Biology subjects

Chan, J.

Publications and source records attributed to Chan, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

macroH2A2 shapes chromatin accessibility at enhancer elements in glioblastoma to modulate a targetable self-renewal epigenetic network

Self-renewal is a crucial property of glioblastoma cells and is enabled by the choreographed function of chromatin regulators and transcription factors. Identifying targetable epigenetic mechanisms of self-renewal could represent an important step toward developing new and effective treatments for this universally lethal cancer. Here we uncover a targetable epigenetic axis of self-renewal mediated by the histone variant macroH2A2. Using patient-derived in vitro and in vivo models, we show that macroH2A2 has a direct role in shaping chromatin accessibility at enhancer elements to antagonize transcriptional programs of self-renewal. Pharmaceutical inhibition of the chromatin remodeler Menin increased macroH2A2 levels and repressed self- renewal. Our results reveal a targetable epigenetic mechanism of self-renewal controlled by macroH2A2 and suggest new treatment approaches for glioblastoma patients. SIGNIFICANCEGlioblastoma is an incurable brain cancer. Malignant self-renewing cells have been shown to drive tumor growth, to be refractory to current treatment approaches and to seed relapses, which ultimately prove lethal. Identifying new and targetable mechanisms associated with self-renewal could be a fundamental first step in designing effective therapies that slow or prevent glioblastoma relapses. Using patient-derived models of glioblastoma, we deployed epigenomic approaches and functional assays to define the role of the histone variant macroH2A2 in repressing self-renewal. We identified compounds that increase macroH2A2 levels and repress self-renewal, including a Menin inhibitor. As Menin inhibitors are being tested in clinical trials, these compounds could be used in new therapeutic paradigms to target self-renewing cell populations in glioblastoma.

cancer biology↗

bioRxiv2021

Simultaneous Control of Infection and Inflammation by Keratin-Derived Antimicrobial Peptides (KAMPs) Targeting TLRs and Co-receptors

The use and the timing of initiation of steroids for controlling unwanted infectious inflammation are major clinical dilemmas due to their possible adverse effects including delayed microbial clearance and wound healing. Compounding this difficulty is the continued emergence of drug-resistant bacteria; yet anti-infective strategies aiming at augmenting inflammatory responses to facilitate bacterial killing cannot be used to treat infections involving vulnerable tissues. As is the case with bacterial keratitis, excessive inflammation jeopardizes corneal transparency leading to devastating vision loss. Hence, a two-pronged remedy possessing both anti-infective and anti-inflammatory properties would be helpful for tackling antibiotic resistance and enabling prompt inflammation control at once. Using murine primary neutrophils, macrophages and sterile corneal inflammation models, we found that non-toxic and pro-healing human keratin 6a-derived antimicrobial peptides (KAMPs) with a native 10-or 18-amino-acid sequence suppress LTA- and LPS-induced NF-[kcy]B and IRF3 activation, proinflammatory cytokine production, as well as phagocyte recruitment, independently of their bactericidal function. Mechanistically, direct binding of KAMPs to cell surface TLR2 and TLR co-receptors CD14 and MD-2 not only blocks their bacterial ligand docking sites, but also reduces cell surface availability of TLR2 and TLR4 through promotion of receptor endocytosis. Benefitting from the dual functions of topical KAMPs, experimental bacterial keratitis caused was effectively prevented or controlled, as evidenced by significant reductions of corneal opacification and inflammatory cell infiltration in addition to enhanced bacterial clearance. These findings reveal multiple TLR-targeting activities of KAMPs and demonstrate their therapeutic potential as a multifunctional drug for managing sterile and infectious inflammatory diseases. One Sentence SummaryBifunctional native keratin peptides allow concurrent alleviation of inflammation and infection to avoid functional damages in vulnerable tissues.

immunology↗

bioRxiv2020

Inferring the spatial code of cell-cell interactions and communication across a whole animal body

