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Allen, R. J.

Publications and source records attributed to Allen, R. J..

At least 19 recordsLinked to original sources

ULK1 and ULK2 Restrain Skeletal Myofiber Growth by Balancing Protein Synthesis and Degradation

Background Skeletal muscle is vital for mobility and metabolic regulation, impacting independence and overall health. Increases in skeletal muscle mass and contractile function during development, and their maintenance during adulthood and aging, rely on an intricate coordination between protein synthesis and degradation processes that remains incompletely understood. Here, we investigated a potential role for the autophagy-initiating kinases ULK1 and ULK2 in broadly modulating protein metabolism in skeletal muscle. Methods Studies were conducted in young (4-6 wk-old) and adult (7-10 mo.-old) mice with skeletal muscle-specific knockout of Ulk1 and Ulk2 (i.e., Ulk1/2skmDKO) and wild-type littermates (WT). Short-term deficiency of these proteins was achieved via electroporation of plasmids (encoding specific microRNAs targeting Ulk1 and Ulk2) into muscles of 4 mo.-old wild-type mice. Protein metabolism was assessed via deuterium oxide (D2O) labeling, whereas anabolic signaling was investigated under insulin and leucine administration. Results Lifelong Ulk1/2 deficiency markedly impaired autophagy flux (i.e., LC3-II accumulated with colchicine treatment only in wild-type mice, P<0.001), compromised muscle quality, as evidenced by an increase in centrally nucleated fibers (from 0.1% to 4.5% in females, and from 0.8% to 22.7% in males (P<0.001), primarily involving MyHC type 2b fibers) and impaired force of dorsiflexors and plantar flexors in males (20%, P<0.01), and plantar flexors in females (24%, P<0.01). Despite these deficits, Ulk1/2 deficiency promoted robust muscle hypertrophy, evidenced by increased diameters of all major MyHC fiber types in the tibialis anterior and soleus muscles (i.e., by 10-15% in males, and 14-20% in females, P<0.05). Short-term deficiency (up to 4 weeks) of Ulk1/2 in adult skeletal muscle, however, led to myofiber hypertrophy (13%, P<0.05) without impairments in force or changes in central nucleation of fibers, pointing to an initial period of muscle quality preservation. Mechanistically, Ulk1/2 deficiency led to elevated myofibrillar protein synthesis (23% higher Ksyn, P<0.05) and decreased mitochondrial and sarcoplasmic protein degradation (16% and 14% lower Kdeg, P=0.09 and P<0.05, respectively). Further mechanistic studies revealed that hypertrophy was accompanied by enhanced mTORC1 activity independent of AKT in Ulk1/2-deficient muscle. Conclusions These results indicate that ULK1 and ULK2 jointly sustain autophagy and limit mTORC1-driven protein synthesis to govern skeletal muscle protein metabolism, with lifelong deficiency increasing muscle size at the expense of quality and function, while short-term deficiency permits hypertrophy without impairment. These findings identify ULK1/2 as a novel node coordinating protein turnover in skeletal muscle, warranting investigation as a therapeutic strategy for atrophy and weakness.

cell biology↗

Loss of PKN2 drives fibroblast reprogramming and extracellular matrix remodelling in pulmonary fibrosis

