Biology subjects

Banerjee, A.

Publications and source records attributed to Banerjee, A..

At least 181 records · Page 10Linked to original sources

bioRxiv2020

Energetics based epitope screening in SARS CoV-2 (COVID 19) spike glycoprotein by Immuno-informatic analysis aiming to a suitable vaccine development.

The recent outbreak by SARS-CoV-2 has generated a chaos in global health and economy and claimed/infected a large number of lives. Closely resembling with SARS CoV, the present strain has manifested exceptionally higher degree of spreadability, virulence and stability possibly due to some unidentified mutations. The viral spike glycoprotein is very likely to interact with host Angiotensin-Converting Enzyme 2 (ACE2) and transmits its genetic materials and hijacks host machinery with extreme fidelity for self propagation. Few attempts have been made to develop a suitable vaccine or ACE2 blocker or virus-receptor inhibitor within this short period of time. Here, attempt was taken to develop some therapeutic and vaccination strategies with a comparison of spike glycoproteins among SARS-CoV, MERS-CoV and the SARS-CoV-2. We verified their structure quality (SWISS-MODEL, Phyre2, Pymol) topology (ProFunc), motifs (MEME Suite, GLAM2Scan), gene ontology based conserved domain (InterPro database) and screened several epitopes (SVMTrip) of SARS CoV-2 based on their energetics, IC50 and antigenicity with regard to their possible glycosylation and MHC/paratopic binding (Vaxigen v2.0, HawkDock, ZDOCK Server) effects. We screened here few pairs of spike protein epitopic regions and selected their energetic, IC50, MHC II reactivity and found some of those to be very good target for vaccination. A possible role of glycosylation on epitopic region showed profound effects on epitopic recognition. The present work might be helpful for the urgent development of a suitable vaccination regimen against SARS CoV-2.

immunology↗

bioRxiv2020

Stabilising selection causes grossly altered but stable karyotypes in metastatic colorectal cancer

Aneuploidy, the loss and gain of whole and part chromosomes, is near-ubiquitous in cancer genomes and likely defines cancer cell biology. However, the temporal evolutionary dynamics that select for aneuploidy remain uncharacterised. Here we perform longitudinal genomic analysis of 755 samples from a total of 167 patients with colorectal-derived neoplastic lesions that represent distinct stages of tumour evolution through metastasis and treatment. Adenomas typically had few copy number alterations (CNAs) and most were subclonal, whereas cancers had many clonal CNAs, suggesting that progression goes through a CNA bottleneck. Individual CRC glands from the same tumour typically had very similar karyotypes, despite evidence of ongoing instability at the cell level in patient tumours, cell lines and organoids. CNAs in metastatic lesions sampled from liver and other organs, after chemotherapy or targeted therapies, and in late recurrences were typically similar to the primary tumour. Mathematical modelling and statistical inference indicated that these data are consistent with the action of negative selection on CNAs that traps cancer cell genomes on a fitness peak defined by the specific pattern of chromosomal aberrations. These data suggest that the initial progression of colorectal cancer requires the traversal of a rugged fitness landscape and subsequent CNA evolution, including metastatic dissemination and therapeutic resistance, is constrained by negative selection.

cancer biology↗

bioRxiv2020

Value-guided remapping of sensory circuits by lateral orbitofrontal cortex in reversal learning

