bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective killing of cancer cells harboring mutant RAS by concomitant inhibition of NADPH oxidase and glutathione biosynthesis
Authors: Liu Muyun , Wang Dan , Luo Yongde , Hu Lianghao , Bi Yawei , Ji Juntao , Huang Haojie , Wang Guoqiang , Zhu Liang , Ma Jianjia , Kim Eunice , Luo Catherine K. , Abbruzzese James L. , Li Xiaokun , Yang Vincent W. , Li Zhaoshen , Lu Weiqin 
Published: February 2021

AbstractOncogenic RAS is a critical driver for the initiation and progression of several types of cancers. However, effective therapeutic strategies by targeting RAS, in particular RASG12D and RASG12V, and associated downstream pathways have been so far unsuccessful. Treatment of oncogenic RAS-ravaged cancer patients remains a currently unmet clinical need. Consistent with a major role in cancer metabolism, oncogenic RAS activation elevates both reactive oxygen species (ROS)-generating NADPH oxidase (NOX) activity and ROS-scavenging glutathione biosynthesis. At a certain threshold, the heightened oxidative stress and antioxidant capability achieve a higher level of redox balance, on which cancer cells depend to gain a selective advantage on survival and proliferation. However, this prominent metabolic feature may irrevocably render cancer cells vulnerable to concurrent inhibition of both NOX activity and glutathione biosynthesis, which may be exploited as a novel therapeutic strategy. In this report, we test this hypothesis by treating the HRASG12V-transformed ovarian epithelial cells, mutant KRAS-harboring pancreatic and colon cancer cells of mouse and human origins, as well as cancer xenografts, with diphenyleneiodonium (DPI) and buthionine sulfoximine (BSO) combination, which inhibit NOX activity and glutathione biosynthesis, respectively. Our results demonstrate that concomitant targeting of NOX and glutathione biosynthesis induces a highly potent lethality to cancer cells harboring oncogenic RAS. Therefore, our studies provide a novel strategy against RAS-bearing cancers that warrants further mechanistic and translational investigation.
BMP2-dependent gene regulatory network analysis reveals Klf4 as a novel transcription factor of osteoblast differentiation
Authors: Yu Shuaitong , Guo Jinqiang , Sun Zheyi , Lin Chujiao , Tao Huangheng , Zhang Qian , Cui Yu , Zuo Huanyan , Lin Yuxiu , Chen Shuo , Liu Huan , Chen Zhi 
Published: February 2021

AbstractTranscription factors (TFs) regulate the expression of target genes, inducing changes in cell morphology or activities needed for cell fate determination and differentiation. The BMP signaling pathway is widely regarded as one of the most important pathways in vertebrate skeletal biology, of which BMP2 is a potent inducer, governing the osteoblast differentiation of bone marrow stromal cells (BMSCs). However, the mechanism by which BMP2 initiates its downstream transcription factor cascade and determines the direction of differentiation remains largely unknown. In this study, we used RNA-seq, ATAC-seq, and animal models to characterize the BMP2-dependent gene regulatory network governing osteoblast lineage commitment. Sp7-Cre; Bmp2fx/fx mice (BMP2-cKO) were generated and exhibited decreased bone density and lower osteoblast number (n > 6). In vitro experiments showed that BMP2-cKO mouse bone marrow stromal cells (mBMSCs) had an impact on osteoblast differentiation and deficient cell proliferation. Osteogenic medium induced mBMSCs from BMP2-cKO mice and control were subjected to RNA-seq and ATAC-seq analysis to reveal differentially expressed TFs, along with their target open chromatin regions. Combined with H3K27Ac CUT&Tag during osteoblast differentiation, we identified 2338 BMP2-dependent osteoblast-specific active enhancers. Motif enrichment assay revealed that over 80% of these elements were directly targeted by RUNX2, DLX5, MEF2C, OASIS, and KLF4. We deactivated Klf4 in the Sp7 + lineage to validate the role of KLF4 in osteoblast differentiation of mBMSCs. Compared to the wild-type, Sp7-Cre; Klf4fx/+ mice (KLF4-Het) were smaller in size and had abnormal incisors resembling BMP2-cKO mice. Additionally, KLF4-Het mice had fewer osteoblasts and decreased osteogenic ability. RNA-seq and ATAC-seq revealed that KLF4 mainly “co-bound” with RUNX2 to regulate downstream genes. Given the significant overlap between KLF4- and BMP2-dependent NFRs and enriched motifs, our findings outline a comprehensive BMP2-dependent gene regulatory network specifically governing osteoblast differentiation of the Sp7 + lineage, in which Klf4 is a novel transcription factor.
Distinct functions of transforming growth factor-β signaling in c-MYC driven hepatocellular carcinoma initiation and progression
Authors: Wang Haichuan , Wang Pan , Xu Meng , Song Xinhua , Wu Hong , Evert Matthias , Calvisi Diego F. , Zeng Yong , Chen Xin 
Published: February 2021

