bluuebunny/crossref_metadata_2025_split huggingface dataset:
PD-1/LAG-3 Dysfunctionality Signatures in Human Cancers
Authors: Chocarro Luisa , Fernandez-Rubio Leticia , García-Granda María Jesús , Blanco Ester , Bocanegra Ana , Echaide Miriam , Garnica Maider , Zuazo Miren , Johnston Colette , Edwards Carolyn J. , Legg James , Pierce Andrew J , Arasanz Hugo , Vera Ruth , Ausin Karina , Santamaría Enrique , Fernández-Irigoyen Joaquín , Kochan Grazyna , Escors David 
Published: March 2023

ABSTRACTA significant number of cancer patients do not benefit from PD-L1/PD-1 blockade immunotherapies. PD-1 and LAG-3 co-upregulation in T-cells is one of the major mechanisms of resistance by establishing a highly dysfunctional state in T-cells. To identify shared features associated to PD- 1/LAG-3 dysfunctionality in human cancers and T-cells, multiomic expression profiles were obtained for all TCGA cancers with high T-cell infiltration. A PD-1/LAG-3 dysfunctional signature was found which regulated immune, metabolic, genetic and epigenetic pathways. These results were validated in T-cell lines with constitutively active PD-1, LAG-3 pathways and their combination. These results uncovered distinct degrees of T-cell dysfunctionality. Global changes were cross-evaluated among T- cell lines with multiomic biopsy data to identify genetic, metabolic, and proteomic programmes regulated by PD-1/LAG-3 dysfunctionality. One of these relied on differential regulation of E3 ubiquitin ligases CBL-B and C-CBL. PD-1/LAG-3 co-blockade with a bispecific drug under clinical development but not with a combination of anti-PD-1/anti-LAG-3 antibodies achieved both CBL-B and C-CBL inhibition, reverting T-cell dysfunctionality in lung cancer patients resistant to PD-L1/PD- 1 blockade.
Testing a polygenic risk score for morphological microglial activation in Alzheimer’s disease and aging
Authors: Tio Earvin S. , Hohman Timothy J. , Milic Milos , Bennett David A. , Felsky Daniel ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: March 2023

AbstractNeuroinflammation and the activation of microglial cells are among the earliest events in Alzheimer’s disease (AD). However, direct observation of microglia in living people is not currently possible. Here, we indexed the heritable propensity for neuroinflammation with polygenic risk scores (PRS), using results from a recent genome-wide analysis of a validated post-mortem measure of morphological microglial activation. We sought to determine whether a PRS for microglial activation (PRSmic) could augment the predictive performance of existing AD PRSs for late-life cognitive impairment. First, PRSmicwere calculated and optimized in a calibration cohort (Alzheimer’s Disease Neuroimaging Initiative (ADNI), n=450), with resampling. Second, predictive performance of optimal PRSmicwas assessed in two independent, population-based cohorts (total n=212,237). Our PRSmicshowed no significant improvement in predictive power for either AD diagnosis or cognitive performance. Finally, we explored associations of PRSmicwith a comprehensive set of imaging and fluid AD biomarkers in ADNI. This revealed some nominal associations, but with inconsistent effect directions. While genetic scores capable of indexing risk for neuroinflammatory processes in aging are highly desirable, more well-powered genome-wide studies of microglial activation are required. Further, biobank-scale studies would benefit from phenotyping of proximal neuroinflammatory processes to improve the PRS development phase.
FRESH™ 3D Bioprinted Cardiac Tissue, a Bioengineered Platform for in vitro Toxicology and Pharmacology
Authors: Finkel Samuel , Sweet Shannon , Locke Tyler , Smith Sydney , Wang Zhefan , Sandini Christopher , Imredy John P. , He Yufang , Durante Marc , Lagrutta Armando , Feinberg Adam , Lee Andrew 
Published: March 2023

