Biology subjects

Hart, A.

Publications and source records attributed to Hart, A..

18 recordsLinked to original sources

bioRxiv2026

Investigating biotic, chemical, and physical drivers of periphyton and invertebrate biomass in boreal streams supporting juvenile Atlantic salmon

1. Atlantic salmon (Salmo salar) are an anadromous fish with a broad distribution from eastern North America to western Europe, with ecological, economic, and cultural significance. Despite their expansive range, wild populations across the North Atlantic have experienced decline. Survival to reproductive age is a management concern, with a focus on identifying factors affecting the juvenile freshwater life stage. Specifically, research is needed to identify potential bottlenecks limiting freshwater productivity. 2. We addressed this research gap with a case study on the Exploits River, Newfoundland - a watershed that receives one of the largest anadromous Atlantic salmon returns in North America. We aimed to identify biotic, chemical, and physical predictors of food resources for juvenile salmon (i.e., invertebrates) and food resources for invertebrates (i.e., periphyton). To test our hypotheses, we collected data on a suite of biotic (e.g., invertebrates and periphyton), chemical (e.g., total dissolved N), and physical (e.g., wetted width) variables at 42 sites within and around this watershed. 3. We observed evidence for relationships between invertebrate biomass and biotic and temporal variables. Specifically, invertebrate biomass was higher at sites with high periphyton biomass that were sampled later in the season. In addition, we observed that periphyton biomass was related to biotic, chemical, and physical variables. Here, we present evidence for bottom-up control, with increased periphyton biomass supporting increased invertebrate biomass. 4. We expect knock-on effects where increased invertebrate biomass results in increased juvenile Atlantic salmon biomass. Our large sample size revealed some predictors of invertebrate biomass and periphyton biomass. However, we found no evidence of correlation between invertebrate biomass and chemical or physical variables. The low productivity of our maritime boreal forest system could be an outlier in expected biotic, chemical, and physical relationships in streams. 5. Our findings provide an important step forward in furthering boreal stream ecology, producing novel invertebrate and periphyton knowledge for watershed managers.

ecology↗

bioRxiv2026

Trichomonas vaginalis targets Lactobacillus jensenii via pseudopodia-independent phagocytosis and secreted lysozyme TvGH25

A low abundance or absence of protective lactobacilli during acute trichomoniasis is a well-known phenomenon that is associated with T. vaginalis (TV) infection. However, a crucial question that remains unanswered is whether alterations in the lactobacilli population precede TV infection or whether the parasite plays an active role in lactobacilli disappearance. Our findings showed that TV efficiently phagocytosed one of the dominant Lactobacillus species L. jensenii (LJ). Phagocytosis proceeds via a pseudopodia-independent mechanism reminiscent of sinking with a preference for viable cells. The presence of viable LJ leads to an increase in secretion of 27 TV proteins, including TvGH25 lysozyme. This enzyme cleaves peptidoglycan, a major component of the bacterial cell wall. TV overexpressing TvGH25 effectively lowers the bacterial cell count, evidencing the enzymes antimicrobial potential. These data support the notion that TV cells can suppress the Lactobacillus population through a combination of targeted secretory response and phagocytic activity, revealing novel potential targets for developing alternative therapeutic strategies against trichomoniasis. Significance StatementTrichomonas vaginalis (TV) is a sexually transmitted parasite that causes trichomoniasis and is connected to the disruption of the healthy vaginal microbiome, dominated by Lactobacillus species. However, the nature of the interactions between TV and Lactobacillus is poorly understood. In this study, we show that TV uses an unusual form of pseudopodia-independent phagocytosis to engulf L. jensenii alongside a targeted secretory response to the bacterial encounter, involving TvGH25 lysozyme. We found that TV acquired this enzyme by lateral gene transfer from bacteria and repurposed it against bacteria to degrade the major bacterial cell wall component peptidoglycan. TvGH25 thus represents an effective component of TVs antibacterial arsenal. Our findings provide new insights into the mechanistic disruption of the protective Lactobacillus microbiota.

microbiology↗

bioRxiv2026

Network topology dictates sequential drug efficacy through bistability-mediated state switching

