bluuebunny/crossref_metadata_2025_split huggingface dataset:
AnnexinA7 promotes epithelial–mesenchymal transition by interacting with Sorcin and contributes to aggressiveness in hepatocellular carcinoma
Authors: Ling Fei , Zhang Huan , Sun Yunliang , Meng Jinyi , Sanches Jaceline Gislaine Pires , Huang He , Zhang Qingqing , Yu Xiao , Wang Bo , Hou Li , Zhang Jun 
Published: October 2021

AbstractHepatocellular carcinoma (HCC) is one of the most common cancers worldwide, and metastasis is the major cause of the high mortality of HCC. In this study, we identified that AnnexinA7 (ANXA7) and Sorcin (SRI) are overexpressed and interacting proteins in HCC tissues and cells. In vitro functional investigations revealed that the interaction between ANXA7 and SRI regulated epithelial–mesenchymal transition (EMT), and then affected migration, invasion, and proliferation in HCC cells. Furthermore overexpression/knockdown of ANXA7 was remarkably effective in promoting/inhibiting tumorigenicity and EMT in vivo. Altogether, our study unveiled a mechanism that ANXA7 promotes EMT by interacting with SRI and further contributes to the aggressiveness in HCC, which provides a novel potential therapeutic target for preventing recurrence and metastasis in HCC.
BET protein inhibition evidently enhances sensitivity to PI3K/mTOR dual inhibition in intrahepatic cholangiocarcinoma
Authors: Miao Xiaolong , Liu Chen , Jiang Yuancong , Wang Yao , Kong Deqiang , Wu Zelai , Wang Xinyi , Tian Rui , Yu Xing , Zhu Xuhang , Gong Weihua 
Published: October 2021

AbstractIntrahepatic cholangiocarcinoma (ICC), the second most common primary liver cancer, is a fatal malignancy with a poor prognosis and only very limited therapeutic options. Although molecular targeted therapy is emerged as a promising treatment strategy, resistance to molecular-targeted therapy occurs inevitably, which represents a major clinical challenge. In this study, we confirmed that mammalian target of rapamycin (mTOR) signaling is the most significantly affected pathways in ICC. As a novel phosphoinositide 3-kinase (PI3K)/mTOR dual inhibitor, BEZ235, exerts antitumour activity by effectively and specifically blocking the dysfunctional activation of the PI3K/serine/threonine kinase (AKT)/mTOR pathway. We generate the orthotopic ICC mouse model through hydrodynamic transfection of AKT and yes-associated protein (YAP) plasmids into the mouse liver. Our study confirmed that BEZ235 can suppress the proliferation, invasion and colony conformation abilities of ICC cells in vitro but cannot effectively inhibit ICC progression in vivo. Inhibition of PI3K/mTOR allowed upregulation of c-Myc and YAP through suppressed the phosphorylation of LATS1. It would be a novel mechanism that mediated resistance to PI3K/mTOR dual inhibitor. However, Bromo- and extraterminal domain (BET) inhibition by JQ1 downregulates c-Myc and YAP transcription, which could enhance the efficacy of PI3K/mTOR inhibitors. The efficacy results of combination therapy exhibited effective treatment on ICC in vitro and in vivo. Our data further confirmed that the combination of PI3K/mTOR dual inhibitor and BET inhibition induces M1 polarization and suppresses M2 polarization in macrophages by regulating the expression of HIF-1α. Our study provides a novel and efficient therapeutic strategy in treating primary ICC.
p32 promotes melanoma progression and metastasis by targeting EMT markers, Akt/PKB pathway, and tumor microenvironment
Authors: Sinha Sunita , Singh Satyendra Kumar , Jangde Nitish , Ray Rashmi , Rai Vivek 
Published: October 2021