Flexible decision-making is crucial for adaptive behaviour. Such behaviour in mammals largely relies on the frontal cortex, and specifically, the orbitofrontal cortex (OFC). How OFC neurons encode decision variables and instruct sensory areas to guide adaptive behaviour is a key open question. Here we developed a reversal learning task for head-fixed mice together with two-photon calcium imaging to monitor the activity of lateral OFC neuronal populations and investigated their dynamic interaction with primary somatosensory cortex (S1). Mice trained on this task learned to discriminate go/no-go tactile stimuli and adapt their behaviour upon changes in stimulus-reward contingencies ( rule-switch). Longitudinal imaging at cellular resolution across weeks during all behavioural phases revealed a distinct engagement of S1 and lateral OFC neurons: S1 neural activity reflected task learning-related responses, while neurons in the lateral OFC saliently and transiently responded to the rule-switch. A subset of OFC neurons conveyed a value prediction error signal via feedback projections to S1, as direct anatomical long-range projections were revealed by retrograde tracing combined with whole-brain light-sheet microscopy. Top-down signals implemented an update of sensory representations and functionally reconfigured a small subpopulation of S1 neurons that were differentially modulated by reward-history. Functional remapping of these neurons crucially depended on top-down inputs, as chemogenetic silencing of lateral OFC neurons disrupted reversal learning and impaired plastic changes in these outcome-sensitive S1 neurons. Our results reveal the presence of long-range cortical interactions between cellular ensembles in higher and lower-order brain areas specifically recruited during context-dependent learning and task-switching. Such interactions crucially implement history-dependent reward-value computations and error heuristics, which, in turn, help guide adaptive behaviour.

neuroscience↗

bioRxiv2020

Mechanical Instability of Adherens Junctions Overrides Intrinsic Quiescence of Hair Follicle Stem Cells

Vinculin, a mechanotransducer associated with both adherens junctions (AJ) and focal adhesions (FA) plays a central role in force transmission through these cell-cell and cell-substratum contacts. Here we describe the conditional knock out (KO) of vinculin in murine skin. Remarkably, we find that the loss of vinculin function results in the loss of bulge stem cell (BuSC) quiescence. We demonstrate that vinculin KO cells are impaired in force generation resulting in mechanically weak AJs. Mechanistically, vinculin functions by keeping -catenin in a stretched conformation, which in turn regulates the retention of YAP1, another potent mechanotransducer and regulator of cell proliferation, to the junctions. Conditional KO of -catenin specifically in the BuSCs further corroborates the importance of stable AJs in the maintenance of quiescence and stemness. Altogether, our data provides definitive mechanistic insights into the hitherto unexplored regulatory link between the mechanical stability of cell-junctions and the maintenance of BuSC quiescence.

cell biology↗

bioRxiv2020

Amino-alcohol Bio-conjugate of Naproxen Exhibits Anti-inflammatory Activity through NF-κB Signaling Pathway

Naproxen sodium (Ns) is a well-known synthetic compound used vastly as a nonsteroidal anti-inflammatory drug (NSAID). Previously, we demonstrated that the hydrogels, made of Ns bio-conjugate (NBC), either with amino alcohol (NBC-1 and 2) or amino acid (NBC-3 and 4), displayed anti-inflammatory properties better than Ns, but the effectiveness was not well explored. Here, we investigated that NBC-2, conjugated with {gamma}-amino alcohol, significantly reduces the expression of pro-inflammatory proteins; such as inducible nitric oxide synthase (iNOS) and cyclooxygenase isoform-2 (COX-2), and the production of pro-inflammatory mediator nitric oxide (NO) in lipopolysaccharide and interferon-{gamma} (LPS/IFN-{gamma}) treated mouse macrophage RAW 264.7 cells, compared with bio-conjugation of {beta}-amino alcohol (NBC-1) or {beta}-amino acid (NBC-3) or -amino acid NBC (NBC-4). NBC-2 decreases the nuclear localization of transcription factors NF-{kappa}B by stabilizing its cytoplasmic functional inhibitor I{kappa}B. Moreover, NBC-2 also displays selective inhibitory effect towards COX-1 enzyme activity as determined by enzymatic assay and in silico molecular docking analysis. Thus, we suggest that NBC-2 may be used as a self-delivery anti-inflammatory drug as compared with other NBCs. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/901223v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1ab255borg.highwire.dtl.DTLVardef@121aa6eorg.highwire.dtl.DTLVardef@13c4b86org.highwire.dtl.DTLVardef@1827207_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

Opportunities for prioritizing and expanding conservation enterprise in India using carnivores as flagships

