bluuebunny/crossref_metadata_2025_split huggingface dataset:
IL-11 is a therapeutic target in idiopathic pulmonary fibrosis
Authors: Ng Benjamin , Dong Jinrui , Viswanathan Sivakumar , D’Agostino Giuseppe , Widjaja Anissa A. , Lim Wei-Wen , Ko Nicole SJ. , Tan Jessie , Chothani Sonia P. , Huang Benjamin , Xie Chen , Chacko Ann-Marie , Guimarães-Camboa Nuno , Evans Sylvia M. , Byrne Adam J. , Maher Toby M. , Liang Jiurong , Noble Paul W. , Schafer Sebastian , Cook Stuart A. 
Published: June 2018

AbstractIdiopathic pulmonary fibrosis (IPF) remains a progressive disease despite best medical management. We previously identified IL-11 as a critical factor for cardiovascular fibrosis and examine here its role in pulmonary fibrosis.IL-11is consistently upregulated in IPF genomic datasets, which we confirmed by histology. Pulmonary fibroblasts stimulated with IL-11 transform into invasive myofibroblasts whereas fibroblasts fromIl11radeleted mice did not respond to pro-fibrotic stimuli. In the mouse, injection of recombinant Il-11 or fibroblast-specific expression of Il-11 caused pulmonary fibrosis. We then generated a neutralising IL-11 binding antibody that blocks lung fibroblast activation across species. In a mouse model of IPF, anti-IL-11 therapy attenuated lung fibrosis and specifically blocked Erk activation. These data prioritise IL-11 as an accessible drug target in IPF.One Sentence SummaryNon-canonical IL-11 signalling is a central hallmark of idiopathic pulmonary fibrosis and represents a novel target for antibody therapies.
Hook-length of the bacterial flagellum is optimized for maximal stability of the flagellar bundle
Authors: Spöring Imke , Martinez Vincent A. , Hotz Christian , Schwarz-Linek Jana , Grady Keara L. , Nava-Sedeño Josué M. , Vissers Teun , Singer Hanna M. , Rohde Manfred , Bourquin Carole , Hatzikirou Haralampos , Poon Wilson C. K. , Dufour Yann S. , Erhardt Marc 
Published: June 2018

AbstractMost bacteria swim in liquid environments by rotating one or several flagella. The long external filament of the flagellum is connected to a membrane-embedded basal-body by a flexible universal joint, the hook, which allows the transmission of motor torque to the filament. The length of the hook is controlled on a nanometer-scale by a sophisticated molecular ruler mechanism. However, why its length is stringently controlled has remained elusive. We engineered and studied a diverse set of hook-length variants ofSalmonella enterica. Measurements of plate-assay motility, single-cell swimming speed and directional persistence in quasi 2D and population-averaged swimming speed and body angular velocity in 3D revealed that the motility performance is optimal around the wild type hook-length. We conclude that too short hooks may be too stiff to function as a junction and too long hooks may buckle and create instability in the flagellar bundle. Accordingly, peritrichously flagellated bacteria move most efficiently as the distance travelled per body rotation is maximal and body wobbling is minimized. Thus, our results suggest that the molecular ruler mechanism evolved to control flagellar hook growth to the optimal length consistent with efficient bundle formation. The hook-length control mechanism is therefore a prime example of how bacteria evolved elegant, but robust mechanisms to maximize their fitness under specific environmental constraints.Author summaryMany bacteria use flagella for directed movement in liquid environments. The flexible hook connects the membrane-embedded basal-body of the flagellum to the long, external filament. Flagellar function relies on self-assembly processes that define or self-limit the lengths of major parts. The length of the hook is precisely controlled on a nanometer-scale by a molecular ruler mechanism. However, the physiological benefit of tight hook-length control remains unclear. Here, we show that the molecular ruler mechanism evolved to control the optimal length of the flagellar hook, which is consistent with efficient motility performance. These results highlight the evolutionary forces that enable flagellated bacteria to optimize their fitness in diverse environments and might have important implications for the design of swimming micro-robots.
Nociceptor translational profiling reveals the RagA-mTORC1 network as a critical generator of neuropathic pain
Authors: Megat Salim , Ray Pradipta R. , Moy Jamie K. , Lou Tzu-Fang , Barragan-Iglesias Paulino , Li Yan , Pradhan Grishma , Wangzhou Andi , Ahmad Ayesha , North Robert Y. , Dougherty Patrick M. , Khoutorsky Arkady , Sonenberg Nahum , Webster Kevin R. , Dussor Gregory , Campbell Zachary T. , Price Theodore J. 
Published: June 2018