Sequential drug combinations can significantly enhance therapeutic efficacy, yet the general principles governing when and why sequential administration outperforms concurrent treatment remain poorly understood. While empirical evidence demonstrates that the order and timing of drug exposure can be critical, a mechanistic framework to predict which regulatory architectures are primed for sequential benefit is currently lacking. Here, we systematically enumerated and dynamically analysed 59,040 four-node network topologies to identify the structural design principles that dictate sequential efficacy. Our analysis reveals that only a small fraction of network architectures robustly confer a sequential advantage and identifies a minimal structural requirement for this benefit: a positive feedback loop between the primary drug target and its downstream oncogenic output, coupled with antagonistic crosstalk from a secondary drug target. We demonstrate that this architecture enables bistability, allowing the first drug to reconfigure the network into a suppressed attractor state that is inaccessible through concurrent administration. The treatment schedule determines which of two coexisting stable states the system ultimately occupies, with the gap time between doses defining a critical therapeutic window. Only when the first drug is given sufficient time to displace the system past a threshold does the sequential regimen achieve superior suppression. Our findings establish bistability-enabling network motifs as predictive determinants of sequential drug efficacy and provide a topology-based framework for the rational design of time-dependent combination therapies.

systems biology↗

bioRxiv2026

The role of integrins in T cell-mediated resistance to Cryptosporidium parvum

Cryptosporidium is a protozoan that infects epithelial cells of the small intestine and is a cause of diarrhea and death in immunocompromised individuals and malnourished children. Immunity to this parasite is mediated by an intestinal T cell response, which is generated in gut-associated lymphoid tissues and dependent on type 1 conventional dendritic cells (cDC1s). The initial priming of T cells is accompanied by changes in integrin expression and subsequent trafficking to the site of infection. The role of specific integrins in trafficking to the ileum during cryptosporidiosis is largely unknown. The development of a transgenic Cryptosporidium strain that expresses MHCI and MHCII-restricted model antigens provides the ability to track T cell responses to this parasite. Our studies in this system revealed marked changes in the integrin profile of parasite-specific T cells as they are activated and traffic to the gut, and demonstrate that cDC1s contribute to the expression of the integrins 4, {beta}7, {beta}1, and L. Surprisingly, blockade of the canonical gut-homing integrin 4{beta}7 does not impact the ability of parasite-specific T cells to access the gut. However, blockade of integrin L decreases the parasite-specific T cell frequency at the site of infection and delays control of parasite burden. These datasets highlight an 4{beta}7-independent mechanism of T cell trafficking to the small intestine and indicate that L is an integrin required for T cell-mediated resistance to Cryptosporidium.

immunology↗

bioRxiv2026

Two axolotl-adapted cell-ablation platforms reveal macrophage-dependent processes essential for spinal-cord and skeletal regeneration

The axolotl (Ambystoma mexicanum) has emerged as the premier model organism for studying scarless repair and adult tissue regeneration, supported by an expanding collection of tissue-specific transgenic lines and translucent skin that enables high-quality live imaging and cell tracking. However, functional characterization of specific cell types during regeneration has been limited by the absence of validated cell-specific ablation systems. Here, we developed and rigorously compared two independent inducible genetic cell-ablation platforms -- bacterial nitroreductase (NTR 2.0) and mammalian inducible caspase-9 (iCasp9), across developmental stages, animal sizes, and administration routes using various transgenic lines and grafting approaches. The NTR 2.0 platform showed limited applicability due to drug toxicity and solubility constraints, restricting its use primarily to larval stages via immersion. In contrast, the iCasp9 system demonstrated superior efficacy across all life stages, including large adults, with multiple viable administration routes. We further validated these platforms by systematically ablating CD68+ macrophages and examined functional consequences during tail regeneration. Sustained depletion revealed essential macrophage-dependent processes despite continuous macrophage repopulation from hematopoietic reservoirs: skeletal-element regeneration was completely abolished, spinal-cord axons degenerated without recovery, and neural crest-derived cells exhibited severe disorganization. These findings establish macrophages as critical orchestrators of central and peripheral nervous-system regeneration and skeletogenesis in axolotls, while providing validated tools for cell-type-specific functional studies across the axolotl lifespan.

developmental biology↗

bioRxiv2025

Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial-immune cell interactions

