bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation and Sensitivity Analysis and Cross-Validation, Demonstrating the Utility of Genteract GxE Discovery methods
Authors: Holohan Brody , Laderman Raphael 
Published: November 2020

AbstractGene-environment interactions are at the heart of why many complex traits are not fully heritable, and why prediction of disease incidence and individual response to environmental changes based on genetics has been underwhelming in utility. Understanding these interactions is the primary limiting factor for the application of personalized medicine, but current methods are not well suited for dealing with complex traits that pose both a dimensionality and sparse data problem to unsupervised analysis methods. Genteract has developed a proprietary analytical technique that allows for detection and interpretation of GxEs regarding specific pairs of a single phenotype with a single environmental factor; these methods allow us to develop a platform that can be used to predict how individuals will respond to changes in their environment based on their genetics. To validate the methods we performed two types of testing: cross-validation against a dataset of clinical study results, and application of the methods in a simulated dataset. These tests enable a greater understanding of the methods’ utility, statistical power and predictive capabilities.
Non-targeting control for MISSION® shRNA library silences SNRPD3 leading to cell death or permanent growth arrest
Authors: Czarnek Maria , Sarad Katarzyna , Karaś Agnieszka , Kochan Jakub , Bereta Joanna 
Published: November 2020

AbstractIn parallel with the expansion of RNA interference techniques evidence has been accumulating that RNAi analyses may be seriously biased due to off-target effects of gene-specific shRNAs. Our work points to another possible source of misinterpretations of shRNA-based data – off-target effects of non-targeting shRNA. We found that one such control for the MISSION® library (commercialized TRC library), SHC016, is cytotoxic. Using a lentiviral vector with inducible expression of SHC016 we proved that this shRNA induces apoptosis in murine cells and, depending on p53 status, senescence or mitotic catastrophe in human tumor cell lines. We identified SNRPD3, a core spliceosomal protein, as a major SHC016 target in several cell lines and confirmed in A549 and U251 cell lines that CRISPRi-knockdown of SNRPD3 mimics the effects of SHC016 expression. Our finding disqualifies non-targeting SHC016 shRNA and adds a new premise to the discussion about the sources of uncertainty of RNAi results.
Electrophysiological signatures of acute systemic lipopolysaccharide: potential implications for delirium science
Authors: Sultan Ziyad W , Jaeckel Elizabeth R , Krause Bryan M , Grady Sean M , Murphy Caitlin A , Sanders Robert D , Banks Matthew I 
Published: November 2020

AbstractBackgroundNovel preventive therapies are needed for postoperative delirium, which especially affects aged patients. A mouse model is presented that captures inflammation-associated cortical slow wave activity (SWA) observed in patients, allowing exploration of the mechanistic role of prostaglandin-adenosine signaling.MethodsEEG and cortical cytokine measurements (interleukin 6 [IL-6], monocyte chemoattractant protein-1 [MCP-1]) were obtained from adult and aged mice. Behavior, SWA, and functional connectivity (alpha-band weighted phase lag index) were assayed before and after systemic administration of lipopolysaccharide (LPS) +/- piroxicam (cyclooxygenase inhibitor) or caffeine (adenosine receptor antagonist). To avoid confounds from inflammation-driven changes in movement, which alter SWA and connectivity, electrophysiological recordings were classified as occurring during quiescence or movement, and propensity score matching used to match distributions of movement magnitude between baseline and LPS.ResultsLPS produces increases in cortical cytokines and behavioral quiescence. In movement-matched data, LPS produces increases in SWA (likelihood-ratio test: χ2(4)=21.51, p=0.00057), but not connectivity (χ2(4)=6.39, p=0.17). Increases in SWA associate with IL6 (p<0.001) and MCP-1 (p=0.001) and are suppressed by piroxicam (p<0.001) and caffeine (p=0.046). Aged animals compared to adult show similar LPS-induced SWA during movement, but exaggerated cytokine response and increased SWA during quiescence.ConclusionsCytokine-SWA correlations during wakefulness are consistent with observations in patients with delirium. Absence of connectivity effects after accounting for movement changes suggests decreased connectivity in patients is a biomarker of hypoactivity. Exaggerated effects in quiescent aged animals are consistent with increased hypoactive delirium in older patients. Prostaglandin-adenosine signaling may link inflammation to neural changes and hence delirium.
Physiological role of the 3’IgH CBEs super-anchor in antibody class switching
Authors: Zhang Xuefei , Yoon Hye Suk , Chapdelaine-Williams Aimee M. , Kyritsis Nia , Alt Frederick W. 
Published: November 2020