Introduction Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease characterised by aberrant fibroblast function, extracellular matrix (ECM) remodelling and defective tissue repair. Protein kinase N2 (PKN2) is associated with accelerated forced vital capacity decline in IPF, but its functional role in pulmonary fibrosis remains unknown. We hypothesised that PKN2 regulates fibroblast phenotype and tissue repair. Methods PKN2 expression was assessed in human lung tissue, induced sputum and primary airway and parenchymal fibroblasts from non-fibrotic controls and patients with interstitial lung disease (ILD). DNA methylation was profiled using the Illumina HumanMethylationEPIC array. PKN2 function was investigated by siRNA-mediated depletion in primary human lung fibroblasts using transcriptomic, proteomic and functional analyses. Tissue repair was assessed following pharmacological PKN inhibition in zebrafish. Results PKN2 expression was reduced in ILD lung tissue and primary airway and parenchymal fibroblasts and further suppressed by TGF-{beta}1. Differential methylation was identified across the PKN2 locus in both fibroblast populations. Integrated transcriptomic and proteomic profiling following PKN2 depletion revealed coordinated remodelling of ECM, cell adhesion, non-canonical WNT and VEGF pathways, including dysregulation of COL1A1, WNT, VEGF and MMP1. PKN2 loss increased VEGF and MMP-1 secretion and accelerated fibroblast wound closure. PKN inhibition altered epithelial organisation and collagen fibre alignment during zebrafish wound repair. Conclusion PKN2 loss drives fibroblast reprogramming and aberrant ECM remodelling, establishing PKN2 as an important regulator of pulmonary fibroblast homeostasis and tissue repair.

cell biology↗

Small shifts, big ripples: multi-omics studies reveal how ambient temperatures govern Chlamydomonas cellular responses

Photosynthetic protists, known as microalgae, face increasing temperatures due to climate change. The green biflagellate alga Chlamydomonas reinhardtii serves as a model for thermoregulation. While responses to thermal stress are well characterized, much less is known about the impact of ambient temperature shifts. Understanding microalgal responses to environmental temperature changes is critical, as these primary producers drive ecosystem productivity and food web dynamics. Here, C. reinhardtii grew mixotrophically at ambient temperatures from 18 {degrees}C to 33 {degrees}C. Transcriptomic profiling revealed extensive reorganization, with over 5,000 transcripts significantly affected, including those involved in algal-bacterial interactions, photoreception, lipid metabolism, photosynthesis, cilia formation, and the secretome. CO2 transfer rates and acetate levels measured at 18 {degrees}C and 28 {degrees}C suggest decreased photoautotrophic algal growth at 28 {degrees}C at first. Antagonistic bacterial activity was sustained longer at lower temperatures. Proteomic analyses of isolated cilia and secreted proteins corroborate major abundance changes within these sub-proteomes, particularly in ciliary intraflagellar transport complexes and mating-related proteins in the secretome. Together, these molecular alterations resulted in pronounced changes in growth, the lengths of cells and cilia swimming behavior, mating ability and bacterial antagonism. These data reveal major cellular responses caused by ambient, even short-term temperature shifts.

cell biology↗

Altered Relaxation and Mitochondria-Endoplasmic Reticulum Contact Sites Precede Major (Mal)adaptations in Aging Skeletal Muscle and are Prevented by Exercise

Sarcopenia, or age-related muscle dysfunction, contributes to morbidity and mortality. Besides decreases in muscle force, sarcopenia is associated with atrophy and fast-to-slow fiber type switching, which is typically secondary to denervation in humans and rodents. However, very little is known about cellular changes preceding these important (mal)adaptations. To this matter, mitochondria and the sarcoplasmic reticulum are critical for tension generation in myofibers. They physically interact at the boundaries of sarcomeres forming subcellular hubs called mitochondria-endo/sarcoplasmic reticulum contacts (MERCs). Yet, whether changes at MERCs ultrastructure and proteome occur early in aging is unknown. Here, studying young adult and older mice we reveal that aging slows muscle relaxation leading to longer excitation-contraction-relaxation (ECR) cycles before maximal force decreases and fast-to-slow fiber switching takes place. We reveal that muscle MERC ultrastructure and mitochondria-associated ER membrane (MAM) protein composition are also affected early in aging and are closely associated with rate of muscle relaxation. Additionally, we demonstrate that regular exercise preserves muscle relaxation rate and MERC ultrastructure in early aging. Finally, we profile a set of muscle MAM proteins involved in energy metabolism, protein quality control, Ca2+ homeostasis, cytoskeleton integrity and redox balance that are inversely regulated early in aging and by exercise. These may represent new targets to preserve muscle function in aging individuals.

