate-Pair library from a breast cancer sample revealed a high level of somatic duplications in the tumor and, to a lesser extent, in the blood sample as well. Altogether, these results show that Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes.

Asthma, allergy and the risk of prostate cancer: results from the Montreal PROtEuS study

BACKGROUND

The few previous studies examining the association between asthma or allergy and prostate cancer (PCa) risk were inconclusive. This study aimed to evaluate these associations, and to explore in details the possible influence of current versus former allergic condition, age at onset, time since onset, and duration of each allergic condition.

METHODS

Detailed information on self-reported asthma and allergy was collected in the context of a large population-based case-control study conducted in Montreal, Canada. Study subjects included 1936 cases, diagnosed between 2005 and 2009, and 1995 population controls. Unconditional multivariate logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) adjusting for age, ancestry and familial history of prostate cancer.

RESULTS

The ORs were 1.11 (95% CI: 0.89-1.40) and 0.98 (95% CI: 0.84-1.14) for ever reporting of asthma and allergy, respectively. These ORs did not substantially vary according to status (former or current), age at onset, time since onset, and duration of each allergic condition. PCa screening was not associated with allergic diseases reporting.

CONCLUSIONS

Overall, our findings are in line with the absence of an association between a history of asthma or allergy, and PCa risk.

The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum

Background

Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA methylation and gene silencing activities. Yet, the biogenesis and regulatory function of small RNAs (sRNAs) remain ill defined in diatoms.

Results

Here we report the first comprehensive characterization of the sRNA landscape and its correlation with genomic and epigenomic information in Phaeodactylum tricornutum. The majority of sRNAs is 25 to 30 nt-long and maps to repetitive and silenced Transposable Elements marked by DNA methylation. A subset of this population also targets DNA methylated protein-coding genes, suggesting that gene body methylation might be sRNA-driven in diatoms. Remarkably, 25-30 nt sRNAs display a well-defined and unprecedented 180 nt-long periodic distribution at several highly methylated regions that awaits characterization. While canonical miRNAs are not detectable, other 21-25 nt sRNAs of unknown origin are highly expressed. Besides, non-coding RNAs with well-described function, namely tRNAs and U2 snRNA, constitute a major source of 21-25 nt sRNAs and likely play important roles under stressful environmental conditions.

Conclusions

P. tricornutum has evolved diversified sRNA pathways, likely implicated in the regulation of largely still uncharacterized genetic and epigenetic processes. These results uncover an unexpected complexity of diatom sRNA population and previously unappreciated features, providing new insights into the diversification of sRNA-based processes in eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-698) contains supplementary material, which is available to authorized users.