Cell-cell interactions shape cellular function and ultimately organismal phenotype. However, the code embedded in the molecular interactions driving and sustaining the spatial organization of cells remains to be elucidated. Here we present a computational framework to infer the spatial code underlying cell-cell interactions from the transcriptomes of the cell types across the whole body of a multicellular organism. As core of this framework, we introduce our tool cell2cell, which uses the coexpression of ligand-receptor pairs to compute the potential for intercellular interactions, and we test it across the Caenorhabditis elegans body. Leveraging a 3D atlas of C. elegans cells, we also implement a genetic algorithm to identify the ligand-receptor pairs most informative of the spatial organization of cells. Validating the spatial code extracted with this strategy, the resulting intercellular distances are negatively correlated with the inferred cell-cell interactions. Furthermore, for selected cell-cell and ligand-receptor pairs, we experimentally confirm the communicatory behavior inferred with cell2cell and the genetic algorithm. Thus, our framework helps identify a code that predicts the spatial organization of cells across a whole-animal body.

bioinformatics↗

bioRxiv2020

Acetylcholine is released in the basolateral amygdala in response to predictors of reward and enhances learning of cue-reward contingency

The basolateral amygdala (BLA) is critical for associating initially neutral cues with appetitive and aversive stimuli and receives dense neuromodulatory acetylcholine (ACh) projections. We measured BLA ACh signaling and principal neuron activity in mice during cue-reward learning using a fluorescent ACh sensor and calcium indicators. We found that ACh levels and activity of nucleus basalis of Meynert (NBM) cholinergic terminals in the BLA (NBM-BLA) increased sharply in response to reward-related events and shifted as mice learned the tone-reward contingency. BLA principal neuron activity followed reward retrieval and moved to the reward-predictive tone after task acquisition. Optical stimulation of cholinergic NBM-BLA terminal fibers during cue-reward learning led to more rapid learning of the cue-reward contingency. These results indicate that BLA ACh signaling carries important information about salient events in cue-reward learning and provides a framework for understanding how ACh signaling contributes to shaping BLA responses to emotional stimuli.

neuroscience↗

bioRxiv2020

Membrane-proximal external region is a superior target for mediating effector activity of HIV-1 specific chimeric antigen receptor modified T cells.

The use of chimeric antigen receptor modified-T (CAR-T) cells in adoptive immunotherapy has been popularized through recent success in the field of cancer treatment research. CD4{zeta} CAR, which targets HIV-1-infected cells, has been developed and evaluated in patients. Though well-tolerated for over a decade, efficacy was disappointingly limited. This result encourages us to develop a novel CAR more effective than CD4{zeta} CAR. To quantitatively compare anti-HIV-1 activity of different CAR constructs in a highly sensitive and reproducible manner, we developed a multicolor flow cytometry method for assessing anti-HIV-1 effector T-cell activity. "Target" Jurkat cells inducibly expressing an HIV-1HXBC2 envelope protein and "Non-target" control cells were genetically labeled with red and blue fluorescent protein, respectively, and co-incubated with human primary T cells transduced with anti-HIV-1 "Effector" CARs at various Effector vs Target cell ratios. Absolute cell numbers of each population were collected by MACSQuant Analyzer and used for calculation of relative cytotoxicity. We successfully ranked the cytotoxicity of three previously reported single chain-antibody CARs and six newly developed single-domain antibody CARs in comparison to CD4{zeta} CAR. Interestingly, three CARs--10E8, 2E7, and 2H10--which demonstrate high cytotoxic activity were all known to target the membrane-proximal external region. Use of this novel assay will simplify assessment of new CAR constructs and in turn accelerate the development of new effective CARs against HIV-1. Author SummaryAdoptive immunotherapies that utilize autologous T cells expressing a desired antigen-specific CAR aim to elicit directed immune responses. In recent years, CAR immunotherapies have been promoted extensively in B cell malignancy treatments. The HIV-1-targeting CAR, known as CD4{zeta}, was developed over 20 years ago and has been widely and longitudinally tested in patients. However, its effectiveness was hindered by poor survival and functionality of the transduced cells. To conduct quantitative evaluation of newly designed anti-HIV-1 CARs, we developed a novel multicolor flow-based assay for HIV-1-specific cytotoxicity, enabling sensitive and quantitative assessment in a high-throughput fashion. This assay would be also useful in screening HIV-1-targeting immune receptors--including CARs and T cell receptors--and other immunotherapeutic drugs such as anti-HIV-1 antibodies.

