bluuebunny/crossref_metadata_2025_split huggingface dataset:
Therapeutic vulnerability to PARP1/2 inhibition inRB1-mutant osteosarcoma
Authors: Zoumpoulidou Georgia , Mendoza Carlos A , Mancusi Caterina , Ahmed Ritika M , Denman Milly , Steele Christopher D , Manji Jiten , Pillay Nischalan , Strauss Sandra J , Mittnacht Sibylle 
Published: December 2020

ABSTRACTBackgroundLoss-of-function mutations of the retinoblastoma tumour suppressorRB1are key drivers in cancer, with prominent involvement in the natural history of Osteosarcoma (OS).RB1loss-of-function compromises genome maintenance in cells and hence could yield vulnerability to therapeutics targeting such processes.MethodWe assessed the response to Poly-ADP-Polymerase1/2 inhibitors (PARPi) in histiotype-matched cancer cell lines differing inRB1status including an extended panel of OS lines, measuring viability, clonogenic activity and inhibition of xenograft growthin vivo. We used mutational signature analysis and RAD51 immunostaining to assess competence for homologous repair defect (HRd).ResultsWe report selective hypersensitivity to clinically-approved PARPi in OS lines with RB1 mutation, which extends to other cancer histiotypes and is induced in RB1-normal OS following engineered RB1 loss. PARPi treatment caused extensive cell death in RB1-mutated OS and extended survival of mice carrying human RB1-mutated OS grafts. Sensitivity in OS with natural or engineered RB1 loss surpassed that seen in BRCA-mutated backgrounds where PARPi are showing clinical benefit. PARPi sensitivity was not associated with loss of RAD51 recruitment and HRd-linked mutational signatures, which predict PARPi sensitivity in cancers with BRCA1/2 loss, but linked to rapid activation of replication checkpoint signalling with S phase transit critical for the death response observed.ConclusionOur work demonstrates that mutations inRB1causes clinically relevant hypersensitivity to approved PARP1/2-targeting therapeutics and advocates PARP1/2 inhibition as a novel, genome lead strategy forRB1-mutated osteosarcoma.
The SYP123-VAMP727 SNARE complex is involved in the delivery of inner cell wall components to the root hair shank in Arabidopsis
Authors: Hirano Tomoko , Ebine Kazuo , Ueda Takashi , Higaki Takumi , Nakayama Takahiro , Konno Hiroki , Takigawa-Imamura Hisako , Sato Masa H. 
Published: December 2020

AbstractA root hair is a long tubular protrusion from a root hair cell established via tip growth, which is accomplished by the polarized deposition of membranous and cell wall components at the root hair apex accompanied by simultaneous hardening of the shank. The polarized secretion of materials to the root hair apex is well investigated; however, little is known about the deposition of inner cell wall materials at the root hair shank. We have previously reported that phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P2)/ROP10 signaling is required for the regulation of cortical microtubule construction and the deposition of inner cell wall components at the root hair shank during hardening. To unravel the alternate secretion mechanism for delivery of the inner cell wall components to root hair shank, here, we demonstrate that root hair-specific Qa-SNARE, SYP123, localizes to the subapical zone and shank of elongating root hairs in Arabidopsis. SYP123-mediated root hair elongation was inhibited by the FAB1 inhibitor YM201636, and inhibition of PtdIns(3,5)P2production impaired the plasma membrane localization of SYP123. We also showed that SYP123 forms a SNARE complex with VAMP727 on the plasma membrane, andsyp123andvamp727mutants exhibited lower cell wall stiffness in the root hair shank because of impaired deposition of inner cell wall components. These results indicate that SYP123/VAMP727-mediated secretion is involved in the transport of inner cell wall components for hardening of the root hair shank.
Myofiber / pro-inflammatory macrophage interplay controls muscle damage in mdx mice
Authors: Saclier Marielle , Ben Larbi Sabrina , Moulin Eugénie , Mounier Rémi , Chazaud Bénédicte , Juban Gaëtan 
Published: December 2020

