bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cdc42 reactivation at growth sites is regulated by local cell-cycle-dependent loss of its GAP Rga4
Authors: Rich-Robinson Julie , Russell Afton , Mancini Eleanor , Das Maitreyi 
Published: August 2020

AbstractIn fission yeast, polarized cell growth stops during division and resumes after cell separation. We uncoupled these sequential events by delaying cytokinesis with a temporary Latrunculin A treatment. Mitotic cells recovering from treatment initiate end growth without cell separation, displaying apolar elongationsansseparation (PrESS) phenotype. PrESS cell ends reactivate Cdc42, a major regulator of polarized growth, before cell separation, but at a fixed time after anaphase B. A candidate screen implicates Rga4, a negative regulator of Cdc42, in this process. We show that Rga4 appears punctate at the cell sides during G2, but is diffuse during mitosis, extending to the ends. While the Morphogenesis Orb6 (MOR) pathway is known to promote cell separation and growth by activating protein synthesis, we find that for polarized growth, removal of Rga4 from the ends is also necessary. Therefore, we propose that growth resumes after division once the MOR pathway is activated and the ends lose Rga4 in a cell-cycle-dependent manner.
A combined proteomics and Mendelian randomization approach to investigate the effects of aspirin-targeted proteins on colorectal cancer
Authors: Nounu Aayah , Greenhough Alexander , Heesom Kate J , Richmond Rebecca C , Zheng Jie , Weinstein Stephanie J , Albanes Demetrius , Baron John A , Hopper John L , Figueiredo Jane C , Newcomb Polly A , Lindor Noralane M , Casey Graham , Platz Elizabeth A , Le Marchand Loïc , Ulrich Cornelia M , Li Christopher I , van Duijnhoven Fränzel JB , Gsur Andrea , Campbell Peter T , Moreno Víctor , Vodicka Pavel , Vodickova Ludmila , Brenner Hermann , Chang-Claude Jenny , Hoffmeister Michael , Sakoda Lori C , Slattery Martha L , Schoen Robert E , Gunter Marc J , Castellví-Bel Sergi , Kim Hyeong Rok , Kweon Sun-Seog , Chan Andrew T , Li Li , Zheng Wei , Bishop D Timothy , Buchanan Daniel D , Giles Graham G , Gruber Stephen B , Rennert Gad , Stadler Zsofia K , Harrison Tabitha A , Lin Yi , Keku Temitope O , Woods Michael O , Schafmayer Clemens , Van Guelpen Bethany , Gallinger Steven J , Hampel Heather , Berndt Sonja I , Pharoah Paul D P , Lindblom Annika , Wolk Alicja , Wu Anna H , White Emily , Peters Ulrike , Drew David A , Scherer Dominique , Bermejo Justo Lorenzo , Williams Ann C , Relton Caroline L 
Published: August 2020

AbstractBackgroundEvidence for aspirin’s chemopreventative properties on colorectal cancer (CRC) is substantial, but its mechanism of action is not well-understood. We combined a proteomic approach with Mendelian randomization (MR) to identify possible new aspirin targets that decrease CRC risk.MethodsHuman colorectal adenoma cells (RG/C2) were treated with aspirin (24 hours) and a stable isotope labelling with amino acids in cell culture (SILAC) based proteomics approach identified altered protein expression. Protein quantitative trait loci (pQTLs) from INTERVAL (N=3,301) and expression QTLs (eQTLs) from the eQTLGen Consortium (N=31,684) were used as genetic proxies for protein and mRNA expression levels. Two-sample MR of mRNA/protein expression on CRC risk was performed using eQTL/pQTL data combined with CRC genetic summary data from the Colon Cancer Family Registry (CCFR), Colorectal Transdisciplinary (CORECT), Genetics and Epidemiology of Colorectal Cancer (GECCO) consortia and UK Biobank (55,168 cases and 65,160 controls).ResultsAltered expression was detected for 125/5886 proteins. Of these, aspirin decreased MCM6, RRM2 and ARFIP2 expression and MR analysis showed that a standard deviation increase in mRNA/protein expression was associated with increased CRC risk (OR:1.08, 95% CI:1.03-1.13, OR:3.33, 95% CI:2.46-4.50 and OR:1.15, 95% CI:1.02-1.29, respectively).ConclusionMCM6 and RRM2 are involved in DNA repair whereby reduced expression may lead to increased DNA aberrations and ultimately cancer cell death, whereas ARFIP2 is involved in actin cytoskeletal regulation indicating a possible role in aspirin’s reduction of metastasis.ImpactOur approach has shown how laboratory experiments and population-based approaches can combine to identify aspirin-targeted proteins possibly affecting CRC risk.
A non-canonical function for Centromere-associated protein-E (CENP-E) controls centrosome integrity and orientation of cell division
Authors: Owa Mikito , Dynlacht Brian 
Published: August 2020

