bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathological mechanisms and candidate therapeutic approaches in the hearing loss of mice carrying humanMIR96mutations
Authors: Lewis Morag A , Lachgar-Ruiz Maria , Di Domenico Francesca , Duddy Graham , Chen Jing , Fernandez Sergio , Morin Matias , Williams Gareth , Moreno Pelayo Miguel Angel , Steel Karen P 
Published: February 2024

AbstractProgressive hearing loss is a common problem in the human population with no effective therapeutics currently available. However, it has a strong genetic contribution, and investigating the genes and regulatory interactions underlying hearing loss offers the possibility of identifying therapeutic candidates. Mutations in regulatory genes are particularly useful for this, and an example is the microRNA miR-96, a transcriptional regulator which controls hair cell maturation. Mice and humans carrying mutations inMir96all develop hearing loss, but different mutations result in different physiological, structural and transcriptional phenotypes.Here we present our characterisation of two lines of mice carrying different human mutations knocked-in toMir96. While mice homozygous for either mutation are profoundly deaf from two weeks old, the heterozygous phenotypes differ markedly, with only one mutation resulting in hearing impairment in heterozygosis. Investigations of the structural phenotype showed that one mutation appears to lead to synaptic defects, while the other has a much more severe effect on the hair cell stereociliary bundles. Transcriptome analyses revealed a wide range of misregulated genes in both mutants which were notably dissimilar. We used the transcriptome analyses to investigate candidate therapeutics, and tested one, finding that it delayed the progression of hearing loss in heterozygous mice.Our work adds further support for the importance of the gain of novel targets in microRNA mutants, and offers a proof of concept for the identification of pharmacological interventions to maintain hearing.
The polyamine transporter ATP13A3 mediates DFMO-induced polyamine uptake in neuroblastoma
Authors: Azfar Mujahid , Gao Weiman , Van den Haute Chris , Xiao Lin , Karsa Mawar , Pandher Ruby , Ronca Emma , Bongers Angelika , Karsa Ayu , Spurling Dayna , Guo Xinyi , Mayoh Chelsea , Burns Mark R. , Verhelst Steven H.L. , Norris Murray D. , Haber Michelle , Vangheluwe Peter , Somers Klaartje 
Published: February 2024

AbstractHigh-risk neuroblastomas, often associated withMYCNoncogene amplification, are addicted to polyamines, small polycations vital for cellular functioning. We have shown that neuroblastoma cells increase polyamine uptake when exposed to the polyamine biosynthesis inhibitor DFMO, currently in clinical trial, and that this mechanism limits the efficacy of the drug. While this finding resulted in the clinical development of polyamine transport inhibitors including AMXT 1501, presently under clinical investigation in combination with DFMO, the mechanisms and transporters involved in DFMO-induced polyamine uptake are unknown. Knockdown of ATP13A3, a member of the P5B-ATPase family, limited basal and DFMO-induced polyamine uptake, attenuatedMYCN-amplified and non-MYCN-amplified neuroblastoma cell growth and potentiated the inhibitory effects of DFMO. Overexpression of ATP13A3 in neuroblastoma cells increased polyamine uptake, which was inhibited by AMXT 1501, highlighting ATP13A3 as a key target of the drug. The association between high ATP13A3 expression and poorer survival in neuroblastoma further supports a role of this transporter in neuroblastoma progression. Thus, this study identified ATP13A3 as a critical regulator of basal and DFMO-induced polyamine uptake and a novel therapeutic target for neuroblastoma.Graphical Abstract
Identification of SEC61B as a novel regulator of calcium flux and platelet hyperreactivity in diabetes mellitus
Authors: Kong Yvonne X , Rehan Rajan , Moreno Cesar L , Madsen Søren , Zhang Yunwei , Zhao Huiwen , Houlahan Callum , Cartland Siân P , Robertshaw Declan , Trang Vincent , Liang Ong Frederick Jun , Cielesh Michelle , Cooke Kristen C , Potter Meg , Stӧckli Jacqueline , Morahan Grant , Kalev-Zylinska Maggie , Rondina Matthew T , Schulman Sol , Yang Jean , Neely G Gregory , James David , Kavurma Mary M , Hocking Samantha , Twigg Stephen M , Weaver James , Larance Mark , Passam Freda H 
Published: February 2024