The distal small intestine plays vital roles in host physiology by regulating nutrient and fluid homeostasis. Despite being impacted in Crohns disease and a major target for a range of infections, we know relatively little about the complexity of cellular responses and cell-cell communication in the ileum during infection. Single cell and spatial transcriptomics have emerged as powerful technologies to study tissue heterogeneity in the gut, but these tools have focused on the large intestine, in part due to the accessibility of this tissue for biopsies and its importance in cancer. Here we present GutPath, an atlas of over 500,000 single cells with RNA and protein expression profiles for 91 cell states in the ileum across diverse infectious archetypes. We show that GutPath accurately captures established immune responses to infection while revealing pathogen-specific responses in enterocytes. To highlight the discovery potential of this atlas, we identify a novel enterocyte cell state present during Yersinia pseudotuberculosis infection that is spatially linked to bacterial load and tissue pathology. GutPath establishes a much-needed resource for the immunology community that will accelerate the study of the transcriptional diversity of cellular landscapes in the small intestine.

immunology↗

bioRxiv2025

Threatened bat species reduce their activity in presence of traffic noise playback, and may shout louder

Anthropogenic sound is a prevalent pollutant with broad effects on wildlife. As human populations grow, exposure of natural environments to anthropogenic noise will increase. Automobile traffic is a notably pervasive source of noise pollution; transportation networks often cross otherwise relatively undisturbed habitats and the sound they produce is typically chronic and of high intensity. How this noise interferes with the production and reception of animal acoustic signals for communication and navigation remains largely unknown. In particular, bats (order Chiroptera) have received limited attention in anthropogenic noise studies, despite being the second most diverse mammalian group and relying strongly on acoustic signals. We used a phantom road paradigm to experimentally isolate and assess the effect of traffic sound playback on the behaviour of the two extant bat species in Aotearoa New Zealand. To begin to understand how bats might behaviourally respond to a noisy environment, we also investigated whether bats call sequence and structure differed with and without sound playback. We found an approximate 50% reduction in the mean number of sequences per night of both bat species during sound playback, suggesting bats avoid noisy areas. We also found that calls from the bats that were present were emitted at higher frequencies and increased intensities (loudness) during playback. As avoidance of areas reduces the amount of quality habitat accessible and call modulation can impose metabolic costs, chronic noise may impose fitness costs on declining populations of native bats. With increasing areas of natural habitat exposed to anthropogenic noise, untangling the effects of high sound levels is crucial for conservation of bats and the ecosystem services they provide.

ecology↗

bioRxiv2025

WEE1 inhibitors synergise with mRNA translation defects via activation of the kinase GCN2

Inhibitors of the protein kinase WEE1 have emerged as promising agents for cancer therapy. In this study, we uncover synergistic interactions between WEE1 small- molecule inhibitors and defects in mRNA translation, mediated by activation of the integrated stress response (ISR) through the kinase GCN2. Using a pooled CRISPRi screen, we identify GSPT1 and ALKBH8 as factors whose depletion confer hypersensitivity to the WEE1 inhibitor, AZD1775. We demonstrate that this synergy depends on ISR activation, which is induced by the off-target activity of WEE1 inhibitors. Furthermore, PROTAC-based WEE1 inhibitors and molecular glues show reduced or no ISR activation, suggesting potential strategies to minimise off-target toxicity. Our findings reveal that certain WEE1 inhibitors elicit dual toxicity via ISR activation and genotoxic stress, with ISR activation being independent of WEE1 itself or cell-cycle status. This dual mechanism highlights opportunities for combination therapies, such as pairing WEE1 inhibitors with agents targeting the mRNA translation machinery. This study also underscores the need for more precise WEE1 targeting strategies to mitigate off-target effects, with implications for optimising the therapeutic potential of WEE1 inhibitors.

cancer biology↗

bioRxiv2024

Pharming: Joint Clonal Tree Reconstruction of SNV and CNAEvolution from Single-cell DNA Sequencing of Tumors