microbiology↗

bioRxiv2019

A genome-wide almanac of co-essential modules assigns function to uncharacterized genes

A central remaining question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into co-essential pathways, but this approach has been limited by ubiquitous false positives. Here, we develop a statistical method that enables robust identification of gene co-essentiality and yields a genome-wide set of functional modules. This almanac recapitulates diverse pathways and protein complexes and predicts the functions of 102 uncharacterized genes. Validating top predictions, we show that TMEM189 encodes plasmanylethanolamine desaturase, the long-sought key enzyme for plasmalogen synthesis. We also show that C15orf57 binds the AP2 complex, localizes to clathrin-coated pits, and enables efficient transferrin uptake. Finally, we provide an interactive web tool for the community to explore the results (coessentiality.net). Our results establish co-essentiality profiling as a powerful resource for biological pathway identification and discovery of novel gene functions.

genomics↗

bioRxiv2019

RobNorm: Model-Based Robust Normalization for High-Throughput Proteomics from Mass Spectrometry Platform

MotivationData normalization is an important step in processing proteomics data generated in mass spectrometry (MS) experiments, which aims to reduce sample-level variation and facilitate comparisons of samples. Previously published methods for normalization primarily depend on the assumption that the distribution of protein expression is similar across all samples. However, this assumption fails when the protein expression data is generated from heterogenous samples, such as from various tissue types. This led us to develop a novel data-driven method for improved normalization to correct the systematic bias meanwhile maintaining underlying biological heterogeneity. MethodsTo robustly correct the systematic bias, we used the density-power-weight method to down-weigh outliers and extended the one-dimensional robust fitting method described in the previous work of (Windham, 1995, Fujisawa and Eguchi, 2008) to our structured data. We then constructed a robustness criterion and developed a new normalization algorithm, called RobNorm. ResultsIn simulation studies and analysis of real data from the genotype-tissue expression (GTEx) project, we compared and evaluated the performance of RobNorm against other normalization methods. We found that the RobNorm approach exhibits the greatest reduction in systematic bias while maintaining across-tissue variation, especially for datasets from highly heterogeneous samples. Availabilityhttps://github.com/mwgrassgreen/RobNorm Contacthuatang@stanford.edu and mpsnyder@stanford.edu

bioinformatics↗

bioRxiv2019

Trimester-specific Zika virus infection affects placental responses in women

Zika virus (ZIKV) infection during pregnancy is associated with neurologic birth defects, but the effects on placental development are unclear. Full-term placentas from three women, each infected with ZIKV during specific pregnancy trimesters, were harvested for anatomic, immunologic and transcriptomic analysis. In this study, each woman exhibited a unique immune response, but they collectively diverged from healthy controls with raised IL-1RA, IP-10, EGF and RANTES expression, and neutrophil numbers during the acute infection phase. Although ZIKV NS3 antigens co-localized to placental Hofbauer cells, the placentas showed no anatomical defects. Transcriptomic analysis of samples from the placentas revealed that infection during trimester 1 caused a disparate cellular response centered on differential eIF2 signaling, mitochondrial dysfunction and oxidative phosphorylation. These findings should translate to improve clinical prenatal screening procedures for virus-infected pregnant patients.