AbstractPain sensing neurons, nociceptors, are key drivers of neuropathic pain. We used translating ribosome affinity purification (TRAP) to comprehensively characterize up-and down-regulated mRNA translation in Scn10a-positive nociceptors in chemotherapy-induced neuropathic pain. We provide evidence that an underlying mechanism driving these changes in gene expression is a sustained mTORC1 activation driven by MNK1-eIF4E signaling. RagA, a GTPase controlling mTORC1 activity, is identified as a novel target of MNK1-eIF4E signaling, demonstrating a new link between these distinct signaling pathways. Neuropathic pain and RagA translation are strongly attenuated by genetic ablation of eIF4E phosphorylation, MNK1 elimination or treatment with the MNK inhibitor eFT508. We reveal a novel translational circuit for the genesis of neuropathic pain with important implications for next generation neuropathic pain therapeutics.One Sentence SummaryCell-specific sequencing of translating mRNAs elucidates signaling pathology that can be targeted to reverse neuropathic pain
Ataxia Telangiectasia triggers deficits in Reelin pathway
Authors: Canet-Pons Júlia , Schubert Ralf , Duecker Ruth Pia , Schrewe Roland , Wölke Sandra , Schnölzer Martina , Auburger Georg , Zielen Stefan , Warnken Uwe 
Published: June 2018

AbstractAutosomal recessive Ataxia Telangiectasia (A-T) is characterized by radiosensitivity, immunodeficiency and cerebellar neurodegeneration. A-T is caused by inactivating mutations in the Ataxia-Telangiectasia-Mutated (ATM) gene, a serine-threonine protein kinase involved in DNA-damage response and excitatory neurotransmission. The selective vulnerability of cerebellar Purkinje neurons (PN) to A-T is not well understood.Employing global proteomic profiling of cerebrospinal fluid from patients at ages around 15 years we detected reduced Calbindin, Reelin, Cerebellin-1, Cerebellin-3, Protocadherin Fat 2, Sempahorin 7A and increased Apolipoprotein -B, -H, -J peptides. Bioinformatic enrichment was observed for pathways of chemical response, locomotion, calcium binding and complement immunity. This seemed important, since secretion of Reelin from glutamatergic afferent axons is crucial for PN radial migration and spine homeostasis. Reelin expression is downregulated by irradiation and its deficiency is a known cause of ataxia. Validation efforts in 2-month-oldAtm-/- mice before onset of motor deficits confirmed transcript reductions for Reelin receptorsApoer2/Vldlrwith increases for their ligandsApoe/Apohand cholesterol 24-hydroxylaseCyp46a1. Concomitant dysregulations were found forVglut2/Sema7aas climbing fiber markers, glutamate receptors likeGrin2band calcium homeostasis factors (Atp2b2, Calb1, Itpr1), while factors involved in DNA damage, oxidative stress, neuroinflammation and cell adhesion were normal at this stage.These findings show that deficient levels of Reelin signaling factors reflect the neurodegeneration in A-T in a sensitive and specific way. As an extracellular factor, Reelin may be accessible for neuroprotective interventions.
Selecting precise reference normal tissue samples for cancer research using a deep learning approach
Authors: Zeng William , Glicksberg Benjamin S. , Li Yangyan , Chen Bin 
Published: June 2018