Cancer arises through an evolutionary process in which somatic mutations, including single nucleotide variants (SNVs) and copy number aberrations (CNAs), drive the development of a malignant, heterogeneous tumor. Reconstructing this evolutionary history from sequencing data is critical for understanding the order in which mutations are acquired and the dynamic interplay between different types of alterations. Advances in modern whole genome single-cell sequencing now enable the accurate inference of copy number profiles in individual cells. However, the low sequencing coverage of these low pass sequencing technologies poses a challenge for reliably inferring the presence or absence of SNVs within tumor cells, limiting the ability to simultaneously study the evolutionary relationships between SNVs and CNAs. In this work, we introduce a novel tumor phylogeny inference method, PO_SCPLOWHARMINGC_SCPLOW, that jointly infers the evolutionary histories of SNVs and CNAs. Our key insight is to leverage the high accuracy of copy number inference methods and the fact that SNVs co-occur in regions with CNAs in order to enable more precise tumor phylogeny reconstruction for both alteration types. We demonstrate via simulations that PO_SCPLOWHARMINGC_SCPLOW outperforms state-of-the-art single-modality tumor phylogeny inference methods. Additionally, we apply PO_SCPLOWHARMINGC_SCPLOW to a triple-negative breast cancer case, achieving high-resolution, joint reconstruction of CNA and SNV evolution, including the de novo detection of a clonal whole-genome duplication event. Thus, PO_SCPLOWHARMINGC_SCPLOW offers the potential for more comprehensive and detailed tumor phylogeny inference for high-throughput, low-coverage single-cell DNA sequencing technologies compared to existing approaches. Availabilityhttps://github.com/elkebir-group/Pharming

bioinformatics↗

bioRxiv2024

Detecting the bodys reproductive hormonal brake against tissue overgrowth: micrin/SgII-70

A new humoral factor has been detected, within a project aiming to disclose the bodys reproductive hormonal brake against tissue overgrowth, micrin ( my-crin). It is hypothesized that micrin braking, gonadal and hypothalamic, is lifted at puberty and wanes with age, bringing on prostatic enlargement and cancers. Factor purification has involved fractionation of ovine and bovine ovarian follicular fluid and blood plasma and serum, with evaluation via rat bioassays in vivo and in vitro. Analysis averse, the molecular effector provided a chemical conundrum. Evidence from mass spectrometry (MS) has been problematic, with spectra from MALDI-TOF, the only productive MS modality, confused by a target polypeptide exhibiting artefacts during processing, storage and MALDI set-up in terms of C-terminal truncation and water losses, together with N-terminal grand fragmentations and dimerizations (factor fragments doubled up). Evidence from chemical sequencing of amino acid (aa) residues was likewise baffling, but consistent with a spiralised depolymerisation within the Edman reaction chamber of a unitary polypeptide. Data decryption has overcome molecular intractability, supported by the results of tryptic digestion and epitope mapping using immunohistochemistry (IHC). The detected inhibitory factor is sleuthed to relate to secretogranin II (SgII), the neurosecretory prohormone, in the form of a secreted acidic 70-aa polypeptide derivative called here SgII-70 ( sig two seventy). The product of peptide splicing, micrin/SgII-70 is potentially an amphipathic molecular ampersand (&), with ends entwined (via salt bridging), the knotty totality compromising Edman and MALDI analyses and molecular modelling whilst conferring protease and heat resistance. The two ends of the factor are conceptualised as binding at the same time to a dimeric cellular receptor, to stoichiometric effect, providing fewer smaller cells within a counting mechanism of tissue-mass regulation. Hexapeptide mimetics simulating both ends of the hormone together have been demonstrated in different species and settings, in the cause of antiorganotrophism (tissue reduction) and reproductive modulation. Therapeutic exploitation beckons for mimetics of the bodys hormonal brake, micrin/SgII-70, in tissue overgrowth conditions such as endometriosis, PCOS, BPH and cancer, and in infertility.

immunology↗

bioRxiv2024

Life-history adaptation under climate warming magnifies the agricultural footprint of a cosmopolitan insect pest

Climate change is affecting population growth rates of ectothermic pests with potentially dire consequences for agriculture, but how rapid genetic adaptation impacts these dynamics remains unclear. To address this challenge, we predicted how climate change adaptation in life-history traits of insect pests may affect future agricultural yields by unifying thermodynamics based on first principles with classic life-history theory. Our model predicts that warming temperatures favour changes in resource allocation decisions coupled with increased larval host consumption, resulting in a predicted double-blow on agricultural yields under future climate change. We find support for these predictions by studying thermal adaptation in life-history traits and underlying gene expression in the wide-spread insect pest, Callosobruchus maculatus, with five years of life-history evolution under experimental warming causing an almost two-fold increase in its predicted agricultural footprint. These results emphasize the need for integrating a mechanistic understanding of life-history evolution into forecasts of pest impact.