immunology↗

bioRxiv2019

Identification of type 2 diabetes loci in 433,540 East Asian individuals

Meta-analyses of genome-wide association studies (GWAS) have identified >240 loci associated with type 2 diabetes (T2D), however most loci have been identified in analyses of European-ancestry individuals. To examine T2D risk in East Asian individuals, we meta-analyzed GWAS data in 77,418 cases and 356,122 controls. In the main analysis, we identified 298 distinct association signals at 178 loci, and across T2D association models with and without consideration of body mass index and sex, we identified 56 loci newly implicated in T2D predisposition. Common variants associated with T2D in both East Asian and European populations exhibited strongly correlated effect sizes. New associations include signals in/near GDAP1, PTF1A, SIX3, ALDH2, a microRNA cluster, and genes that affect muscle and adipose differentiation. At another locus, eQTLs at two overlapping T2D signals act through two genes, NKX6-3 and ANK1, in different tissues. Association studies in diverse populations identify additional loci and elucidate disease genes, biology, and pathways.\n\nType 2 diabetes (T2D) is a common metabolic disease primarily caused by insufficient insulin production and/or secretion by the pancreatic {beta} cells and insulin resistance in peripheral tissues1. Most genetic loci associated with T2D have been identified in populations of European (EUR) ancestry, including a recent meta-analysis of genome-wide association studies (GWAS) of nearly 900,000 individuals of European ancestry that identified >240 loci influencing the risk of T2D2. Differences in allele frequency between ancestries affect the power to detect associations within a population, particularly among variants rare or monomorphic in one population but more frequent in another3,4. Although smaller than studies in European populations, a recent T2D meta-analysis in almost 200,000 Japanese individuals identified 28 additional loci4. The relative contributions of different pathways to the pathophysiology of T2D may also differ between ancestry groups. For example, in East Asian (EAS) populations, T2D prevalence is greater than in European populations among people of similar body mass index (BMI) or waist circumference5. We performed the largest meta-analysis of East Asian individuals to identify new genetic associations and provide insight into T2D pathogenesis.

genetics↗

bioRxiv2019

Novel Strategies for Glutamate Clearance in the Glia-Deprived Synaptic Hub of C. elegans

Brain function requires the ability to form neuronal circuits that mediate focused and accurate communication. Since the vast majority of brain synapses use Glutamate (Glu) as their neurotransmitter, unintended spillover of Glu between adjacent synapses is a critical challenge. To ensure accurate neurotransmission and avert synaptic mix-up, specialized Glu Transporters (GluTs) clear the synapse of released Glu. While classical views of neuronal morphology and physiology depict isolated spiny synapses enwrapped by GluT-expressing glia, in reality, a considerable portion of synapses are flat, glial coverage in some parts of the brain is rather sparse, and extracellular space is larger than previously estimated. This suggests that diffusion in interstitial fluids might have an important role in Glu clearance in these synapses. To understand basic principles of Glu clearance in flat-, glia-deprived synapses, we study the physiology of neuronal circuits in the C. elegans nerve ring, the nematodes aspiny synaptic hub. We use behavioral assays, Ca2+ imaging, and iGluSnFR to follow synaptic activity in intact animals. We find that synapses in a nociceptive avoidance circuit are dramatically affected by distal GluTs, while an adjacent chemoattraction circuit is controlled by proximal GluTs. We also find that pharyngeal pulsatility and mobility, which could agitate interstitial fluids, are critical for synaptic physiology. We therefore conclude that robust Glu clearance in the nematode is provided differentially by distal and proximal GluTs, aided by agitation of interstitial fluids. Such principles might be informative in determining additional factors that contribute to robust Glu clearance in other neuronal systems.\n\nSignificance StatementThe nervous system depends on faithful relay of information without inadvertent mixing of signals between neuronal circuits. Classical views of the nervous system depict isolated synapses, enwrapped by glia that express neurotransmitter-transporters. However, this view is incomplete, since many synapses are flat, deprived of glia, and exposed to a larger-than-expected extracellular space. We use optogenetic tools to investigate glutamate clearance strategies in the aspiny and glia-deprived synaptic hub of intact nematodes. We find a division of labor among Glutamate transporters: while some transporters display classical localization near the synapses, others are distal, and cooperate with agitation of interstitial fluids to prevent glutamate accumulation. These novel principles might contribute to synaptic clearance in higher animals, affecting normal neuronal physiology and disease.