ABSTRACTIgH class switch recombination (CSR) replaces Cμ constant region (CH) exons with one of six downstream CHS by joining transcription-targeted DSBs in the Cμ switch (S) region to DSBs in a downstream S region. Chromatin loop extrusion underlies fundamental CSR mechanisms including 3’IgH regulatory region (3’IgHRR)-mediated S region transcription, CSR center formation, and deletional CSR joining. There are ten consecutive CTCF binding elements (CBEs) downstream of the 3’IgHRR, termed the “3’IgH CBEs”. Prior studies showed that deletion of eight 3’IgH CBEs did not detectably affect CSR. Here, we report that deletion of all 3’IgH CBEs impacts, to varying degrees, germline transcription and CSR of upstream S regions, except Sγ1. Moreover, deletion of all 3’IgH CBEs rendered the 6kb region just downstream highly transcribed and caused sequences within to be aligned with Sμ, broken, and joined to form aberrant CSR rearrangements. These findings implicate the 3’IgH CBEs as a critical insulator for focusing loop extrusion-mediated 3’IgHRR transcriptional and CSR activities on upstream CH locus targets.SignificanceB lymphocytes change antibody heavy chain (IgH) isotypes by a recombination/deletion process called IgH class switch recombination (CSR). CSR involves introduction of DNA breaks into a donor switch (S) region and also into one of six downstream S regions, with joining of the breaks changing antibody isotype. A chromatin super-anchor, of unknown function, is located just downstream of the IgH locus. We show that complete deletion of this super-anchor variably decreases CSR to most S regions and creates an ectopic S region downstream of IgH locus that undergoes aberrant CSR-driven chromosomal rearrangements. Based on these and other findings, we conclude that the super-anchor downstream of IgH is a critical insulator for focusing potentially dangerous CSR rearrangements to the IgH locus.
Establishment of Multi-stage Intravenous Self-administration Paradigms in Mice
Authors: Slosky Lauren M. , Pires Andrea , Bai Yushi , Clark Nicholas , Hauser Elizabeth R. , Gross Joshua D. , Porkka Fiona , Zhou Yang , Chen Xiaoxiao , Pogorelov Vladimir M. , Toth Krisztian , Wetsel William C. , Barak Lawrence S. , Caron Marc G. 
Published: November 2020

ABSTRACTA genetically tractable animal model would provide a needed strategy to resolve the biological basis of drug addiction. Intravenous self-administration (IVSA) is the gold standard for modeling cocaine and opioid addiction in animals, but technical limitations have precluded the widespread use of IVSA in mice. Here, we describe the first IVSA paradigms for mice that capture the multi-stage nature of the disease and permit predictive modeling. Mice with long-standing indwelling jugular catheters engaged in cocaine or opioid-associated lever responding that was fixed ratio- and dose-dependent, extinguished by the withholding of drug, and reinstated by the presentation of paired cues. Machine learning revealed that vulnerability to drug seeking and relapse were predicted by a mouse’sa prioriresponse to novelty, sensitivity to drug-induced locomotion, and drug-taking behavior. Application of this behavioral and analysis approach to genetically-engineered mice will facilitate the identification of the neural circuits driving addiction susceptibility and relapse and focused therapeutic development.
Using distance on the Riemannian manifold to compare representations in brain and models
Authors: Shahbazi Mahdiyar , Shirali Ali , Aghajan Hamid , Nili Hamed 
Published: November 2020