Conservation interventions in developing countries are frequently thwarted by socio-economic agendas, severely limiting the scope and rigor of biodiversity and habitat conservation. Very few ecological assessments incorporate human interests in conservation prioritization, creating asynchrony between planning and implementation. For conservation actions to be logistically feasible, multiple criteria including ecological, social, economic and administrative aspects must be considered. Understanding how these different dimensions interact spatially is also important for gauging the potential for conservation success. Here, we use a guild of select mammalian carnivores (wild canids and hyenas) in India to (i) generate distribution maps at the spatial scale of administrative sub-districts, that is relevant to management, (ii) examine ecological, social and biogeographic factors associated with their distribution, quantify key threats, and identify areas important for their conservation, (iii) use prioritization tools for balancing habitat conservation, human needs and economic growth, and (iv) evaluate the spatial congruence between areas with high conservation potential, and areas currently in focus for protection efforts, conservation investments, and infrastructure development. We find that the current Protected Area system does not adequately cover or represent diverse habitats, that there is immense potential for States to increase financial investments towards alternative conservation strategies, and, most infrastructure projects may be jeopardizing important carnivore habitats. Our framework allowed for identifying locations where conservation investments would lead to the highest dividends for flagship carnivores and associated species across habitats. We make a case for re-evaluating how large-scale prioritization assessments are made, and for broadening the purview of conservation policies in India and other developing countries.

ecology↗

bioRxiv2019

Alpha oscillations for processing saliency are generated by common cortical networks in visual attention tasks spanning wide spatial and spatio-temporal scales

The Ventral Attention Network (VAN) is involved in reorienting attention from an ongoing task when a salient (pop-out) stimulus is detected in the environment. Previous neuroimaging studies have extensively evaluated the structural and functional connectivity of the VAN. However, directed effective connectivity within the network and the neural oscillations driving it still remain elusive. Functional magnetic resonance imaging (fMRI) studies have not been able to address this issue due to lack of appropriate temporal resolution required to capture the process of reorientation. In this study, we recorded scalp electroencephalography (EEG) and behavioural data from healthy human volunteers, obtained saliency-specific spectral changes, localized the sources underlying the spectral power modulations with individual-specific structural MRI scans, reconstructed the waveforms of the sources and investigated the causal relationships between the areas of the VAN using Granger causality (GC). Using a custom-designed experiment involving visual search on static images and a dynamic motion tracking task, we investigated the neural processing of salient distractors operating at very slow and very fast time scales, respectively. Our results revealed how a task-independent but context-specific VAN encompassing the right insula, the right lateral pre-frontal cortex, the anterior and the posterior right temporo-parietal junction communicating in the alpha frequency band (8-12 Hz) supports saliency processing.

neuroscience↗

bioRxiv2019

How do thalamocortical connections shape causal structure among resting state brain networks during aging?

The human brain undergoes significant structural and functional changes across the lifespan. Our current understanding of the underlying causal relationships of dynamical changes in functional connectivity with age is limited. On average, functional connectivity within resting-state networks (RSNs) weakens in magnitude, while connections between RSNs tend to increase with age. Recent studies show that effective connectivity within and between large scale resting-state functional networks changes over the healthy lifespan. The vast majority of previous studies have focused primarily on characterizing cortical networks, with little work exploring the influence of subcortical nodes such as the thalamus on large-scale network interactions across the lifespan. Using directed connectivity and weighted net causal outflow measures applied to resting-state fMRI data, we examine the age-related changes in both cortical and thalamocortical causal interactions within and between RSNs. The three core neurocognitive networks from the triple network theory (default mode: DMN, salience: SN, and central executive: CEN) were identified independently using ICA and spatial matching of hub regions with these important RSNs previously reported in the literature. Multivariate granger causal analysis (GCA) was performed to test for directional connectivity and weighted causal outflow between selected nodes of RSNs accounting for thalamo-cortical interactions. Firstly, we observe that within-network causal connections become progressively weaker with age, and network dynamics are substantially reconfigured via strong thalamic drive particularly in the young group. Our findings manifest stronger between-network directional connectivity, which is further strongly mediated by the SN in flexible co-ordination with the CEN, and DMN in the old group compared with the young group. Hence, causal within- and between- triple network connectivity largely reflects age-associated effects of resting-state functional connectivity. Thalamo-cortical causality effects on the triple networks with age were next explored. We discovered that left and right thalamus exhibit substantial interactions with the triple networks and play a crucial role in the reconfiguration of directed connections and within network causal outflow. The SN displayed directed functional connectivity in strongly driving both the CEN and DMN to a greater extent in the older group. Notably, these results were largely replicated on an independent dataset of matched young and old individuals. Our findings based on directed functional connectivity and weighted causal outflow measures strengthen the hypothesis that balancing within and between network connectivity is perhaps critical for the preservation and flexibility of cognitive functioning with aging.