SummaryCentromere-associated protein-E (CENP-E) is a kinesin motor localizing at kinetochores. Although its mitotic functions have been well studied, it has been challenging to investigate direct consequences of CENP-E removal using conventional methods because CENP-E depletion results in mitotic arrest. In this study, we harnessed an auxin-inducible degron system to achieve acute degradation of CENP-E. We revealed a kinetochore-independent role for CENP-E that removes pericentriolar material 1 (PCM1) from centrosomes in G2phase. After acute loss of CENP-E, centrosomal Polo-like kinase 1 (Plk1) is sequestered by accumulated PCM1, resulting in aberrant phosphorylation and destabilization of centrosomes, which triggers loss of astral microtubules and oblique cell divisions. Furthermore, we also observed centrosome and cell division defects in cells from a microcephaly patient with mutations inCENPE. Orientation of cell division is deregulated in some microcephalic patients, and our unanticipated findings provide a unifying principle that explains how microcephaly can result from centrosomal defects.
DPP9 directly sequesters the NLRP1 C-terminus to repress inflammasome activation
Authors: Hollingsworth L. Robert , Sharif Humayun , Griswold Andrew R. , Fontana Pietro , Mintseris Julian , Dagbay Kevin B. , Paulo Joao A. , Gygi Steven P. , Bachovchin Daniel A. , Wu Hao 
Published: August 2020

AbstractNLRP1 is a cytosolic inflammasome sensor that mediates activation of caspase-1, which in turn induces cytokine maturation and pyroptotic cell death1-6. Gain-of-function NLPR1 mutations cause skin inflammatory diseases including carcinoma, keratosis, and papillomatosis7-14. NLRP1 contains a unique function-to-find domain (FIIND) that autoproteolyzes into noncovalently associated subdomains15-18. Proteasomal degradation of the autoinhibitory N-terminal fragment (NT) activates NLRP1 by releasing the inflammatory C-terminal fragment (CT)19,20. Cytosolic dipeptidyl peptidases 8 and 9 (DPP8/9) interact with NLRP1, and small-molecule DPP8/9 inhibitors activate NLRP1 by poorly characterized mechanisms11,19,21. Here, we report cryo-EM structures of the human NLRP1-DPP9 complex, alone and in complex with the DPP8/9 inhibitor Val-boroPro (VbP). Surprisingly, the NLRP1-DPP9 complex is a ternary complex comprised of DPP9, one intact FIIND of a non-degraded full-length NLRP1 (NLRP1-FL) and one NLRP1-CT freed by NT degradation. The N-terminus of the NLRP1-CT unfolds and inserts into the DPP9 active site but is not cleaved by DPP9, and this binding is disrupted by VbP. Structure-based mutagenesis reveals that the binding of NLRP1-CT to DPP9 requires NLRP1-FL and vice versa, and inflammasome activation by ectopic NLRP1-CT expression is rescued by co-expressing autoproteolysis-deficient NLRP1-FL. Collectively, these data indicate that DPP9 functions as a “bomb-diffuser” to prevent NLRP1-CTs from inducing inflammation during homeostatic protein turnover.
Single-cell dynamics of pannexin-1-facilitated programmed ATP loss during apoptosis
Authors: Imamura Hiromi , Sakamoto Shuichiro , Yoshida Tomoki , Matsui Yusuke , Penuela Silvia , Laird Dale W. , Mizukami Shin , Kikuchi Kazuya , Kakizuka Akira 
Published: August 2020