SummaryDuchenne Muscular Dystrophy is a genetic muscle disease characterized by chronic inflammation and fibrosis, which is mediated by a pro-fibrotic macrophage population expressing pro-inflammatory markers. The aim of this study was to characterize cellular events leading to the alteration of macrophage properties, and to modulate macrophage inflammatory status using the gaseous mediator H2S. We first analyzed the relationship between myofibers and macrophages in the mdx mouse model of Duchenne Muscular Dystrophy using coculture experiments. We showed that normal myofibers derived from mdx mice strongly skewed the polarization of resting macrophages towards a pro-inflammatory phenotype. Treatment of mdx mice with NaHS, an H2S donor, reduced the number of pro-inflammatory macrophages in skeletal muscle, which was associated with a decrease in the number of nuclei per fiber, a reduction of myofiber branching and a reduced fibrosis. These results identify an interplay between myofibers and macrophages where dystrophic myofibers contribute to the maintenance of a highly inflammatory environment that skews the macrophage status, which in turn favors myofiber damage, myofiber branching and fibrosis establishment. They also identify H2S donors as a potential therapeutic strategy to improve dystrophic muscle phenotype by modulating macrophage inflammatory status.
Single-cell Individual Complete mtDNA Sequencing Uncovers Hidden Mitochondrial Heterogeneity in Human and Mouse Oocytes
Authors: Bi Chongwei , Wang Lin , Fan Yong , Ramos-Mandujano Gerardo , Yuan Baolei , Zhou Xuan , Wang Jincheng , Shao Yanjiao , Zhang Pu-Yao , Huang Yanyi , Yu Yang , Izpisua Belmonte Juan Carlos , Li Mo 
Published: December 2020

AbstractThe ontogeny and dynamics of mtDNA heteroplasmy remain unclear due to limitations of current mtDNA sequencing methods. We developed individualMitochondrialGenomesequencing (iMiGseq) of full-length mtDNA for ultra-sensitive variant detection, complete haplotyping, and unbiased evaluation of heteroplasmy levels, all at the individual mtDNA molecule level. iMiGseq uncovers unappreciated levels of heteroplasmic variants in single healthy human oocytes well below the current 1% detection limit, of which numerous variants are detrimental and could contribute to late-onset mitochondrial disease and cancer. Extreme mtDNA heterogeneity among oocytes of the same mouse female, and a strong selection against deleterious mutations in human oocytes are observed. iMiGseq could comprehensively characterize and haplotype single-nucleotide and structural variants of mtDNA and their genetic linkage in NARP/Leigh syndrome patient-derived cells. Therefore, iMiGseq could not only elucidate the mitochondrial etiology of diseases, but also help diagnose and prevent mitochondrial diseases with unprecedented precision.
An open platform for high-resolution light-based control of microscopic collectives
Authors: Rubio Denniss Ana , Gorochowski Thomas E. , Hauert Sabine 
Published: December 2020

AbstractEngineering microscopic collectives of cells or microrobots is challenging due to the often-limited capabilities of the individual agents, our inability to program their motion and local interactions, and difficulties visualising their behaviours. Here, we present a low-cost, modular and open-source Dynamic Optical MicroEnvironment (DOME) and demonstrate its ability to augment microagent capabilities and control collective behaviours using light. The DOME offers an accessible means to study complex multicellular phenomena and implementde-novomicroswarms with desired functionalities.
Occurrence and associated characteristics of a mutatedant(6’)-Iagene amongEnterococcus faeciumstrains expressing phenotypic susceptibility to high levels of streptomycin
Authors: Rodrigues Souza Stephanie Silva , Faria Adriana Rocha , Rangel Freitas Andréa Andrade , Planet Paul J , Carreira Merquior Vânia Lúcia , Teixeira Lúcia Martins 
Published: December 2020

