bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of IFNγ production by ZFP36L2 in T cells is context-dependent
Authors: Zandhuis Nordin D. , Guislain Aurélie , Popalzij Abeera , Engels Sander , Popović Branka , Turner Martin , Wolkers Monika C. 
Published: February 2024

ABSTRACTCD8+T cells kill target cells by releasing cytotoxic molecules and pro-inflammatory cytokines, such as TNF and IFNγ. The magnitude and duration of cytokine production is defined by post-transcriptional regulation, and a critical regulator herein are RNA-binding proteins (RBPs). Although the functional importance of RBPs in regulating cytokine production is established, the kinetics and mode of action through which RBPs control cytokine production is not well understood. Previously, we showed that the RBP ZFP36L2 blocks translation of pre-formed cytokine encoding mRNA in quiescent memory T cells. Here, we uncover that ZFP36L2 regulates cytokine production in a context-dependent manner. T cell-specific deletion of ZFP36L2 (CD4-cre) had no effect on T cell development, or on cytokine production during early time points (2-6h) of T cell activation. In contrast, ZFP36L2 specifically dampened the production of IFNγ during prolonged T cell activation (20-48h). ZFP36L2 deficiency also resulted in increased production of IFNγ production in tumour-infiltrating T cells that are chronically exposed to antigen. Mechanistically, ZFP36L2 regulates IFNγ production at late time points of activation by destabilizingIfngmRNA in an AU-rich element-dependent manner. Together, our results reveal that ZFP36L2 employs different regulatory nodules in effector and memory T cells to regulate cytokine production.
Synthesis and Biological Evaluation of Novel MB327 Analogs as Resensitizers for Desensitized Nicotinic Acetylcholine Receptors after Intoxication with Nerve Agents
Authors: Bernauer Tamara , Nitsche Valentin , Kaiser Jesko , Gertzen Christoph G.W. , Höfner Georg , Niessen Karin V. , Seeger Thomas , Steinritz Dirk , Worek Franz , Gohlke Holger , Wanner Klaus T. , Paintner Franz F. 
Published: February 2024

AbstractPoisoning with organophosphorus compounds, which can lead to a cholinergic crisis due to the inhibition of acetylcholinesterase and the subsequent accumulation of acetylcholine (ACh) in the synaptic cleft, is a serious problem for which treatment options are currently insufficient. Our approach to broadening the therapeutic spectrum is to use agents that interact directly with desensitized nicotinic acetylcholine receptors (nAChRs) in order to induce functional recovery after ACh overstimulation. Although MB327, one of the most prominent compounds investigated in this context, has already shown positive properties in terms of muscle force recovery, this compound is not suitable for use as a therapeutic agent due to its insufficient potency. By means ofin silicostudies based on our recently presented allosteric binding pocket at the nAChR, i.e. the MB327-PAM-1 binding site, three promising 4-aminopyridinium ion-substituted MB327 analogs (PTM0056, PTM0062 and PTM0063) were identified. In this study, we present the synthesis and biological evaluation of a series of new 4-aminopyridinium ion-substituted analogs of the aforementioned compounds (PTM0064-PTM0072), as well as hydroxy-substituted analogs of MB327 (PTMD90-0012 and PTMD90-0015) designed to substitute energetically unfavorable water clusters identified during molecular dynamics simulations. The compounds were characterized in terms of their binding affinity towards the aforementioned binding site by applying the UNC0642 MS Binding Assays and in terms of their muscle force reactivation in rat diaphragm myography. More potent compounds were identified compared to MB327, as some of them showed a higher affinity towards MB327-PAM-1 and also a higher recovery of neuromuscular transmission at lower compound concentrations. To improve the treatment of organophosphate poisoning, direct targeting of nAChRs with appropriate compounds is a key step, and this study is an important contribution to this research.
Cell state transition analysis reveals a causal network that controls critical limb ischemia
Authors: Rukhlenko Oleksii S. , McClung Joseph M. , Tuliakova Anna , Annex Brian H. , Kholodenko Boris N. 
Published: February 2024