AbstractATP is essential for all living cells. However, how dead cells lose ATP has not been well investigated. In this study, we developed new FRET biosensors for dual imaging of intracellular ATP level and caspase-3 activity in single apoptotic cultured human cells. We show that the cytosolic ATP level starts to decrease immediately after the activation of caspase-3, and this process is completed typically within 2 hours. The ATP decrease was facilitated by caspase-dependent cleavage of the plasma membrane channel pannexin-1, indicating that the intracellular decrease of the apoptotic cell is a “programmed” process. Apoptotic cells deficient of pannexin-1 sustained the ability to produce ATP through glycolysis and to consume ATP, and did not stop wasting glucose much longer period than normal apoptotic cells. Thus, the pannexin-1 plays a role in arresting the metabolic activity of dead apoptotic cells, most likely through facilitating the loss of intracellular ATP. (148 words)
PRG2 and AQPEP are misexpressed in fetal membranes in placenta previa and percreta
Authors: Zhang Elisa T. , Hannibal Roberta L. , Badillo Rivera Keyla M. , Song Janet H.T. , McGowan Kelly , Zhu Xiaowei , Meinhardt Gudrun , Knöfler Martin , Pollheimer Jürgen , Urban Alexander E. , Folkins Ann K. , Lyell Deirdre J. , Baker Julie C. 
Published: August 2020

AbstractThe obstetrical conditions placenta accreta spectrum (PAS) and placenta previa are a significant source of pregnancy-associated morbidity and mortality, yet the specific molecular and cellular underpinnings of these conditions are not known. In this study, we identified misregulated gene expression patterns in tissues from placenta previa and percreta (the most extreme form of PAS) compared with control cases. By comparing this gene set with existing placental single-cell and bulk RNA-Seq datasets, we show that the upregulated genes predominantly mark extravillous trophoblasts. We performed immunofluorescence on several candidate molecules and found that PRG2 and AQPEP protein levels are upregulated in both the fetal membranes and the placental disk in both conditions. While this increased AQPEP expression remains restricted to trophoblasts, PRG2 is mislocalized and is found throughout the fetal membranes. Using a larger patient cohort with a diverse set of gestationally aged-matched controls, we validated PRG2 as a marker for both previa and PAS and AQPEP as a marker for only previa in the fetal membranes membranes. Our findings suggest that the extraembryonic tissues surrounding the conceptus, including both the fetal membranes membranes and the placental disk, harbor a signature of previa and PAS that reflects increased trophoblast invasiveness.Summary sentence3SEQ and immunofluorescence reveal that extravillous trophoblast factors, most notably PRG2 and AQPEP, define the diseases placenta previa and placenta accreta spectrum (PAS) in both the chorioamniotic membranes and the placental disk.
The origins and consequences ofUPF1variants in pancreatic adenosquamous carcinoma
Authors: Polaski Jacob T. , Udy Dylan B. , Escobar-Hoyos Luisa F. , Askan Gokce , Leach Steven D. , Ventura Andrea , Kannan Ram , Bradley Robert K. 
Published: August 2020

ABSTRACTPancreatic adenosquamous carcinoma (PASC) is a rare and aggressive subtype of pancreatic cancer whose mutational origins are poorly understood. An early study reported somatic mutations inUPF1, which encodes a core component of the nonsense-mediated mRNA decay (NMD) pathway, as a common signature of PASC, but subsequent studies did not observe these lesions in other PASC cohorts. The corresponding controversy about whetherUPF1mutations are important contributors to PASC has been exacerbated by a paucity of functional studies of these lesions. Here, we systematically assessed the potential roles ofUPF1mutations in PASC. We modeled two reportedUPF1mutations to find no consistent effects on pancreatic cancer growth, acquisition of adenosquamous features,UPF1splicing, UPF1 protein levels, or NMD efficiency. We subsequently discovered that ~40% ofUPF1mutations reportedly present in PASCs are identical to standing genetic variation in the human population, suggesting that they are likely non-pathogenic inherited variation rather than pathogenic mutations. Our data suggest thatUPF1is not a common functional driver of PASC and motivate further attempts to identify unique genetic features defining these malignancies.
Multicellular Organoids of the Neurovascular Blood-Brain Barrier: A New Platform for Precision Neuronanomedicine
Authors: Kumarasamy Murali , Sosnik Alejandro 
Published: August 2020