physiology↗

Targeting of a STING Agonist to Perivascular Macrophages in Prostate Tumors Delays Resistance to Androgen Deprivation Therapy

BackgroundAndrogen deprivation therapy (ADT) is a frontline treatment for prostate cancer but often leads to the development of castration resistant prostate cancer (CRPC). This causes tumors to regrow and metastasize, despite ongoing treatment, and impacts negatively on patient survival. ADT is known to stimulate the accumulation of immunosuppressive cells like protumoral tumor-associated macrophages (TAMs), myeloid-derived suppressor cells and regulatory T cells in prostate tumors, as well as hypofunctional T cells. Protumoral TAMs have been shown to accumulate around tumor blood vessels during chemotherapy and radiotherapy, where they drive tumor relapse. Our aim was to see if such perivascular (PV) TAMs accumulated in ADT-treated prostate tumors prior to CRPC, and, if so, to selectively target these PV cells with a potent immunostimulant, interferon beta (IFN{beta}), an attempt to stimulate anti-tumor immunity and delay CRPC. MethodsWe first used quantitative, multiplex immunofluorescence to assess the effects of ADT on distribution and activation status of TAMs, CD4+ T cells, CD8+ T cells and NK cells in mouse and human prostate tumors. We then used antibody-coated, lipid nanoparticles to selectively target a STING agonist, 2'3'-cGAMP (cGAMP), to PV TAMs in mouse prostate tumors during ADT. ResultsTAMs accumulated at high density around blood vessels in ADT-treated primary mouse and human prostate tumors prior to CRPC, where they expressed markers of a protumoral phenotype, folate receptor beta (FR{beta}), MRC1 (CD206), SIGLEC1 (CD169) and VISTA. Additionally, higher numbers of inactive (PD-1-) CD8+ T cells and reduced numbers of active (CD69+) NK cells were also present in PV tumor areas after ADT. LNPs coated with antibody to FR{beta} selectively delivered cGAMP to PV TAMs in ADT-treated tumors where they activated STING and expression of IFN{beta} by these cells. This resulted in a marked increase in the density of active CD4+ T cells, CD8+T cells and NK cells in PV tumor areas, and significantly delayed in the onset of CRPC. ConclusionTogether, our data indicate that targeting a STING agonist to PV TAMs could be used to extend the treatment window for ADT in prostate cancer. KEY MESSAGESO_ST_ABSWhat is already known about the topicC_ST_ABSAndrogen deprivation therapy (ADT) is a frontline treatment for prostate cancer. However, tumors often develop resistance and start to regrow and metastasize - a condition called castration resistance prostate cancer (CRPC). Prostate cancer is considered to be an immunologically cold tumor type and while ADT stimulates tumor infiltration by cytotoxic (CD8+) T cells, they are largely hypofunctional, possibly due to the immunosuppressive tumor microenvironment. What this study addsThis study is the first to demonstrate that FR{beta}+ macrophages with a immunosuppressive phenotype accumulate around blood vessels in mouse and human prostate tumors during ADT, prior to the onset of CRPC. Lipid nanoparticles coated with an antibody to FR{beta}+ were then used to deliver a STING agonist selectively to these perivascular (PV) cells during ADT. This triggered STING signalling and the release of the potent immunostimulant, interferon beta, by PV macrophages, which then activated tumour-infiltrating CD4+ and CD8+ T cells, and delayed the onset of CRPC. How this study might affect research, practice or policyThe delivery of an immunostimulant specifically to PV regions of tumors represents a new, more targeted form of immunotherapy that ensures the activation of T cells as soon as they cross the vasculature into tumors. This new approach could be used to extend the treatment window for neoadjuvant ADT in men with localised prostate tumors. In doing so, it would delay/circumvent the need for additional treatments like radiotherapy and/or or prostatectomy.