ecology↗

bioRxiv2023

Invariant natural killer T-cell and CD4+ T-cell derived IL22 is a regulator of epithelial-to-mesenchymal transition and extracellular matrix remodelling in perianal fistulas

Background and aimsPerianal fistulization is a challenging phenotype of Crohns disease (CD). Unravelling the cytokine networks and cellular mediators driving tissue injury in perianal CD (pCD) will help inform much needed novel treatment strategies. MethodsThe phenotype of different T-cell subsets, including unconventional lineages, such as {gamma}{delta} T-cells, MAIT and iNKT-cells in fistula tract tissue and blood samples of patients with pCD or cryptoglandular perianal fistulas was determined using multiparameter flow cytometry. Transcriptomic profiling of fistula tract tissue was performed by RNA-sequencing. ResultsCD161+ CD4+ T-cells and CD161+ CD4- CD8- iNKT-cells significantly accumulated in fistula tissue and produced interleukin-(IL)22 and IL13. Transcripts associated with epithelial-to-mesenchymal transition (EMT), extracellular matrix (ECM) remodelling, interferon-gamma, JAK-STAT and lymphocyte signalling were enriched in pCD, as well as inhibition of pathways associated with wound closure. IL22-responsive transcripts were significantly enriched in fistulas and network analysis identified IL22-mediated regulation of EMT, ECM and other inflammatory pathways. ConclusionThis study provides novel molecular and cellular insights into fistula pathogenesis, identifying IL22 producing lymphocytes as novel immune regulators of EMT and ECM dysregulation in perianal fistulas. Targeting the regulatory networks controlling IL22 producing lymphocytes may offer novel therapeutic strategies in pCD.

immunology↗

bioRxiv2023

The G-alpha Gpa1 directs septin localization in the mating projection of Saccharomyces cerevisiae through its Ubiquitination Domain and Endocytic Machinery

The septin cytoskeleton plays a key role in the morphogenesis of the yeast mating projection, forming structures at the base of the projection. The yeast mating response uses the G-protein coupled receptor (GPCR), Ste2, to detect mating pheromone and initiate mating projection morphogenesis. Desensitization of the G, Gpa1, by the Regulator of G-protein Signaling (RGS), Sst2, is required for proper septin organization and morphogenesis. We hypothesized that Gpa1 would utilize known septin regulators to control septin organization. We found that single deletions of the septin chaperone Gic1, the Cdc42 GAP Bem3, and the endocytic adaptor proteins Ent1 and Ent2 rescued the polar cap accumulation of septins in the hyperactive G. We hypothesized that hyperactive G might increase the rate of endocytosis of a pheromone-responsive cargo, thereby altering where septins are localized. Mathematical modeling predicted that changes in endocytosis could explain the septin organizations we find in WT and mutant cells. Our results show that Gpa1-induced disorganization of septins requires clathrin-mediated endocytosis. Both the GPCR and the G are known to be internalized by clathrin-mediated endocytosis during the pheromone response. Deletion of the GPCR C-terminus to block internalization partially rescued septin organization. However, deleting the Gpa1 ubiquitination domain required for its endocytosis completely abrogated septin accumulation at the polarity site. Our data support a model where the location of endocytosis serves as a spatial mark for septin structure assembly and that desensitization of the G delays its endocytosis sufficiently that septins are placed peripheral to the site of Cdc42 polarity.

cell biology↗

bioRxiv2023

Evaluating key evidence and formulating regulatory alternatives regarding the UK Hunting Trophies (Import Prohibition) Bill

