bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epithelial-mesenchymal transition is the main driver of intrinsic metabolism in cancer cell lines
Authors: Cherkaoui Sarah , Durot Stephan , Bradley Jenna , Critchlow Susan , Dubuis Sebastien , Masiero Mauro Miguel , Wegmann Rebekka , Snijder Berend , Othman Alaa , Bendtsen Claus , Zamboni Nicola 
Published: November 2021

AbstractA fundamental feature of cancer cells is genomic heterogeneity. It is a main driver of phenotypic differences, including the response to drugs, and therefore a key factor in therapy selection. Motivated by the increasing role attributed to metabolic reprogramming in tumor development, we wondered how genomic heterogeneity affects metabolic phenotype. To this end, we profiled the intracellular metabolome of 180 cancer cell lines grown in similar conditions to exclude environmental factors. For each cell line, we estimate activity for 49 pathways across the whole metabolic network. Upon clustering of activity data, we found a convergence into only two major metabolic types. These were further characterized by 13C-flux analysis, lipidomics, and analysis of sensitivity to perturbations. These experiments revealed differences in lipid, mitochondrial, and carbohydrate metabolism between the two major types. Finally, a thorough integration of our metabolic data with multiple omics data revealed a strong association with markers of epithelial-mesenchymal transition (EMT). Our analysis indicates that in absence of variations imposed by the microenvironment, the metabolism of cancer cell lines falls into only two major classes despite genetic heterogeneity.
Optimal trade-off control in machine learning-based library design, with application to adeno-associated virus (AAV) for gene therapy
Authors: Zhu Danqing , Brookes David H. , Busia Akosua , Carneiro Ana , Fannjiang Clara , Popova Galina , Shin David , Donohue Kevin. C. , Chang Edward F. , Nowakowski Tomasz J. , Listgarten Jennifer , Schaffer David. V. 
Published: November 2021

AbstractAdeno-associated viruses (AAVs) hold tremendous promise as delivery vectors for clinical gene therapy, but they need improvement. AAVs with enhanced properties, such as more efficient and/or cell-type specific infection, can be engineered by creating a large, diverse starting library and screening for desired phenotypes, in some cases iteratively. Although this approach has succeeded in numerous specific cases, such as infecting cell types from the brain to the lung, the starting libraries often contain a high proportion of variants unable to assemble or package their genomes, a general prerequisite for engineering any gene delivery goal. Herein, we develop and showcase a machine learning (ML)-based method for systematically designing more effective starting libraries — ones that have broadly good packaging capabilities while being as diverse as possible. Such carefully designed but general libraries stand to significantly increase the chance of success in engineering any property of interest. Furthermore, we use this approach to design a clinically-relevant AAV peptide insertion library that achieves 5-fold higher packaging fitness than the state-of-the-art library, with negligible reduction in diversity. We demonstrate the general utility of this designed library on a downstream task to which our approach was agnostic: infection of primary human brain tissue. The ML-designed library had approximately 10-fold more successful variants than the current state-of-the-art library. Not only should our new library serve useful for any number of other engineering goals, but our library design approach itself can also be applied to other types of libraries for AAV and beyond.
NASP maintains histone H3–H4 homeostasis through two distinct H3 binding modes
Authors: Bao Hongyu , Carraro Massimo , Flury Valentin , Liu Yanhong , Luo Min , Chen Liu , Groth Anja , Huang Hongda 
Published: November 2021

ABSTRACTHistone chaperones regulate all aspects of histone metabolism. NASP is a major histone chaperone for H3–H4 dimers critical for preventing histone degradation. Here, we identify two distinct histone binding modes of NASP and reveal how they cooperate to ensure histone H3–H4 supply. We determine the structures of a sNASP dimer, a complex of sNASP with an H3 α3 peptide, and the sNASP–H3–H4–ASF1b co-chaperone complex. This captures distinct functionalities of NASP and identifies two distinct binding modes involving the H3 α3 helix and the H3 αN region, respectively. Functional studies demonstrate the H3 αN-interaction represents the major binding mode of NASP in cells and shielding of the H3 αN region by NASP is essential in maintaining the H3–H4 histone soluble pool. In conclusion, our studies uncover the molecular basis of NASP as a major H3–H4 chaperone in guarding histone homeostasis.
Inhibition of BET family proteins suppresses African swine fever virus infection
Authors: Zhao Yaru , Niu Qingli , Yang Saixia , Yang Jifei , Zhang Zhonghui , Geng Shuxian , Fan Jie , Liu Zhijie , Guan Guiquan , Liu Zhiqing , Zhou Jia , Hu Haitao , Luo Jianxun , Yin Hong 
Published: November 2021