cancer biology↗

Spatial partitioning of a microbial population enhances collective enzymatic defence

Microbes often inhabit complex, spatially partitioned geometries such as host tissue or soil, but the effects of habitat fragmentation on microbial infection dynamics and ecology are poorly understood. Here we investigate how habitat fragmentation impacts a prevalent microbial collective defence mechanism: enzymatic degradation of an environmental toxin. Using a theoretical model, we predict that habitat fragmentation can strongly enhance the collective benefits of enzymatic toxin degradation. For the clinically relevant case where {beta}-lactamase producing bacteria mount a collective defence by degrading a {beta}-lactam antibiotic, we find that realistic levels of habitat fragmentation can allow a population to survive antibiotic doses that would far exceed those required to kill a non-fragmented population. This "habitat-fragmentation rescue" is a stochastic effect that originates from variation in bacterial density among different subpopulations and demographic noise. In contrast, the stochastic effects of habitat fragmentation are weaker in a model of collective enzymatic nutrient foraging. Our model suggests that treatment of a spatially complex, fragmented infection showing collective resistance may be far less effective than expected based on bulk population assumptions. This may help to explain lack of correlation between lab-measured antibiotic susceptibility values and clinical treatment success.

biophysics↗

Bacterial aggregation triggered by low-level antibiotic-mediated lysis

Suspended bacterial aggregates play a central role in ocean biogeochemistry, industrial processes and probably many clinical infections - yet the factors that trigger aggregation remain poorly understood, as does the relationship between suspended aggregates and surface-attached biofilms. Here we show that very low doses of cell-wall targeting antibiotic, far below the minimal inhibitory concentration, can trigger aggregation of Escherichia coli cells. This occurs when a few cells lyse, releasing extracellular DNA - thus, cell-to-cell variability in antibiotic response leads to population-level aggregation. Although lysis-triggered aggregation echoes known trigger mechanisms for surface-attached biofilms, these aggregates appear to be of a distinct type, since they do not show typical biofilm characteristics such as protection from antibiotics, or increased biofilm-forming potential. Our work contributes to understanding the nature of bacterial aggregates and the factors that trigger their formation, and the consequences of widespread low-dose antibiotic exposure in the environment and in the body.

microbiology↗

Urine production rate is critical in a model for catheter-associated urinary tract infection

Urinary catheters are used extensively in hospitals and long-term care and they are highly prone to infection. Understanding the pathways by which bacteria colonise a urinary catheter could guide strategies to mitigate infection, but quantitative models for this colonisation process are lacking. Here we present a mathematical model for bacterial colonisation of a urinary catheter, that integrates population dynamics and fluid dynamics. The model describes bacteria migrating up the outside surface of the catheter, spreading into the bladder and being swept through the catheter lumen. Computer simulations of the model reveal that clinical outcomes for long-term versus short-term catheterisation are controlled by different factors: the rate of urine production by the kidneys as opposed to urethral length, catheter surface properties and bacterial motility. Our work may help explain variable susceptibility to catheter-associated urinary tract infection (CAUTI) among individuals, and the mixed success of antimicrobial surface coatings. Our model suggests that for long-term catheterised patients, increasing fluid intake or reducing residual urine volume in the bladder may help prevent infection, while antimicrobial surface coatings are predicted to be effective only for short-term catheterised patients. Therefore, different catheter management strategies could be rationally targeted to long-term vs short-term catheterised patients.

biophysics↗

Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures

Pseudomonas aeruginosa forms suspended multicellular aggregates when cultured in liquid media. Such aggregates may be important in disease, and/or as a pathway to biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have both been implicated in aggregation, but previous results depend strongly on the experimental conditions. Here we develop a quantitative microscopy-based method for assessing changes in the size distribution of suspended aggregates over time in growing cultures. For exponentially growing cultures of P. aeruginosa PAO1, we find that aggregation is mediated by cell-associated Psl, rather than by either eDNA or se-creted Psl. These aggregates arise de novo within the culture via a growth process that involves both collisions and clonal growth. They are "non-cheatable" since Psl non-producing cells do not aggregate with producers. In contrast, we find that stationary phase (overnight) cultures contain a different type of multicelullar aggregate, in which both eDNA and Psl mediate cohesion. Our findings suggest that the physical and bi-ological properties of multicellular aggregates may be very different in early-stage vs late-stage bacterial cultures.

