The predictive accuracy of cardiovascular risk prediction tools in inflammatory arthritis and psoriasis: an observational validation study using the Clinical Practice Research Datalink.

OBJECTIVES: Cardiovascular risk prediction tools developed for the general population often underperform for individuals with rheumatoid arthritis (RA), and their predictive accuracy are unclear for other inflammatory conditions that also have increased cardiovascular risk. We investigated performance of QRISK-3, Framingham Risk Score (FRS) and Reynolds Risk Score (RRS) in RA, psoriatic disease (psoriatic arthritis (PsA) and psoriasis) and ankylosing spondylitis (AS). We considered osteoarthritis as a non-inflammatory comparator. METHODS: We utilised primary care records from the Clinical Practice Research Datalink (CPRD) Aurum database to identify individuals with each condition and calculated 10-year cardiovascular risk using each prediction tool. Discrimination and calibration of each tool in each disease was assessed. RESULTS: Time-dependent AUC for QRISK3 was 0.752 for RA (95% CI 0.734-0.777), 0.794 for AS (95% CI 0.764-0.812), 0.764 for PsA (95% CI 0.741-0.791),0.815 for psoriasis (95% CI 0.789-0.835), and 0.698 for osteoarthritis (95% CI 0.670-0.717) indicating reasonably good predictive performance. AUC for FRS were similar, and slightly lower for RRS. FRS was reasonably well calibrated for each condition but underpredicted risk for patients with RA. RRS tended to underpredict CVD risk, whilst QRISK3 overpredicted CVD risk, especially for the most high-risk individuals. CONCLUSIONS: CVD risk for individuals with RA, AS and psoriatic disease were generally less accurately predicted using each of the 3 CVD risk prediction tools than reported accuracies in the original publications. Individuals with osteoarthritis also had less accurate predictions suggesting inflammation is not the sole reason for underperformance. Disease specific risk prediction tools may be required.

Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers.

Throughout their lifetime, cells are subject to extrinsic and intrinsic mutational processes leaving behind characteristic signatures in the genome. DNA mismatch repair (MMR) deficiency leads to hypermutation and is found in different cancer types. Although it is possible to associate mutational signatures extracted from human cancers with possible mutational processes, the exact causation is often unknown. Here, we use C. elegans genome sequencing of pms-2 and mlh-1 knockouts to reveal the mutational patterns linked to C. elegans MMR deficiency and their dependency on endogenous replication errors and errors caused by deletion of the polymerase ε subunit pole-4 Signature extraction from 215 human colorectal and 289 gastric adenocarcinomas revealed three MMR-associated signatures, one of which closely resembles the C. elegans MMR spectrum and strongly discriminates microsatellite stable and unstable tumors (AUC = 98%). A characteristic difference between human and C. elegans MMR deficiency is the lack of elevated levels of NCG > NTG mutations in C. elegans, likely caused by the absence of cytosine (CpG) methylation in worms. The other two human MMR signatures may reflect the interaction between MMR deficiency and other mutagenic processes, but their exact cause remains unknown. In summary, combining information from genetically defined models and cancer samples allows for better aligning mutational signatures to causal mutagenic processes.

The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors.

Within the genomes of metazoans, nucleosomes are highly organised adjacent to the binding sites for a subset of transcription factors. Here we have sought to investigate which chromatin remodelling enzymes are responsible for this. We find that the ATP-dependent chromatin remodelling enzyme SNF2H plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding. At many other factor binding sites SNF2H and the related enzyme SNF2L contribute to nucleosome organisation. The action of SNF2H at CTCF sites is functionally important as depletion of CTCF or SNF2H affects transcription of a common group of genes. This suggests that chromatin remodelling ATPase's most closely related to the Drosophila ISWI protein contribute to the function of many human gene regulatory elements.

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

RNA-seq is now the technology of choice for genome-wide differential gene expression experiments, but it is not clear how many biological replicates are needed to ensure valid biological interpretation of the results or which statistical tools are best for analyzing the data. An RNA-seq experiment with 48 biological replicates in each of two conditions was performed to answer these questions and provide guidelines for experimental design. With three biological replicates, nine of the 11 tools evaluated found only 20%-40% of the significantly differentially expressed (SDE) genes identified with the full set of 42 clean replicates. This rises to >85% for the subset of SDE genes changing in expression by more than fourfold. To achieve >85% for all SDE genes regardless of fold change requires more than 20 biological replicates. The same nine tools successfully control their false discovery rate at ≲5% for all numbers of replicates, while the remaining two tools fail to control their FDR adequately, particularly for low numbers of replicates. For future RNA-seq experiments, these results suggest that at least six biological replicates should be used, rising to at least 12 when it is important to identify SDE genes for all fold changes. If fewer than 12 replicates are used, a superior combination of true positive and false positive performances makes edgeR and DESeq2 the leading tools. For higher replicate numbers, minimizing false positives is more important and DESeq marginally outperforms the other tools.