ABSTRACTAfrican swine fever (ASF), an acute, severe, highly contagious disease caused by African swine fever virus (ASFV) infection in domestic pigs and boars, has a mortality rate of up to 100%. Because effective vaccines and treatments for ASF are lacking, effective control of the spread of ASF remains a great challenge for the pig industry. Host epigenetic regulation is essential for the viral gene transcription. Bromodomain and extraterminal (BET) family proteins, including BRD2, BRD3, BRD4, and BRDT, are epigenetic “readers” critical for gene transcription regulation. Among these proteins, BRD4 recognizes acetylated histones via its two bromodomains (BD1 and BD2) and recruits transcription factors, thereby playing a pivotal role in transcriptional regulation and chromatin remodeling during viral infection. However, how BET/BRD4 regulates ASFV replication and gene transcription is unknown. Here, we randomly selected 12 representative BET family inhibitors and compared their effects on ASFV infection in pig’s primary alveolar macrophages (PAMs). They were found to inhibit viral infection by interfering with the different stages of viral life cycle (attachment, internalization, desencapsidation and formation of viral factories). The four most effective inhibitors (ARV-825, ZL0580, I-BET-762 and PLX51107) were selected for further antiviral activity analysis. These BET/BRD4 inhibitors dose-dependently decreased the ASFV titer, viral RNA transcription and protein production in PAMs. Collectively,our study reported novel activity of BET/BRD4 inhibitors in inducing suppression of ASFV infection, providing insights into role of BET/BRD4 in epigenetic regulation of ASFV and potential new strategies for ASF prevention and control.IMPORTANCESince the continuing spread of the ASFV in the world, and lack of commercial vaccines, the development of improved control strategies including antiviral drugs are urgently needed. BRD4 is an important epigenetic factor and has been commonly used for drug development for tumor treatment. Furthermore, the latest research showed that BET/BRD4 inhibition could suppress replication of virus. In this study, we first showed the inhibitory effect of agents targeting BET/BRD4 on ASFV infection with no significant host cytotoxicity. Then, we found 4 BET/BRD4 inhibitors which can inhibit ASFV replication, RNA transcription and protein synthesis. Finally, we analyzed 4 inhibitors’ biological effect on BRD4 according to the structure of BRD4, and docking analysis of BET-762, PLX51107, ARV-825 and ZL0580 binding to BD1 and BD2 domains of BRD4 was performed. Our findings support the hypothesis that BET/BRD4 can be considered as attractive host targets in antiviral drug discovery against ASFV.
Dense granule protein, GRA64 interacts with host cell ESCRT proteins duringToxoplasma gondiiinfection
Authors: Mayoral Joshua , Guevara Rebekah B. , Rivera-Cuevas Yolanda , Tu Vincent , Tomita Tadakimi , Romano Julia , Gunther-Cummins Leslie , Sidoli Simone , Coppens Isabelle , Carruthers Vernon B. , Weiss Louis M. 
Published: November 2021