ABSTRACTEnterococcal high-level resistance to streptomycin (HLR-S) (MIC ≥ 2000 µg/ml), conferred by production of a variety of aminoglycoside modifying enzymes (AMES), has been reported worldwide and a nucleotidyltransferase (ANT) enzyme encoded by theant(6’)-Iagene is frequently associated with this phenotype. However, during a study conducted by our group on whole genome sequencing (WGS) analyses ofEnterococcus faeciumisolates, we observed that 32E. faeciumstrains identified as susceptible to high-levels of streptomycin by the disk diffusion method had the ofant(6’)-Iagene annotated in their genomes. Antimicrobial susceptibility to streptomycin was reassessed by phenotypic testing and the presence of theant(6’)-Iagene was confirmed by PCR in all the isolates. Alignment of theant(6’)-Iagene with a reference sequence revealed a deletion of the first 48 nucleotides and four nonsynonymous mutations, leading to the substitution of a Glutamine to Methionine and an Aspartic Acid to Asparagine in the amino acid sequence. The protein structure was modelled by using the Phyre2 platform and the results indicated alterations in the N-terminus region leading to changes in the predicted binding site. Also, by searching the NCBI database we identified the genomes of 71 strains carrying the mutated gene. MLST analysis revealed that most strains carrying the mutated gene, including those described in this study belonged to hospital-adapted lineages, suggesting the occurrence of clonal dissemination of a subset of mutated isolates.HIGHLIGHTSThe presence of a mutatedant(6’)-Iagene was identified amongEnterococcus faeciumisolates expressing phenotypic susceptibility to high levels of streptomycin.Nonsynonymous mutations and inactivating changes in theant(6’)-Iagene led to incongruities between phenotypes and genotypes.Alterations in the amino acid sequence had impacts on protein structure, with changes in the N-terminus region and the binding site.
Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions and monocytes for optimal therapeutic protection
Authors: Winkler Emma S. , Gilchuk Pavlo , Yu Jinsheng , Bailey Adam L. , Chen Rita E. , Zost Seth J. , Jang Hyesun , Huang Ying , Allen James D. , Case James Brett , Sutton Rachel E. , Carnahan Robert H. , Darling Tamarand L. , Boon Adrianus C. M. , Mack Matthias , Head Richard D. , Ross Ted M. , Crowe James E. , Diamond Michael S. 
Published: December 2020

SUMMARYSARS-CoV-2 has caused the global COVID-19 pandemic. Although passively delivered neutralizing antibodies against SARS-CoV-2 show promise in clinical trials, their mechanism of actionin vivois incompletely understood. Here, we define correlates of protection of neutralizing human monoclonal antibodies (mAbs) in SARS-CoV-2-infected animals. Whereas Fc effector functions are dispensable when representative neutralizing mAbs are administered as prophylaxis, they are required for optimal protection as therapy. When given after infection, intact mAbs reduce SARS-CoV-2 burden and lung disease in mice and hamsters better than loss-of-function Fc variant mAbs. Fc engagement of neutralizing antibodies mitigates inflammation and improves respiratory mechanics, and transcriptional profiling suggests these phenotypes are associated with diminished innate immune signaling and preserved tissue repair. Immune cell depletions establish that neutralizing mAbs require monocytes for therapeutic efficacy. Thus, potently neutralizing mAbs require Fc effector functions for maximal therapeutic benefit during therapy to modulate protective immune responses and mitigate lung disease.
Horizontal and vertical transmission of transgenerational memories via theCer1transposon
Authors: Moore Rebecca S. , Kaletsky Rachel , Lesnik Chen , Cota Vanessa , Blackman Edith , Parsons Lance R. , Gitai Zemer , Murphy Coleen T. 
Published: December 2020

AbstractAnimals face both external and internal dangers: pathogens threaten from the environment, and unstable genomic elements threaten from within. Previously, we discovered thatC. elegansprotects itself from pathogens by “reading” bacterial small RNAs and using this information to both induce avoidance and transmit memories for several generations. Here we found that these memories can be transferred to naïve animals viaCer1retrotransposon-encoded capsids.Cer1functions at the step of transmission of information from the germline to neurons, and is required forC. elegans’learned avoidance ability and for mothers to pass this information on to progeny. The presence of theCer1retrotransposon in wildC. elegansstrains correlates with the ability to learn and inherit small RNA-induced pathogen avoidance. Together, these results suggest thatC. eleganshas co-opted a potentially dangerous retrotransposon to instead protect itself and its progeny from a common pathogen through its inter-tissue signaling ability, hijacking this genomic element for its own adaptive immunity benefit.
Transcriptome-wide high-throughput mapping of protein-RNA occupancy profiles using POP-seq
Authors: Srivastava Mansi , Srivastava Rajneesh , Janga Sarath Chandra 
Published: December 2020