AbstractHigh platelet reactivity is associated with adverse clinical events and is more frequent in people with diabetes mellitus (DM). To better understand platelet dysfunction in DM, we performed a proteomic analysis in platelets from a matched cohort of 34 people without, and 42 people with type 2 DM. The cohorts were matched by clinical characteristics including age, sex, and coronary artery disease burden. Using high sensitivity unbiased proteomics, we consistently identified over 2,400 intracellular proteins, and detected proteins that are differentially released by platelets from people with diabetes in response to low dose thrombin. Importantly, we identified the endoplasmic reticulum (ER) protein SEC61 translocon subunit beta (SEC61B) was increased in platelets from humans and mice within vivohyperglycemia. SEC61B was increased in megakaryocytes in mouse models of diabetes, in association with megakaryocyte ER stress. A rise in cytosolic calcium is a key aspect in platelet activation, and the SEC61 translocon is known to act as a channel for ER calcium leak. We demonstrate that cultured cells overexpressing SEC61B have increased calcium flux and decreased protein synthesis. In accordance, hyperglycemic mouse platelets mobilized more calcium to the cytosol and had lower protein synthesis compared with normoglycemic platelets. Independently,in vitroinduction of ER stress increased platelet SEC61B expression and markers of platelet activation. We propose a mechanism whereby ER stress-induced upregulation of platelet SEC61B leads to increased cytosolic calcium, potentially contributing to platelet hyperactivity in people with diabetes.Key PointsPlatelet SEC61B is increased in hyperglycemia and contributes to increased endoplasmic reticulum (ER) calcium leakIncreased ER calcium leak is associated with ER stress and platelet hyperactivity
Local Delivery of Soluble Fractalkine (CX3CL1) Peptide Restore Ribbon Synapses After Noise-Induced Cochlear Synaptopathy
Authors: Manickam Vijayprakash , Maity Sibaprasad , Murali Sree Varshini , Gawande Dinesh Y. , Stothert Andrew R. , Batalkina Lyudamila , Cardona Astrid , Kaur Tejbeer 
Published: February 2024

AbstractEfficacy of chemokine fractalkine isoforms was evaluated for restoration of loss of inner hair cell ribbon synapses and hearing after noise-induced cochlear synaptopathy (NICS). Previously, we have demonstrated a critical role for fractalkine signaling axis (CX3CL1-CX3CR1) in synaptic repair where in the presence of fractalkine receptor (CX3CR1) expressed by cochlear macrophages, the damaged synapses are spontaneously repaired. Here, we examined whether overexpression of fractalkine ligand (CX3CL1 or FKN) in the form of a peptide is effective in restoring the lost synapses and hearing after NICS. Remarkably, single transtympanic (TT) injection of soluble isoform of FKN (sFKN) peptide at 1 day after synaptopathic noise trauma showed significant recovery of ABR thresholds, ABR peak I amplitudes and ribbon synapses in both FKN-wildtype and knockout mice when compared to mice injected with full length membrane-bound FKN peptide (mFKN). Mechanistically, sFKN peptide treatment increased macrophage numbers in the cochlea and in the absence of those macrophages, sFKN failed to restore loss of synapses and hearing after NICS. Furthermore, sFKN treatment attenuated cochlear inflammation after noise overexposure without altering the expression of CX3CR1. Finally, sFKN peptide was detectable inside the cochlea localized to the sensory epithelium for 24 hours after TT injection. These data provide a robust proof-of-principle that local delivery of an immune factor, sFKN is effective in restoring lost ribbon synapses and hearing after NICS in a macrophage-dependent manner and highlights the potential of sFKN as an immunotherapy for cochlear synaptopathy due to noise or aging.SummaryTranstympanic delivery of soluble FKN peptide is effective in restoring lost inner hair cell ribbon synapses and hearing after noise-induced cochlear synaptopathy in a macrophage-dependent manner.
Uncovering the Interleukin-12 Pharmacokinetic Desensitization Mechanism and Its Consequences with Mathematical Modeling
Authors: DeBonis Jonathon , Veiseh Omid , Igoshin Oleg A. 
Published: February 2024