ABSTRACTThe intracellular parasiteToxoplasma gondiiadapts to diverse host cell environments within a replicative compartment that is heavily decorated by secreted proteins. In attempts to identify novel parasite secreted proteins that influence host cell activity, we identified and characterized a trans-membrane dense granule protein dubbed GRA64 (TGME49_202620). We found that GRA64 is on the parasitophorous vacuolar membrane (PVM) and is partially exposed to the host cell cytoplasm in both tachyzoite and bradyzoite parasitophorous vacuoles. Using co-immunoprecipitation and proximity-based biotinylation approaches, we demonstrate that GRA64 appears to interact with certain components of the host Endosomal Sorting Complexes Required for Transport (ESCRT). Genetic disruption of GRA64 does not affect acuteToxoplasmavirulence in mice nor encystation as observed via tissue cyst burdens in mice during chronic infection. However, ultrastructural analysis of Δgra64tissue cysts using electron tomography revealed enlarged vesicular structures underneath the cyst membrane, suggesting a role for GRA64 in organizing the recruitment of ESCRT proteins and subsequent intracystic vesicle formation. This study uncovers a novel host-parasite interaction that contributes to an emerging paradigm in which specific host ESCRT proteins are recruited to the limiting membranes (PVMs) of tachyzoite and bradyzoite vacuoles formed during acute and chronicToxoplasmainfection.IMPORTANCEToxoplasma gondiiis a widespread foodborne parasite that causes congenital disease and life-threatening complications in immune compromised individuals. Part of this parasite’s success lies in its ability to infect diverse organisms and host cells, as well as to persist as a latent infection within parasite constructed structures called tissue cysts. In this study, we characterized a protein secreted byT. gondiiinto its parasitophorous vacuole during intracellular infection, which we dub GRA64. On the vacuole, this protein is exposed to the host cell and interacts with specific host ESCRT proteins. Parasites lacking the GRA64 protein exhibit ultrastructural changes in tissue cysts during chronic infection. This study lays the foundation for future studies on the mechanics and consequences of host ESCRT-parasite protein interactions.
Metabolome-defined obesity and the risk of future diabetes and mortality
Authors: Ottosson Filip , Smith Einar , Ericson Ulrika , Di Somma Salvatore , Antonini Paola , Nilsson Peter M , Fernandez Céline , Melander Olle 
Published: November 2021

BackgroundObesity is a key risk factor for type 2 diabetes, however, up to 20% of patients are normal weight. Our aim was to identify metabolite patterns reproducibly predictive of BMI, and subsequently to test if lean individuals who carry an obese metabolome are at hidden high risk of obesity related diseases, such as diabetes.MethodsWe measured 109 metabolites in fasted plasma samples of 7663 individuals from two Swedish and one Italian population-based cohort. Ridge regression models were used to predict BMI using the plasma metabolites. Individuals with a predicted BMI either more than 5 kg/m2higher (overestimated) or lower (underestimated) than their actual BMI were characterized as outliers and further investigated for obesity related risk factors and future risk of diabetes and mortality.ResultsThe plasma metabolome could predict BMI in all cohorts (r2= 0.48, 0.26 and 0.19). The overestimated group had a BMI similar to individuals correctly predicted as normal weight, similar waist circumference, were not more likely to change weight over time but had a 2 times higher risk of future diabetes and an 80 % increased risk of all-cause mortality. These associations remained after adjustments for obesity-related risk factors and lifestyle parameters.ConclusionsWe found that lean individuals with an obese metabolome, have an increased risk for diabetes and all-cause mortality compared to lean individuals with a healthy metabolome. Metabolomics may be used to identify hidden high-risk individuals, in order to initiate lifestyle and pharmacological interventions.
Phase-locked transcranial electrical brain stimulation for tremor suppression in dystonic tremor syndromes
Authors: Nieuwhof Freek , Toni Ivan , Buijink Arthur W.G. , van Rootselaar Anne-Fleur , van de Warrenburg Bart P.C. , Helmich Rick C. 
Published: November 2021

AbstractBackgroundTremor is a common and burdensome symptom in patients with dystonia, which is clinically heterogeneous and often resistant to treatment. The pathophysiology is suggested to involve abnormal activity in the cerebellum and motor cortex, but the causal role of these brain regions remains to be established. Transcranial alternating current stimulaton (TACS) can suppress rhytmic cerebral activity in other tremor disorders when phase-locked to the ongoing arm tremor, but the effect on dystonic tremor syndromes is unknown.Objective/HypothesisWe aimed to establish the causal role of the cerebellum and motor cortex in dystonic tremor syndromes, and explore the therapeutic efficacy of phase-locked TACS.MethodsWe applied phase-locked TACS over the ipsilateral cerebellum (N=14) and contralateral motor cortex (N=17) in dystonic tremor syndrome patients, while patients assumed a tremor-evoking posture. We measured tremor power using accelerometery during 30s stimulation periods at 10 different phase-lags (36-degrees increments) between tremor and TACS for each target. Post-hoc, TACS-effects were related to a key clinical feature: the jerkiness (regularity) of tremor.ResultsCerebellar TACS modulated tremor amplitude in a phase-dependent manner, such that tremor amplitude was suppressed or enhanced at opposite sides of the phase-cycle. This effect was specific for patients with non-jerky (sinusoidal) tremor (n=10), but absent in patients with jerky (irregular) tremor (n=4). Phase-locked stimulation over the motor cortex did not modulate tremor amplitude.ConclusionsThis study indicates that the cerebellum plays a causal role in the generation of (non-jerky) dystonic tremor syndrome. Our findings suggest pathophysiologic heterogeneity between patients with dystonic tremor syndrome, which mirrors clinical variability.
Fidaxomicin as first line: What will it cost in the USA and Canada?
Authors: Patel Devangi , Senecal Julien , Spellberg Brad , Morris Andrew M. , Saxinger Lynora , Footer Brent W. , McDonald Emily G. , Lee Todd C. 
Published: November 2021