neuroscience↗

bioRxiv2018

Analysis of 100 high coverage genomes from a pedigreed captive baboon colony

Baboons (genus Papio) are broadly studied in the wild and in captivity. They are widely used as a non-human primate model for biomedical studies, and the Southwest National Primate Research Center (SNPRC) at Texas Biomedical Research Institute has maintained a large captive baboon colony for more than 50 years. Unlike other model organisms though, the genomic resources for baboons are severely lacking. This has hindered the progress of studies using baboons as a model for basic biology or human disease. Here, we describe a dataset of 100 high-coverage whole-genome sequences obtained from the mixed colony of olive (P. anubis) and yellow (P. cynocephalus) baboons housed at the SNPRC. These data provide a comprehensive catalog of common genetic variation in baboons, as well as a fine-scale genetic map. We show how the data can be used to learn about ancestry and admixture, and to correct errors in the colony records. Finally, we investigated the consequences of inbreeding within the SNPRC colony and found clear evidence for increased rates of juvenile mortality and increased homozygosity of putatively deleterious alleles in inbred individuals.

genomics↗

bioRxiv2018

DR-SIP: Protocols for Higher Order Structure Modeling with Distance Restraints- and Cyclic Symmetry-Imposed Packing

MotivationQuaternary structure determination for proteins is difficult especially for transmembrane proteins. Even if the monomeric constituents of complexes have been experimentally resolved, computational prediction of quaternary structures is a challenging task particularly for higher order complexes. It is essential to have a reliable computational protocol to predict quaternary structures of both transmembrane and soluble proteins leveraging experimentally determined distance restraints and/or cyclic symmetry (Cn symmetry) found in most homo-oligomeric transmembrane proteins.\n\nResultsWe survey 115 X-ray crystallographically solved structures of homo-oligomeric transmembrane proteins (HoTPs) to discover that 90% of them are Cn symmetric. Given the prevalence of Cn symmetric HoTPs and the benefits of incorporating geometry restraints in aiding quaternary structure determination, we introduce two new filters, the distance-restraints (DR) filter and the Symmetry-Imposed Packing (SIP) filter which takes advantage of the statistically derived tilt angle cutoff and the Cn symmetry of HoTPs without prior knowledge of the number (\"n\") of monomers. Using only the geometrical filter, SIP, near-native poses of the 115 HoTPs can be correctly identified in the top-5 for 52% of all cases, or 49% among the HoTPs having an n >2 (~60% of the dataset), while ZDOCK alone returns 41% and 24%, respectively. Applying only SIP to three HoTPs with distance restraints, the near-native poses for two HoTPs are ranked 1st and the other 7th among 54,000 possible decoys. With both filters, the two remain 1st while the other improved to 2nd. While a soluble system with distance restraints is recovered at the 1st-ranked pose by applying only DR.\n\nAvailability and Implementationhttps://github.com/capslockwizard/drsip\n\nSupplementary informationSupplementary methods and results are available.

bioinformatics↗

bioRxiv2018

Macaque anterior cingulate cortex deactivation impairs performance and alters lateral prefrontal oscillatory activities in a rule-switching task