AbstractIncreased endothelial cell (EC) permeability significantly contributes to peripheral arterial disease and its severe manifestation, critical limb ischemia (CLI). CLI remains refractory to current pharmacological interventions, often requiring limb amputation and showing how limited our knowledge is about signaling pathways that control EC states. Here, we utilize a two-pronged approach, employing cell State Transition Assessment and Regulation (cSTAR) analyses to both the published knowledge (e.g., LINCS data portal) and our own transcriptomics data collected from CLI patients and healthy adult (HA) control. We identified CLI and HA transcriptomics patterns and reconstructed causal network that controls transitions between EC states associated with CLI and HA. Contrary to general belief, our study demonstrates that VEGF administration slightly promotes the CLI EC states, indicating VEGF ineffectiveness in enhancing perfusion of CLI tissue.Based on the unveiled control network, we suggest targets whose inhibition would reverse CLI EC states closer to HA states.
Closed-loop electrical stimulation to prevent focal epilepsy progression and long-term memory impairment
Authors: Ferrero Jose J. , Hassan Ahnaf R. , Yu Zelin , Zhao Zifang , Ma Liang , Wu Cynthia , Shao Shan , Kawano Takeshi , Engel Judah , Doyle Werner , Devinsky Orrin , Khodagholy Dion , Gelinas Jennifer N. 
Published: February 2024

AbstractInterictal epileptiform discharges (IEDs) are ubiquitously expressed in epileptic networks and disrupt cognitive functions. It is unclear whether addressing IED-induced dysfunction could improve epilepsy outcomes as most therapeutics target seizures. We show in a model of progressive hippocampal epilepsy that IEDs produce pathological oscillatory coupling which is associated with prolonged, hypersynchronous neural spiking in synaptically connected cortex and expands the brain territory capable of generating IEDs. A similar relationship between IED-mediated oscillatory coupling and temporal organization of IEDs across brain regions was identified in human subjects with refractory focal epilepsy. Spatiotemporally targeted closed-loop electrical stimulation triggered on hippocampal IED occurrence eliminated the abnormal cortical activity patterns, preventing spread of the epileptic network and ameliorating long-term spatial memory deficits in rodents. These findings suggest that stimulation-based network interventions that normalize interictal dynamics may be an effective treatment of epilepsy and its comorbidities, with a low barrier to clinical translation.One-Sentence SummaryTargeted closed-loop electrical stimulation prevents spread of the epileptic network and ameliorates long-term spatial memory deficits.
Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex
Authors: Huuki-Myers Louise A. , Montgomery Kelsey D. , Kwon Sang Ho , Cinquemani Sophia , Eagles Nicholas J. , Gonzalez-Padilla Daianna , Maden Sean K. , Kleinman Joel E. , Hyde Thomas M. , Hicks Stephanie C. , Maynard Kristen R. , Collado-Torres Leonardo 
Published: February 2024

AbstractBackgroundCellular deconvolution of bulk RNA-sequencing (RNA-seq) data using single cell or nuclei RNA-seq (sc/snRNA-seq) reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as human brain. Computational methods for deconvolution have been developed and benchmarked against simulated data, pseudobulked sc/snRNA-seq data, or immunohistochemistry reference data. A major limitation in developing improved deconvolution algorithms has been the lack of integrated datasets with orthogonal measurements of gene expression and estimates of cell type proportions on the same tissue sample. Deconvolution algorithm performance has not yet been evaluated across different RNA extraction methods (cytosolic, nuclear, or whole cell RNA), different library preparation types (mRNA enrichment vs. ribosomal RNA depletion), or with matched single cell reference datasets.ResultsA rich multi-assay dataset was generated in postmortem human dorsolateral prefrontal cortex (DLPFC) from 22 tissue blocks. Assays included spatially-resolved transcriptomics, snRNA-seq, bulk RNA-seq (across six library/extraction RNA-seq combinations), and RNAScope/Immunofluorescence (RNAScope/IF) for six broad cell types. TheMean Ratiomethod, implemented in theDeconvoBuddiesR package, was developed for selecting cell type marker genes. Six computational deconvolution algorithms were evaluated in DLPFC and predicted cell type proportions were compared to orthogonal RNAScope/IF measurements.ConclusionsBisqueandhspewere the most accurate methods, were robust to differences in RNA library types and extractions. This multi-assay dataset showed that cell size differences, marker genes differentially quantified across RNA libraries, and cell composition variability in reference snRNA-seq impact the accuracy of current deconvolution methods.
Genome-wide Nucleosome Positioning and Associated Features uncovered with Interpretable Deep Residual Networks
Authors: Masoudi-Sobhanzadeh Yosef , Li Shuxiang , Peng Yunhui , Panchenko Anna R 
Published: February 2024

