Biology subjects

Fisher, J.

Publications and source records attributed to Fisher, J..

34 records · Page 2Linked to original sources

bioRxiv2023

Multi-scale characterisation of homologous recombination deficiency in breast cancer

BackgroundHomologous recombination is a robust, broadly error-free mechanism of double strand break repair, and deficiencies cause reliance on alternative repair processes, leading to sensitivity to PARP inhibitors. Patients displaying homologous recombination deficiency can be identified using mutational signatures. However, these patterns are difficult to reliably infer from exome sequencing. Additionally, as mutational signatures are a historical record of mutagenic processes, this limits their utility in describing the current status of a tumour. ResultsHere, we apply two methods for classifying homologous recombination deficiency in breast cancer to explore the features and heterogeneity associated with this phenotype. Firstly, we apply a likelihood-based method which leverages small insertions and deletions to improve classification of homologous recombination deficiency in exome sequenced breast cancers. We find that whilst BRCA+ homologous recombination deficient samples display strong similarities to those harbouring BRCA defects, they deviate in microenvironmental features such as hypoxic signalling. Secondly, using this classification we develop a 228-gene transcriptional signature which simultaneously characterises homologous recombination deficiency and BRCA1/2-defect status, and is linked with PARP inhibitor response. Finally, we apply this signature to single-cell RNA-sequenced breast cancer cohorts to study homologous recombination deficiency at single cell resolution and demonstrate that these cells present a distinct milieu of interactions with immune cells in their microenvironment compared to their HR proficient counterparts, which could inform checkpoint blockade for HRD tumours. ConclusionsWe apply multi-scale approaches to characterise homologous recombination deficiency in breast cancer through the development of mutational and transcriptional signatures. We show that indels, even at low levels, can improve homologous recombination deficiency classification. Additionally, we demonstrate the heterogeneity of homologous recombination deficiency, especially in relation to BRCA status, and show that indications of this feature can be captured at a single-cell level, enabling further investigations into interactions between DNA repair deficient cells and their tumour microenvironment.

genomics↗

bioRxiv2023

Waning Immunity Against XBB.1.5 Following Bivalent mRNA Boosters

The SARS-CoV-2 Omicron variant has continued to evolve. XBB is a recombinant between two BA.2 sublineages, XBB.1 includes the G252V mutation, and XBB.1.5 includes the G252V and F486P mutations. XBB.1.5 has rapidly increased in frequency and has become the dominant virus in New England. The bivalent mRNA vaccine boosters have been shown to increase neutralizing antibody (NAb) titers to multiple variants, but the durability of these responses remains to be determined. We assessed humoral and cellular immune responses in 30 participants who received the bivalent mRNA boosters and performed assays at baseline prior to boosting, at week 3 after boosting, and at month 3 after boosting. Our data demonstrate that XBB.1.5 substantially escapes NAb responses but not T cell responses after bivalent mRNA boosting. NAb titers to XBB.1 and XBB.1.5 were similar, suggesting that the F486P mutation confers greater transmissibility but not increased immune escape. By month 3, NAb titers to XBB.1 and XBB.1.5 declined essentially to baseline levels prior to boosting, while NAb titers to other variants declined less strikingly.

immunology↗

bioRxiv2023

Measuring the long arm of childhood in real-time: Epigenetic predictors of BMI and social determinants of health across childhood and adolescence