microbiology↗

A model for quorum-sensing mediated stochastic biofilm nucleation

Surface-attached bacterial biofilms cause disease and industrial biofouling, as well as being widespread in the natural environment. Density-dependent quorum sensing is one of the mechanisms implicated in biofilm initiation. Here we present and analyse a model for quorum-sensing triggered biofilm initiation. In our model, individual, planktonic bacteria adhere to a surface, pro-liferate and undergo a collective transition to a biofilm phenotype. This model predicts a stochastic transition between a loosely attached, finite, layer of bacteria near the surface, and a growing biofilm. The transition is governed by two key parameters: the collective transition density relative to the carrying capacity, and the immigration rate relative to the detachment rate. Biofilm initiation is complex, but our model suggests that stochastic nucleation phenomena may be relevant.

biophysics↗

Pinning transition in biofilm structure driven by active layer dynamics

Surface-attached communities of microbes, known as biofilms, are diverse in their morphologies. Characterising distinct types of biofilm spatial structure, and understanding how they emerge, can shed light on the fundamental biological and biophysical mechanisms involved, and can improve our understanding of evolution in biofilms. Here, we perform long-time individual-based simulations of growing biofilms. We observe distinct types of biofilm spatial structure depending on the parameters, and we classify these into three phases according to the behaviour of the active layer of growing cells at the biofilm interface. In the unpinned phase, the biofilm is smooth and the active layer is unbroken with no gaps. In the transiently pinned phase, short-lived gaps in the active layer arise, which can cause local parts of the biofilm interface to pin, or become stationary relative to the moving front. In the pinned phase these pinning sites persist, leading to fingering of the biofilm interface. We show that pinning arises due to the dynamical behaviour of active layer gaps, and observe that the relative magnitudes of the active layer thickness and the active layer fluctuations are important in this process. We demonstrate a direct connection between biofilm pinning and interface roughness, and we show that the pinning phase transition is well described by a control parameter that combines the average and standard deviation of the active layer thickness. Taken together, our work suggests a role for active layer dynamics in controlling pinning of the biofilm interface and hence biofilm morphology.

biophysics↗

Stability of β-lactam antibiotics in bacterial growth media

Laboratory assays such as MIC tests assume that antibiotic molecules are stable in the chosen growth medium - but rapid degradation has been observed for antibiotics including {beta}-lactams under some conditions in aqueous solution. Degradation rates in bacterial growth medium are less well known. Here, we develop a delay time bioassay that provides a simple way to estimate antibiotic stability in bacterial growth media. We use the bioassay to measure degradation half-lives of the {beta}-lactam antibiotics mecillinam, aztreonam and cefotaxime in widely-used bacterial growth media based on MOPS and Luria-Bertani (LB) broth. We find that mecillinam degradation can occur rapidly, with a half-life as short as 2 hours in MOPS medium at 37{degrees}C and pH 7.4, and 4-5 hours in LB, but that adjusting the pH and temperature can increase its stability to a half-life around 6 hours without excessively perturbing growth. Aztreonam and cefotaxime were found to have half-lives longer than 6 hours in MOPS medium at 37{degrees}C and pH 7.4, but still shorter than the timescale of a typical minimum inhibitory concentration (MIC) assay. Taken together, our results suggest that care is needed in interpreting MIC tests and other laboratory growth assays for {beta}-lactam antibiotics, since there may be significant degradation of the antibiotic during the assay.