AbstractNucleosomes represent elementary building units of eukaryotic chromosomes and consist of DNA wrapped around a histone octamer flanked by linker DNA segments. Nucleosomes are central in epigenetic pathways and their genomic positioning is associated with regulation of gene expression, DNA replication, DNA methylation and DNA repair, among other functions. Building on prior discoveries, that DNA sequences noticeably affect nucleosome positioning, our objective is to identify nucleosome positions and related features across entire genome. Here we introduce an interpretable framework based on the concepts of deep residual networks (NuPose). Trained on high-coverage human experimental MNase-seq data, NuPose is able to learn sequence and structural patterns and their dependencies associated with nucleosome organization in human genome. NuPoSe can be used to identify nucleosomal regions, not covered by experiments, and be applied to unseen data from different organisms and cell types. Our findings point to 43 informative DNA sequence features, most of them constitute tri-nucleotides, di-nucleotides and one tetra-nucleotide. Most features are significantly associated with the structural characteristics, namely, periodicity of nucleosomal DNA and its location with respect to a histone octamer. Importantly, we show that linker DNA features contribute ∼10% to the quality of the prediction model, which together with comprehensive training sets, deep-learning architecture and feature selection may explain the advanced performance of NuPose of 80-89% accuracy.
Determination of Absolute Intramolecular Distances in Proteins by Anomalous X-ray Scattering Interferometry
Authors: Stubhan Samuel , Baptist Anna V. , Körösy Caroline , Narducci Alessandra , Moya Muñoz Gustavo Gabriel , Wendler Nicolas , Lak Aidin , Sztucki Michael , Cordes Thorben , Lipfert Jan 
Published: February 2024

ABSTRACTBiomolecular structures are typically determined using frozen or crystalline samples. Measurement of intramolecular distances in solution can provide additional insights into conformational heterogeneity and dynamics of biological macromolecules and their complexes. The established molecular ruler techniques used for this (NMR, FRET, and EPR) are, however, limited in their dynamic range and require model assumptions to determine absolute distance (distributions). Here, we introduce anomalous X-ray scattering interferometry (AXSI) for intramolecular distance measurements in proteins, which are labeled at two sites with small gold nanoparticles of 0.7 nm radius. We apply AXSI to two different cysteine-variants of maltose binding protein in the presence and absence of its ligand maltose and find distances in quantitative agreement with single-molecule FRET experiments. Our study shows that AXSI enables determination of absolute intramolecular distance distributions under virtually arbitrary solution conditions and we anticipate its broad use to characterize protein conformational ensembles and dynamics.
Medulloblastoma oncogene aberrations are not involved in tumor initiation, but essential for disease progression and therapy resistance
Authors: Okonechnikov Konstantin , Joshi Piyush , Körber Verena , Rademacher Anne , Bortolomeazzi Michele , Mallm Jan-Philipp , da Silva Patricia Benites Goncalves , Statz Britta , Sepp Mari , Sarropoulos Ioannis , Yamada-Saito Tetsuya , Vaillant Jan , Wittmann Andrea , Schramm Kathrin , Blattner-Johnson Mirjam , Fiesel Petra , Jones Barbara , Milde Till , Pajtler Kristian , van Tilburg Cornelis M. , Witt Olaf , Bochennek Konrad , Weber Katharina Johanna , Nonnenmacher Lisa , Reimann Christian , Schüller Ulrich , Mynarek Martin , Rutkowski Stefan , Jones David T.W. , Korshunov Andrey , Rippe Karsten , Westermann Frank , Thongjuea Supat , Höfer Thomas , Kaessmann Henrik , Kutscher Lena M. , Pfister Stefan M. 
Published: February 2024