Children who are socioeconomically disadvantaged are at increased risk for high body mass index (BMI) and multiple diseases in adulthood. The developmental origins of health and disease hypothesis proposes that early life conditions affect later-life health in a manner that is only partially modifiable by later-life experiences. Epigenetic mechanisms may regulate the influence of early life conditions on later life health. Recent epigenetic studies of adult blood samples have identified DNA-methylation sites associated with higher BMI and worse health (epigenetic-BMI). Here, we used longitudinal and twin study designs to examine whether epigenetic predictors of BMI developed in adults are valid biomarkers of child BMI and are sensitive to early life social determinants of health. Salivary epigenetic-BMI was calculated from two samples: (1) N=1,183 8-to-19-year-olds (609 female, mean age=13.4) from the Texas Twin Project (TTP), and (2) N=2,020 children (1,011 female) measured at 9 and 15 years from the Future of Families and Child Well-Being Study (FFCWS). We found that salivary epigenetic-BMI is robustly associated with childrens BMI (r=0.36 to r=0.50). Longitudinal analysis suggested that epigenetic-BMI is highly stable across adolescence, but remains both a leading and lagging indicator of BMI change. Twin analyses showed that epigenetic-BMI captures differences in BMI between monozygotic twins. Moreover, children from more disadvantaged socioeconomic status (SES) and marginalized race/ethnic groups had higher epigenetic-BMI, even when controlling for concurrent BMI, pubertal development, and tobacco exposure. SES at birth relative to concurrent SES best predicted epigenetic-BMI in childhood and adolescence. We show for the first time that epigenetic predictors of BMI calculated from pediatric saliva samples are valid biomarkers of childhood BMI that are sensitive to social inequalities. Our findings are in line with the hypothesis that early life conditions are especially important factors in epigenetic regulation of later life health. Research showing that health later in life is linked to early life conditions have important implications for the development of early-life interventions that could significantly extend healthy life span.

genomics↗

bioRxiv2023

Alterations in Germinal Center Formation and B Cell Activation during Severe Orientia tsutsugamushi Infection in Mice

Scrub typhus is a poorly studied but life-threatening disease caused by the intracellular bacterium Orientia tsutsugamushi (Ot). Cellular and humoral immunity in Ot-infected patients is not long-lasting, waning as early as one-year post-infection; however, its underlying mechanisms remain unclear. To date, no studies have examined germinal center (GC) or B cell responses in Ot-infected humans or experimental animals. This study was aimed at evaluating humoral immune responses at acute stages of severe Ot infection and possible mechanisms underlying B cell dysfunction. Following inoculation with Ot Karp, a clinically dominant strain known to cause lethal infection in C57BL/6 mice, we measured antigen-specific antibody titers, revealing IgG2c as the dominant isotype induced by infection. Splenic GC responses were evaluated by immunohistology, co-staining for B cells (B220), T cells (CD3), and GCs (GL-7). Organized GCs were evident at day 4 post-infection (D4), but they were nearly absent at D8, accompanied by scattered T cells throughout splenic tissues. Flow cytometry revealed comparable numbers of GC B cells and T follicular helper (Tfh) cells at D4 and D8, indicating that GC collapse was not due to excessive death of these cell subtypes at D8. B cell RNAseq analysis revealed significant differences in expression of genes associated with B cell adhesion and co-stimulation at D8 versus D4. The significant downregulation of S1PR2 (a GC-specific adhesion gene) was most evident at D8, correlating with disrupted GC formation. Signaling pathway analysis uncovered downregulation of 71% of B cell activation genes at D8, suggesting attenuation of B cell activation during severe infection. This is the first study showing the disruption of B/T cell microenvironment and dysregulation of B cell responses during Ot infection, which may help understand the transient immunity associated with scrub typhus. Author SummaryScrub typhus is an understudied disease caused by the intracellular bacterium O. tsutsugamushi. A hallmark of scrub typhus is the unexplained, non-durable immunity after infection. While cellular immune responses are known to be important for controlling this infection, our understanding of B cell and GC responses remains limited. In this study, we examined B cell activation and GC responses using our recently established murine model of severe scrub typhus. We measured bacterial antigen-specific antibody titers and identified IgG2c, an IFN-{gamma}-driven isotype, as the major IgG subtype. We also found that O. tsutsugamushi infection disrupted spleen morphology, exemplified by randomly dispersed T cells and lost GC structures. Transcriptomic analysis of purified splenic B cells demonstrated reduced expression of genes encoding critical adhesion and co-stimulation molecules, including GC-adhesion gene S1PR2, at severe stages of infection. Several humoral immune response pathways relevant to B cell receptor signaling, B cell activation and differentiation were significantly downregulated during infection. This study is the first report describing humoral immunity in a scrub typhus mouse model and provides detailed evidence that B cell and GC responses are impaired during acute infection.