AbstractRepresentational similarity analysis (RSA) summarizes activity patterns for a set of experimental conditions into a matrix composed of pairwise comparisons between activity patterns. Two examples of such matrices are the condition-by-condition inner product matrix or the correlation matrix. These representational matrices reside on the manifold of positive semidefinite matrices, called the Riemannian manifold. We hypothesize that representational similarities would be more accurately quantified by considering the underlying manifold of the representational matrices. Thus, we introduce the distance on the Riemannian manifold as a metric for comparing representations. Analyzing simulated and real fMRI data and considering a wide range of metrics, we show that the Riemannian distance is least susceptible to sampling bias, results in larger intra-subject reliability, and affords searchlight mapping with high sensitivity and specificity. Furthermore, we show that the Riemannian distance can be used for measuring multi-dimensional connectivity. This measure captures both univariate and multivariate connectivity and is also more sensitive to nonlinear regional interactions compared to the state-of-the-art measures. Applying our proposed metric to neural network representations of natural images, we demonstrate that it also possesses outstanding performance in quantifying similarity in models. Taken together, our results lend credence to the proposition that RSA should consider the manifold of the representational matrices to summarize response patterns in the brain and models.
Profiling sensory neuron microenvironment after peripheral and central axon injury reveals key pathways for neural repair
Authors: Avraham Oshri , Feng Rui , Ewan Eric E. , Rustenhoven Justin , Zhao Guoyan , Cavalli Valeria 
Published: November 2020

ABSTRACTSensory neurons with cell bodies in dorsal root ganglia (DRG) represent a useful model to study axon regeneration. Whereas regeneration and functional recovery occurs after peripheral nerve injury, spinal cord injury or dorsal root injury is not followed by regenerative outcomes. Regeneration of sensory axons in peripheral nerves is not entirely cell autonomous. Whether the DRG microenvironment influences the different regenerative capacities after injury to peripheral or central axons remains largely unknown. To answer this question, we performed a single cell transcriptional profiling of mouse DRG in response to peripheral (sciatic nerve crush) and central axon injuries (dorsal root crush and spinal cord injury). Each cell type responded differently to the three types of injuries. All injuries increased the proportion of a cell type that shares features of both immune cells and glial cells. A distinct subset of satellite glial cells (SGC) appeared specifically in response to peripheral nerve injury. Activation of the PPARα signaling pathway in SGC, which promotes axon regeneration after peripheral nerve injury, failed to occur after central axon injuries. Treatment with the FDA-approved PPARα agonist fenofibrate increased axon regeneration after dorsal root injury. This study provides a map of the distinct DRG microenvironment responses to peripheral and central injuries at the single cell level and highlights that manipulating non-neuronal cells could lead to avenues to promote functional recovery after CNS injuries or disease.
Mucosal vaccination with cyclic-di-nucleotide adjuvants induces effective T cell homing and IL-17 dependent protection againstM. tuberculosisinfection
Authors: Jong Robyn M. , Van Dis Erik , Nguyenla Xammy , Baltodano Alexander , Pastenkos Gabrielle , Xu Chenling , Yosef Nir , McWhirter Sarah M. , Stanley Sarah A. 
Published: November 2020

AbstractThe only licensed vaccine for tuberculosis,Mycobacterium bovisBacille Calmette-Guérin (BCG), is not reliably effective against adult pulmonary tuberculosis. A major hurdle to tuberculosis vaccine development is incomplete understanding of successful immunity against the causative agentMycobacterium tuberculosis. Recently, we demonstrated that a protein subunit vaccine adjuvanted with STING-activating cyclic-di-nucleotides (CDNs) robustly protects against tuberculosis infection in mice. Here we show mucosal vaccination with this vaccine induces production of T cells that home to lung parenchyma and penetrate lesions in the lung. Protection is partially dependent on IL-17, type I interferon (IFN), and IFN-γ, while the transcription factor STAT-6 is dispensable. Single cell transcriptomics reveals mucosal vaccination with a CDN vaccine increases transcriptional heterogeneity in CD4 cells, including a significant population of non-classical IFN-γ and IL-17 co-expressing Th1-Th17 cells, as well as markers of memory and activation. Th1-Th17 cells in vaccinated mice are enriched for expression of the T cell functional markersTnfsf8andIl1r1relative to more conventional Th1 cells. These data provide critical insight into the immune mediators and diversity of T cell responses that can contribute to vaccine efficacy againstM. tuberculosisinfection.
Pharmacologic manipulation of complement receptor 3 prevents dendritic spine loss and cognitive impairment after acute cranial radiation
Authors: Hinkle Joshua J. , Olschowka John A. , Williams Jacqueline P. , O’Banion M. Kerry 
Published: November 2020