AbstractDespite recent advances in understanding disease biology, treatment of Group 3/4 medulloblastoma remains a therapeutic challenge in pediatric neuro-oncology. Bulk-omics approaches have identified considerable intertumoral heterogeneity in Group 3/4 medulloblastoma, including the presence of clear single-gene oncogenic drivers in only a subset of cases, whereas in the majority of cases, large-scale copy-number aberrations prevail. However, intratumoral heterogeneity, the role of oncogene aberrations, and broad CNVs in tumor evolution and treatment resistance remain poorly understood. To dissect this interplay, we used single-cell technologies (snRNA-seq, snATAC-seq, spatial transcriptomics) on a cohort of Group 3/4 medulloblastoma with known alterations in the oncogenesMYC, MYCN, andPRDM6. We show that large-scale chromosomal aberrations are early tumor initiating events, while the single-gene oncogenic events arise late and are typically sub-clonal, butMYCcan become clonal upon disease progression to drive further tumor development and therapy resistance. We identify that the subclones are mostly interspersed across tumor tissue using spatial transcriptomics, but clear segregation is also present. Using a population genetics model, we estimate medulloblastoma initiation in the cerebellar unipolar brush cell-lineage starting from the first gestational trimester. Our findings demonstrate how single-cell technologies can be applied for early detection and diagnosis of this fatal disease.
A long non-coding RNA at thecortexlocus controls adaptive colouration in butterflies
Authors: Livraghi Luca , Hanly Joseph J. , Evans Elizabeth , Wright Charlotte J. , Loh Ling S. , Mazo-Vargas Anyi , Kamrava Kiana , Carter Alexander , van der Heijden Eva S.M. , Reed Robert D. , Papa Riccardo , Jiggins Chris D. , Martin Arnaud 
Published: February 2024

AbstractEvolutionary variation in the wing pigmentation of butterflies and moths offers striking examples of adaptation by crypsis and mimicry. Thecortexlocus has been independently mapped as the locus controlling colour polymorphisms in 14 lepidopteran species, suggesting it acts as a genomic hotspot for the diversification of wing patterns, but functional validation through protein-coding knockouts has proven difficult to obtain. Our study unveils the role of a novel long non-coding RNA (lncRNA) which we nameivory, transcribed from thecortexlocus, in modulating colour patterning in butterflies. Strikingly,ivoryexpression prefigures most melanic patterns during pupal development, suggesting an early developmental role in specifying scale identity. To test this, we generated CRISPR mosaic knock-outs in five nymphalid butterfly species and show thativorymutagenesis yields transformations of dark pigmented scales into white or light-coloured scales. Genotyping ofVanessa carduigermline mutants associates these phenotypes to small on-target deletions at the conserved first exon ofivory. In contrast,cortexgermline mutant butterflies with confirmed null alleles lack any wing phenotype, and exclude a colour patterning role for this adjacent gene. Overall, these results show that a lncRNA acts as a master switch of colour pattern specification, and played key roles in the adaptive diversification of colour patterns in butterflies.Significance statementDeciphering the genetic underpinnings of adaptive variation is fundamental for a comprehensive understanding of evolutionary processes. Long non-coding RNAs (lncRNAs) represent an emerging category of genetic modulators within the genome, yet they have been overlooked as a source of phenotypic diversity. In this study, we unveil the pivotal role of a lncRNA in orchestrating colour transitions between dark and light patterns during butterfly wing development. Remarkably, this lncRNA gene is nested within thecortexlocus, a genetic region known to control multiple cases of adaptive variation in butterflies and moths, including iconic examples of natural selection. These findings highlight the significant influence of lncRNAs in developmental regulation, and also underscore their potential as key genetic players in the evolutionary process itself.
Chondroitin sulfate glycan sulfation patterns influence histochemical labeling of perineuronal nets: a comparative study of interregional distribution in human and mouse brain
Authors: Belliveau Claudia , Théberge Stéphanie , Netto Stefanie , Rahimian Reza , Fakhfouri Gohar , Hosdey Clémentine , Davoli Maria Antonietta , Hendrickson Aarun , Hao Kathryn , Giros Bruno , Turecki Gustavo , Alonge Kimberly M. , Mechawar Naguib 
Published: February 2024