immunology↗

bioRxiv2022

OPS-γδ: allogeneic opsonin-secreting γδT cell immunotherapy for solid tumours mediates direct and bystander immunity

T cell-based cancer immunotherapy has typically relied on membrane-bound cytotoxicity enhancers such as chimeric antigen receptors expressed in autologous {beta}T cells. These approaches are limited by tonic signalling of synthetic constructs and costs associated with manufacture of bespoke patient products. {gamma}{delta}T cells are an emerging alternative chassis for cellular therapy, possessing innate anti-tumour activity, potent antibody-dependent cytotoxicity (ADCC) and minimal alloreactivity. We present an immunotherapeutic platform technology built around the V{gamma}9V{delta}2 {gamma}{delta}T cell chassis, harnessing specific characteristics of this cell type and offering an allo-compatible means of delivering cellular therapy that recruits bystander immunity. We engineered {gamma}{delta}T cells to secrete synthetic opsonins and stabilized IL15 (stIL15). Using GD2 as a model antigen we show how opsonin-secreting V{gamma}9V{delta}2 (OPS-{gamma}{delta}) have enhanced cytotoxicity and also confer this benefit on lymphoid and myeloid bystander cells. Reflecting the secreted nature of the engineered efficacy modules, the entire product rather than just the gene-modified fraction exhibited enhanced activation and cytotoxic profiles, superior persistence and proliferative capacity even upon repeated tumour challenge. Secretion of stIL15 abrogated the need for exogenous cytokine supplementation during expansion and further mediated functional licensing of bystander NK cells. Compared to unmodified {gamma}{delta}T cells, stIL15-OPS-{gamma}{delta} cells exhibited superior in-vivo control of subcutaneous tumour and persistence in the blood. stIL15-OPS-{gamma}{delta} cells were further efficacious in 3D patient-derived osteosarcoma models, where efficacy could be boosted with the addition of immunomodulatory aminobisphosphonate drug, zoledronic acid. Together the data identify stIL15-OPS-{gamma}{delta} cells as a novel allogeneic platform combining direct cytolysis with bystander activation to effect solid tumour control. One Sentence SummaryArmoured, opsonin-secreting OPS-{gamma}{delta} cell immunotherapy is built on the innate strengths of the V{gamma}9V{delta}2 cell chassis for allogeneic solid tumour targeting.

immunology↗

bioRxiv2022

Biochemical and metabolic maladaption defines pathological niches in progressive multiple sclerosis

Progressive multiple sclerosis (MS) is driven by demyelination, neuroaxonal loss, and mitochondrial damage occurring behind a closed blood-brain barrier (BBB).1,2 Patients with progressive MS typically fail to respond to available immunomodulatory drugs that reduce relapses in early disease.2 This indicates a dire need to identify non-canonical therapeutic avenues to limit neurodegeneration and promote protection and repair.3 Here, we have employed high-resolution multiomic profiling to characterise the biochemical and metabolic adaptations underpinning MS pathology, as these have been incompletely described but critically, may be amenable to BBB-permeable drug targeting. Using synchrotron radiation (SR)- and focal plane array (FPA)-based Fourier transform infrared microspectroscopy (FTIR), we spatially mapped the biochemical features present in human progressive MS and control post-mortem brain and rare spinal cord tissue. By employing single-nuclear RNA sequencing (snRNA-seq), 10x Genomics Visium spatial transcriptomics and spatial proteomics to resolve their cellular context, we found that these biochemical features provide a uniquely and highly disease-specific barcode for distinct pathological niches within the tissue. Characterisation of the metabolic processes underpinning these niches revealed an associated re-organisation of the astrocytic landscape in the grey and white matter, with implications for the treatment of progressive MS.