AbstractThe cytokine interleukin-12 (IL-12) is a potential immunotherapy because of its ability to induce a Th1 immune response. However, success in the clinic has been limited due to a phenomenon called IL-12 desensitization – the trend where repeated exposure to IL-12 leads to reduced IL-12 concentrations (pharmacokinetics) and biological effects (pharmacodynamics). Here, we investigated IL-12 pharmacokinetic desensitization via a modeling approach to (i) validate proposed mechanisms in literature and (ii) develop a mathematical model capable of predicting IL-12 pharmacokinetic desensitization. Two potential causes of IL-12 pharmacokinetic desensitization were identified: increased clearance or reduced bioavailability of IL-12 following repeated doses. Increased IL-12 clearance was previously proposed to occur due to the upregulation of IL-12 receptor on T-cells that causes increased receptor-mediated clearance in the serum. However, our model with this mechanism, the accelerated-clearance model, failed to capture trends in clinical trial data. Alternatively, our novel reduced-bioavailability model assumed that upregulation of IL-12 receptor on T-cells in the lymphatic system leads to IL-12 sequestration, inhibiting the transport to the blood. This model accurately fits IL-12 pharmacokinetic data from three clinical trials, supporting its biological relevance. Using this model, we analyzed the model parameter space to illustrate that IL-12 desensitization occurs over a robust range of parameter values and to identify the conditions required for desensitization. We next simulated local, continuous IL-12 delivery and identified several methods to mitigate systemic IL-12 exposure. Ultimately, our results provide quantitative validation of our proposed mechanism and allow for accurate prediction of IL-12 pharmacokinetics over repeated doses.
The evolutionary dynamics of alternative splicing during primate neuronal differentiation
Authors: Ritter Alex , Wallace Andrew , Ronaghi Neda , Sanford Jeremy R 
Published: February 2024

ABSTRACTAlternative splicing (AS) is emerging as an important regulatory process for complex biological processes such as neuronal differentiation. To uncover the functional consequences of AS during neuronal differentiation we performed a comparative transcriptomic analysis using human, rhesus, chimpanzee and orangutan pluripotent stem cells. Transcriptomic studies commonly involve the identification and quantification of alternative processing events, but the need for predicting the functional consequences of changes to the relative inclusion of alternative events remains largely unaddressed. Many tools exist for the former task, albeit often limited to rudimentary event types. Few tools exist for the latter task; each with significant limitations. To address these issues we developed junctionCounts, which captures both simple and complex pairwise AS events and quantifies them with straightforward exon-exon and exon-intron junction reads in RNA-seq data, performing competently among similar tools in terms of sensitivity, false discovery and quantification accuracy. Its partner utility, cdsInsertion identifies transcript coding sequence information, including the presence of premature termination codons, gathered viain silicotranslation from annotated start codons. It then couples transcript-level information to AS events to predict functional effects, i.e. nonsense-mediated decay (NMD). We used junctionCounts and related tools to discover both conserved and species-specific splicing dynamics as well as regulation of NMD during differentiation. Our work demonstrates this tool’s capacity to robustly characterize AS and bridge the gap of predicting its potential effect on mRNA isoform fate.GRAPHICAL ABSTRACTjunctionCounts is an alternative splicing analysis tool that identifies both simple and complex splicing events from a gene annotation and then measures their percent spliced-in from mapped RNA-seq junction reads.
The Dorsal Column Nuclei Scale Mechanical Sensitivity in Naive and Neuropathic Pain States
Authors: Upadhyay Aman , Gradwell Mark A. , Vajtay Thomas J. , Conner James , Sanyal Arnab A. , Azadegan Chloe , Patel Komal R. , Thackray Joshua K. , Bohic Manon , Imai Fumiyasu , Ogundare Simon O. , Yoshida Yutaka , Abdus-Saboor Ishmail , Azim Eiman , Abraira Victoria E. 
Published: February 2024

SUMMARYTactile perception relies on reliable transmission and modulation of low-threshold information as it travels from the periphery to the brain. During pathological conditions, tactile stimuli can aberrantly engage nociceptive pathways leading to the perception of touch as pain, known as mechanical allodynia. Two main drivers of peripheral tactile information, low-threshold mechanoreceptors (LTMRs) and postsynaptic dorsal column neurons (PSDCs), terminate in the brainstem dorsal column nuclei (DCN). Activity within the DRG, spinal cord, and DCN have all been implicated in mediating allodynia, yet the DCN remains understudied at the cellular, circuit, and functional levels compared to the other two. Here, we show that the gracile nucleus (Gr) of the DCN mediates tactile sensitivity for low-threshold stimuli and contributes to mechanical allodynia during neuropathic pain in mice. We found that the Gr contains local inhibitory interneurons in addition to thalamus-projecting neurons, which are differentially innervated by primary afferents and spinal inputs. Functional manipulations of these distinct Gr neuronal populations resulted in bidirectional changes to tactile sensitivity, but did not affect noxious mechanical or thermal sensitivity. During neuropathic pain, silencing Gr projection neurons or activating Gr inhibitory neurons was able to reduce tactile hypersensitivity, and enhancing inhibition was able to ameliorate paw withdrawal signatures of neuropathic pain, like shaking. Collectively, these results suggest that the Gr plays a specific role in mediating hypersensitivity to low-threshold, innocuous mechanical stimuli during neuropathic pain, and that Gr activity contributes to affective, pain-associated phenotypes of mechanical allodynia. Therefore, these brainstem circuits work in tandem with traditional spinal circuits underlying allodynia, resulting in enhanced signaling of tactile stimuli in the brain during neuropathic pain.
Subunit Communication within Dimeric SF1 DNA Helicases
Authors: Nguyen Binh , Hsieh John , Fischer Christopher J. , Lohman Timothy M. 
Published: February 2024