AbstractDysregulation of transforming growth factor-beta (TGFβ) signaling has been implicated in liver carcinogenesis with both tumor promoting and inhibiting activities. Activation of the c-MYC protooncogene is another critical genetic event in hepatocellular carcinoma (HCC). However, the precise functional crosstalk between c-MYC and TGFβ signaling pathways remains unclear. In the present investigation, we investigated the expression of TGFβ signaling in c-MYC amplified human HCC samples as well as the mechanisms whereby TGFβ modulates c-Myc driven hepatocarcinogenesis during initiation and progression. We found that several TGFβ target genes are overexpressed in human HCCs with c-MYC amplification. In vivo, activation of TGFβ1 impaired c-Myc murine HCC initiation, whereas inhibition of TGFβ pathway accelerated this process. In contrast, overexpression of TGFβ1 enhanced c-Myc HCC progression by promoting tumor cell metastasis. Mechanistically, activation of TGFβ promoted tumor microenvironment reprogramming rather than inducing epithelial-to-mesenchymal transition during HCC progression. Moreover, we identified PMEPA1 as a potential TGFβ1 target. Altogether, our data underline the divergent roles of TGFβ signaling during c-MYC induced HCC initiation and progression.
Distinct Ring1b complexes defined by DEAD-box helicases and EMT transcription factors synergistically enhance E-cadherin silencing in breast cancer
Authors: Wang Yawei , Sun Yingying , Shang Chao , Chen Lili , Chen Hongyu , Wang Dake , Zeng Xianlu 
Published: February 2021

AbstractRing1b is a core subunit of polycomb repressive complex 1 (PRC1) and is essential in several high-risk cancers. However, the epigenetic mechanism of Ring1b underlying breast cancer malignancy is poorly understood. In this study, we showed increased expression of Ring1b promoted metastasis by weakening cell–cell adhesions of breast cancer cells. We confirmed that Ring1b could downregulate E-cadherin and contributed to an epigenetic rewiring via PRC1-dependent function by forming distinct complexes with DEAD-box RNA helicases (DDXs) or epithelial-mesenchymal transition transcription factors (EMT TFs) on site-specific loci of E-cadherin promoter. DDXs-Ring1b complexes moderately inhibited E-cadherin, which resulted in an early hybrid EMT state of epithelial cells, and EMT TFs-Ring1b complexes cooperated with DDXs-Ring1b complexes to further repress E-cadherin in mesenchymal-like cancer cells. Clinically, high expression of Ring1b with DDXs or EMT TFs predicted low levels of E-cadherin, metastatic behavior, and poor prognosis. These findings provide an epigenetic regulation mechanism of Ring1b complexes in E-cadherin expression. Ring1b complexes may be potential therapeutic targets and biomarkers for diagnosis and prognosis in invasion breast cancer.
Structural characterization of ice XIX as the second polymorph related to ice VI
Authors: Gasser Tobias M. , Thoeny Alexander V. , Fortes A. Dominic , Loerting Thomas 
Published: February 2021

AbstractIce polymorphs usually appear as hydrogen disorder-order pairs. Ice VI has a wide range of thermodynamic stability and exists in the interior of Earth and icy moons. Our previous work suggested ice β-XV as a second polymorph deriving from disordered ice VI, in addition to ice XV. Here we report thermal and structural characterization of the previously inaccessible deuterated polymorph using ex situ calorimetry and high-resolution neutron powder diffraction. Ice β-XV, now called ice XIX, is shown to be partially antiferroelectrically ordered and crystallising in a √2×√2×1 supercell. Our powder data recorded at subambient pressure fit best to the structural model in space group $$P\bar 4$$
P

4

¯

. Key to the synthesis of deuterated ice XIX is the use of a DCl-doped D2O/H2O mixture, where the small H2O fraction enhances ice XIX nucleation kinetics. In addition, we observe the transition from ice XIX to its sibling ice XV upon heating, which proceeds via a transition state (ice VI‡) containing a disordered H-sublattice. To the best of our knowledge this represents the first order-order transition known in ice physics.
Real-space imaging of acoustic plasmons in large-area graphene grown by chemical vapor deposition
Authors: Menabde Sergey G. , Lee In-Ho , Lee Sanghyub , Ha Heonhak , Heiden Jacob T. , Yoo Daehan , Kim Teun-Teun , Low Tony , Lee Young Hee , Oh Sang-Hyun , Jang Min Seok 
Published: February 2021