neuroscience↗

bioRxiv2022

Host transcriptomic profiling of CD-1 outbred mice with severe clinical outcomes following infection with Orientia tsutsugamushi

Orientia tsutsugamushi is an obligately intracellular bacterium with endothelial tropism and can cause mild to lethal scrub typhus in humans. No vaccine is available for this reemerging and severely neglected infection. Previous scrub typhus studies have utilized inbred mice, yet such models have intrinsic limitations. Thus, the development of suitable mouse models that better mimic human diseases is in great need for immunologic investigation and future vaccine studies. This study is aimed at establishing scrub typhus in outbred CD-1 mice and defining immune biomarkers related to disease severity. CD-1 mice received O. tsutsugamushi Karp strain via the i.v. route; major organs were harvested at 2-12 days post-infection for kinetic analyses. We found that for our given infection doses, CD-1 mice were significantly more susceptible (90-100% lethal) than were inbred C57BL/6 mice (0-10% lethal). Gross pathology of infected CD-1 mouse organs revealed features that mimicked human scrub typhus, including pulmonary edema, interstitial pneumonia, perivascular lymphocytic infiltrates, and vasculitis. Alteration in angiopoietin/receptor expression in inflamed lungs implied endothelial dysfunction. Lung immune gene profiling using NanoString analysis displayed a Th1/CD8-skewed, but Th2 repressed profile, including novel biomarkers not previously investigated in other scrub typhus models. Bio-plex analysis revealed a robust inflammatory response in CD-1 mice as evidenced by increased serum cytokine and chemokine levels, correlating with immune cell recruitment during the severe stages of the disease. This study provides an important framework indicating a value of CD-1 mice for delineating host susceptibility to O. tsutsugamushi, immune dysregulation, and disease pathogenesis. This preclinical model is particularly useful for future translational and vaccine studies for severe scrub typhus. Author SummaryScrub typhus is a severely neglected and potentially fatal disease caused by Orientia tsutsugamushi, a genetically intractable, obligately intracellular bacterium that annually infects at least one million people worldwide. There is no vaccine available, and our current understanding of the host immunological response and mechanisms remains very limited. Appropriate animal models of infection that recapitulate the disease are essential to the development of effective therapeutics and vaccines. In this study, we characterized the immunologic responses by transcriptomics and Bio-plex assays in outbred CD-1 mice with lethal O. tsutsugamushi infection. We found that CD-1 mice were highly susceptible to infection and that the high mortality correlated with a Th1/CD8-skewed, but Th2 repressed, immune profile during the acute phase of disease. This proinflammatory state was further confirmed by elevated cytokine and chemokine levels in the sera. Collectively, this study established CD-1 mice as a practical, preclinical model to define pathogenic mechanisms underlying severe scrub typhus and for future immunologic and translational studies during O. tsutsugamushi infection.

microbiology↗

bioRxiv2022

Unexpected proteinopathies in hippocampal PDE11A4 promote age-related cognitive decline of social associative memories