neuroscience↗

bioRxiv2019

Biophysical mechanisms to relate large-scale brain network dynamics to individual-specific variability of perception

Perception necessitates interaction amongst neuronal ensembles, the dynamics of which can be conceptualized as the emergent behavior of coupled dynamical systems. Here, we propose a detailed neurobiologically realistic model that captures the neural mechanisms of inter-individual variability observed in cross-modal speech perception. From raw EEG signals recorded from human participants when they were presented with speech vocalizations of McGurk-incongruent and congruent audio-visual (AV) stimuli, we computed the global coherence metric to capture the neural variability of large-scale networks. We identified that participants McGurk susceptibility was negatively correlated to their alpha-band global coherence. The proposed biophysical model conceptualized the global coherence dynamics emerge from coupling between the interacting neural masses - representing the sensory specific auditory/visual areas and modality non-specific associative/integrative regions. Subsequently, we could predict that an extremely weak direct AV coupling result in a decrease in alpha band global coherence - mimicking the cortical dynamics of participants with higher McGurk susceptibility. Source connectivity analysis also showed decreased connectivity between sensory specific regions in participants more susceptible to McGurk effect, thus establishing an empirical validation to the prediction. Overall, our study provides an outline to link variability in structural and functional connectivity metrics to variability of performance that can be useful for several perception & action task paradigms.

neuroscience↗

bioRxiv2019

DHHC20 palmitoyl-transferase reshapes the membrane to foster catalysis

Cysteine palmitoylation, a form of S-acylation, is a key post-translational modification in cellular signaling. This type of reversible lipidation is catalyzed by a family of integral membrane proteins known as DHHC acyltransferases. The first step in the S-acylation process is the recognition of free acyl-CoA from the lipid bilayer. The DHHC enzyme then becomes auto-acylated, at a site defined by a conserved Asp-His-His-Cys motif. This reaction entails ionization of the catalytic Cys. Intriguingly, in known DHHC structures this catalytic Cys appears to be exposed to the hydrophobic interior of the lipid membrane, which would be highly unfavorable for a negatively charged nucleophile, thus hindering auto-acylation. Here, we use biochemical and computational methods to reconcile these seemingly contradicting facts. First, we experimentally demonstrate that human DHHC20 is active when reconstituted in POPC nanodiscs. Microsecond-long all-atom molecular dynamics simulations are then calculated for hDHHC20 and for different acyl-CoA forms, also in POPC. Strikingly, we observe that hDHHC20 induces a drastic deformation in the membrane, particularly on the cytoplasmic side where auto-acylation occurs. As a result, the catalytic Cys becomes hydrated and optimally positioned to encounter the cleavage site in acyl-CoA. In summary, we hypothesize that DHHC enzymes locally reshape the membrane to foster a morphology that is specifically adapted for acyl-CoA recognition and auto-acylation.\n\nSignificance StatementPalmitoylation, the most common form of S-acylation and the only reversible type of protein lipidation, is ubiquitous in eukaryotic cells. In humans, for example, it has been estimated that as much as [~]10% of the proteome becomes palmitoylated, i.e. thousands of proteins. Accordingly, protein palmitoylation touches every important aspect of human physiology, both in health and disease. Despite its biological and biomedical importance, little is known about the molecular mechanism of the enzymes that catalyze this post-translational modification, known as DHHC acyltransferases. Here, we leverage the recently-determined atomic-resolution structure of human DHHC20 to gain novel insights into the mechanism of this class of enzymes, using both experimental and computational approaches.