AbstractPerineuronal nets (PNNs) are a condensed subtype of extracellular matrix that form a net-like coverings around certain neurons in the brain. PNNs are primarily composed of chondroitin sulfate (CS) proteoglycans from the lectican family that consist of CS-glycosaminoglycan (CS-GAG) side chains attached to a core protein. CS disaccharides can exist in various isoforms with different sulfation patterns. Literature suggests that CS disaccharide sulfation patterns can influence the function of PNNs as well as their labeling. This study was conducted to characterize such interregional CS disaccharide sulfation pattern differences in adult human (N = 81) and mouse (N = 19) brains. Liquid chromatography tandem mass spectrometry was used to quantify five different CS disaccharide sulfation patterns, which were then compared to immunolabeling of PNNs usingWisteria Floribunda Lectin(WFL) to identify CS-GAGs and anti-aggrecan to identify CS proteoglycans. In healthy brains, significant regional and species-specific differences in CS disaccharide sulfation and single versus double-labeling pattern were identified. A secondary analysis to investigate how early-life stress (ELS) impacts these PNN features discovered that although ELS increases WFL+ PNN density, the CS-GAG sulfation code and single versus double PNN-labeling distributions remained unaffected in both species. These results underscore PNN complexity in traditional research, emphasizing the need to consider their heterogeneity in future experiments.
Increased excitability of dentate gyrus mossy cells occurs early in life in the Tg2576 model of Alzheimer’s disease
Authors: Alcantara-Gonzalez David , Kennedy Meghan , Criscuolo Chiara , Botterill Justin , Scharfman Helen E 
Published: February 2024

ABSTRACTINTRODUCTIONHyperexcitability in Alzheimer’s disease (AD) emerge early and contribute to disease progression. The dentate gyrus (DG) is implicated in hyperexcitability in AD. We hypothesized that mossy cells (MCs), regulators of DG excitability, contribute to early hyperexcitability in AD. Indeed, MCs generate hyperexcitability in epilepsy.METHODSUsing the Tg2576 model and WT mice (∼1month-old), we compared MCs electrophysiologically, assessed c-Fos activity marker, Aβ expression and mice performance in a hippocampal-dependent memory task.RESULTSTg2576 MCs exhibit increased spontaneous excitatory events and decreased inhibitory currents, increasing the charge transfer excitation/inhibition ratio. Tg2576 MC intrinsic excitability was enhanced, and showed higher c-Fos, intracellular Aβ expression, and axon sprouting. Granule cells only showed changes in synaptic properties, without intrinsic changes. The effects occurred before a memory task is affected.DISCUSSIONEarly electrophysiological and morphological alterations in Tg2576 MCs are consistent with enhanced excitability, suggesting an early role in DG hyperexcitability and AD pathophysiology.HIGHLIGHTS∘MCs from 1 month-old Tg2576 mice had increased spontaneous excitatory synaptic input.∘Tg2576 MCs had reduced spontaneous inhibitory synaptic input.∘Several intrinsic properties were abnormal in Tg2576 MCs.∘Tg2576 GCs had enhanced synaptic excitation but no changes in intrinsic properties.∘Tg2576 MCs exhibited high c-Fos expression, soluble Aβ and axonal sprouting.
Inferring Metabolic Objectives and Tradeoffs in Single Cells During Embryogenesis
Authors: Lin Da-Wei , Zhang Ling , Zhang Jin , Chandrasekaran Sriram 
Published: February 2024

AbstractWhile proliferating cells optimize their metabolism to produce biomass, the metabolic objectives of cells that perform non-proliferative tasks are unclear. The opposing requirements for optimizing each objective results in a trade-off that forces single cells to prioritize their metabolic needs and optimally allocate limited resources. To define metabolic objectives and tradeoffs in biological systems mathematically, we integrated bulk and single-cell omics data with a novel framework to infer cell objectives using metabolic modeling and machine learning. We validated this framework by identifying essential genes from CRISPR-Cas9 screens in embryonic stem cells, and by inferring the metabolic objectives of quiescent cells and during different cell-cycle phases. Applying this to embryonic cell states, we observed a decrease in metabolic entropy upon development. We further uncovered a trade-off between glutathione and biosynthetic precursors in 1-cell zygote, 2-cell embryo, and blastocyst cells, potentially representing a trade-off between pluripotency and proliferation.