Examining the role of individual movement in promoting coexistence in a spatially explicit prisoner's dilemma.

The emergence of cooperation is a major conundrum of evolutionary biology. To unravel this evolutionary riddle, several models have been developed within the theoretical framework of spatial game theory, focussing on the interactions between two general classes of player, "cooperators" and "defectors". Generally, explicit movement in the spatial domain is not considered in these models, with strategies moving via imitation or through colonisation of neighbouring sites. We present here a spatially explicit stochastic individual-based model in which pure cooperators and defectors undergo random motion via diffusion and also chemotaxis guided by the gradient of a semiochemical. Individual movement rules are derived from an underlying system of reaction-diffusion-taxis partial differential equations which describes the dynamics of the local number of individuals and the concentration of the semiochemical. Local interactions are governed by the payoff matrix of the classical prisoner's dilemma, and accumulated payoffs are translated into offspring. We investigate the cases of both synchronous and non-synchronous generations. Focussing on an ecological scenario where defectors are parasitic on cooperators, we find that random motion and semiochemical sensing bring about self-generated patterns in which resident cooperators and parasitic defectors can coexist in proportions that fluctuate about non-zero values. Remarkably, coexistence emerges as a genuine consequence of the natural tendency of cooperators to aggregate into clusters, without the need for them to find physical shelter or outrun the parasitic defectors. This provides further evidence that spatial clustering enhances the benefits of mutual cooperation and plays a crucial role in preserving cooperative behaviours.

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment.

MOTIVATION: High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read-count variability. These estimates are typically based on statistical models such as the negative binomial distribution, which is employed by the tools edgeR, DESeq and cuffdiff. Until now, the validity of these models has usually been tested on either low-replicate RNA-seq data or simulations. RESULTS: A 48-replicate RNA-seq experiment in yeast was performed and data tested against theoretical models. The observed gene read counts were consistent with both log-normal and negative binomial distributions, while the mean-variance relation followed the line of constant dispersion parameter of ∼0.01. The high-replicate data also allowed for strict quality control and screening of 'bad' replicates, which can drastically affect the gene read-count distribution. AVAILABILITY AND IMPLEMENTATION: RNA-seq data have been submitted to ENA archive with project ID PRJEB5348. CONTACT: g.j.barton@dundee.ac.uk.

What's in a name? Word inflation, punctuation, abbreviation and cloud formation.

The title of a journal paper offers a crucial portal into any scientific field. It determines whether interested readers locate the paper and whether others have enough interest sparked to lead them to read the abstract. This article looks at authored journal paper titles in Medical Education over its first 50 years (n = 6357) of publication and Medical Teacher over its first 35 years of publication, revealing both trends in areas of interest and how those interests are worded. Word clouds per decade showed a shift from teaching to learning and from examination to assessment, and new foci on learning, patients, research and feedback in both journals. The average length of title in Medical Education peeked in the 2000s, dropping to 70 characters in the 2010s, with no titles being longer than 140 characters (the length of a tweet) in this last decade. Abbreviations were used sparingly. The use of humorous titles, although not common, has increased in recent years. The use of the colon showed a marked increase in the 1980s, dropping a little in the 2000s but resurging in the 2010s. Titles posed as a question increased steadily, appearing to plateau in the 2000s at 11%. The use of humour and questions suggests that the authors of these articles are submitting papers to be selected by the human rather than just the virtual eye. We also hypothesise that the use of humour may indicate a maturation of medical education as a subject.

Autocrine activation of MAPK signaling mediates intrinsic tolerance to androgen deprivation in LY6D prostate cancer cells.

The emergence of castration-resistant prostate cancer remains an area of unmet clinical need. We recently identified a subpopulation of normal prostate progenitor cells, characterized by an intrinsic resistance to androgen deprivation and expression of LY6D. We here demonstrate that conditional deletion of PTEN in the murine prostate epithelium causes an expansion of transformed LY6D+ progenitor cells without impairing stem cell properties. Transcriptomic analyses of LY6D+ luminal cells identified an autocrine positive feedback loop, based on the secretion of amphiregulin (AREG)-mediated activation of mitogen-activated protein kinase (MAPK) signaling, increasing cellular fitness and organoid formation. Pharmacological interference with this pathway overcomes the castration-resistant properties of LY6D+ cells with a suppression of organoid formation and loss of LY6D+ cells in vivo. Notably, LY6D+ tumor cells are enriched in high-grade and androgen-resistant prostate cancer, providing clinical evidence for their contribution to advanced disease. Our data indicate that early interference with MAPK inhibitors can prevent progression of castration-resistant prostate cancer.