AbstractAn acoustic plasmon mode in a graphene-dielectric-metal structure has recently been spotlighted as a superior platform for strong light-matter interaction. It originates from the coupling of graphene plasmon with its mirror image and exhibits the largest field confinement in the limit of a sub-nm-thick dielectric. Although recently detected in the far-field regime, optical near-fields of this mode are yet to be observed and characterized. Here, we demonstrate a direct optical probing of the plasmonic fields reflected by the edges of graphene via near-field scattering microscope, revealing a relatively small propagation loss of the mid-infrared acoustic plasmons in our devices that allows for their real-space mapping at ambient conditions even with unprotected, large-area graphene grown by chemical vapor deposition. We show an acoustic plasmon mode that is twice as confined and has 1.4 times higher figure of merit in terms of the normalized propagation length compared to the graphene surface plasmon under similar conditions. We also investigate the behavior of the acoustic graphene plasmons in a periodic array of gold nanoribbons. Our results highlight the promise of acoustic plasmons for graphene-based optoelectronics and sensing applications.
Thermodynamics of structure-forming systems
Authors: Korbel Jan , Lindner Simon David , Hanel Rudolf , Thurner Stefan 
Published: February 2021

AbstractStructure-forming systems are ubiquitous in nature, ranging from atoms building molecules to self-assembly of colloidal amphibolic particles. The understanding of the underlying thermodynamics of such systems remains an important problem. Here, we derive the entropy for structure-forming systems that differs from Boltzmann-Gibbs entropy by a term that explicitly captures clustered states. For large systems and low concentrations the approach is equivalent to the grand-canonical ensemble; for small systems we find significant deviations. We derive the detailed fluctuation theorem and Crooks’ work fluctuation theorem for structure-forming systems. The connection to the theory of particle self-assembly is discussed. We apply the results to several physical systems. We present the phase diagram for patchy particles described by the Kern-Frenkel potential. We show that the Curie-Weiss model with molecule structures exhibits a first-order phase transition.
Gold(I)-catalyzed intramolecular cyclization/intermolecular cycloaddition cascade as a fast track to polycarbocycles and mechanistic insights
Authors: Zhang Cheng , Hong Kemiao , Pei Chao , Zhou Su , Hu Wenhao , Hashmi A. Stephen K. , Xu Xinfang 
Published: February 2021

AbstractMetal carbene is an active synthetic intermediate, which has shown versatile applications in synthetic chemistry. Although a variety of catalytic methods have been disclosed for the generation of carbene species from different precursors, there is an increasing demand for the development of efficient and practical approaches for the in-situ formation of metal carbene intermediates with structural diversity and unrevealed reactivity. Herein we report a gold-catalyzed cascade protocol for the assembly of polycarbocyclic frameworks in high yields under mild reaction conditions. Mechanistic studies indicate that the unique β-aryl gold-carbene species, generated via gold-promoted 6-endo-dig diazo-yne cyclization, is the key intermediate in this reaction, followed by a [4 + 2]-cycloaddition with external alkenes. In comparison to the well-documented metal carbene cycloadditions, this carbene intermediate serves as a 4-C synthon in a cycloaddition reaction. A variety of elusive π-conjugated polycyclic hydrocarbons (CPHs) with multiple substituents are readily accessible from the initially generated products by a mild oxidation procedure.
20S proteasomes secreted by the malaria parasite promote its growth
Authors: Dekel Elya , Yaffe Dana , Rosenhek-Goldian Irit , Ben-Nissan Gili , Ofir-Birin Yifat , Morandi Mattia I. , Ziv Tamar , Sisquella Xavier , Pimentel Matthew A. , Nebl Thomas , Kapp Eugene , Ohana Daniel Yael , Karam Paula Abou , Alfandari Daniel , Rotkopf Ron , Malihi Shimrit , Temin Tal Block , Mullick Debakshi , Revach Or-Yam , Rudik Ariel , Gov Nir S. , Azuri Ido , Porat Ziv , Bergamaschi Giulia , Sorkin Raya , Wuite Gijs J. L. , Avinoam Ori , Carvalho Teresa G. , Cohen Sidney R. , Sharon Michal , Regev-Rudzki Neta 
Published: February 2021