AbstractMelanoma originates from melanin-producing cells called melanocytes. Melanoma poses a great risk because of its rapid ability to spread and invade new organs. Cellular metastasis involves alteration in the gene expression profile and their transformation from epithelial to mesenchymal state. Despite of several advances, metastatic melanoma being a key cause of therapy failure and mortality remains poorly understood. p32 has been found to be involved in various physiological and pathophysiological conditions. However, the role of p32 in melanoma progression and metastasis remains underexplored. Here, we identify the role of p32 in the malignancy of both murine and human melanoma. p32 knockdown leads to reduced cell proliferation, migration, and invasion in murine and human melanoma cells. Furthermore, p32 promotes in vitro tumorigenesis, inducing oncogenes and EMT markers. Mechanistically, we show p32 regulates tumorigenic and metastatic properties through the Akt/PKB signaling pathway in both murine and human melanoma. Furthermore, p32 silencing attenuates melanoma tumor progression and lung metastasis in vivo, modulating the tumor microenvironment by inhibiting the angiogenesis, infiltration of macrophages, and leukocytes in mice. Taken together, our findings identify that p32 drives melanoma progression, metastasis, and regulates the tumor microenvironment. p32 can be a target of a novel therapeutic approach in the regulation of melanoma progression and metastasis.
Age-related neurodegeneration and cognitive impairments of NRMT1 knockout mice are preceded by misregulation of RB and abnormal neural stem cell development
Authors: Catlin James P. , Marziali Leandro N. , Rein Benjamin , Yan Zhen , Feltri M. Laura , Schaner Tooley Christine E. 
Published: October 2021

AbstractN-terminal methylation is an important posttranslational modification that regulates protein/DNA interactions and plays a role in many cellular processes, including DNA damage repair, mitosis, and transcriptional regulation. Our generation of a constitutive knockout mouse for the N-terminal methyltransferase NRMT1 demonstrated its loss results in severe developmental abnormalities and premature aging phenotypes. As premature aging is often accompanied by neurodegeneration, we more specifically examined how NRMT1 loss affects neural pathology and cognitive behaviors. Here we find that Nrmt1−/− mice exhibit postnatal enlargement of the lateral ventricles, age-dependent striatal and hippocampal neurodegeneration, memory impairments, and hyperactivity. These morphological and behavior abnormalities are preceded by alterations in neural stem cell (NSC) development. Early expansion and differentiation of the quiescent NSC pool in Nrmt1−/− mice is followed by its subsequent depletion and many of the resulting neurons remain in the cell cycle and ultimately undergo apoptosis. These cell cycle phenotypes are reminiscent to those seen with loss of the NRMT1 target retinoblastoma protein (RB). Accordingly, we find misregulation of RB phosphorylation and degradation in Nrmt1−/− mice, and significant de-repression of RB target genes involved in cell cycle. We also identify novel de-repression of Noxa, an RB target gene that promotes apoptosis. These data identify Nα-methylation as a novel regulatory modification of RB transcriptional repression during neurogenesis and indicate that NRMT1 and RB work together to promote NSC quiescence and prevent neuronal apoptosis.
Alterations in the gut microbiota and metabolite profiles of patients with Kashin-Beck disease, an endemic osteoarthritis in China
Authors: Wang Xi , Ning Yujie , Li Cheng , Gong Yi , Huang Ruitian , Hu Minhan , Poulet Blandine , Xu Ke , Zhao Guanghui , Zhou Rong , Lammi Mikko J. , Guo Xiong 
Published: October 2021

AbstractKashin-Beck disease (KBD) is a severe osteochondral disorder that may be driven by the interaction between genetic and environmental factors. We aimed to improve our understanding of the gut microbiota structure in KBD patients of different grades and the relationship between the gut microbiota and serum metabolites. Fecal and serum samples collected from KBD patients and normal controls (NCs) were used to characterize the gut microbiota using 16S rDNA gene and metabolomic sequencing via liquid chromatography-mass spectrometry (LC/MS). To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria in the KBD patients, metagenomic sequencing of fecal samples from grade I KBD, grade II KBD and NC subjects was performed. The KBD group was characterized by elevated levels of Fusobacteria and Bacteroidetes. A total of 56 genera were identified to be significantly differentially abundant between the two groups. The genera Alloprevotella, Robinsoniella, Megamonas, and Escherichia_Shigella were more abundant in the KBD group. Consistent with the 16S rDNA analysis at the genus level, most of the differentially abundant species in KBD subjects belonged to the genus Prevotella according to metagenomic sequencing. Serum metabolomic analysis identified some differentially abundant metabolites among the grade I and II KBD and NC groups that were involved in lipid metabolism metabolic networks, such as that for unsaturated fatty acids and glycerophospholipids. Furthermore, we found that these differences in metabolite levels were associated with altered abundances of specific species. Our study provides a comprehensive landscape of the gut microbiota and metabolites in KBD patients and provides substantial evidence of a novel interplay between the gut microbiome and metabolome in KBD pathogenesis.
miR548ai antagonism attenuates exosome-induced endothelial cell dysfunction
Authors: Xie Xiujie , Guo Lian-Wang , Kent Craig K. 
Published: October 2021