AbstractImportanceRecent changes in the Infectious Diseases and Healthcare Epidemiology Societies of America (IDSA-SHEA) guidelines for managing Clostridioides difficile infections (CDI) have placed fidaxomicin as first-line treatment.ObjectiveTo estimate the net cost of first line fidaxomicin compared to vancomycin in the American and Canadian healthcare systems and to estimate the price points at which fidaxomicin would become cost saving. In Canada, net costs were from the public payer perspective. In the US, costs were from a healthcare and payer perspective.Data sourcesWe identified all randomized controlled trials comparing fidaxomicin with vancomycin through the 2021 IDSA-SHEA guideline update. Medication costs were obtained from internet prices (US) and the Quebec drug formulary (Canada). The average cost of a CDI recurrence was established through a systematic review for each country.Study selectionFor fidaxomicin efficacy, we included double-blind and placebo-controlled trials. For the systematic review of recurrence costs, studies were included if they were primary research articles, had a cost-analysis of CDI, included cases of recurrent CDI, and were calculated with cost parameters from American or Canadian healthcare systems. Studies were excluded if the population was solely pediatric or hospitalized.Data extraction and SynthesisFor the efficacy meta-analysis, data was pooled using a restricted maximal likelihood random effects model. For the cost review, the mean cost across identified studies was adjusted to reflect July 2022 dollars.Main Outcomes and MeasuresThe primary outcome of the meta-analysis was CDI recurrence at Day 40. The primary outcome of the systematic review was the average cost of a CDI recurrence in the American and Canadian healthcare systems. The objective was to estimate the net cost per recurrence prevented and the price point below which fidaxomicin would be cost saving to either the public payer (Canada) or the insurer (US).ResultsThe estimated mean system cost of a CDI recurrence was $15147USD and $8806CAD, respectively. At current drug pricing, to prevent one recurrence by using first line fidaxomicin over vancomycin would cost $43904USD (95%CI $35123-$65856) and $13,760CAD (95%CI $11,008-$20,640), respectively. The likelihood of fidaxomicin offering cost savings varies by country, with a 95% probability of fidaxomicin being cost saving if priced below $1180USD or $860CAD respectively.Conclusions and RelevanceAn increased drug expenditure on fidaxomicin will not be offset through recurrence prevention unless the fidaxomicin price is negotiated.
Structural insights into human excitatory amino acid transporter EAAT2
Authors: Kato Takafumi , Kusakizako Tsukasa , Jin Chunhuan , Quan LiLi , Ohgaki Ryuichi , Okuda Suguru , Kobayashi Kan , Yamashita Keitaro , Nishizawa Tomohiro , Kanai Yoshikatsu , Nureki Osamu 
Published: November 2021

AbstractGlutamate is a pivotal excitatory neurotransmitter in mammalian brains, but excessive glutamate causes numerous neural disorders. Almost all extracellular glutamate is retrieved by the glial transporter, Excitatory Amino Acid Transporter 2 (EAAT2), belonging to the SLC1A family. However, in some cancers, EAAT2 expression is enhanced and causes resistance to therapies by metabolic disturbance. Despite its crucial roles, the detailed structural information about EAAT2 has not been available. Here, we report cryo-EM structures of human EAAT2 in substrate-free and selective inhibitor WAY213613-bound states. EAAT2 forms a trimer, with each protomer consisting of transport and scaffold domains. Along with a glutamate-binding site, the transport domain possesses a cavity, that could be disrupted during the transport cycle. WAY213613 occupies both the glutamate-binding site and cavity of EAAT2 to interfere with its alternating access, where the sensitivity is defined by the inner environment of the cavity. This is the first characterization of molecular features of EAAT2 and the selective inhibition mechanism, underlying structure-based drug design for EAAT2.
Mis6/CENP-I maintains CENP-A nucleosomes against centromeric non-coding transcription during mitosis
Authors: Hirai Hayato , Shogaki Yuki , Sato Masamitsu 
Published: November 2021