ABSTRACTThere is critical need for a predictive model of human cardiac physiology in the drug development process for assessment of compound toxicology and pharmacology. In vitro two-dimensional monolayer culture of cardiomyocytes provides biochemical and cellular readouts, and in vivo small and large animal models provide information on systemic cardiovascular response. However, there remains a significant gap in these models due to an incomplete recapitulation of adult human cardiovascular physiology, which results in more difficult safety interpretations. Recent efforts in developing in vitro models from engineered heart tissues have demonstrated potential for bridging this gap using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) in a three-dimensional tissue structure. Here we advance this paradigm by implementing FRESH™ 3D bioprinting to build human cardiac tissues in a medium throughput, well-plate format with controlled tissue architecture, tailored cellular composition, and native-like physiological function, specifically in its adrenergic agonist drug response. To do this, we combined hiPSC-CMs, endothelial cells and fibroblasts in a cellular bioink and FRESH™ 3D bioprinted this mixture in the format of a thin tissue strip stabilized on a tissue fixture. Our results confirmed that FRESH™ 3D bioprinted cardiac tissues could be fabricated directly in a 24-well plate format, were composed of dense and highly aligned hiPSC-CMs at >600 million cells/mL, and within 14 days demonstrated reproducible calcium transients and fast conduction velocity of ∼25 cm/s. Interrogation of these cardiac tissues with the ß-adrenergic receptor agonist isoproterenol showed native-like positive chronotropic and inotropic responses, a combination of responses that is not typically observed in 2D monolayer models or standard 3D engineered heart tissue approaches. These results confirm that FRESH™ 3D bioprinted cardiac tissues represents a novel in vitro platform that enables early in vitro pharmacology and toxicology screening.
Portable X-ray Fluorescence for Measuring Lead in the Hair of Wild Mammals
Authors: Jones Evie M. , Bengsen Andrew J. , Specht Aaron J. , Koch Amelia J. , Hamede Rodrigo K. , Jones Menna E. , Hampton Jordan O. 
Published: March 2023

AbstractLead exposure threatens scavenging wildlife globally. For inexpensive estimation of lead concentration in bones from avian scavengers, portable X-ray fluorescence (XRF) devices have been trialed. However, portable XRF has not been validated for tissue lead measurement in non-human mammalian scavengers. We evaluated portable XRF for hair lead measurement in the endangered Tasmanian devil (Sarcophilus harrisii). We first analyzed large (∼1.0 g) hair samples from 39 deceased animals from southeastern Tasmania via portable XRF and then inductively-coupled plasma mass spectrometry (ICP-MS) (validation study). We then measured lead concentrations via portable XRF only in 61 small (∼0.1 g) hair samples from live devils from a plantation landscape (plantation study). Portable XRF measures of hair lead levels were positively correlated with ICP-MS values (R2= 0.61). In the validation study, 95% of sampled Tasmanian devils had relatively low lead levels (< 2 mg/kg), but the remaining two showed elevated lead levels (> 15 mg/kg). Mean lead levels in the plantation study and validation study were not significantly different. Our preliminary results suggest that portable XRF can provide a useful measure of differences in lead levels in wildife hair over a coarse scale. We provide recommendations for further research and refinement of this method.SynopsisPortable XRF can provide inexpensive and non-destructive analysis of environmental contaminants in wildlife. We present the first evaluation of portable XRF for analysis of lead contamination in mammalian scavenger hair.
Constitutively synergistic multiagent drug formulations targeting MERTK, FLT3, and BCL-2 for treatment of AML
Authors: Kelvin James M , Jain Juhi , Thapa Aashis , Qui Min , Birnbaum Lacey A , Moore Samuel G , Zecca Henry , Summers Ryan J , Costanza Emma , Uricoli Biaggio , Wang Xiaodong , Jui Nathan T , Fu Haian , Du Yuhong , DeRyckere Deborah , Graham Douglas K , Dreaden Erik C 
Published: March 2023