Inequalities in incident and prevalent multimorbidity in England, 2004-19: a population-based, descriptive study.

BACKGROUND: The increasing burden of multimorbidity and its socioeconomic gradient poses unique challenges to the provision and structure of health care. We aimed to describe inequalities and trends over time in multimorbidity prevalence, incidence, and case fatality among adults of all ages in England using primary care electronic health records. METHODS: We used a random sample of 991 243 individuals from the Clinical Practice Research Datalink Aurum database registered at participating general practices within England between Jan 1, 2004, and Dec 31, 2019, linked to the 2015 English Index of Multiple Deprivation (IMD). We used the following two outcome measures: basic multimorbidity, comprising two or more chronic conditions; and complex multimorbidity, comprising at least three chronic conditions affecting at least three body systems. We calculated crude, age-standardised, and age-sex-standardised annual incidence, prevalence, and case fatality rates, along with median age of onset for both multimorbidity types. We calculated absolute and relative inequalities for each outcome. FINDINGS: In 2004, 30·8% of our study population had basic multimorbidity and 15·1% had complex multimorbidity. This increased to 52·8% and 32·7%, respectively, in 2019. Although the overall incidence of basic multimorbidity remained stable over the 16-year study period, the incidence among people of working age and the incidence of complex multimorbidity increased gradually. Socioeconomic deprivation was associated with an increased incidence of both multimorbidity types in working-age adults. The median age at onset of complex multimorbidity was 7 years younger for the most deprived quintile of the IMD compared with the least deprived quintile. INTERPRETATION: The burden of multimorbidity in England has increased substantially over the past 16 years with persistent inequalities, which are worse in working-age adults and for complex multimorbidity. Prevention efforts to reduce the onset and slow the progression of multimorbidity are essential to reduce the increasing impact on patients and health systems alike. FUNDING: University of Liverpool and UK National Institute for Health Research School for Public Health Research.

Modelling contact spread of infection in host-parasitoid systems: vertical transmission of pathogens can cause chaos.

All animals and plants are, to some extent, susceptible to disease caused by varying combinations of parasites, viruses and bacteria. In this paper, we develop a mathematical model of contact spread infection to investigate the effect of introducing a parasitoid-vectored infection into a one-host-two-parasitoid competition model. We use a system of ordinary differential equations to investigate the separate influences of horizontal and vertical pathogen transmission on a model system appropriate for a variety of competitive situations. Computational simulations and steady-state analysis show that the transient and long-term dynamics exhibited under contact spread infection are highly complex. Horizontal pathogen transmission has a stabilising effect on the system whilst vertical transmission can destabilise it to the point of chaotic fluctuations in population levels. This has implications when considering the introduction of host pathogens for the control of insect vectored diseases such as bovine tuberculosis or yellow fever.

Profiling of Circulating Free DNA Using Targeted and Genome-wide Sequencing in Patients with SCLC.

INTRODUCTION: SCLC accounts for approximately 250,000 deaths worldwide each year. Acquisition of adequate tumor biopsy samples is challenging, and liquid biopsies present an alternative option for patient stratification and response monitoring. METHODS: We applied whole genome next-generation sequencing to circulating free DNA (cfDNA) from 39 patients with limited-stage (LS) SCLC and 30 patients with extensive-stage SCLC to establish genome-wide copy number aberrations and also performed targeted mutation analysis of 110 SCLC associated genes. Quantitative metrics were calculated for copy number aberrations, including percent genome amplified (PGA [the percentage of genomic regions amplified]), Z-score (a measure of standard deviation), and Moran's I (a measure of spatial autocorrelation). In addition CellSearch, an epitope-dependent enrichment platform, was used to enumerate circulating tumor cells (CTCs) from a parallel blood sample. RESULTS: Genome-wide and targeted cfDNA sequencing data identified tumor-related changes in 94% of patients with LS SCLC and 100% of patients with extensive-stage SCLC. Parallel analysis of CTCs based on at least 1 CTC/7.5 mL of blood increased tumor detection frequencies to 95% for LS SCLC. Both CTC counts and cfDNA readouts correlated with disease stage and overall survival. CONCLUSIONS: We demonstrate that a simple cfDNA genome-wide copy number approach provides an effective means of monitoring patients through treatment and show that targeted cfDNA sequencing identifies potential therapeutic targets in more than 50% of patients. We are now incorporating this approach into additional studies and trials of targeted therapies.

Hypoxia induces rapid changes to histone methylation and reprograms chromatin.