AbstractEndothelial cell (EC) and smooth muscle cell (SMC) are major cell types adjacent in the vascular wall. Recent progress indicates that their communication is crucial for vascular homeostasis and pathogenesis. In particular, dysfunctional (proliferative) SMCs through exosomes can induce EC dysfunction (impaired growth). The current study suggests that miR548ai, a rarely known microRNA, may provide a molecular target for protection against SMC/exosome-induced EC dysfunction. We performed microarray profiling of microRNAs of dysfunctional human primary aortic SMCs induced by different cytokines (PDGF-BB, TGFβ1, TNFα, IL1β). Among the microRNAs commonly upregulated by these cytokines, miR548ai showed the most robust changes, as also validated through quantitative PCR. This cytokine-induced miR548ai upregulation was recapitulated in the qPCR determination of SMC-derived exosomal microRNAs. Consistent with SMC-to-EC communication, the exosomes extracted from cytokine-stimulated SMCs impaired human EC proliferation and migration. Of particular interest, this SMC exosomal impingement on ECs was countered by transfection of miR548ai inhibitor microRNA into ECs. Furthermore, the miR548ai inhibitor transfected into SMCs attenuated SMC dysfunction/proliferation. Thus, these results identify miR548ai as a novel target; namely, miR548ai inhibitor mitigates EC dysfunction induced by exosomes derived from dysfunctional SMCs. This new knowledge may aid the future development of microRNA-based treatment of vascular disorders.
Overexpression of HMGA1 confers radioresistance by transactivating RAD51 in cholangiocarcinoma
Authors: Song Jianping , Cui Donghai , Wang Jing , Qin Junchao , Wang Shourong , Wang Zixiang , Zhai Xiangyu , Ma Huan , Ma Delin , Liu Yanfeng , Jin Bin , Liu Zhaojian 
Published: October 2021

AbstractCholangiocarcinomas (CCAs) are rare but aggressive tumors of the bile ducts. CCAs are often diagnosed at an advanced stage and respond poorly to current conventional radiotherapy and chemotherapy. High mobility group A1 (HMGA1) is an architectural transcription factor that is overexpressed in multiple malignant tumors. In this study, we showed that the expression of HMGA1 is frequently elevated in CCAs and that the high expression of this gene is associated with a poor prognosis. Functionally, HMGA1 promotes CCA cell proliferation/invasion and xenograft tumor growth. Furthermore, HMGA1 transcriptionally activates RAD51 by binding to its promoter through two HMGA1 response elements. Notably, overexpression of HMGA1 promotes radioresistance whereas its knockdown causes radiosensitivity of CCA cells to X-ray irradiation. Moreover, rescue experiments reveal that inhibition of RAD51 reverses the effect of HMGA1 on radioresistance and proliferation/invasion. These findings suggest that HMGA1 functions as a novel regulator of RAD51 and confers radioresistance in cholangiocarcinoma.
BAMboozle removes genetic variation from human sequence data for open data sharing
Authors: Ziegenhain Christoph , Sandberg Rickard 
Published: October 2021

AbstractThe risks associated with re-identification of human genetic data are severely limiting open data sharing in life sciences, even in studies where donor-related genetic variant information is not of primary interest. Here, we developed BAMboozle, a versatile tool to eliminate critical types of sensitive genetic information in human sequence data by reverting aligned reads to the genome reference sequence. Applying BAMboozle to functional genomics data, such as single-cell RNA-seq (scRNA-seq) and scATAC-seq datasets, confirmed the removal of donor-related single nucleotide polymorphisms (SNPs) and indels in a manner that did not disclose the altered positions. Importantly, BAMboozle only removes the genetic sequence variants of the sample (i.e., donor) while preserving other important aspects of the raw sequence data. For example, BAMboozled scRNA-seq data contained accurate cell-type associated gene expression signatures, splice kinetic information, and can be used for methods benchmarking. Altogether, BAMboozle efficiently removes genetic variation in aligned sequence data, which represents a step forward towards open data sharing in many areas of genomics where the genetic variant information is not of primary interest.
Assessing the importance of thermogenic degassing from the Karoo Large Igneous Province (LIP) in driving Toarcian carbon cycle perturbations
Authors: Heimdal Thea H. , Goddéris Yves , Jones Morgan T. , Svensen Henrik H. 
Published: October 2021