ABSTRACTAlthough high-dose, multi-agent chemotherapy has improved leukemia survival rates in recent years, treatment outcomes remain poor in high-risk subsets, including acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) in infants. Development of new, more effective therapies for these patients is therefore an urgent, unmet clinical need. To address this challenge, we developed a nanoscale combination drug formulation that exploits ectopic expression of MERTK tyrosine kinase and dependency on BCL-2 family proteins for leukemia cell survival in pediatric AML andMLL-rearranged precursor B-cell ALL (infant ALL). In a novel, high-throughput combination drug screen, the MERTK/FLT3 inhibitor MRX-2843 synergized with venetoclax and other BCL-2 family protein inhibitors to reduce AML cell densityin vitro. Neural network models based on drug exposure and target gene expression were used to identify a classifier predictive of drug synergy in AML. To maximize the therapeutic potential of these findings, we developed a combination monovalent liposomal drug formulation that maintains ratiometric drug synergy in cell-free assays and following intracellular delivery. The translational potential of these nanoscale drug formulations was confirmed in a genotypically diverse set of primary AML patient samples and both the magnitude and frequency of synergistic responses were not only maintained but were improved following drug formulation. Together, these findings demonstrate a systematic, generalizable approach to combination drug screening, formulation, and development that maximizes therapeutic potential, was effectively applied to develop a novel nanoscale combination therapy for treatment of AML, and could be extended to other drug combinations or diseases in the future.
LiverZap: A chemoptogenetic tool for global and locally restricted hepatocyte ablation to study cellular behaviours in liver regeneration
Authors: Ambrosio Elizabeth M. G. , Bailey Charlotte S. L. , Unterweger Iris A. , Christensen Jens B. , Bruchez Marcel P. , Lundegaard Pia R. , Ober Elke A. 
Published: March 2023

AbstractThe liver restores its mass and architecture after injury. Yet, investigating morphogenetic cell behaviours and signals that repair tissue architecture at high spatiotemporal resolution remains challenging. We developed LiverZap, a tuneable chemoptogenetic liver injury model in zebrafish. LiverZap employs formation of a binary FAP-TAP photosensitiser followed by brief near-infrared illumination inducing hepatocyte-specific death and recapitulating mammalian liver injury types. The tool enables local hepatocyte ablation and extendedliveimaging of regenerative cell behaviours, critical for studying cellular interactions at the interface of healthy and damaged tissue. Applying LiverZap, we show that targeted hepatocyte ablation in a small region-of-interest is unexpectedly sufficient to trigger Liver Progenitor-like Cell (LPC)-mediated regeneration, challenging the current understanding of LPC activation. Associated dynamic bilary network rearrangement and E-cadherin relocalisation suggest modulation of cell adhesion as an integral step of LPC-mediated liver regeneration. This precisely targetable live cell ablation model will enable addressing of key regeneration paradigms.
Rhythmic tapping to a moving beat: motion kinematics overrules motion naturalness
Authors: Pérez Oswaldo , Monache Sergio Delle , Lacquaniti Francesco , Bosco Gianfranco , Merchant Hugo 
Published: March 2023

AbstractBeat induction is the cognitive ability that allow humans to listen to a regular pulse in music and move in synchrony with it. Although auditory rhythmic cues are known to induce more consistent synchronization than flashing visual metronomes, this asymmetry can be canceled out by visual moving metronomes. Here, we investigated whether the naturalness of the visual motion or its kinematics could provide a synchronization advantage over flashing metronomes. Subjects tap in sync with visual isochronous metronomes defined by vertically or horizontally accelerating and decelerating motion, either congruent or not with natural gravity, and then continue tapping with no metronome. We found that motion kinematics was the predominant factor determining rhythm synchronization, as accelerating moving metronomes in either cardinal direction produced more precise and predictive tapping than decelerating or flashing conditions. Notably, a Bayesian observer model revealed that error correction during tapping synchronization and regression towards the mean in accuracy during tapping continuation in the absence of external cues are optimal control strategies independently of the moving properties of the visual metronomes. Our results support the notion that accelerating visual metronomes convey a strong sense of beat as seen in the cueing movements of an orchestra director.
ChemEM: flexible docking of small molecules in Cryo-EM structures using difference maps
Authors: Sweeney Aaron , Mulvaney Thomas , Topf Maya 
Published: March 2023

AbstractThe rapid advancement of the “resolution revolution” has propelled cryo-electron microscopy (cryo-EM) to the forefront of structure-based drug discovery. However, the majority of cryo-EM structures are solved at medium resolution (3-4Å), an unexplored territory for small-molecule docking, due to difficulty in positioning ligands and the surrounding side-chains. Therefore, the development of software capable of reliably and automatically docking ligands into cryo-EM maps at such resolutions is of utmost importance. ChemEM is a novel method that employs cryo-EM data, difference mapping, and a physico-chemical scoring function to flexibly dock one or multiple ligands in a protein binding site. To validate its effectiveness, ChemEM was assessed using a highly curated benchmark containing 33 experimental cryo-EM structures, spanning a resolution range of 2.2-5.6 Å. In all but one case, the method placed the ligands in the density in an accurate conformation, often better than the PDB deposited solutions. Even without the use of cryo-EM density, the ChemEM scoring function outperformed the well-established docking software AutoDock Vina. Furthermore, the study demonstrates that useful information is present in the map even at low resolutions. ChemEM unlocks the potential of medium-resolution cryo-EM structures for drug discovery.
Global parameter optimisation and sensitivity analysis of antivenom pharmacokinetics and pharmacodynamics
Authors: Morris Natalie M , Blee Johanna A , Hauert Sabine 
Published: March 2023