AbstractBackgroundNormal tissue samples are often employed as a control for understanding disease mechanisms, however, collecting matched normal tissues from patients is difficult in many instances. In cancer research, for example, the open cancer resources such as TCGA and TARGET do not provide matched tissue samples for every cancer or cancer subtype. The recent GTEx project has profiled samples from healthy individuals, providing an excellent resource for this field, yet the feasibility of using GTEx samples as the reference remains unanswered.MethodsWe analyze RNA-Seq data processed from the same computational pipeline and systematically evaluate GTEx as a potential reference resource. We use those cancers that have adjacent normal tissues in TCGA as a benchmark for the evaluation. To correlate tumor samples and normal samples, we explore top varying genes, reduced features from principal component analysis, and encoded features from an autoencoder neural network. We first evaluate whether these methods can identify the correct tissue of origin from GTEx for a given cancer and then seek to answer whether disease expression signatures are consistent between those derived from TCGA and from GTEx.ResultsAmong 32 TCGA cancers, 18 cancers have less than 10 matched adjacent normal tissue samples. Among three methods, autoencoder performed the best in predicting tissue of origin, with 12 of 14 cancers correctly predicted. The reason for misclassification of two cancers is that none of normal samples from GTEx correlate well with any tumor samples in these cancers. This suggests that GTEx has matched tissues for the majority cancers, but not all. While using autoencoder to select proper normal samples for disease signature creation, we found that disease signatures derived from normal samples selected via an autoencoder from GTEx are consistent with those derived from adjacent samples from TCGA in many cases. Interestingly, choosing top 50 mostly correlated samples regardless of tissue type performed reasonably well or even better in some cancers.ConclusionsOur findings demonstrate that samples from GTEx can serve as reference normal samples for cancers, especially those do not have available adjacent tissue samples. A deep-learning based approach holds promise to select proper normal samples.
Increased Cerebral Blood Flow after single dose of antipsychotics in healthy volunteers depends on dopamine D2 receptor density profiles
Authors: Selvaggi Pierluigi , Hawkins Peter C.T. , Dipasquale Ottavia , Rizzo Gaia , Bertolino Alessandro , Dukart Juergen , Sambataro Fabio , Pergola Giulio , Williams Steven C.R. , Turkheimer Federico , Zelaya Fernando , Veronese Mattia , Mehta Mitul A. 
Published: June 2018

AbstractAs a result of neuro-vascular coupling, the functional effects of antipsychotics in human brain have been investigated in both healthy and clinical populations using haemodynamic markers such as regional Cerebral Blood Flow (rCBF). However, the relationship between observed haemodynamic effects and the pharmacological action of these drugs has not been fully established. Here, we analysed MRI-based rCBF data from a placebo-controlled study in healthy volunteers, who received a single dose of three different D2 receptor antagonists and tested the association of the main effects of the drugs on rCBF against normative population maps of D2R protein density and gene-expression data. In particular, we correlated CBF changes after antipsychotic administration with non-displaceable binding potential (BPND) template maps of the high affinity D2-antagonist Positron Emission Tomography (PET) ligand [18F]Fallypride and brain post-mortem microarray mRNA expression data for the DRD2 gene. For all antipsychotics, rCBF changes were directly proportional to brain D2R densities and DRD2 mRNA expression measures, although PET BPND spatial profiles explained more variance as compared with mRNA profiles (PET R2 range= 0.20-0.60, mRNA PET R2 range 0.04-0.20, pairwise-comparisons all p<0.05). In addition, the spatial coupling between ΔCBF and D2R profiles varied between the different antipsychotics tested, possibly reflecting differential affinities. Overall, these results indicate that the functional effects of antipsychotics as measured with rCBF are tightly correlated with the distribution of their target receptors in striatal and extra-striatal regions. Our results further demonstrate the link between neurotransmitter targets and haemodynamic changes reinforcing rCBF as a robust in-vivo marker of drug effects. This work is important in bridging the gap between pharmacokinetic and pharmacodynamics of novel and existing compounds.
Lightweight bioinformatics: evaluating the utility of Single Board Computer (SBC) clusters for portable, scalable Real-Time Bioinformatics in fieldwork environments via benchmarking
Authors: Parker Joe 
Published: June 2018