AbstractCranial irradiation induces healthy tissue damage that can lead to neurocognitive complications and negatively impact patient quality of life. One type of damage associated with cognitive impairment is loss of neuronal spine density. Based on developmental and disease studies implicating microglia and complement in dendritic spine loss, we hypothesized that irradiation-mediated spine loss is microglial complement receptor 3 (CR3)-dependent, and associated with late-delayed cognitive deficits. Utilizing a model of cranial irradiation (acute, 10 Gy gamma) in C57BL/6 mice we found that male mice demonstrate irradiation-mediated spine loss and cognitive deficits whereas female mice and CR3 knockout mice do not. Moreover, pharmacological blockade of CR3 with leukadherin-1 (LA1) prevented these changes in irradiated male mice. Interestingly, CR3 KO mice showed reduced behavioral task performance suggesting that CR3 is important for normal learning and memory. Improving our understanding of irradiation-mediated mechanisms and sexual dimorphic responses is essential for the identification of novel therapeutics to reduce irradiation-induced cognitive decline and improve patient quality of life.
Identification of mutations that cooperate with defects in B cell transcription factors to initiate leukemia
Authors: Heltemes-Harris Lynn M. , Hubbard Gregory K. , La Rue Rebecca S. , Munro Sarah A. , Knudson Todd P. , Yang Rendong , Henzler Christine M. , Starr Timothy K. , Sarver Aaron L. , Kornblau Steven M. , Farrar Michael A. 
Published: November 2020

AbstractThe transcription factors EBF1 and PAX5 are frequently mutated in B cell acute lymphoblastic leukemia (B-ALL). We demonstrate that Pax5+/-x Ebf1+/- compound heterozygous mice develop highly penetrant leukemia. Similar results were seen in Pax5+/-x Ikzf1+/- and Ebf1+/-x Ikzf1+/- mice for B-ALL, or in Tcf7+/-x Ikzf1+/- mice for T cell leukemia. To identify genetic defects that cooperate with Pax5 and Ebf1 compound heterozygosity to initiate leukemia, we performed a Sleeping Beauty (SB) transposon screen that identified cooperating partners including gain-of-function mutations in Stat5 (∼65%) and Jak1(∼68%), or loss-of-function mutations in Cblb (61%) and Myb (32%). These findings underscore the role of JAK/STAT5 signaling in B cell transformation and demonstrate unexpected roles for loss-of-function mutations in Cblb and Myb in leukemic transformation. RNA-Seq studies demonstrated upregulation of a PDK1>SGK3>MYC pathway; treatment of Pax5+/-x Ebf1+/- leukemia cells with PDK1 inhibitors blocked proliferation in vitro. Finally, we identified conserved transcriptional variation in a subset of genes between human leukemias and our mouse B-ALL models. Thus, compound haploinsufficiency for B cell transcription factors likely plays a critical role in transformation of human B cells and suggest that PDK1 inhibitors may be effective for treating patients with such defects.
Plume dynamics structure the spatiotemporal activity of glomerular networks in the mouse olfactory bulb
Authors: Lewis Suzanne M. , Xu Lai , Rigolli Nicola , Tariq Mohammad F. , Stern Merav , Seminara Agnese , Gire David H. 
Published: November 2020