AbstractMonomers of the Superfamily (SF) 1 helicases,E. coliRep and UvrD, can translocate directionally along single stranded (ss) DNA, but must be activated to function as helicases. In the absence of accessory factors, helicase activity requires Rep and UvrD homo-dimerization. The ssDNA binding sites of SF1 helicases contain a conserved aromatic amino acid (Trp250 in Rep and Trp256 in UvrD) that stacks with the DNA bases. Here we show that mutation of this Trp to Ala eliminates helicase activity in both Rep and UvrD. Rep(W250A) and UvrD(W256A) can still dimerize, bind DNA, and monomers still retain ATP-dependent ssDNA translocase activity, although with lower processivity than wild type monomers. Although neither wtRep monomers nor Rep(W250A) monomers possess helicase activity by themselves, using both ensemble and single molecule methods, we show that helicase activity is achieved upon formation of a Rep(W250A)/wtRep hetero-dimer. An ATPase deficient Rep monomer is unable to activate a wtRep monomer indicating that ATPase activity is needed in both subunits of the Rep hetero-dimer. We find the same results withE. coliUvrD and its equivalent mutant (UvrD(W256A)). Importantly, Rep(W250A) is unable to activate a wtUvrD monomer and UvrD(W256A) is unable to activate a wtRep monomer indicating that specific dimer interactions are required for helicase activity. We also demonstrate subunit communication within the dimer by virtue of Trp fluorescence signals that only are present within the Rep dimer, but not the monomers. These results bear on proposed subunit switching mechanisms for dimeric helicase activity.
Engineering a three-dimensional multilayer multicellular model of endometrial cancer for high throughput drug screening and novel treatment methods
Authors: Cadena Ines A , Rowlands Claire , Buchanan Mina R , Jenne Molly A , Keefe Bailey , Almer Alyssa , Obasi Ndubuisi , Harris Conor G , Rochefort Willie E , Givens Brittany E. , Fogg Kaitlin C 
Published: February 2024

ABSTRACTEndometrial cancer is one of the most common gynecological cancers in the world, with an estimated 382,000 new cases and 90,000 deaths each year. There is no specific treatment, as the underlying causes of endometrial cancer neoplasia are poorly understood. This study focuses on the development and validation of a three-dimensional (3D)in vitromultilayer, multicellularhydrogel that facilitates drug screening analysis. We hypothesized that a specific combination of natural (collagen type I and IV, fibrinogen, fibronectin, Laminin) and synthetic (GELMA, PEGDA) polymers would maximize microvessel formation and cell invasion. The 3D model incorporates human microvascular endothelial cells (hMVEC) and endometrial cancer cells (HEC-1A) atop hydrogel formulations mimicking cell-specific extracellular matrix components. Using a D-optimal experimental design, 45 hydrogel combinations were generated. The predicted hydrogel formulation to maximize all cell responses enhanced higher microvessel formation and cancer invasion compared to the gold standard Matrigel. Subsequent validation emphasizes the importance of a disease-specific model and cell crosstalk in maximizing microvessel formation and cancer invasion. The optimized 3D model adeptly captures variances in cell responses among endometrial cancer cell lines from distinct stages. Finally, the platform is employed to compare cell viability, microvessel formation, and cancer invasion across Ishikawa, KLE, and HEC-1A cells after Paclitaxel exposure, delivered both as a free drug and loaded in poly(caprolactone) (PCL) nanoparticles. Overall, this study provides a valuable tool for exploring intricate interactions within the tumor microenvironment, offering a holistic understanding of cell responses and fostering the development of targeted therapeutic strategies for endometrial cancer.
Label free metabolic imaging to enhance the efficacy of Chimeric Antigen Receptor T cell therapy
Authors: Pham Dan L. , Cappabianca Daniel , Forsberg Matthew H. , Weaver Cole , Mueller Katherine P. , Tommasi Anna , Vidugiriene Jolanta , Lauer Anthony , Sylvester Kayla , Bugel Madison , Capitini Christian M. , Saha Krishanu , Skala Melissa C. 
Published: February 2024