AbstractIn recent years it has become possible to design snakebite antivenoms with diverse pharmacokinetic properties. Owing to the pharmacokinetic variability of venoms, the choice of antivenom scaffold may influence a treatment’s neutralisation coverage. Computation offers a useful medium through which to assess the pharmacokinetics and pharmacodynamics of envenomation-treatment systems, as antivenoms with identical neutralising capacities can be simulated. In this study, we simulate envenomation and treatment with a variety of antivenoms, to define the properties of effective antivenoms. Systemic envenomation and treatment were described using a two-compartment pharmacokinetic model. Treatment ofNaja sumatranaandCryptelytrops purpureomaculatusenvenomation was simulated with a set of 200,000 theoretical antivenoms across 10 treatment time delays. These two venoms are well-characterised and have differing pharmacokinetic properties. The theoretical antivenom set varied across molecular weight, dose, kon, koff, and valency. The best and worst treatments were identified using an area under the curve metric, and a global sensitivity analysis was performed to quantify the influence of the input parameters on treatment outcome. The simulations show that scaffolds of diverse molecular formats can be effective. Molecular weight and valency have a negligible direct impact on treatment outcome, however low molecular weight scaffolds offer more flexibility across the other design parameters, particularly when treatment is delayed. The simulations show konto primarily mediate treatment efficacy, with rates above 105M-1s-1required for the most effective treatments. koffhas the greatest impact on the performance of less effective scaffolds. While the same scaffold preferences for improved treatment are seen for both model snakes, the parameter bounds forC. purpureomaculatusenvenomation are more constrained. This paper establishes a computational framework for the optimisation of antivenom design.
Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops
Authors: Harada Taku , Kalfon Jérémie , Perez Monika W. , Eagle Kenneth , Braes Flora Dievenich , Batley Rashad , Heshmati Yaser , Ferrucio Juliana Xavier , Ewers Jazmin , Mehta Stuti , Kossenkov Andrew , Ellegast Jana M. , Bowker Allyson , Wickramasinghe Jayamanna , Nabet Behnam , Paralkar Vikram R. , Dharia Neekesh V. , Stegmaier Kimberly , Orkin Stuart H. , Pimkin Maxim 
Published: March 2023

AbstractLineage-defining transcription factors form densely interconnected circuits in chromatin occupancy assays, but the functional significance of these networks remains underexplored. We reconstructed the functional topology of a leukemia cell transcription network from the direct gene-regulatory programs of eight core transcriptional regulators established in pre-steady state assays coupling targeted protein degradation with nascent transcriptomics. The core regulators displayed narrow, largely non-overlapping direct transcriptional programs, forming a sparsely interconnected functional hierarchy stabilized by incoherent feed-forward loops. BET bromodomain and CDK7 inhibitors disrupted the core regulators’ direct programs, acting as mixed agonists/antagonists. The network is predictive of dynamic gene expression behaviors in time-resolved assays and clinically relevant pathway activity in patient populations.
Developing QSAR Models for the Identification of Inhibitors TargetingMycobacterium tuberculosisEnoyl-ACP Reductase Enzyme
Authors: Karolczak Aureo André , Timmers Luis Fernando S. M. , Caceres Rafael Andrade 
Published: March 2023