AbstractThe treatment of neurological disorders (NDs) is challenged by low drug permeability from the systemic circulation into the central nervous system (CNS) owing to the presence of the blood-brain barrier (BBB). Neuronanomedicine investigates nanotechnology strategies to target the brain and improve the therapeutic outcome in NDs. Two-dimensional adherent cell BBB models show substantial phenogenomic heterogeneity and their ability to predict the permeability of molecules and nanoparticles into the brain is extremely limited. Thus, the high-throughput screening of CNS nanomedicines relies on the use of animal models. To address this dearth, 3D organoids that mimic thein vivophysiology are under development. Still, there exist concerns about the standardization and scale-up of the production process, their proper characterisation, and their industrial application. In this work, we report on a novel multicellular organoid of the neurovascular blood–brain barrier (NV-BBB) that recapitulates the regulated syncytium of human endothelial cells and the function of the human BBB. For this, an advanced organoid comprising human brain microvascular endothelial cells, brain vascular pericytes and human astrocytes combined with primary neurons and microglia isolated from neonate rats is bio-fabricated without the use of an extracellular matrix. The structure and function are fully characterized by confocal laser scanning fluorescence microscopy, light sheet fluorescence microscopy, scanning transmission electron microscopy, cryogenic-scanning electron microscopy, western blotting, RNA-sequencing and quantitative gene expression by quantitative polymerase chain reaction analysis. This bulk of these self-assembloids is comprised of neural cells and microglia and the surface covered by endothelial cells that act as a biological barrier that resembles the BBB endothelium. In addition, the formation of neuron-microglia morphofunctional communication sites is confirmed. Analysis of key transcriptomic expressions show the up-regulation of selected BBB-related genes including tight junction proteins, solute carriers, transporters of the ATP-binding cassette superfamily, metabolic enzymes, and prominent basement membrane signatures. Results confirmed the more efficient cell-cell communication in 3D organoids made of multiple neural-tissue cells than in 2D endothelial cell monocultures. These multicellular organoids are utilized to screen the permeability of different polymeric, metallic, and ceramic nanoparticles. Results reveal penetration through different mechanisms such as clathrin-mediated endocytosis and distribution patterns in the organoid that depend on the nanoparticle type, highlighting the promise of this simple, reproducible and scalable multicellular NV-BBB organoid platform to investigate the BBB permeability of different nanomaterials in nanomedicine, nanosafety, and nanotoxicology.
Mathematical Modeling of Multiple Pathways in Colorectal Carcinogenesis using Dynamical Systems with Kronecker Structure
Authors: Haupt Saskia , Zeilmann Alexander , Ahadova Aysel , von Knebel Doeberitz Magnus , Kloor Matthias , Heuveline Vincent 
Published: August 2020

AbstractLike many other tumors, colorectal cancers develop through multiple pathways containing different driver mutations. This is also true for colorectal carcinogenesis in Lynch syndrome, the most common inherited colorectal cancer syndrome. However, a comprehensive understanding of Lynch syndrome tumor evolution which allows for tailored clinical treatment and even prevention is still lacking.We suggest a linear autonomous dynamical system modeling the evolution of the different pathways. Starting with the gene mutation graphs of the driver genes, we formulate three key assumptions about how these different mutations might be combined. This approach leads to a dynamical system that is built by the Kronecker sum of the adjacency matrices of the gene mutation graphs. This Kronecker structure makes the dynamical system amenable to a thorough mathematical analysis and medical interpretation, even if the number of incorporated genes or possible mutation states is increased.For the case that some of the mathematical key assumptions are not satisfied, we explain possible extensions to our model. Additionally, improved bio-medical measurements or novel medical insights can be integrated into the model in a straightforward manner, as all parameters in the model have a biological interpretation. Modifications of the model are able to account for other forms of colorectal carcinogenesis, such as Lynch-like and familial adenomatous polyposis cases.Graphical Abstract:From the Medical Hypothesis Over the Modeling Approach To the Mathematical Structure.The medical hypothesis of multiple pathways in carcinogenesis is widely known for various types of cancer.Left:We present a model for this phenomenon at the example of Lynch syndrome, the most common inherited colorectal cancer syndrome, with specific key driver events in the MMR genes,CTNNB1,APC,KRASandTP53.Middle:This current medical understanding of carcinogenesis is translated into a mathematical model using a specific dynamical system, which can be represented by a graph structure, where each vertex in the graph represents a genotypic state and the edges correspond to the transition probabilities between those states. Starting with all colonic crypts in the state of all genes being wild-type and a single MMR germline mutation due to Lynch syndrome, we are interested in the distribution of the crypts among the graph at different ages of the patient in order to obtain estimates for the number of crypts in specific states, e.g. adenomatous or cancerous states.Right:The underlying matrix of the dynamical system makes use of the Kronecker sum and product. It is a sparse upper triangular matrix accounting for the assumption that mutations cannot be reverted. This allows fast numerical solving by using the matrix exponential. Each nonzero entry of the matrix represents a connection between genotypic states in the graph.
Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 - Spike Protein InteractionIn Vitro
Authors: Olaleye Omonike A. , Kaur Manvir , Onyenaka Collins , Adebusuyi Tolu 
Published: August 2020