AbstractChimeric antigen receptor (CAR) T cell therapy for solid tumors remains challenging due to the complex manufacturing process and the immunosuppressive tumor microenvironment. The manufacturing condition directly impacts CAR T cell yield, phenotype, and metabolism, which correlate within vivopotency and persistence. Optical metabolic imaging (OMI) is a non-invasive, label-free method to evaluate single cell metabolism based on autofluorescent metabolic coenzymes NAD(P)H and FAD. Using OMI, we identified the dominating impacts of media composition over the selection of antibody stimulation and/or cytokines on anti-GD2 CAR T cell metabolism, activation strength and kinetics, and phenotype. We demonstrated that OMI parameters were indicative of cell cycle stage and optimal gene transfer conditions for both viral transduction and electroporation-based CRISPR/Cas9. Notably, OMI accurately predicted oxidative metabolic phenotype of virus-free CRISPR-edited anti-GD2 CAR T cells that correlated to higherin vivopotency against neuroblastoma. Our data supports OMI’s potential as a robust, sensitive analytical tool that enables dynamic and optimal manufacturing conditions for increased CAR T cell yield and metabolic fitness.One sentence summaryAutofluorescence imaging informs manufacturing conditions that enhance yield and metabolic fitness of CAR T cells for neuroblastoma.
Manipulating syntax without taxing working memory: MEG correlates of syntactic dependencies in a Verb-Second language
Authors: Krogh Simone , Pylkkänen Liina 
Published: February 2024

ABSTRACTThe neural basis of syntax is notoriously difficult to study without working memory and lexico-semantic confounds. To tackle these challenges, we presented dependencies in minimal Danish two-word sentences using Rapid Parallel Visual Presentation (RPVP), which eliminated the tem-poral delay between a filler and gap. Our stimuli involved dependencies high and low in the tree as a function of manipulating syntactic frame (declarative, yes/no question) and verb argument structure (unergative, unaccusative, alternating unaccusative). Neural magnetoencephalography signals were increased and behaviour facilitated for sentences compared to list controls, replicating the Sentence Superiority Effect (SSE) of prior RPVP studies. Our left-lateral neural SSE at 231– 407ms co-occurred with a right-lateral fronto-medial argument structure effect, while syntactic frame affected neural signals at 500–723ms. Thus hierarchically lower dependencies elicited faster neurophysiological correlates, raising the possibility that RPVP may offer a unique window into the brain’s detection of syntax when removing temporally extended parsing decisions.
Ndufs4knockout induces transcriptomic signatures of Alzheimer’s Diseases that are partially reversed by mitochondrial complex I inhibitor
Authors: Gao Huanyao , Jensen Kate , Nesbit Jarred , Ostroot Mark , Baloni Priyanka , Funk Cory , Trushina Eugenia 
Published: February 2024

AbstractMitochondrial dysfunction is well documented in Alzheimer’s Disease (AD). However, whether it instigates the onset of AD remains unclear. We demonstrate that a reduction of complex I activity in wild type (WT) mice caused by a global knockout ofNdufs4, an accessory mitochondrial complex I subunit, was sufficient to induce transcriptomic changes in the brain reminiscent of those observed in AD patients and familial mouse models of AD. Reduced complex I activity affected expression of genes in the networks related to mitochondrial homeostasis, neuronal and synaptic function. Transcriptomic signatures in male and femaleNdufs4-/-mice reflected a different severity of AD phenotype. Unexpectedly, these changes were partially rescued by a neuroprotective small molecule mild complex I inhibitor CP2. Consistent with studies in AD mice, CP2 treatment inNdufs4-/-mice augmented the expression of genes associated with mitochondrial biogenesis and turnover, synaptic activity, autophagy, redox balance, and reduced expression of genes related to inflammation. FemaleNdufs4-/-mice demonstrated a greater reversal of gene expression toward WT mice. These studies provide further support for mitochondria as a causative factor of AD pathophysiology and complex I as a putative therapeutic target.