pharmacology and toxicology↗

Predictable Properties of Fitness Landscapes Induced by Adaptational Tradeoffs

Fitness effects of mutations depend on environmental parameters. For example, mutations that increase fitness of bacteria at high antibiotic concentration often decrease fitness in the absence of antibiotic, exemplifying a tradeoff between adaptation to environmental extremes. We develop a mathematical model for fitness landscapes generated by such tradeoffs, based on experiments that determine the antibiotic dose-response curves of Escherichia coli strains, and previous observations on antibiotic resistance mutations. Our model generates a succession of landscapes with predictable properties as antibiotic concentration is varied. The landscape is nearly smooth at low and high concentrations, but the tradeoff induces a high ruggedness at intermediate antibiotic concentrations. Despite this high ruggedness, however, all the fitness maxima in the landscapes are evolutionarily accessible from the wild type. This implies that selection for antibiotic resistance in multiple mutational steps is relatively facile despite the complexity of the underlying landscape.

evolutionary biology↗

Phenotypic delay: mechanistic models and their implications for the evolution of resistance to antibiotics

Phenotypic delay - the time delay between genetic mutation and expression of the corresponding phenotype - is generally neglected in evolutionary models, yet recent work suggests that it may be more common than previously assumed. Here, we use computer simulations and theory to investigate the significance of phenotypic delay for the evolution of bacterial resistance to antibiotics. We consider three mechanisms which could potentially cause phenotypic delay: effective polyploidy, dilution of antibiotic-sensitive molecules and accumulation of resistance-enhancing molecules. We find that the accumulation of resistant molecules is relevant only within a narrow parameter range, but both the dilution of sensitive molecules and effective polyploidy can cause phenotypic delay over a wide range of parameters. We further investigate whether these mechanisms could affect population survival under drug treatment and thereby explain observed discrepancies in mutation rates estimated by Luria-Delbruck fluctuation tests. While the effective polyploidy mechanism does not affect population survival, the dilution of sensitive molecules leads both to decreased probability of survival under drug treatment and underestimation of mutation rates in fluctuation tests. The dilution mechanism also changes the shape of the Luria-Delbruck distribution of mutant numbers, and we show that this modified distribution provides an improved fit to previously published experimental data. Author SummaryUnderstanding precisely how some bacteria survive exposure to antibiotics is a major research focus. Specific mutations in the bacterial genome are known to provide protection. However, it remains unclear how much time passes between a bacterium acquiring the genetic change and being able to tolerate antibiotics - termed the phenotypic delay - and what controls this delay. Here, using computer simulations and mathematical arguments we discuss three biologically plausible mechanisms of phenotypic delay. We investigate how each mechanism would affect the outcome of laboratory experiments often used to study the evolution of antibiotic resistance, and we highlight how the delay might be detected in such experiments. We also show that the existence of the delay could explain an observed discrepancy in the measurement of mutation rates, and demonstrate that one of our models provides a superior fit to experimental data. Our work exposes how molecular details at the intracellular level can have a direct effect on evolution at the population level.

evolutionary biology↗

A roadblock-and-kill model explains the action of the DNA-targeting antibiotic ciprofloxacin

Fluoroquinolones - antibiotics that cause DNA damage by inhibiting DNA topoisomerases - are clinically important, but their mechanism of action is not yet fully understood. In particular, the dynamical response of bacterial cells to fluoroquinolone exposure has hardly been investigated, although the SOS response, triggered by DNA damage, is often thought to play a key role. Here we investigate growth inhibition of the bacterium Escherichia coli by the fluoroquinolone ciprofloxacin at low doses (up to 5x the minimum inhibitory concentration). We measure the long-term and short-term (dynamic) response of the growth rate and DNA production rate to ciprofloxacin, at both population- and single-cell level. We show that despite the molecular complexity of DNA metabolism, a simple `roadblock-and-kill model focusing on replication fork blockage and DNA damage by ciprofloxacin-poisoned DNA topoisomerase II (gyrase) quantitatively reproduces long-term growth rates. The model also predicts dynamical changes in DNA production rate in wild type E. coli and in an SOS-deficient mutant, following a step-up of ciprofloxacin. Our work reveals new insights into the dynamics of fluoroquinolone action, with important implications for predicting the rate of resistance evolution. Most importantly, our model explains why the response is delayed: it takes many doubling times to fragment the DNA sufficiently to inhibit gene expression. Our model also challenges the view that the SOS response plays a central role: the dynamical response is controlled by the timescale of DNA replication and gyrase binding/unbinding to the DNA rather than by the SOS response. More generally, our work highlights the importance of including biophysical processes in biochemical-systems models to fully understand bacterial response to antibiotics.