AbstractThe emplacement of the Karoo Large Igneous Province (LIP) occurred synchronously with the Toarcian crisis (ca. 183 Ma), which is characterized by major carbon cycle perturbations. A marked increase in the atmospheric concentration of CO2(pCO2) attests to significant input of carbon, while negative carbon isotope excursions (CIEs) in marine and terrestrial records suggest the involvement of a12C-enriched source. Here we explore the effects of pulsed carbon release from the Karoo LIP on atmosphericpCO2and δ13C of marine sediments, using the GEOCLIM carbon cycle model. We show that a total of 20,500 Gt C replicates the ToarcianpCO2and δ13C proxy data, and that thermogenic carbon (δ13C of −36 ‰) represents a plausible source for the observed negative CIEs. Importantly, an extremely isotopically depleted carbon source, such as methane clathrates, is not required in order to replicate the negative CIEs. Although exact values of individual degassing pulses represent estimates, we consider our emission scenario realistic as it incorporates the available geological knowledge of the Karoo LIP and a representative framework for Earth system processes during the Toarcian.
Uncovering the out-of-plane nanomorphology of organic photovoltaic bulk heterojunction by GTSAXS
Authors: Xia Xinxin , Lau Tsz-Ki , Guo Xuyun , Li Yuhao , Qin Minchao , Liu Kuan , Chen Zeng , Zhan Xiaozhi , Xiao Yiqun , Chan Pok Fung , Liu Heng , Xu Luhang , Cai Guilong , Li Na , Zhu Haiming , Li Gang , Zhu Ye , Zhu Tao , Zhan Xiaowei , Wang Xun-Li , Lu Xinhui 
Published: October 2021

AbstractThe bulk morphology of the active layer of organic solar cells (OSCs) is known to be crucial to the device performance. The thin film device structure breaks the symmetry into the in-plane direction and out-of-plane direction with respect to the substrate, leading to an intrinsic anisotropy in the bulk morphology. However, the characterization of out-of-plane nanomorphology within the active layer remains a grand challenge. Here, we utilized an X-ray scattering technique, Grazing-incident Transmission Small-angle X-ray Scattering (GTSAXS), to uncover this new morphology dimension. This technique was implemented on the model systems based on fullerene derivative (P3HT:PC71BM) and non-fullerene systems (PBDBT:ITIC, PM6:Y6), which demonstrated the successful extraction of the quantitative out-of-plane acceptor domain size of OSC systems. The detected in-plane and out-of-plane domain sizes show strong correlations with the device performance, particularly in terms of exciton dissociation and charge transfer. With the help of GTSAXS, one could obtain a more fundamental perception about the three-dimensional nanomorphology and new angles for morphology control strategies towards highly efficient photovoltaic devices.
Improvement of a synthetic live bacterial therapeutic for phenylketonuria with biosensor-enabled enzyme engineering
Authors: Adolfsen Kristin J. , Callihan Isolde , Monahan Catherine E. , Greisen Per , Spoonamore James , Momin Munira , Fitch Lauren E. , Castillo Mary Joan , Weng Lindong , Renaud Lauren , Weile Carl J. , Konieczka Jay H. , Mirabella Teodelinda , Abin-Fuentes Andres , Lawrence Adam G. , Isabella Vincent M. 
Published: October 2021

AbstractIn phenylketonuria (PKU) patients, a genetic defect in the enzyme phenylalanine hydroxylase (PAH) leads to elevated systemic phenylalanine (Phe), which can result in severe neurological impairment. As a treatment for PKU,Escherichia coliNissle (EcN) strain SYNB1618 was developed under Synlogic’s Synthetic Biotic™ platform to degrade Phe from within the gastrointestinal (GI) tract. This clinical-stage engineered strain expresses the Phe-metabolizing enzyme phenylalanine ammonia lyase (PAL), catalyzing the deamination of Phe to the non-toxic producttrans-cinnamate (TCA). In the present work, we generate a more potent EcN-based PKU strain through optimization of whole cell PAL activity, using biosensor-based high-throughput screening of mutant PAL libraries. A lead enzyme candidate from this screen is used in the construction of SYNB1934, a chromosomally integrated strain containing the additional Phe-metabolizing and biosafety features found in SYNB1618. Head-to-head, SYNB1934 demonstrates an approximate two-fold increase in in vivo PAL activity compared to SYNB1618.
Ion-dependent structure, dynamics, and allosteric coupling in a non-selective cation channel
Authors: Lewis Adam , Kurauskas Vilius , Tonelli Marco , Henzler-Wildman Katherine 
Published: October 2021