Oxygen is essential for the life of most multicellular organisms. Cells possess enzymes called molecular dioxygenases that depend on oxygen for activity. A subclass of molecular dioxygenases is the histone demethylase enzymes, which are characterized by the presence of a Jumanji-C (JmjC) domain. Hypoxia can alter chromatin, but whether this is a direct effect on JmjC-histone demethylases or due to other mechanisms is unknown. Here, we report that hypoxia induces a rapid and hypoxia-inducible factor-independent induction of histone methylation in a range of human cultured cells. Genomic locations of histone-3 lysine-4 trimethylation (H3K4me3) and H3K36me3 after a brief exposure of cultured cells to hypoxia predict the cell's transcriptional response several hours later. We show that inactivation of one of the JmjC-containing enzymes, lysine demethylase 5A (KDM5A), mimics hypoxia-induced cellular responses. These results demonstrate that oxygen sensing by chromatin occurs via JmjC-histone demethylase inhibition.

Disease induced dynamics in host-parasitoid systems: chaos and coexistence.

All animals and plants are, to some extent, susceptible to disease caused by varying combinations of parasites, viruses and bacteria. In this paper, we present a mathematical model of interactions between a host, two parasitoids and a pathogen which shows that the presence of an infection can preserve and promote diversity in such multi-species systems. Initially, we use a system of ordinary differential equations to investigate interactions between two species of parasitoids, a host and a host infection. We show that the presence of all four species is necessary for the system as a whole to persist, and that in particular, the presence of the pathogen is necessary for the coexistence of the two parasitoid species. The inclusion of infection induces a wide range of dynamics, including chaos, and these dynamics are robust for a wide range of parameter values. We then extend the model to include spatial effects by introducing random motility (diffusion) of all three species and examine the subsequent spatio-temporal dynamics, including travelling waves and other more complicated heterogeneous behaviour. The computational simulation results of the model suggest that infection in the hosts can blunt the effects of competition between parasitoids, allowing the weaker competitor to survive. Regardless of the nature of the stability of the coexistent steady state of the system, there is an initial period of transient dynamics, the length of which can be extended by an appropriate choice of initial conditions. The existence of these transient dynamics suggests that systems subject to regular restoration to a starting state, such as agro-ecosystems, may be kept in a continual state of dynamic transience, and this has implications for the use of natural enemies to control insect pests, the preservation of biodiversity in farmland habitats and the more general dynamics of disease processes.

Proteotoxic stress reprograms the chromatin landscape of SUMO modification.

The small ubiquitin-like modifier 2 (SUMO-2) is required for survival when cells are exposed to treatments that induce proteotoxic stress by causing the accumulation of misfolded proteins. Exposure of cells to heat shock or other forms of proteotoxic stress induces the conjugation of SUMO-2 to proteins in the nucleus. We investigated the chromatin landscape of SUMO-2 modifications in response to heat stress. Through chromatin immunoprecipitation assays coupled to high-throughput DNA sequencing and mRNA sequencing, we showed that in response to heat shock, SUMO-2 accumulated at nucleosome-depleted, active DNA regulatory elements, which represented binding sites for large protein complexes and were predominantly associated with active genes. However, SUMO did not act as a direct transcriptional repressor or activator of these genes during heat shock. Instead, integration of our results with published proteomics data on heat shock-induced SUMO-2 substrates supports a model in which the conjugation of SUMO-2 to proteins acts as an acute stress response that is required for the stability of protein complexes involved in gene expression and posttranscriptional modification of mRNA. We showed that the conjugation of SUMO-2 to chromatin-associated proteins is an integral component of the proteotoxic stress response, and propose that SUMO-2 fulfills its essential role in cell survival by contributing to the maintenance of protein complex homeostasis.

A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization.

The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here, we show that the combined action of Isw1 and Chd1 nucleosome-spacing enzymes is required to maintain this organization. In the absence of these enzymes, regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome, and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicate that adenosine triphosphate-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome.

High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

Chemotaxis-induced spatio-temporal heterogeneity in multi-species host-parasitoid systems.

When searching for hosts, parasitoids are observed to aggregate in response to chemical signalling cues emitted by plants during host feeding. In this paper we model aggregative parasitoid behaviour in a multi-species host-parasitoid community using a system of reaction-diffusion-chemotaxis equations. The stability properties of the steady-states of the model system are studied using linear stability analysis which highlights the possibility of interesting dynamical behaviour when the chemotactic response is above a certain threshold. We observe quasi-chaotic dynamic heterogeneous spatio-temporal patterns, quasi-stationary heterogeneous patterns and a destabilisation of the steady-states of the system. The generation of heterogeneous spatio-temporal patterns and destabilisation of the steady state are due to parasitoid chemotactic response to hosts. The dynamical behaviour of our system has both mathematical and ecological implications and the concepts of chemotaxis-driven instability and coexistence and ecological change are discussed.