In primates, both the dorsal anterior cingulate cortex (dACC) and the dorsolateral prefrontal cortex (dlPFC) are key regions of the frontoparietal cognitive control network. To study the role of the dACC and its communication with the dlPFC in cognitive control, we recorded the local field potentials from the dlPFC before and during the reversible deactivation of the dACC, in macaque monkeys engaging in uncued switches between two stimulus-response rules. Cryogenic dACC deactivation impaired response accuracy during rule-maintenance, but not rule-switching, which coincided with a reduction in the correct-error difference in dlPFC beta activities specifically during maintenance of the more challenging rule. During both rule switching and maintenance, dACC deactivation prolonged the animals reaction time and reduced task-related theta/alpha activities in the dlPFC; it also weakened dlPFC theta-gamma phase-amplitude modulation. Thus, the dACC and its interaction with the dlPFC plays a critical role in the maintenance of a new, challenging rule.

neuroscience↗

bioRxiv2018

An efficient timer and sizer of protein motions reveals the time scales of functional dynamics in the ribosome

The clock of life ticks as fast as how efficiently proteins could perform their functional dynamics. Protein complexes execute functions via several large-scale intrinsic motions across multiple conformational states, which occur at a timescale of nano-to milliseconds for well-folded proteins. Computationally expensive molecular dynamics (MD) simulation has been the only theoretical tool to time and size these motions, though barely to their slowest ends. Here, we convert a simple elastic network model (ENM), which takes a few seconds (ubiquitin) to hours (ribosome) for the analysis, into a molecular timer and sizer to gauge the slowest functional motions of proteins. Quasi-harmonic analysis, fluctuation-profile matching (FPM) and the Wiener-Khintchine theorem (WKT) are used to define the \"time-periods\", t, for anharmonic principal components (PCs) which are validated by NMR order parameters. The PCs with their respective \"time-periods\" are mapped to the eigenvalues ({lambda}ENM) of the corresponding ENM modes. Thus, the power laws t(ns) = 86.9{lambda}ENM-1.9 and {sigma}2([A]2) = 46.1 {lambda}ENM-2.5 are established allowing the characterization of the time scales of Nuclear Magnetic Resonance (NMR)-solved conformers, crystallographic anisotropic displacement parameters, and important ribosomal motions, as well as motional sizes of the latter.\n\nAuthor SummaryThe time scale of biological processes is governed by protein functional dynamics that often corresponds to the largest conformational spread and the longest time scales among all possible motions. Current simulation methodologies cannot reach the slowest, often functional, motions especially for supramolecular machineries. Borrowing the spring-bead model used in polymer physics since 60s, the efficient elastic network model (ENM), introduced in 90s, captured all modes of protein motions but largely underestimated the time scales of slowest modes due to its harmonic approximation.\n\nHere we map water-damped modes sampled by MD simulations to corresponding ones in ENM and thereby establish 2 power laws that describe the authentic time scales and sizes for the slowest anharmonic modes as functions of ENM eigenvalues. With that, we adequately describe the sizes and time scales for three proteins, confirmed by NMR spectroscopy, and ribosome that contains ~0.2 million heavy atoms (~ 20 thousands coarse-grained nodes).

biophysics↗

bioRxiv2018

Regulation of neural stem cell fate by the transcriptional repressor Capicua

Capicua (Cic) is a transcriptional repressor mutated in the brain cancer oligodendroglioma. Despite its cancer link, little is known of Cics function in the brain. Here, we investigated the relationship between Cic expression and cell type specification in the brain. Cic is strongly expressed in astrocytic and neuronal lineage cells but is more weakly expressed in stem cells and oligodendroglial lineage cells. Using a new conditional Cic knockout mouse, we show that forebrain-specific Cic deletion increases proliferation and self-renewal of neural stem cells. Furthermore, Cic loss biases neural stem cells toward glial lineage selection, expanding the pool of oligodendrocyte precursor cells (OPCs). These proliferation and lineage selection effects in the developing brain are dependent on de-repression of Ets transcription factors. In patient-derived oligodendroglioma cells, CIC re-expression or ETV5 blockade decreases lineage bias, proliferation, self-renewal and tumorigenicity. Our results identify Cic is an important regulator of cell fate in neurodevelopment and oligodendroglioma, and suggest that its loss contributes to oligodendroglioma by promoting proliferation and an OPC-like identity via Ets overactivity.