AbstractThe versatility of the current DNA sequencing platforms and the development of portable, nanopore sequencers means that it has never been easier to collect genetic data for unknown sample ID. In fact, the distinction between fieldwork and the laboratory is becoming blurred since genome-scale data can now be collected in challenging conditions in a matter of hours. However, the full scientific and societal benefits of these new methods can only be realised with equally rapid and portable analyses. At present, field-based analyses of genomic data, despite advances in computing technology, remain problematic; laptop computers are relatively expensive and limited in scalability, while cloud- and cluster-based analyses depend, for the time being, on sufficiently reliable high-bandwidth data uplinks to transmit primary data for analysis.Single board computers (SBCs), such as the Raspberry Pi, offer a potential solution to this problem: while less powerful than their laptop cousins, their very individual low cost and power consumption mean modest arrays of SBCs could be used for field-based preprocessing, or complete analyses or primary data. In this study we investigate the performance of one SBC, the Pi 3 Model B+, on a range of typical field-sequencing tasks versus laptop and cloud-based form-factors. Our data analysis pipeline has been made available as a workflow on Github for simple, scalable deployment for a range of uses.
PARP10 promotes cellular proliferation and tumorigenesis by alleviating replication stress
Authors: Schleicher Emily M. , Galvan Adri M. , Moldovan George-Lucian , Nicolae Claudia M. 
Published: June 2018

ABSTRACTDuring carcinogenesis, cells are exposed to increased replication stress due to replication fork arrest at sites of DNA lesions and other difficult to replicate regions. Efficient fork restart and DNA repair are important for cancer cell proliferation. We previously showed that the ADP-ribosyltransferase PARP10 interacts with the replication protein PCNA and promotes lesion bypass by recruiting specialized, non-replicative DNA polymerases. Here, we show that PARP10 is overexpressed in a large proportion of human tumors. To understand the role of PARP10 in cellular transformation, we inactivated PARP10 in HeLa cancer cells by CRISPR/Cas9-mediated gene knockout, and overexpressed it in non-transformed RPE-1 cells. We found that PARP10 promotes cellular proliferation and replication fork elongation. Mechanistically, PARP10 overexpression alleviated cellular sensitivity to replication stress by fostering the restart of stalled replication forks. Importantly, mouse xenograft studies indicated that loss of PARP10 reduces the tumorigenesis activity of HeLa cells, while its overexpression results in tumor formation by non-transformed RPE-1 cells. Our findings indicate that PARP10 promotes cellular transformation by alleviating replication stress, and suggest that targeting PARP10 may represent a novel therapeutic approach.
Evaluating cell lines as models for metastatic cancer through integrative analysis of open genomic data
Authors: Liu Ke , Newbury Patrick A. , Glicksberg Benjamin S. , Zeng William ZD , Andrechek Eran R. , Chen Bin 
Published: June 2018

AbstractMetastasis is the most common cause of cancer-related death and, as such, there is an urgent need to discover new therapies to treat metastasized cancers. Cancer cell lines are widely-used models to study cancer biology and test drug candidates. However, it is still unknown to what extent they adequately resemble the disease in patients. The recent accumulation of large-scale genomic data in cell lines, mouse models, and patient tissue samples provides an unprecedented opportunity to evaluate the suitability of cell lines for metastatic cancer research. In this work, we used breast cancer as a case study. The comprehensive comparison of the genetic profiles of 57 breast cancer cell lines with those of metastatic breast cancer samples revealed substantial genetic differences. In addition, we identified cell lines that more closely resemble different subtypes of metastatic breast cancer. Surprisingly, a combined analysis of mutation, copy number variation and gene expression data suggested that MDA-MB-231, the most commonly used triple negative cell line for metastatic breast cancer research, had little genomic similarity with Basal-like metastatic breast cancer samples. We further compared cell lines with organoids, a new type of preclinical model which are becoming more popular in recent years. We found that organoids outperformed cell lines in resembling the transcriptome of metastatic breast cancer samples. However, additional differential expression analysis suggested that both types of models could not mimic the effects of tumor microenvironment and meanwhile had their own bias towards modeling specific biological processes. Our work provides a guide of cell line selection in metastasis-related study and sheds light on the potential of organoids in translational research.
An expanded toolkit for gene tagging based on MiMIC and scarless CRISPR tagging in Drosophila
Authors: Li-Kroeger David , Kanca Oguz , Lee Pei-Tseng , Cowan Sierra , Lee Michael , Jaiswal Manish , Salazar Jose Luis , He Yuchun , Bellen Hugo J. 
Published: June 2018