AbstractAlthough mice locate resources using turbulent airborne odor plumes, the stochasticity and intermittency of fluctuating plumes create challenges for interpreting odor cues in natural environments. Population activity within the olfactory bulb (OB), is thought to process this complex spatial and temporal information, but how plume dynamics impact odor representation in this early stage of the mouse olfactory system is not known. Limitations in odor detection technology have made it impossible to measure plume fluctuations while simultaneously recording from the mouse’s brain. Thus, previous studies have measured OB activity following controlled odor pulses of varying profiles or frequencies, but this approach only captures a subset of features found within olfactory plumes. Adequately sampling this feature space is difficult given a lack of knowledge regarding which features the brain extracts during exposure to natural olfactory scenes. Here we measured OB responses to naturally fluctuating odor plumes using a miniature, adapted odor sensor combined with wide-field GCaMP6f signaling from the dendrites of mitral and tufted (MT) cells imaged in olfactory glomeruli of head-fixed mice. We precisely tracked plume dynamics and imaged glomerular responses to this fluctuating input, while varying flow conditions across a range of ethologically-relevant values. We found that a consistent portion of MT activity in glomeruli follows odor concentration dynamics, and the strongest responding glomeruli are the best at following fluctuations within odor plumes. Further, the reliability and average response magnitude of glomerular populations of MT cells are affected by the flow condition in which the animal samples the plume, with the fidelity of plume following by MT cells increasing in conditions of higher flow velocity where odor dynamics result in intermittent whiffs of stronger concentration. Thus, the flow environment in which an animal encounters an odor has a large-scale impact on the temporal representation of an odor plume in the OB. Additionally, across flow conditions odor dynamics are a major driver of activity in many glomerular networks. Taken together, these data demonstrate that plume dynamics structure olfactory representations in the first stage of odor processing in the mouse olfactory system.
NMDA receptor signalling controls R-type calcium channel levels at the neuronal synapse
Authors: Glebov Oleg O. 
Published: November 2020

AbstractRegulation of extracellular Ca++ influx by neuronal activity is a key mechanism underlying synaptic plasticity. At the neuronal synapse, activity-dependent Ca++ entry involves NMDA-type glutamate receptors (NMDARs) and voltage-gated calcium channels (VGCCs); the relationship between NMDARs and VGCCs, however, is poorly understood. Here, I report that neuronal activity specifically regulates synaptic levels of R-type VGCCs through synaptic NMDAR signalling and protein translation. This finding reveals a link between two key neuronal signalling pathways, suggesting a feedback mode for regulation of Ca++ signalling at the synapse.
Accelerating Drug Discovery and Repurposing by Combining Transcriptional Signature Connectivity with Docking
Authors: Thorman Alexander W. , Reigle James , Chutipongtanate Somchai , Shamsaei Behrouz , Pilarczyk Marcin , Fazel-Najafabadi Mehdi , Adamczak Rafal , Kouril Michal , Morrow Ardythe L. , Czyzyk-Krzeska Maria F. , McCullumsmith Robert , Seibel William , Nassar Nicolas , Zheng Yi , Hildeman David , Herr Andrew B. , Medvedovic Mario , Meller Jarek 
Published: November 2020

AbstractThe development of targeted treatment options for precision medicine is hampered by a slow and costly process of drug screening. While small molecule docking simulations are often applied in conjunction with cheminformatic methods to reduce the number of candidate molecules to be tested experimentally, the current approaches suffer from high false positive rates and are computationally expensive. Here, we present a novel in silico approach for drug discovery and repurposing, dubbed connectivity enhanced Structure Activity Relationship (ceSAR) that improves on current methods by combining docking and virtual screening approaches with pharmacogenomics and transcriptional signature connectivity analysis. ceSAR builds on the landmark LINCS library of transcriptional signatures of over 20,000 drug-like molecules and ~5,000 gene knock-downs (KDs) to connect small molecules and their potential targets. For a set of candidate molecules and specific target gene, candidate molecules are first ranked by chemical similarity to their ‘concordant’ LINCS analogs that share signature similarity with a knock-down of the target gene. An efficient method for chemical similarity search, optimized for sparse binary fingerprints of chemical moieties, is used to enable fast searches for large libraries of small molecules. A small subset of candidate compounds identified in the first step is then re-scored by combining signature connectivity with docking simulations. On a set of 20 DUD-E benchmark targets with LINCS KDs, the consensus approach reduces significantly false positive rates, improving the median precision 3-fold over docking methods at the extreme library reduction. We conclude that signature connectivity and docking provide complementary signals, offering an avenue to improve the accuracy of virtual screening while reducing run times by multiple orders of magnitude.