In humans, associative memories are more susceptible to age-related cognitive decline (ARCD) than are recognition memories. Reduced cAMP/cGMP signaling in the hippocampus may contribute to ARCD. Here, we found that both aging and traumatic brain injury-associated dementia increased expression of the cAMP/cGMP-degrading enzyme phosphodiesterase 11A (PDE11A) in the human hippocampus. Further, age-related increases in hippocampal PDE11A4 mRNA and protein were conserved in mice, as was the increased vulnerability of associative versus recognition memories to ARCD. Interestingly, mouse PDE11A4 protein in the aged ventral hippocampus (VHIPP) ectopically accumulated in the membrane fraction and filamentous structures we term "ghost axons". These age-related increases in expression were driven by reduced exoribonuclease-mediated degradation of PDE11A mRNA and increased PDE11A4-pS117/pS124, the latter of which also drove the punctate accumulation of PDE11A4. In contrast, PDE11A4-pS162 caused dispersal. Importantly, preventing age-related increases in PDE11 expression via genetic deletion protected mice from ARCD of short-term and remote long-term associative memory (aLTM) in the social transmission of food preference assay, albeit at the expense of recent aLTM. Further, mimicking age-related overexpression of PDE11A4 in CA1 of old KO mice caused aging-like impairments in CREB function and remote social--but not non-social--LTMs. RNA sequencing and phosphoproteomic analyses of VHIPP identified cGMP-PKG--as opposed to cAMP-PKA--as well as circadian entrainment, glutamatergic/cholinergic synapses, calcium signaling, oxytocin, and retrograde endocannabinoid signaling as mechanisms by which PDE11A deletion protects against ARCD. Together, these data suggest that PDE11A4 proteinopathies acutely impair signaling in the aged brain and contribute to ARCD of social memories.

neuroscience↗

bioRxiv2021

European Vintage tomatoes galore: a result of farmers combinatorial assorting/swapping of a few diversity rich loci

A comprehensive collection of 1,254 tomato accessions corresponding to European heirlooms and landraces, together with modern varieties, early domesticates and wild relatives, were analyzed by genotyping by sequencing. A continuous genetic gradient between the vintage and modern varieties was observed. European vintage tomatoes displayed very low genetic diversity, with only 298 loci out of 64,943 variants being polymorphic at the 95% threshold. European vintage tomatoes could be classified in several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed a higher genetic diversity than the rest varieties, suggesting that these regions might be independent secondary centers of diversity and with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a GWAS with fruit morphological traits in the European vintage collection, and the corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise diversity-poor genome suggests a history of balancing selection, in which tomato farmers maintained the morphological variation by applying a high selective pressure within different varietal types. HighlightThe high phenotypic diversity observed among European vintage varieties was created by traditional farmers by combining very few polymorphic loci subjected to balancing selection.

plant biology↗

bioRxiv2021

Executable Network of SARS-CoV-2-Host Interaction Predicts Drug Combination Treatments

The COVID-19 pandemic has pushed healthcare systems globally to a breaking point. The urgent need for effective and affordable COVID-19 treatments calls for repurposing combinations of approved drugs. The challenge is to identify which combinations are likely to be most effective and at what stages of the disease. Here, we present the first disease-stage executable signalling network model of SARS-CoV-2-host interactions used to predict effective repurposed drug combinations for treating early- and late-stage severe disease. Using our executable model, we performed in silico screening of 9870 pairs of 140 potential targets and have identified 12 new drug combinations. Camostat and Apilimod were predicted to be the most promising combination in effectively supressing viral replication in the early stages of severe disease and were validated experimentally in human Caco-2 cells. Our study further demonstrates the power of executable mechanistic modelling to enable rapid pre-clinical evaluation of combination therapies tailored to disease progression. It also presents a novel resource and expandable model system that can respond to further needs in the pandemic.

systems biology↗

bioRxiv2021

HOXA9 acts as a regulatory switch in acute myeloid leukaemia and myeloproliferative neoplasms

Blood malignancies arise from the dysregulation of haematopoiesis. The type of blood cell and the specific order of oncogenic events initiating abnormal growth ultimately determine the cancer subtype and subsequent clinical outcome. HOXA9 plays an important role in acute myeloid leukaemia (AML) prognosis by promoting blood cell expansion and altering differentiation; however, the function of HOXA9 in other blood malignancies is still unclear. Here, we demonstrate the importance of this gene in chronic myeloproliferative neoplasms (MPN) and highlight the biological switch and prognosis marker properties of HOXA9 in AML and MPN. This binary switch function can explain the clinical stratification of these two blood disorders. First, we establish the ability of HOXA9 to stratify AML patients with distinct cellular and clinical outcomes. Then, through the use of a computational network model of MPN, we show that the self-activation of HOXA9 and its relationship to JAK2 and TET2 can explain the branching progression of JAK2/TET2 mutant MPN patients towards divergent clinical characteristics. Finally, we predict a connection between the RUNX1 and MYB genes and a suppressive role for the NOTCH pathway in MPN diseases.