AbstractWe generated new genetic tools to efficiently tag genes in Drosophila. Double Header (DH) utilizes intronic MiMIC/CRIMIC insertions to generate artificial exons for GFP mediated protein trapping or T2A-GAL4 gene trapping in vivo based on CRE recombinase to avoid embryo injections. DH significantly increases integration efficiency compared to previous strategies and faithfully reports the expression pattern of genes and proteins. The second technique targets genes lacking coding introns using a two-step cassette exchange. First, we replace the endogenous gene with an excisable compact dominant marker using CRISPR making a null allele. Second, the insertion is replaced with a protein::tag cassette.This sequential manipulation allows the generation of numerous tagged alleles or insertion of other DNA fragments that facilitates multiple downstream applications. Both techniques allow precise gene manipulation and facilitate detection of gene expression, protein localization and assessment of protein function, as well as numerous other applications.
Enhanced Synthesis of Poly Gamma Glutamic Acid by Increasing the Intracellular Reactive Oxygen Species in the Bacillus licheniformis Δ1-pyrroline-5-carboxylate Dehydrogenase Gene ycgN Deficient Strain
Authors: Li Bichan , Cai Dongbo , Hu Shiying , Zhu Anting , He Zhili , Chen Shouwen 
Published: June 2018

AbstractPoly gamma glutamic acid (γ-PGA) is an anionic polyamide with numerous applications. Proline metabolism influences the formation of reactive oxygen species (ROS), and is involved in a wide range of cellular processes. However, the relation between proline metabolism and γ-PGA synthesis has not yet been analyzed. In this study, our results indicated that the deletion of Δ1-pyrroline-5-carboxylate dehydrogenase encoded gene ycgN resulted in 85.22% higher yield of γ-PGA in B. licheniformis WX-02. But the deletion of proline dehydrogenase encoded gene ycgM had no effect on γ-PGA synthesis. Meanwhile, a 2.92-fold higher level of P5C was detected in ycgN deficient strain WXΔycgN, while the P5C levels in WXΔycgM and double mutant strain WXΔycgMN remained the same, compared to WX-02. The ROS level of WXΔycgN was 1.18-fold higher than that of WX-02, and the addition of n-acetylcysteine (antioxidant) into medium could decrease its ROS level, further reduced the γ-PGA yield. Our results showed that proline catabolism played an important role in maintaining ROS homeostasis, and the deletion of ycgN caused P5C accumulation, which induced a transient ROS signal to promote γ-PGA synthesis in B. licheniformis.Importanceγ-PGA is an anionic polyamide with various applications in biomedical and industrial fields. Proline metabolism influences the intracellular reactive oxygen species (ROS) and is involved in a wide range of cellular processes. Here, we report the effects of proline metabolism on γ-PGA synthesis. Our results indicated that deletion of ycgN promoted the synthesis of γ-PGA by increasing the intracellular levels of Δ1-pyrroline-5-carboxylate to generate a transient ROS signal in B. licheniformis WX-02. This study provides the valuable information that enhanced synthesis of γ-PGA by knocking out of ycgN.
Deregulation of LRSAM1 expression impairs the levels of TSG101, UBE2N, VPS28, MDM2 and EGFR
Authors: Minaidou Anna , Nicolaou Paschalis , Christodoulou Kyproula 
Published: June 2018

AbstractCMT is the most common hereditary neuromuscular disorder of the peripheral nervous system with a prevalence of 1/2500 individuals and it is caused by mutations in more than 80 genes. LRSAM1, a RING finger ubiquitin ligase also known as TSG101-associated ligase (TAL), has been associated with Charcot-Marie-Tooth disease type 2P (CMT2P) and to date eight causative mutations have been identified. Little is currently known on the pathogenetic mechanisms that lead to the disease. We investigated the effect of LRSAM1 deregulation on possible LRSAM1 interacting molecules in cell based models. Possible LRSAM1 interacting molecules were identified using protein-protein interaction databases and literature data. Expression analysis of these molecules was performed in both CMT2P patient and control lymphoblastoid cell lines as well as in LRSAM1 and TSG101 downregulated SH-SY5Y cells.TSG101, UBE2N, VPS28, EGFR and MDM2 levels were significantly decreased in the CMT2P patient lymphoblastoid cell line as well as in LRSAM1 downregulated cells. TSG101 downregulation had a significant effect only on the expression of VPS28 and MDM2 and it did not affect the levels of LRSAM1. This study confirms that LRSAM1 is a regulator of TSG101 expression. Furthermore, deregulation of LRSAM1 significantly affects the levels of UBE2N, VPS28, EGFR and MDM2.