systems biology↗

Genome-wide association study of susceptibility to idiopathic pulmonary fibrosis

RationaleIdiopathic pulmonary fibrosis (IPF) is a complex lung disease characterised by scarring of the lung that is believed to result from an atypical response to injury of the epithelium. The mechanisms by which this arises are poorly understood and it is likely that multiple pathways are involved. The strongest genetic association with IPF is a variant in the promoter of MUC5B where each copy of the risk allele confers a five-fold risk of disease. However, genome-wide association studies have reported additional signals of association implicating multiple pathways including host defence, telomere maintenance, signalling and cell-cell adhesion.\n\nObjectivesTo improve our understanding of mechanisms that increase IPF susceptibility by identifying previously unreported genetic associations.\n\nMethods and measurementsWe performed the largest genome-wide association study undertaken for IPF susceptibility with a discovery stage comprising up to 2,668 IPF cases and 8,591 controls with replication in an additional 1,467 IPF cases and 11,874 controls. Polygenic risk scores were used to assess the collective effect of variants not reported as associated with IPF.\n\nMain resultsWe identified and replicated three new genome-wide significant (P<5x10-8) signals of association with IPF susceptibility (near KIF15, MAD1L1 and DEPTOR) and confirm associations at 11 previously reported loci. Polygenic risk score analyses showed that the combined effect of many thousands of as-yet unreported IPF risk variants contribute to IPF susceptibility.\n\nConclusionsNovel association signals support the importance of mTOR signalling in lung fibrosis and suggest a possible role of mitotic spindle-assembly genes in IPF susceptibility.

genomics↗

Adjustment for index event bias in genome-wide association studies of subsequent events

Following numerous genome-wide association studies of disease susceptibility, there is increasing interest in genetic associations with disease prognosis, survival or other subsequent events. Such associations are vulnerable to index event bias, by which selection of subjects according to their disease status creates biased associations if common causes of incidence and prognosis are not accounted for. We propose a novel adjustment for index event bias using the residuals from the regression of genetic effects on prognosis on genetic effects on incidence. Our approach eliminates this bias when direct genetic effects on incidence and prognosis are independent, and otherwise reduces bias in realistic situations. In a study of idiopathic pulmonary fibrosis, we resolved a paradoxical association of the strong susceptibility gene MUC5B with increased survival, identifying instead a significant association with decreased survival. In re-analysis of a study of Crohns disease prognosis, four regions remained associated at genome-wide significance albeit with increased P-values.

epidemiology↗

New genetic signals for lung function highlight pathways and pleiotropy, and chronic obstructive pulmonary disease associations across multiple ancestries

Reduced lung function predicts mortality and is key to the diagnosis of COPD. In a genome-wide association study in 400,102 individuals of European ancestry, we define 279 lung function signals, one-half of which are new. In combination these variants strongly predict COPD in deeply-phenotyped patient populations. Furthermore, the combined effect of these variants showed generalisability across smokers and never-smokers, and across ancestral groups. We highlight biological pathways, known and potential drug targets for COPD and, in phenome-wide association studies, autoimmune-related and other pleiotropic effects of lung function associated variants. This new genetic evidence has potential to improve future preventive and therapeutic strategies for COPD.

genomics↗