biophysics↗

bioRxiv2019

Commensal-derived succinate enhances tuft cell specification and suppresses ileal inflammation

Longitudinal analysis of Crohn's disease (CD) incidence has identified an inverse correlation with helminth infestation and recent studies have revealed that intestinal tuft cell hyperplasia is critical for helminth response. Tuft cell frequency was decreased in the inflamed ilea of CD patients and a mouse model of TNF-induced Crohn's-like ileitis (TNF{Delta}ARE). Single-cell RNA sequencing paired with unbiased differential trajectory analysis of the tuft cell lineage in a genetic model of tuft cell hyperplasia (AtohKO) demonstrated that the tuft cell lineage had increased tricarboxylic acid (TCA) cycle gene signatures. Commensal microbiome-derived succinate was detected in the ileal lumen of these animals while microbiome depletion suppressed tuft cell hyperplasia. Therapeutic succinate treatment in TNF{Delta}ARE animals reduced pathology in correlation with induced tuft cell specification. We provide evidence implicating the modulatory role of intestinal tuft cells in chronic intestinal inflammation, which could facilitate leveraging this rare and elusive cell type for CD treatment.

cell biology↗

bioRxiv2019

Optimization Assisted Discovery of a Conductance Based Neuronal Network Model for the Elementary Motion Detector

We present a general optimization procedure that given a parameterized network of nonspiking conductance based compartmentally modeled neurons, tunes the parameters to elicit a desired network behavior. Armed with this tool, we address the elementary motion detector problem. Central to established theoretical models, the Hassenstein-Reichardt and Barlow-Levick detectors, are delay lines whose outputs from spatially separated locations are prescribed to be nonlinearly integrated with the direct outputs to engender direction selectivity. The neural implementation of the delays--which are substantial as stipulated by interomatidial angles--has remained elusive although there is consensus regarding the neurons that constitute the network. Assisted by the optimization procedure, we identify parameter settings consistent with the connectivity architecture and physiology of the Drosophila optic lobe, that demonstrates that the requisite delay and the concomitant direction selectivity can emerge from the nonlinear dynamics of small recurrent networks of neurons with simple tonically active synapses. Additionally, although the temporally extended responses of the neurons permit simple synaptic integration of their signals to be sufficient to induce direction selectivity, both preferred direction enhancement and null direction suppression is necessary to abridge the overall response. Finally, the characteristics of the response to drifting sinusoidal gratings are readily explained by the charging-up of the recurrent networks and their low-pass nature.

neuroscience↗

bioRxiv2019

Parallel Streams to Interconnected Networks: Organization and Reorganization of Cortical Processing During Visual Perception and Action

Visual dual stream theory posits that two distinct neural pathways of specific functional significance originate from primary visual areas and reach the inferior temporal (ventral) and posterior parietal areas (dorsal). However, there are several unresolved questions concerning the fundamental aspects of this theory. For example, is the functional dissociation between ventral and dorsal stream driven by features in input stimuli or is it driven by categorical differences between visuo-perceptual and visuo-motor functions? Is the dual stream rigid or flexible? What is the nature of the interactions between two streams? We addressed these questions using fMRI recordings on healthy human volunteers and employing stimuli and tasks that can tease out the divergence between visuo-perceptual and visuo-motor models of dual stream theory. fMRI scans were repeated after seven practice sessions that were conducted in a non-MRI environment to investigate the effects of neuroplasticity. Brain activation analysis supports an input-based functional dissociation and existence of context-dependent neuroplasticity in dual stream areas. Intriguingly, premotor cortex activation was observed in the position perception task and distributed deactivated regions were observed in all perception tasks thus, warranting a network level analysis. Dynamic causal modelling (DCM) analysis incorporating activated and deactivated brain areas during perception tasks indicates that the brain dynamics during visual perception and actions could be interpreted within the framework of predictive coding. Effectively, the network level findings point towards the existence of more intricate context-driven functional networks selective of "what" and "where" information rather than segregated streams of processing along ventral and dorsal brain regions.