Public policy addressing biodiversity loss is most likely to be effective when it is informed by appropriate evidence and considers potential unintended consequences. We evaluate key evidence relating to the Hunting Trophies (Import Prohibition) Bill that was discussed in the UK Parliament between 2022 and 2024. We characterize the UKs role in international hunting trophy trade by analyzing CITES trade data for 2000-2021 and 2015-2021. For CITES-listed species imported to/exported from the UK as hunting trophies in these periods we use data from the International Union for Conservation of Nature Red List of Threatened Species to determine whether hunting designated as "trophy hunting" is i) likely a major threat contributing to species being of elevated conservation concern, ii) likely or possibly causing localized declines, or iii) not a threat. We then use the Red List to determine whether such hunting provides, or potentially provides, benefits for species and/or people. Finally, we evaluate the UK Governments impact assessment of the bill. In 2000-2021 an estimated 3494 hunting trophies from 73 CITES-listed species and subspecies were exported to the UK involving an estimated 2549 whole organism equivalents (WOEs), i.e. individual animals. Imports involved 158.86 {+/-} 66.53 (mean {+/-} SD) trophies/year (115.83 {+/-} 32.27 WOEs/year). In 2015-2021, 79% of imports were from countries where populations of the hunted species are stable, increasing, or abundant. Legal hunting for trophies is not a major threat to any of the species or subspecies imported to the UK, but likely or possibly represents a local threat to some populations of nine species. This hunting does, or could potentially, benefit 20 species and subspecies, and people. Among other concerns, the impact assessment failed to adequately consider the costs and benefits to local communities in countries where such hunting occurs. Informed by these analyses we discuss alternative regulatory options.

ecology↗

bioRxiv2022

Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment

Despite the fundamental role of strain variation in gut microbiota function, the number of unique strains of a species that can stably colonize the human gut is still unknown. In this work, we determine the strain richness of common gut species using thousands of sequenced bacterial isolates and metagenomes. We find that strain richness varies across species, is transferable by fecal microbiota transplantation, and is low in the gut compared to other environments. Therapeutic administration of supraphysiologic numbers of strains per species only temporarily increases recipient strain richness, which subsequently converges back to the population average. These results suggest that properties of the gut ecosystem govern the number of strains of each species colonizing the gut and provide a theoretical framework for strain engraftment and replacement in fecal microbiota transplantation and defined live biotherapeutic products.

microbiology↗

bioRxiv2021

Multiomics Integration Elucidates Metabolic Modulators of Drug Resistance in Lymphoma

BackgroundDiffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma (NHL). B-cell NHLs rely on Brutons tyrosine kinase (BTK) mediated B-cell receptor signaling for survival and disease progression. However, they are often resistant to BTK inhibitors or soon acquire resistance after drug exposure resulting in the drug tolerant form. The drug tolerant clones proliferate faster, have increased metabolic activity, and shift to oxidative phosphorylation; however, how this metabolic programming occurs in the drug resistant tumor is poorly understood. MethodsIn this study, we explored for the first time the metabolic regulators of ibrutinib-resistant activated B-cell (ABC) DLBCL using a multi-omics analysis that integrated metabolomics (using high-resolution mass spectrometry) and transcriptomic (gene expression analysis). Overlay of the unbiased statistical analyses, genetic perturbation and pharmaceutical inhibition, were further used to identify the key players that contribute to the metabolic reprograming of the drug resistant clone. ResultsGene-metabolite integration revealed interleukin 4 induced 1 (IL4I1) at the crosstalk of two significantly altered metabolic pathways involved in the production of various amino acids. We showed for the first time that drug resistant clones undergo metabolic reprogramming from glycolysis towards oxidative phosphorylation & is activated via the BTK-PI3K-AKT-IL4I1 axis and can be targeted therapeutically. ConclusionsOur report shows how these cells become dependent on PI3K/AKT signaling for survival after acquiring ibrutinib resistance and shift to sustained Oxidative phosphorylation, additionally we outline the compensatory, pathway that regulates this metabolic reprogramming in the drug resistant cells. These findings from our unbiased analyses highlight the role of metabolic reprogramming during drug resistance development. Furthermore, our work demonstrates that a multi-omics approach can be a powerful and unbiased strategy to uncover genes and pathways that drive metabolic dysregulation in cancer cells.