cancer biology↗

bioRxiv2019

Rora regulates activated T helper cells during inflammation

The transcription factor Rora has been shown to be important for the development of ILC2 and the regulation of ILC3, macrophages and Treg cells. Here we investigate the role of Rora across CD4+ T cells, both in vitro as well as in the context of several in vivo type 2 infection models. We dissect the function of Rora using overexpression and a CD4-conditional Rora-knockout mouse, as well as a RORA-reporter mouse. We establish the importance of Rora in CD4+ T cells for controlling lung inflammation induced by Nippostrongylus brasiliensis infection, and have measured the effect on downstream genes using RNA-seq. Using a systematic stimulation screen of CD4+ T cells, coupled with RNA-seq, we identify upstream regulators of Rora, most importantly IL-33 and CCL7. Our data suggest that Rora is a negative regulator of the immune system, possibly through several downstream pathways, and is under control of the local microenvironment.

immunology↗

bioRxiv2019

The flagellar substrate specificity switch protein FlhB assembles onto the extra-membrane export gate to regulate type three secretion

Export of proteins through type three secretion systems (T3SS) is critical for motility and virulence of many major bacterial pathogens. Proteins are transported through an export gate complex consisting of three proteins (FliPQR in flagellar systems, SctRST in virulence systems) that were initially annotated as membrane proteins, but which we have recently shown assemble into an extra-membranous helical assembly. A fourth putative membrane protein (FlhB/SctU) is essential to the export process, and also functions to \"switch\" secretion substrate specificity once the growing hook/needle structures reach their determined length. Here we present the structure of an export gate containing the switch protein from a Vibrio polar flagellar system at 3.2 [A] resolution by cryo-electron microscopy. The structure reveals that the FlhB/SctU further extends the helical export gate assembly with its four putative transmembrane helices adopting an out-of-membrane location, wrapped around the other export gate components at the base of the structure. The unusual topology of the switch protein helices creates a loop that wraps around the bottom of the closed export gate complex. Structure-informed mutagenesis suggests that this loop is critical in gating secretion and we propose that a series of conformational changes in the type 3 secretion system trigger opening of the export gate through the interactions between FlhB/SctU and FliPQR/SctRST.

microbiology↗

bioRxiv2018

Spatial Mark-Resight for Categorically MarkedPopulations with an Application to GeneticCapture-Recapture

The estimation of animal population density is a fundamental goal in wildlife ecology and management, commonly met using mark recapture or spatial mark recapture (SCR) study designs and statistical methods. Mark-recapture methods require the identification of individuals; however, for many species and sampling methods, particularly noninvasive methods, no individuals or only a subset of individuals are individually identifiable. The unmarked SCR model, theoretically, can estimate the density of unmarked populations; however, it produces biased and imprecise density estimates in many sampling scenarios typically encountered. Spatial mark-resight (SMR) models extend the unmarked SCR model in three ways: 1) by introducing a subset of individuals that are marked and individually identifiable, 2) introducing the possibility of individual-linked telemetry data, and 3) introducing the possibility that the capture-recapture data from the survey used to deploy the marks can be used in a joint model, all improving the reliability of density estimates. The categorical spatial partial identity model (SPIM) improves the reliability of density estimates over unmarked SCR along another dimension, by adding categorical identity covariates that improve the probabilistic association of the latent identity samples. Here, we combine these two models into a \"categorical SMR\" model to exploit the benefits of both models simultaneously. We demonstrate using simulations that SMR alone can produce biased and imprecise density estimates with sparse data and/or when few individuals are marked. Then, using a fisher (Pekania pennanti) genetic capture-recapture data set, we show how categorical identity covariates, marked individuals, telemetry data, and jointly modeling the capture survey used to deploy marks with the resighting survey all combine to improve inference over the unmarked SCR model. As previously seen in an application of the categorical SPIM to a real-world data set, the fisher data set demonstrates that individual heterogeneity in detection function parameters, especially the spatial scale parameter{sigma} , introduces positive bias into latent identity SCR models (e.g., unmarked SCR, SMR), but the categorical SMR model provides more tools to reduce this positive bias than SMR or the categorical SPIM alone. We introduce the possibility of detection functions that vary by identity category level, which will remove individual heterogeneity in detection function parameters than is explained by categorical covariates, such as individual sex. Finally, we provide efficient SMR algorithms that accommodate all SMR sample types, interspersed marking and sighting periods, and any number of identity covariates using the 2-dimensional individual by trap data in conjunction with precomputed constraint matrices, rather than the 3-dimensional individual by trap by occasion data used in SMR algorithms to date.