neuroscience↗

bioRxiv2019

Chemogenetic activation of excitatory neurons alters hippocampal neurotransmission in a dose-dependent manner

Designer Receptors Exclusively Activated by Designer Drugs (DREADD)-based chemogenetic tools are extensively used to manipulate neuronal activity in a cell-type specific manner. Whole-cell patch-clamp recordings indicate membrane depolarization, coupled with increased neuronal firing rate, following administration of the DREADD ligand, Clozapine-N-Oxide (CNO) to activate the Gq-coupled DREADD, hM3Dq. Although hM3Dq has been used to enhance neuronal firing in order to manipulate diverse behaviors, often within thirty minutes to an hour post-CNO administration, the physiological effects on excitatory neurotransmission remain poorly understood. We investigated the influence of CNO-mediated hM3Dq DREADD activation on distinct aspects of hippocampal excitatory neurotransmission at the Schaffer collateral-CA1 synapse in hippocampal slices derived from mice expressing hM3Dq in Ca2+/calmodulin dependent protein kinase (CamKII)-positive excitatory neurons. Our results indicate a clear dose-dependent effect on fEPSP slope, with no change noted at the lower dose of CNO (1 {micro}M) and a significant, long-term decline in fEPSP slope observed at higher doses (5-20 {micro}M). Further, we noted a robust theta burst stimulus (TBS) induced long-term potentiation (LTP) in the presence of the lower CNO (1 {micro}M) dose, which was significantly attenuated at the higher CNO (20 {micro}M) dose. Whole-cell patch clamp recording revealed both complex dose-dependent regulation of excitability, and spontaneous and evoked activity of CA1 pyramidal neurons in response to hM3Dq activation across CNO concentrations. Our data indicate that CNO-mediated activation of the hM3Dq DREADD results in dose-dependent regulation of excitatory hippocampal neurotransmission, and highlight the importance of careful interpretation of behavioral experiments involving chemogenetic manipulation.

neuroscience↗

bioRxiv2019

A stochastic model for error correction of kinetochore-microtubule attachments and its coupling to the spindle assembly checkpoint

To divide replicated chromosomes equally between daughter cells kinetochores must attach to microtubules emanating from opposite poles of the mitotic spindle. Two mechanisms, namely, error correction and spindle assembly checkpoint work together to facilitate this process. The error correction mechanism recognizes and detaches erroneous kinetochore-microtubule attachments, and the spindle assembly checkpoint delays the onset of anaphase until all the kinetochores are properly attached. Kinases and phosphatases at the kinetochore play a key role in proper functioning of these two mechanisms. Here we present a stochastic model to study how the opposing activities of kinases and phosphatases at the kinetochore affect error correction of kinetochore-microtubule attachments and checkpoint signaling in budding yeast, Saccharomyces cerevisiae. We show that error correction and biorientation of chromosomes occurs efficiently when the ratio between kinase activity of Ipl1 and the activity of an opposing phosphatase is a constant (balance point), and derive an approximate analytical formula that defines the balance point. Analysis of the coupling of the spindle assembly checkpoint signal to error correction shows that its strength remains high when the Ipl1 activity is equal to (or larger than) the value specified by the balance point, and the activity of another kinase, Mps1, is much larger (approximately 30 times larger) than its opposing phosphatase (PP1). We also find that the geometrical orientation of sister chromatids does not significantly improve the probability of their reaching biorientation, which depends entirely on Ipl1-dependent microtubule detachment. Author summaryThe kinetochore, the master regulator of chromosome segregation, integrates signals from different chromosome attachment states to generate an appropriate response, like the destabilization of erroneous kinetochore-microtubule attachments, stabilization of correct attachments, maintenance of the spindle assembly checkpoint signal until all kinetochores are properly attached, and finally silencing of checkpoint when biorientation is achieved. At a molecular level the job is carried out by kinases and phosphatases. The complexity of the interactions between these kinases and phosphatases makes intuitive analysis of the control network impossible, and a systems-level model is needed to put experimental information together and to generate testable hypotheses. Here we present such a model for the process of error correction and its coupling to the spindle assembly checkpoint in budding yeast. Using the model, we characterize the balance between kinase and phosphatase activities required for removing erroneous attachments and then establishing correct stable attachments between kinetochore and microtubule. We also analyze how the balance affects the strength of the spindle assembly checkpoint signal.