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent for coronavirus disease 2019 (COVID-19), has emerged as an ongoing global pandemic. Presently, there are no clinically approved vaccines nor drugs for COVID-19. Hence, there is an urgent need to accelerate the development of effective antivirals. Here in, we discovered Clioquinol (5-chloro-7-iodo-8-quinolinol (CLQ)), a FDA approved drug and two of its analogues (7-bromo-5-chloro-8-hydroxyquinoline (CLBQ14); and 5, 7-Dichloro-8-hydroxyquinoline (CLCQ)) as potent inhibitors of SARS-CoV-2 infection induced cytopathic effectin vitro. In addition, all three compounds showed potent anti-exopeptidase activity against recombinant human angiotensin converting enzyme 2 (rhACE2) and inhibited the binding of rhACE2 with SARS-CoV-2 Spike (RBD) protein. CLQ displayed the highest potency in the low micromolar range, with its antiviral activity showing strong correlation with inhibition of rhACE2 and rhACE2-RBD interaction. Altogether, our findings provide a new mode of action and molecular target for CLQ and validates this pharmacophore as a promising lead series for clinical development of potential therapeutics for COVID-19.
CREB mediates theC. elegansdauer polyphenism through direct and cell-autonomous regulation of TGF-β expression
Authors: Park Jisoo , Oh Hyekyung , Kim Do-Young , Cheon YongJin , Park Yeon-Ji , Neal Scott J. , Dar Abdul Rouf , Butcher Rebecca A. , Sengupta Piali , Kim Daewon , Kim Kyuhyung 
Published: August 2020

AbstractAnimals can adapt to dynamic environmental conditions by modulating their developmental programs. Understanding the genetic architecture and molecular mechanisms underlying developmental plasticity in response to changing environments is an important and emerging area of research. Here, we show a novel role of cAMP response element binding protein (CREB)-encodingcrh-1gene in developmental polyphenism ofC. elegans. Under conditions that promote normal development in wild-type animals,crh-1mutants inappropriately form transient pre-dauer (L2d) larva and express the L2d marker gene. L2d formation incrh-1mutants is specifically induced by the ascaroside pheromone ascr#5 (asc-ωC3; C3), andcrh-1functions autonomously in the ascr#5-sensing ASI neurons to inhibit L2d formation. Moreover, we find that CRH-1 directly binds upstream of thedaf-7TGF-β locus and promotes its expression in the ASI neurons. Taken together, these results provide new insight into how animals alter their developmental programs in response to environmental changes.
A benchmarking model for validation and standardization of traction force microscopy analysis tools
Authors: Pardon Gaspard , Castillo Erica , Pruitt Beth L. 
Published: August 2020

AbstractTraction Force Microscopy (TFM) has become a well-established technique to assay the biophysical force produced by cells cultured on soft substrates of controlled stiffness. However, experimental conditions as well as computational implementations can have a large impact on the analysis results accuracy and reproducibility. While this can be alleviated using appropriate controls and a rigorous analytical approach, the comparison of results across studies remains difficult and there is a need for validation and benchmarking tools. To validate the accuracy of and compare various computational TFM analysis algorithms, we developed a virtualin silicomodel of a cell contracting on a soft substrate of controlled stiffness. The model utilizes user-defined parameters for the cell dimensions as well as for the strength and spatial distribution of a contraction dipole to calculate the deformation that would result on a soft substrate due to the cell contraction. The deformation is computed using the forward analytical stress-strain tensor calculation in the Fourier space. The resulting displacement field is used to apply, using image processing, a deformation on a real or simulated image of fluorescent microspheres embedded into a soft hydrogel, which is normally obtain experimentally by TFM imaging. The deformation field and resulting image then serve as input in the PIV and TFM analysis. The model also enables to create movies of a dynamic cell contraction, such as that of a cardiomyocyte, to validate the time accuracy of the TFM analysis after application of image processing algorithm, such as denoising. Our tool therefore addresses the need for validation and standardization of TFM analytical algorithms and its experimental implementations.