AbstractThe selectivity filter (SF) determines which ions are efficiently conducted through ion channel pores. NaK is a non-selective cation channel that conducts Na+ and K+ with equal efficiency. Crystal structures of NaK suggested a rigid SF structure, but later solid-state NMR and MD simulations questioned this interpretation. Here, we use solution NMR to characterize how bound Na+ vs. K+ affects NaK SF structure and dynamics. We find that the extracellular end of the SF is flexible on the ps-ns timescale regardless of bound ion. On a slower timescale, we observe a structural change between the Na+ and K+-bound states, accompanied by increased structural heterogeneity in Na+. We also show direct evidence that the SF structure is communicated to the pore via I88 on the M2 helix. These results support a dynamic SF with multiple conformations involved in non-selective conduction. Our data also demonstrate allosteric coupling between the SF and pore-lining helices in a non-selective cation channel that is analogous to the allosteric coupling previously demonstrated for K+-selective channels, supporting the generality of this model.
Functional metagenomic analysis of quorum sensing signaling in a nitrifying community
Authors: Tan Chuan Hao , Yeo Yee Phan , Hafiz Muhammad , Ng Noele Kai Jing , Subramoni Sujatha , Taj Shireen , Tay Martin , Chao Xie , Kjelleberg Staffan , Rice Scott A. 
Published: October 2021

AbstractQuorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS production and the nitrogen removal process. However, the role of QS in such complex communities is still not fully understood, including the QS-proficient taxa and the functional QS genes involved. To address these questions, we performed a metagenomic screen for AHL genes in an activated sludge microbial community from the Ulu Pandan wastewater treatment plant (WWTP) in Singapore followed by functional validation of luxI activity using AHL biosensors and LC–MSMS profiling. We identified 13 luxI and 30 luxR homologs from the activated sludge metagenome. Of those genes, two represented a cognate pair of luxIR genes belonging to a Nitrospira spp. and those genes were demonstrated to be functionally active. The LuxI homolog synthesized AHLs that were consistent with the dominant AHLs in the activated sludge system. Furthermore, the LuxR homolog was shown to bind to and induce expression of the luxI promoter, suggesting this represents an autoinduction feedback system, characteristic of QS circuits. Additionally, a second, active promoter was upstream of a gene encoding a protein with a GGDEF/EAL domain, commonly associated with modulating the intracellular concentration of the secondary messenger, c-di-GMP. Thus, the metagenomic approach used here was demonstrated to effectively identify functional QS genes and suggests that Nitrospira spp. maybe QS is active in the activated sludge community.
Tunable vertical ferroelectricity and domain walls by interlayer sliding in β-ZrI2
Authors: Ma Xiaonan , Liu Chang , Ren Wei , Nikolaev Sergey A. 
Published: October 2021

AbstractVertical ferroelectricity where a net dipole moment appears as a result of in-plane ionic displacements has gained enormous attention following its discovery in transition metal dichalcogenides. Based on first-principles calculations, we report on the evidence of robust vertical ferroelectricity upon interlayer sliding in layered semiconducting β-ZrI2, a sister material of polar semimetals MoTe2 and WTe2. The microscopic origin of ferroelectricity in ZrI2 is attributed to asymmetric shifts of electronic charges within a trilayer, revealing a subtle interplay of rigid sliding displacements and charge redistribution down to ultrathin thicknesses. We further investigate the variety of ferroelectric domain boundaries and predict a stable charged domain wall with a quasi-two-dimensional electron gas and a high built-in electric field that can increase electron mobility and electromechanical response in multifunctional devices. Semiconducting behaviour and a small switching barrier of ZrI2 hold promise for various ferroelectric applications, and our results provide important insights for further development of slidetronics ferroelectricity.