AbstractInteraction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein-RNA complexes and polyA pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non polyA RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of polyA pulldown. Our study demonstrates that ~68% of the total POP-seq peaks exhibited an overlap with publicly available protein-RNA interaction profiles of 97 RNA binding proteins (RBPs) in K562 cells. We show that POP-seq variants consistently capture protein-RNA interaction sites across a broad range of genes including on transcripts encoding for transcription factors (TFs), RNA-Binding Proteins (RBPs) and long non-coding RNAs (lncRNAs). POP-seq identified peaks exhibited a significant enrichment (p value < 2.2e-16) for GWAS SNPs, phenotypic, clinically relevant germline as well as somatic variants reported in cancer genomes, suggesting the prevalence of uncharacterized genomic variation in protein occupied sites on RNA. We demonstrate that the abundance of POP-seq peaks increases with an increase in expression of lncRNAs, suggesting that highly expressed lncRNA are likely to act as sponges for RBPs, contributing to the rewiring of protein-RNA interaction network in cancer cells. Overall, our data supports POP-seq as a robust and cost-effective method that could be applied to primary tissues for mapping global protein occupancies.
Growth‐mediated negative feedback shapes quantitative antibiotic response
Authors: Angermayr S. Andreas , Chevereau Guillaume , Bollenbach Tobias 
Published: December 2020

AbstractDose‐response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole‐cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose‐response curves. The shape of the dose‐response curve varies drastically between antibiotics and plays a key role for treatments, drug interactions, and resistance evolution. However, the mechanisms shaping the dose‐response curve remain largely unclear. Here, we show inEscherichia colithat the distinctively shallow dose‐response curve of the antibiotic trimethoprim is caused by a negative growth‐ mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends only on growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose‐response curve in a predictable manner, which we corroborate with a mathematical model. Our results indicate that growth‐mediated feedback loops shape drug responses and could be exploited to design evolutionary traps that enable selection against drug resistance.
Locally adaptive inversions modulate genetic variation at different geographic scales in a seaweed fly
Authors: Mérot Claire , Berdan Emma , Cayuela Hugo , Djambazian Haig , Ferchaud Anne-Laure , Laporte Martin , Normandeau Eric , Ragoussis Jiannis , Wellenreuther Maren , Bernatchez Louis 
Published: December 2020

AbstractAcross a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range, and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed flyCoelopa frigidaalong a bioclimatic gradient stretching across 10° of latitude, a salinity gradient and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyse 1,446 low-coverage whole genomes collected along those gradients. We found several large non-recombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.
Endothelial SOCS3 maintains homeostasis and promotes survival in endotoxemic mice
Authors: Martino Nina , Ramos Ramon Bossardi , Lu Shuhan , Leyden Kara , Tomaszek Lindsay , Sadhu Sudeshna , Fredman Gabrielle , Jaitovich Ariel , Vincent Peter A. , Adam Alejandro P. 
Published: December 2020

AbstractSOCS3 is the main inhibitor of the JAK/STAT3 pathway. This pathway is activated by interleukin 6 (IL-6), a major mediator of the cytokine storm during shock. To determine its role in the vascular response to shock, we challenged mice lacking SOCS3 in the adult endothelium (SOCS3iEKo) with a non-lethal dose of lipopolysaccharide (LPS). SOCS3iEKomice died 16-24 hours post-injection after severe kidney failure. Loss of SOCS3 led to an LPS-induced type I interferon-like program, and high expression of pro-thrombotic and pro-adhesive genes. Consistently, we observed intraluminal leukocyte adhesion and NETosis, as well as retinal venular leukoembolization. Notably, heterozygous mice displayed an intermediate phenotype, suggesting a gene dose effect. In vitro studies were performed to study the role of SOCS3 protein levels in the regulation of the inflammatory response. In HUVEC, pulse-chase experiments showed that SOCS3 protein has a half-life below 20 minutes. Inhibition of SOCS3 ubiquitination and proteasomal degradation leads to protein accumulation and a stronger inhibition of IL-6 signaling and barrier function loss. Together, our data demonstrates that the regulation of SOCS3 protein levels is critical to inhibit IL-6-mediated endotheliopathy during shock and provides a promising new therapeutic avenue to prevent MODS though stabilization of endothelial SOCS3.Graphical abstract
YAP1-TAZ/TEAD transcriptional networks restrain differentiation downstream of oncogenic Hedgehog-SMO activity
Authors: Yuan Yao , Parra Natalia Salinas , Chen Qianming , Iglesias-Bartolome Ramiro 
Published: December 2020