SummaryCentromeres are established by nucleosomes containing the histone H3 variant CENP-A. CENP-A is recruited to centromeres by the Mis18–HJURP machinery. During mitosis, CENP-A recruitment ceases, implying the necessity of CENP-A maintenance at centromeres, although the exact underlying mechanism remains elusive. Herein, we show that the kinetochore protein Mis6 (CENP-I) retains CENP-A during mitosis in fission yeast. Eliminating Mis6 during mitosis caused immediate loss of pre-existing CENP-A at centromeres. CENP-A loss occurred due to the transcriptional upregulation of non-coding RNAs at the central core region of centromeres, as confirmed by the observation RNA polymerase II inhibition preventing CENP-A loss from centromeres in the mis6 mutant. Thus, we concluded that Mis6 blocks the indiscriminate transcription of non-coding RNAs at the core centromere, thereby retaining the epigenetic inheritance of CENP-A during mitosis.
Visual category representations in the infant brain
Authors: Xie Siying , Hoehl Stefanie , Moeskops Merle , Kayhan Ezgi , Kliesch Christian , Turtleton Bert , Köster Moritz , Cichy Radoslaw M. 
Published: November 2021

SUMMARYVisual categorization is a human core cognitive capacity1,2that depends on the development of visual category representations in the infant brain3–7. However, the exact nature of infant visual category representations and their relationship to the corresponding adult form remains unknown8. Our results clarify the nature of visual category representations from electroencephalography (EEG) data in 6- to 8-month-old infants and their developmental trajectory towards adult maturity in the key characteristics of temporal dynamics2,9, representational format10–12, and spectral properties13,14. Temporal dynamics change from slowly emerging, developing representations in infants to quickly emerging, complex representations in adults. Despite those differences, infants and adults already partly share visual category representations. The format of infants’ representations is visual features of low to intermediate complexity, whereas adults’ representations also encode high complexity features. Theta band activity contributes to visual category representations in infants, and these representations are shifted to the alpha/beta band in adults. Together, we reveal the developmental neural basis of visual categorization in humans, show how information transmission channels change in development, and demonstrate the power of advanced multivariate analysis techniques in infant EEG research for theory building in developmental cognitive science.
Wnt1-Cre mediated deletion of BMP7 suggests a role for neural crest-derived BMP7 in retina development and function
Authors: Kung Tiffany FC , Baddam Pranidhi , Liu Ruocun , Maripuri Devi Priyanka , Dimopoulos Ioannis S , MacDonald Ian M , Sauve Yves , Graf Daniel 
Published: November 2021

AbstractNeural crest (NC) contributes to various structures of the eye including cornea, ciliary body and retina. The association of NC-derived cells with hyaloid vessels in the form of pericytes is established. Similarly, persistence of NC-derived cells in the inner retina layer of the mature retina has been suggested. To date, no specific function has been attributed to them. NC-derived Bone morphogenetic protein 7 (BMP7) controls neurogenic properties in the brain and regulates glia differentiation. Here, we assessed the role of NC-derived BMP7 in the adult retina.BMP7 expression was determined using Bmp7LacZ reporter mice. BMP7 was expressed in GCL, IPL, OPL, and photoreceptors in P0, P14 and P30 retinas. Lineage tracing confirmed the presence of NC-derived cells in the GCL, INL, and ONL. Some but not all cells associated with vasculature. To test the function of NC-derived Bmp7, Bmp7fl/flWnt1cre (Bmp7ncko) mice were assessed by histological and functional methods. Loss of NC-derived cells in the GCL and INL and mild structural abnormalities were observed in the Bmp7ncko retina. Electroretinography revealed reduced a wave under photopic conditions and b wave under both scotopic and photopic conditions. The neuronal circuitry in the inner retina appeared affected, evidenced by decreased Calbindin in the GCL, IPL and INL. In the outer retina, S-opsin was increased. BMP7 expression in the mutant retina was strongly decreased at birth, but increased expression from cells other than NC was observed in the adult retina. This was associated with an increase in IBA1, suggestive that loss of NC-derived BMP7 predisposes to development of gliosis-like changes in the adult retina. Overall, our data reveal an important contribution of NC-derived BMP7 for the development and function of the inner and outer retina.