ecology↗

bioRxiv2018

A Toolbox for Discrete Modelling of Cell Signalling Dynamics

In an age where the volume of data regarding biological systems exceeds our ability to analyse it, many researchers are looking towards systems biology and computational modelling to help unravel the complexities of gene and protein regulatory networks. In particular, the use of discrete modelling allows generation of signalling networks in the absence of full quantitative descriptions of systems, which are necessary for ordinary differential equation (ODE) models. In order to make such techniques more accessible to mainstream researchers, tools such as the BioModelAnalyzer (BMA) have been developed to provide a user-friendly graphical interface for discrete modelling of biological systems. Here we use the BMA to build a library of discrete target functions of known canonical molecular interactions, translated from ordinary differential equations (ODEs). We then show that these BMA target functions can be used to reconstruct complex networks, which can correctly predict many known genetic perturbations. This new library supports the accessibility ethos behind the creation of BMA, providing a toolbox for the construction of complex cell signalling models without the need for extensive experience in computer programming or mathematical modelling, and allows for construction and simulation of complex biological systems with only small amounts of quantitative data.\n\nAUTHOR SUMMARYOrdinary differential equation (ODE) based models are a popular approach for modelling biological networks. A limitation of ODE models is that they require complete networks and detailed kinetic parameterisation. An alternative is the use of discrete, executable models, in which nodes are assigned discrete value ranges, and the relationship between them defined with simple mathematical operations. One tool for constructing such models is the BioModelAnalyzer (BMA), an open source and publicly available (https://www.biomodelanalyzer.org) software, aimed to be fully usable by researchers without extensive computational or mathematical experience. A fundamental question for executable models is whether the high level of abstraction substantially reduces expressivity relative to continuous approaches. Here, we present a canonical library of biological signalling motifs, initially defined by Tyson et al (2003), translated for the first time into the BMA. We show that; 1) these motifs are easily and fully translatable from continuous to discrete models, 2) Combining these motifs in a computationally naive way generates a fully functional and predictive model of the yeast cell cycle.

systems biology↗

bioRxiv2017

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

Advances in proteomics reveal that pathway databases fail to capture the majority of cellular signaling activity. Our mass spectrometry study of the dynamic epidermal growth factor (EGF) response demonstrates that over 89% of significantly (de)phosphorylated proteins are excluded from individual EGF signaling maps, and 63% are absent from all annotated pathways. We present a computational method, the Temporal Pathway Synthesizer (TPS), to discover missing pathway elements by modeling temporal phosphoproteomic data. TPS uses constraint solving to exhaustively explore all possible structures for a signaling pathway, eliminating structures that are inconsistent with protein-protein interactions or the observed phosphorylation event timing. Applied to our EGF response data, TPS connects 83% of the responding proteins to receptors and signaling proteins in EGF pathway maps. Inhibiting predicted active kinases supports the TPS pathway model. The TPS algorithm is broadly applicable and also recovers an accurate model of the yeast osmotic stress response.

bioinformatics↗