systems biology↗

bioRxiv2019

UK phenomics platform for developing and validating EHR phenotypes: CALIBER

ObjectiveElectronic health records are a rich source of information on human diseases, but the information is variably structured, fragmented, curated using different coding systems and collected for purposes other than medical research. We describe an approach for developing, validating and sharing reproducible phenotypes from national structured Electronic Health Records (EHR) in the UK with applications for translational research. Materials and MethodsWe implemented a rule-based phenotyping framework, with up to six approaches of validation. We applied our framework to a sample of 15 million individuals in a national EHR data source (population based primary care, all ages) linked to hospitalization and death records in England. Data comprised continuous measurements such as blood pressure, medication information and coded diagnoses, symptoms, procedures and referrals, recorded using five controlled clinical terminologies: a) Read (primary care, subset of SNOMED-CT), b) ICD-9, ICD-10 (secondary care diagnoses and cause of mortality), c) OPCS-4 (hospital surgical procedures) and d) Gemscript Drug Codes. ResultsThe open-access CALIBER Portal (https://www.caliberresearch.org/portal) demonstrates phenotyping algorithms for 50 diseases, syndromes, biomarkers and lifestyle risk factors and provides up to six validation layers. These phenotyping algorithms have been used by 40 national/international research groups in 60 peer-reviewed publications. ConclusionHerein, we describe the UK EHR phenomics approach, CALIBER, with initial evidence of validity and use, as an important step towards international use of UK EHR data for health research.

epidemiology↗

bioRxiv2019

Bleeding in cardiac patients prescribed antithrombotic drugs: Electronic health record phenotyping algorithms, incidence, trends and prognosis