AbstractMature red blood cells (RBCs) lack internal organelles and canonical defense mechanisms, making them both a fascinating host cell, in general, and an intriguing choice for the deadly malaria parasite Plasmodium falciparum (Pf), in particular. Pf, while growing inside its natural host, the human RBC, secretes multipurpose extracellular vesicles (EVs), yet their influence on this essential host cell remains unknown. Here we demonstrate that Pf parasites, cultured in fresh human donor blood, secrete within such EVs assembled and functional 20S proteasome complexes (EV-20S). The EV-20S proteasomes modulate the mechanical properties of naïve human RBCs by remodeling their cytoskeletal network. Furthermore, we identify four degradation targets of the secreted 20S proteasome, the phosphorylated cytoskeletal proteins β-adducin, ankyrin-1, dematin and Epb4.1. Overall, our findings reveal a previously unknown 20S proteasome secretion mechanism employed by the human malaria parasite, which primes RBCs for parasite invasion by altering membrane stiffness, to facilitate malaria parasite growth.
Cell non-autonomy amplifies disruption of neurulation by mosaic Vangl2 deletion in mice
Authors: Galea Gabriel L. , Maniou Eirini , Edwards Timothy J. , Marshall Abigail R. , Ampartzidis Ioakeim , Greene Nicholas D. E. , Copp Andrew J. 
Published: February 2021

AbstractPost-zygotic mutations that generate tissue mosaicism are increasingly associated with severe congenital defects, including those arising from failed neural tube closure. Here we report that neural fold elevation during mouse spinal neurulation is vulnerable to deletion of the VANGL planar cell polarity protein 2 (Vangl2) gene in as few as 16% of neuroepithelial cells.Vangl2-deleted cells are typically dispersed throughout the neuroepithelium, and each non-autonomously prevents apical constriction by an average of fiveVangl2-replete neighbours. This inhibition of apical constriction involves diminished myosin-II localisation on neighbour cell borders and shortening of basally-extending microtubule tails, which are known to facilitate apical constriction.Vangl2-deleted neuroepithelial cells themselves continue to apically constrict and preferentially recruit myosin-II to their apical cell cortex rather than to apical cap localisations. Such non-autonomous effects can explain how post-zygotic mutations affecting a minority of cells can cause catastrophic failure of morphogenesis leading to clinically important birth defects.
Innate immune evasion revealed in a colorectal zebrafish xenograft model
Authors: Póvoa Vanda , Rebelo de Almeida Cátia , Maia-Gil Mariana , Sobral Daniel , Domingues Micaela , Martinez-Lopez Mayra , de Almeida Fuzeta Miguel , Silva Carlos , Grosso Ana Rita , Fior Rita 
Published: February 2021

AbstractCancer immunoediting is a dynamic process of crosstalk between tumor cells and the immune system. Herein, we explore the fast zebrafish xenograft model to investigate the innate immune contribution to this process. Using multiple breast and colorectal cancer cell lines and zAvatars, we find that some are cleared (regressors) while others engraft (progressors) in zebrafish xenografts. We focus on two human colorectal cancer cells derived from the same patient that show contrasting engraftment/clearance profiles. Using polyclonal xenografts to mimic intra-tumor heterogeneity, we demonstrate that SW620_progressors can block clearance of SW480_regressors. SW480_regressors recruit macrophages and neutrophils more efficiently than SW620_progressors; SW620_progressors however, modulate macrophages towards a pro-tumoral phenotype. Genetic and chemical suppression of myeloid cells indicates that macrophages and neutrophils play a crucial role in clearance. Single-cell-transcriptome analysis shows a fast subclonal selection, with clearance of regressor subclones associated with IFN/Notch signaling and escaper-expanded subclones with enrichment of IL10 pathway. Overall, our work opens the possibility of using zebrafish xenografts as living biomarkers of the tumor microenvironment.
Characterising open chromatin in chick embryos identifies cis-regulatory elements important for paraxial mesoderm formation and axis extension
Authors: Mok Gi Fay , Folkes Leighton , Weldon Shannon A. , Maniou Eirini , Martinez-Heredia Victor , Godden Alice M. , Williams Ruth M. , Sauka-Spengler Tatjana , Wheeler Grant N. , Moxon Simon , Münsterberg Andrea E. 
Published: February 2021