ABSTRACTTuberculosis is a global concern due to its high prevalence in developing countries and the ability of mycobacteria to develop resistance to current treatment regimens. In this project, we propose the use of QSAR (Quantitative Structure-Activity Relationships) modeling as a means to identify and evaluate the inhibitory activity of candidate molecules for molecular improvement stages and/or in vitro assays. This approach allows for in silico estimation, reducing research time and costs. To achieve this, we utilized the SAR (Structure-Activity Relationships) study conducted by He, Alian, and Montellano (2007), which focused on a series of arylamides tested as inhibitors of the enzyme enoyl-ACP-reductase (InhA) inMycobacterium tuberculosis. We developed both the Hansh-Fujita (classical) and CoMFA (Comparative Molecular Field Analysis) QSAR models. The classical QSAR model produced the most favorable statistical results using Multiple Linear Regression (MLR). It achieved an internal validation correlation factor R2of 0.9012 and demonstrated predictive quality with a Stone-Geisser indicator Q2of 0.8612. External validation resulted in a correlation factor R2of 0.9298 and Q2of 0.720, indicating a highly predictive mathematical model. The CoMFA Model obtained a Q2of 0.6520 in internal validation, enabling the estimation of energy fields around the molecules. This information is crucial for molecular improvement efforts. We constructed a library of small molecules, analogous to those used in the SAR study, and subjected them to the classic QSAR function. As a result, we identified ten molecules with high estimated biological activity. Molecular docking analysis suggests that these ten analogs, identified by the classical QSAR model, exhibit favorable estimated free energy of binding. In conclusion, the QSAR methodology proves to be an efficient and effective tool for searching and identifying promising drug-like molecules.
Molecular mechanisms of catalytic inhibition for active site mutations in glucose-6-phosphatase catalytic subunit 1 linked to glycogen storage disease
Authors: Sinclair Matt , Stein Richard A , Sheehan Jonathan H , Hawes Emily M , O’Brien Richard M , Tajkhorshid Emad , Claxton Derek P 
Published: March 2023

AbstractMediating the terminal reaction of gluconeogenesis and glycogenolysis, the integral membrane protein G6PC1 regulates hepatic glucose production by catalyzing hydrolysis of glucose-6-phosphate (G6P) within the lumen of the endoplasmic reticulum. Consistent with its vital contribution to glucose homeostasis, inactivating mutations in G6PC1 cause glycogen storage disease (GSD) type 1a characterized by hepatomegaly and severe hypoglycemia. Despite its physiological importance, the structural basis of G6P binding to G6PC1 and the molecular disruptions induced by missense mutations within the active site that give rise to GSD type 1a are unknown. Exploiting a computational model of G6PC1 derived from the groundbreaking structure prediction algorithm AlphaFold2 (AF2), we combine molecular dynamics (MD) simulations and computational predictions of thermodynamic stability with a robustin vitroscreening platform to define the atomic interactions governing G6P binding as well as explore the energetic perturbations imposed by disease-linked variants. We identify a collection of side chains, including conserved residues from the signature phosphatidic acid phosphatase motif, that contribute to a hydrogen bonding and van der Waals network stabilizing G6P in the active site. Introduction of GSD type 1a mutations into the G6PC1 sequence elicits changes in G6P binding energy, thermostability and structural properties, suggesting multiple pathways of catalytic impairment. Our results, which corroborate the high quality of the AF2 model as a guide for experimental design and to interpret outcomes, not only confirm active site structural organization but also suggest novel mechanistic contributions of catalytic and non-catalytic side chains.
RSV infection does not induce EMT
Authors: Talukdar Sattya N. , McGregor Brett , Osan Jaspreet K. , Hur Junguk , Mehedi Masfique 
Published: March 2023

AbstractRespiratory syncytial virus (RSV) infection does not cause severe disease in most of us despite suffering from multiple RSV infections in our lives. However, infants, young children, older adults, and immunocompromised patients are unfortunately vulnerable to RSV-associated severe diseases. A recent study suggested that RSV infection causes cell expansion, resulting in bronchial wall thickeningin vitro. Whether the virus-induced changes in the lung airway resemble epithelial-mesenchymal transition (EMT) is still unknown. Here, we report that RSV does not induce EMT in three differentin vitrolung models: the epithelial A549 cell line, primary normal human bronchial epithelial cells, and pseudostratified airway epithelium. We found that RSV increases the cell surface area and perimeter in the infected airway epithelium, which is distinct from the effects of a potent EMT inducer, TGF-β1-driven cell elongation—indicative of cell motility. A genome-wide transcriptome analysis revealed that both RSV and TGF-β1 have distinct modulation patterns of the transcriptome, which suggests that RSV-induced changes are distinct from EMT.