AbstractDisruption of the transcriptional activity of the Hippo pathway members YAP1 and TAZ has become a major target for cancer treatment. However, detailed analysis of the effectivity and networks affected by YAP1/TAZ transcriptional targeting are limited. Here, by comparing the effects of YAP1/TAZ knockdown with those resulting from TEAD blockage, we unveil the consequences of YAP1/TAZ transcriptional inhibition in cancer cells. We utilize TEADi, an inhibitor of the binding of YAP1 and TAZ with their main transcriptional target TEAD. In a mouse model of basal cell carcinoma (BCC) driven by the smoothened oncogene (SmoM2), TEADi and YAP1/TAZ knockdown lead to reduced proliferation and increased differentiation of tumor cells both in vitro and in vivo. We find that TEAD transcriptional networks inactivate differentiation in BCC by regulating KLF4. Furthermore, we determine YAP1/TAZ TEAD-independent effects in cancer cells that impact Stat3 and NF-κB gene networks. Our results reveal the TEAD dependent and independent roles of YAP1/TAZ in cancer and expose potential pitfalls for targeting TEAD transcription in tumors.
The comprehensive roadmaps of reprogramming and transformation unveiled antagonistic roles for bHLH transcription factors in the control of cellular plasticity
Authors: Huyghe A. , Furlan G. , Schroeder J. , Stüder J. , Mugnier F. , De Matteo L. , Wang J. , Yu Y. , Rama N. , Gibert B. , Wajda P. , Goddard I. , Gadot N. , Brevet M. , Siouda M. , Mulligan P. , Dante R. , Liu P. , Gronemeyer H. , Mendoza-Parra M. , Polo J. , Lavial F. 
Published: December 2020

AbstractCoordinated changes of cellular identity and plasticity are critical for pluripotent reprogramming (PR) and malignant transformation (MT). However, the molecular circuitries orchestrating these modifications, as well as their degree of analogy during reprogramming and transformation, remain unknown. To address this question, we generated “repro-transformable” mice models and dissected comparatively the early events underpinning PR - mediated by Oct4, Sox2, Klf4, c-Myc - and MT - triggered by oncogenic Ras and c-Myc. Transcriptomic analyses allowed the identification of a unique set of markers - the cell surface glycoprotein Thy1 and the transcription factor (TF) Bcl11b - that are commonly downregulated during PR and MT and delineate cellular intermediates (CI) highly amenable to generate pluripotent or malignant derivatives. Comprehensive transcriptomic, epigenomic and functional analyses of different CI, prone or refractory to PR/MT, unveiled that cellular plasticity acquisition precedes the broad extinction of cellular identity. It also demonstrated the existence of specific and shared molecular features of PR and MT while ensuring the identification of broad-range regulators of cellular plasticity. As a proof-of-concept, we revealed that the basic helix-loop-helix (bHLH) class A TF Atoh8 constrains rodent and human iPS cells generation as well as MT and direct neuron conversion. Mechanistically, this TF hampers the reactivation of the pluripotent network during PR and limits the acquisition of phenotypic plasticity during MT. Furthermore, an integrated analysis of Atoh8 genome-wide binding, alongside the other bHLH TFs c-Myc, Ascl1 and MyoD promoting reprogramming/transdifferentiation, unveiled how Atoh8 constrains cellular plasticity by occupying a specific subset of MEF enhancers and by finetuning WNT signalling activity. Collectively, by deconvoluting the early steps of the reprogramming and transformation roadmaps, this integrated study uncoupled changes of cellular plasticity and identity to shed light on novel insights into reprogramming and cancer biology.Graphical abstractOne-sentence summaryComparative roadmaps of cellular plasticity acquisition during pluripotent reprogramming and malignant transformation.