cancer biology↗

bioRxiv2018

Characterizing Subpopulations with Better Response to Treatment Using Observational Data - an Epilepsy Case Study

Electronic health records and health insurance claims, providing observational data on millions of patients, offer great opportunities, and challenges, for population health studies. The objective of this study is identifying subpopulations that are likely to benefit from a given treatment using observational data. We refer to these subpopulations as \"better responders\" and focus on characterizing these using linear scores with a limited number of variables. Building upon well-established causal inference techniques for analyzing observational data, we propose two algorithms that generate such scores for identifying better responders, as well as methods for evaluating and comparing these scores. We applied our methodology to a large dataset of ~135,000 epilepsy patients derived from claims data. Out of this sample, 85,000 were used to characterize subpopulations with better response to next-generation (\"Newer\") anti-epileptic drugs (AEDs), compared to an alternative treatment by first-generation (\"Older\") AEDs. The remaining 50,000 epilepsy patients were then used to evaluate our scores. Our results demonstrate the ability of our scores to identify large subpopulations of epilepsy patients with significantly better response to newer AEDs.

epidemiology↗

bioRxiv2018

A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks

An explosion of high-throughput DNA sequencing in the past decade has led to a surge of interest in population-scale inference with whole-genome data. Recent work in population genetics has centered on designing inference methods for relatively simple model classes, and few scalable general-purpose inference techniques exist for more realistic, complex models. To achieve this, two inferential challenges need to be addressed: (1) population data are exchangeable, calling for methods that efficiently exploit the symmetries of the data, and (2) computing likelihoods is intractable as it requires integrating over a set of correlated, extremely high-dimensional latent variables. These challenges are traditionally tackled by likelihood-free methods that use scientific simulators to generate datasets and reduce them to hand-designed, permutation-invariant summary statistics, often leading to inaccurate inference. In this work, we develop an exchangeable neural network that performs summary statistic-free, likelihood-free inference. Our frame-work can be applied in a black-box fashion across a variety of simulation-based tasks, both within and outside biology. We demonstrate the power of our approach on the recombination hotspot testing problem, outperforming the state-of-the-art.

evolutionary biology↗

bioRxiv2017

Nuclear Abl Drives Extracellular-Vesicle Transfer of miR-34c to Induce Bystander Effects of Radiation

SUMMARYIonizing radiation stimulates nuclear accumulation of Abl tyrosine kinase that is required for directly irradiated cells to produce microRNA-34c-containing extracellular vesicles, which transfer the microRNA into non-irradiated cells to induce reactive oxygen species and bystander DNA damage.\n\nABSTRACTIonizing radiation (IR) activates an array of DNA damage response (DDR) that includes the induction of bystander effects (BE) in cells not targeted by radiation. How DDR pathways in irradiated cells stimulate BE in non-targeted cells is mostly unknown. We show here that extracellular vesicles from irradiated cells (EV-IR) induce reactive oxygen species (ROS) and DNA damage when internalized by un-irradiated cells. We found that EV-IR from Abl-NLS-mutated cells could not induce ROS or DNA damage, and restoration of nuclear Abl rescued those defects. Expanding a previous finding that Abl stimulates miR-34c expression, we show here that nuclear Abl also drives the vesicular secretion of miR-34c. Ectopic miR-34c expression, without irradiation, generated EV-miR-34c capable of inducing ROS and DNA damage. Furthermore, EV-IR from miR34-knockout cells could not induce ROS and raised {gamma}H2AX to lesser extent than EV-IR from miR34-wild type cells. These results establish a novel role for the Abl-miR-34c DDR pathway in stimulating radiation-induced bystander effects.

cell biology↗