BackgroundClinical guidelines and public health authorities lack recommendations on scalable approaches to defining and monitoring the occurrence and severity of bleeding in populations prescribed antithrombotic therapy. We aimed to develop electronic health record algorithms for different bleeding phenotypes, and to determine the incidence, time trends and prognosis of bleeding in patients with incident cardiac disorders indicated for antiplatelet and/or vitamin K antagonist (VKA) therapy. MethodsWe examined linked primary care, hospital admission and death registry electronic health records (CALIBER 1998-2010, England) of patients with newly diagnosed atrial fibrillation, acute myocardial infarction, unstable angina or stable angina to develop algorithms for bleeding events. Kaplan-Meier plots were used to estimate the incidence of bleeding events and we used Cox regression models to assess prognosis for all-cause mortality, atherothrombotic events and further bleeding following bleeding events. ResultsWe present electronic health record phenotyping algorithms for bleeding based on bleeding diagnosis in primary or hospital care, symptoms, transfusion, surgical procedures, and haemoglobin values. In validation of the phenotype we estimated a positive predictive value of 0.88 (95% Cl: 0.64, 0.99) for hospitalised bleeding. Amongst 128,815 patients, 27259 (21.2%) had at least one bleeding event, with 5 year risks of bleeding of 29.1%, 21.9%, 25.3% and 23.4% following diagnoses of atrial fibrillation, acute myocardial infarction, unstable angina and stable angina respectively. Rates of hospitalised bleeding per 1000 patients more than doubled from 1.02 (95% Cl: 0.83, 1.22) in January 1998 to 2.68 (95% Cl: 2.49, 2.88) in December 2009 coinciding with increased rates of antiplatelet and VKA prescribing. Patients with hospitalised bleeding and primary care bleeding, with or without markers of severity, were at increased risk of all-cause mortality and atherothrombotic events compared to those with no bleeding. For example the hazard ratio for all-cause mortality was 1.98 (95% Cl: 1.86, 2.11) for primary care bleeding with markers of severity, and 1.99 (95% Cl: 1.92, 2.05) for hospitalised bleeding without markers of severity, compared to patients with no bleeding. ConclusionsElectronic health record bleeding phenotyping algorithms offer a scalable approach to monitoring bleeding in the population. Incidence of bleeding has doubled in incidence since 1998, affects 1 in 4 cardiac patients, and is associated with poor prognosis. Efforts are required to tackle this iatrogenic epidemic. O_LSTWhat is already known?C_LSTO_LIClinical guidelines and public health authorities lack recommendations on how to define or monitor the occurrence and severity of bleeding in populations. C_LIO_LIThis is particularly important because clinical guidelines increasingly recommend the use of one, two or three antiplatelet and vitamin K antagonist drugs to lower the risk of subsequent atherothrombotic events in common heart diseases including atrial fibrillation, acute coronary syndromes and chronic stable angina. C_LIO_LIClinical guidelines lack consistent recommendations of how to reduce the main side effect of bleeding. C_LIO_LIFor acute myocardial infarction it has been shown that combining primary care electronic health records (which include information from hospital discharge summaries) and hospital admission data can generate valid EHR disease phenotypes and provide real-world estimates of disease occurrence. C_LI O_LSTWhat is not known?C_LSTO_LIIt is not known how to define bleeding occurrence and severity in large scale, unselected populations by combining available information on bleeding diagnosis in primary or hospital care, symptoms, transfusion, surgical procedures, and haemoglobin values. C_LIO_LIThe population-based incidence, time trends and long-term prognosis of bleeding have not been evaluated in people with common cardiac disorders. C_LIO_LIComparisons of the population burden of bleeding across common cardiac disorders, such as atrial fibrillation, acute coronary syndromes and stable angina, are lacking. C_LI O_LSTWhat this study adds?C_LSTO_LIPhenotype: We developed standardised replicable EHR phenotyping algorithms defining bleeding and severity measures based on available clinical information across structured primary and hospital care EHR sources. C_LIO_LIIncidence: At 5 years of follow-up, one in five patients with cardiac disease had a bleeding event and 6.5% had fatal or severe bleeding. C_LIO_LITrends: There was approximately a two-fold increase in incidence of primary care and hospitalised bleeding between 1998 and 2010. The rate of fatal bleeding remained stable. C_LIO_LIPrognosis: Patients with bleeding recorded in primary care or in hospital admissions are at increased bleeding between 1998 and 2010. The rate of fatal bleeding remained stable, risk of all-cause death and atherothrombotic events. C_LI

epidemiology↗

bioRxiv2019

Post-translational modifications of Drosophila melanogaster HOX protein, Sex combs reduced

Homeotic selector (HOX) transcription factors (TFs) regulate gene expression that determines the identity of Drosophila segments along the anterior-posterior (A-P) axis. The current challenge with HOX proteins is understanding how they achieve their functional specificity while sharing a highly conserved homeodomain (HD) that recognize the same DNA binding sites. One mechanism proposed to regulate HOX activity is differential post-translational modification (PTM). As a first step in investigating this hypothesis, the sites of PTM on a Sex combs reduced protein fused to a triple tag (SCRTT) extracted from developing embryos were identified by Tandem Mass Spectrometry (MS/MS). The PTMs identified include phosphorylation at S185, S201, T315, S316, T317 and T324, acetylation at K218, S223, S227, K309, K434 and K439, formylation at K218, K309, K325, K341, K369, K434 and K439, methylation at S19, S166, K168 and T364, carboxylation at D108, K298, W307, K309, E323, K325 and K369, and hydroxylation at P22, Y87, P107, D108, D111, P269, P306, R310, N321, K325, Y334, R366, P392 and Y398. Of the 44 modifications, 18 map to functionally important regions of SCR. Besides a highly conserved DNA-binding HD, HOX proteins also have functionally important, evolutionarily conserved small motifs, which may be Short Linear Motifs (SLiMs). SLiMs are proposed to be preferential sites of phosphorylation. Although 6 of 7 phosphosites map to regions of predicted SLiMs, we find no support for the hypothesis that the individual S, T and Y residues of predicted SLiMs are phosphorylated more frequently than S, T and Y residues outside of predicted SLiMs.

biochemistry↗