cancer biology↗

bioRxiv2019

A blood-based prognostic biomarker in inflammatory bowel disease

ObjectiveWe have previously described a prognostic transcriptional signature in CD8 T cells that separates inflammatory bowel disease (IBD) patients into 2 phenotypically-distinct subgroups, which we termed IBD1 and IBD2. Here we sought to develop a blood-based prognostic test that could identify these patient subgroups without the need for cell separation, and thus be suitable for routine clinical use in Crohns disease (CD) and ulcerative colitis (UC). DesignPatients with active IBD were recruited before treatment. Transcriptomic analyses were performed on purified CD8 T cells and/or whole blood. Detailed phenotype information was collected prospectively. IBD1/IBD2 patient subgroups were identified by consensus clustering of CD8 T cell transcriptomes. In a training cohort, statistical (machine) learning was used to identify groups of genes ("classifiers") whose differential expression in whole blood re-created the IBD1/IBD2 patient subgroups. Genes from the best classifiers were qPCR-optimised, and further statistical learning was applied to the qPCR dataset to identify the optimal classifier, which was locked-down for further testing. Independent validation was sought in separate cohorts of CD (n=66) and UC patients (n=57). ResultsIn both independent validation cohorts, a 17-gene qPCR-based classifier stratified patients into two distinct subgroups. Irrespective of the underlying diagnosis, IBDhi patients (analogous to the poor prognosis IBD1 subgroup) experienced significantly more aggressive disease than IBDlo patients (analogous to IBD2), with earlier need for treatment escalation and more escalations over time. ConclusionThis is the first validated prognostic biomarker that can predict prognosis in newly-diagnosed IBD patients, and represents a step towards personalised therapy. What is already known about this subject?The course of CD and UC varies considerably between patients, but reliable prognostic markers are not available in clinical practice. This hinders disease management because treatment approaches that would be optimal for patients with indolent disease - characterised by infrequent flare-ups that can be readily controlled by first-line therapy - will inevitably undertreat those with progressive disease. Conversely, strategies that would appropriately control frequently-relapsing, progressive disease will expose patients with more quiescent disease to the risks and side effects of unnecessary treatment. We have previously described a CD8 T cell gene expression signature that corresponds to differences in T cell exhaustion, is detectable during active untreated disease (including at diagnosis), and predicts disease course in both UC and CD. However, the need for cell separation and microarray-based gene expression analysis would make this difficult to translate to clinical practice. What are the new findings?We have developed, optimised, and independently validated a whole blood qPCR-based classifier - designed to identify the IBD1 and IBD2 patient subgroups - that can reliably predict prognosis in patients with CD or UC from diagnosis without the need for cell separation. We also present a detailed phenotypic update on the disease course experienced by patients in either the IBD1/IBDhi or IBD2/IBDlo subgroups, incorporating both expanded patient cohorts and substantially longer follow-up. This affords new insights into the spectrum of therapies that are differentially required in these patient subgroups, and reinforces their association with disease prognosis. How might it impact on clinical practice in the foreseeable future?The qPCR-based classifier has performance characteristics that compare favourably to prognostic biomarkers currently in use in oncology, and should be sufficient to guide therapy from diagnosis in patients with CD or UC. This represents an important step towards personalised therapy in inflammatory bowel disease.

genomics↗

bioRxiv2018

Association between Parkinson’s Disease subtypes and tests of physical function: the 360-degree turn test is most predictive

BACKGROUND AND PURPOSEPeople with Parkinsons disease (PD) present phenotypes that can be characterized as tremor-dominant (TD) or postural instability / gait difficulty (PIGD) subtypes. Differentiation of subtypes allows clinicians to predict the disease course and adjust treatment accordingly. We examined whether brief mobility and balance measures can discriminate PIGD from TD phenotypes.\n\nMETHODSWe performed a cross-sectional study with individuals with PD (N=104). Blinded raters assessed participants with the UPDRS or MDS-UPDRS, and potential predictor variables: 360-degree turn test, one-leg stance, backward perturbation test and tandem walk. Participant were classified as PIGD or TD based on the Unified Parkinsons Disease Rating Scale or the Movement Disorder Society revision (UPDRS or MDS-UPDRS) assessment results. Differences in study variables between subtype groups were assessed with univariate analyses. Receiver operating characteristic (ROC) curve analyses were performed to investigate the ability of candidate predictor variables to differentiate PD subtypes.\n\nRESULTSMean age and disease duration were 68{+/-}9 and 7{+/-}5 years, respectively, and Hoehn & Yahr Stages I-IV median (1st,3rd quartile) = II (II, III). No differences between subtypes were observed for tandem walk or reactive postural control. PIGD participants performed worse on number of steps (p<0.001) and time to complete (p=0.003) the 360-degree turn test and one-leg stance (p=0.006). ROC curves showed only the 360-degree turn test could discriminate PIGD from TD with high sensitivity.\n\nCONCLUSIONSThe 360-degree turn test requires minimal time to administer and may be useful in mild-moderate PD for distinguishing PIGD from TD subtypes.

neuroscience↗