AbstractSomites arising from paraxial mesoderm are a hallmark of the segmented vertebrate body plan. They form sequentially during axis extension and generate musculoskeletal cell lineages. How paraxial mesoderm becomes regionalised along the axis and how this correlates with dynamic changes of chromatin accessibility and the transcriptome remains unknown. Here, we report a spatiotemporal series of ATAC-seq and RNA-seq along the chick embryonic axis. Footprint analysis shows differential coverage of binding sites for several key transcription factors, including CDX2, LEF1 and members of HOX clusters. Associating accessible chromatin with nearby expressed genes identifies cis-regulatory elements (CRE) for TCF15 and MEOX1. We determine their spatiotemporal activity and evolutionary conservation in Xenopus and human. Epigenome silencing of endogenous CREs disrupts TCF15 and MEOX1 gene expression and recapitulates phenotypic abnormalities of anterior–posterior axis extension. Our integrated approach allows dissection of paraxial mesoderm regulatory circuits in vivo and has implications for investigating gene regulatory networks.
EARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancy
Authors: Azeez Abdul , Zhao Yiru Chen , Singh Rajesh Kumar , Yordanov Yordan S. , Dash Madhumita , Miskolczi Pal , Stojkovič Katja , Strauss Steve H. , Bhalerao Rishikesh P. , Busov Victor B. 
Published: February 2021

AbstractBud-break is an economically and environmentally important process in trees and shrubs from boreal and temperate latitudes, but its molecular mechanisms are poorly understood. Here, we show that two previously reported transcription factors, EARLY BUD BREAK 1 (EBB1) and SHORT VEGETATIVE PHASE-Like (SVL) directly interact to control bud-break. EBB1 is a positive regulator of bud-break, whereas SVL is a negative regulator of bud-break. EBB1 directly and negatively regulates SVL expression. We further report the identification and characterization of the EBB3 gene. EBB3 is a temperature-responsive, epigenetically-regulated, positive regulator of bud-break that provides a direct link to activation of the cell cycle during bud-break. EBB3 is an AP2/ERF transcription factor that positively and directly regulates CYCLIND3.1 gene. Our results reveal the architecture of a putative regulatory module that links temperature-mediated control of bud-break with activation of cell cycle.
Colossal switchable photocurrents in topological Janus transition metal dichalcogenides
Authors: Xu Haowei , Wang Hua , Zhou Jian , Guo Yunfan , Kong Jing , Li Ju 
Published: February 2021

AbstractNonlinear optical properties, such as bulk photovoltaic effects, possess great potential in energy harvesting, photodetection, rectification, etc. To enable efficient light–current conversion, materials with strong photo-responsivity are highly desirable. In this work, we predict that monolayer Janus transition metal dichalcogenides (JTMDs) in the 1T′ phase possess colossal nonlinear photoconductivity owing to their topological band mixing, strong inversion symmetry breaking, and small electronic bandgap. 1T′ JTMDs have inverted bandgaps on the order of 10 meV and are exceptionally responsive to light in the terahertz (THz) range. By first-principles calculations, we reveal that 1T′ JTMDs possess shift current (SC) conductivity as large as 2300 nm μA V−2, equivalent to a photo-responsivity of 2800 mA/W. The circular current (CC) conductivity of 1T′ JTMDs is as large as ∼104 nm μA V−2. These remarkable photo-responsivities indicate that the 1T′ JTMDs can serve as efficient photodetectors in the THz range. We also find that external stimuli such as the in-plane strain and out-of-plane electric field can induce topological phase transitions in 1T′ JTMDs and that the SC can abruptly flip their directions. The abrupt change of the nonlinear photocurrent can be used to characterize the topological transition and has potential applications in 2D optomechanics and nonlinear optoelectronics.
Code interoperability extends the scope of quantum simulations
Authors: Govoni Marco , Whitmer Jonathan , de Pablo Juan , Gygi Francois , Galli Giulia 
Published: February 2021

AbstractThe functionality of many materials is critically dependent on the integration of dissimilar components and on the interfaces that arise between them. The description of such heterogeneous components requires the development and deployment of first principles methods, coupled to appropriate dynamical descriptions of matter and advanced sampling techniques, in order to capture all the relevant length and time scales of importance to the materials’ performance. It is thus essential to build simple, streamlined computational schemes for the prediction and design of multiple properties of broad classes of materials, by developing interoperable codes which can be efficiently coupled to each other to perform complex tasks. We discuss the use of interoperable codes to simulate the structural and spectroscopic characterization of materials, including chemical reactions for catalysis, the description of defects for quantum information science, and heat and charge transport.