bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardiac ventricular myosin and slow skeletal myosin exhibit dissimilar chemo-mechanical properties despite the same myosin heavy chain isoform
Authors: Wang Tianbang , Spahiu Emrulla , Behrens Florentine , Osten Jennifer , Grünhagen Fabius , Scholz Tim , Kraft Theresia , Nayak Arnab , Amrute-Nayak Mamta 
Published: March 2022

AbstractThe myosin II motors are ATP-powered, force-generating machines driving cardiac and muscle contraction. Myosin II heavy chain isoform-beta (β-MyHC) is primarily expressed in the ventricular myocardium and slow-twitch muscle fibers, such as in M. soleus. M. soleus-derived myosin II (SolM-II) is often used as an alternative to the ventricular β-cardiac myosin (βM-II); however, the direct assessment of detailed biochemical and mechanical features of the native myosins is limited. By employing the optical trapping method, we examined the mechanochemical properties of the native myosins isolated from rabbit heart ventricle and M. soleus muscles at the single-molecule level. Contrary to previous reports, the purified motors from the two tissue sources, despite the same MyHC isoform, displayed distinct motile and ATPase kinetic properties. βM-II was ∼threefold faster in the actin filament-gliding assay than SolM-II. The maximum acto-myosin (AM) detachment rate derived in single-molecule assays was ∼threefold higher in βM-II. The stroke size for both myosins was comparable. The stiffness of the ‘AM rigor’ cross-bridge was also similar for both the motor forms. The stiffness of βM-II was found to be determined by the nucleotide state of the actin-bound myosin. Our analysis revealed distinct kinetic differences, i.e., a higher AM detachment rate for the βM-II, corresponding to the ADP release rates from the cross-bridge, thus elucidating the observed differences in the motility driven by βM-II and SolM-II. These studies have important implications for the future choice of tissue sources to gain insights into cardiomyopathies
Loss of tumor suppressor WWOX accelerates pancreatic cancer development through promotion of TGFβ/BMP2 signaling
Authors: Husanie Hussam , Abu-Remaileh Muhannad , Maroun Kian , Abu-Tair Lina , Safadi Hazem , Atlan Karine , Golan Talia , Aqeilan Rami I. 
Published: March 2022

AbstractPancreatic cancer is one of the most lethal cancers, owing to its late diagnosis and resistance to chemotherapy. The tumor suppressor WW domain-containing oxidoreductase (WWOX), one of the most active fragile sites in the human genome (FRA16D), is commonly altered in pancreatic cancer. However, the direct contribution of WWOX loss to pancreatic cancer development and progression remains largely unknown. Here, we report that combined conditional deletion ofWwoxand activation ofKRasG12DinPtf1a-CreER-expressing mice results in accelerated formation of precursor lesions and pancreatic carcinoma. At the molecular level, we found that WWOX physically interacts with SMAD3 and BMP2, which are known activators of the TGF-β signaling pathway. In the absence of WWOX, TGFβ/BMPs signaling was enhanced, leading to increased macrophage infiltration and enhanced cancer stemness. Finally, overexpression of WWOX in patient-derived xenografts led to diminished aggressiveness bothin vitroandin vivo. Overall, our findings reveal an essential role of WWOX in pancreatic cancer development and progression and underscore its role asa bona fidetumor suppressor.
Pan-cancer distribution of cleaved cell-surface Amphiregulin, the target of the GMF-1A3 antibody drug conjugate
Authors: Lofgren Kristopher A. , Reker Nicolette C. , Sreekumar Sreeja , Kenny Paraic A. 
Published: March 2022

ABSTRACTAmphiregulin (AREG) is a transmembrane protein which, following TACE/ADAM17-dependent cleavage, releases a soluble Epidermal Growth Factor Receptor ligand domain that promotes proliferation of normal and malignant cells. Expression of Amphiregulin has been described by immunohistochemistry in several tumor types, including lung, prostate, head and neck, gastric, pancreatic and breast cancers but evidence for a functional requirement for Amphiregulin in these malignancies is more limited. We have previously described the development of a monoclonal antibody, GMF-1A3, that selectively recognizes the Amphiregulin epitope that is revealed following cleavage by TACE/ADAM17 and demonstrated that drug conjugates of this antibody have anti-tumor activity in mouse models. By directly evaluating Amphiregulin cleavage, immunohistochemistry on tissue specimens using this antibody can be used to evaluate the extent to which Amphiregulin is being proteolytically processed in cancer, which is a more direct measure of Amphiregulin activity. As a potential companion diagnostic for this antibody-drug conjugate, this immunohistochemistry assay allows identification of tumors with high levels of the cleaved Amphiregulin target. Here we evaluate levels of cleaved Amphiregulin in 370 specimens from 10 tumor types and demonstrate that it is widely expressed in solid tumors and is especially common (more than 50% of cases) in breast, prostate, liver and lung cancer.
Characterization of Morreton Virus (MORV) as a Novel Oncolytic Virotherapy Platform for Liver Cancers
Authors: Nagalo Bolni Marius , Zhou Yumei , Loeuillard Emilien J. , Dumbauld Chelsae , Barro Oumar , Elliott Natalie M. , Baker Alexander T. , Arora Mansi , Bogenberger James M. , Meurice Nathalie , Petit Joachim , Uson Junior Pedro Luiz Serrano , Aslam Faaiq , Chamcheu Jean Christopher , Simoes Camila C. , Cannon Martin J. , Basnakian Alexei , Post Steven R. , Buetow Kenneth , Barrett Michael T. , Duda Dan G. , Jacobs Bertram , Vile Richard , Barry Michael A. , Roberts Lewis R. , Ilyas Sumera , Borad Mitesh J. 
Published: March 2022

AbstractMorreton virus (MORV) is a novel oncolyticVesiculovirus, genetically distinct from vesicular stomatitis virus (VSV). we report that MORV induced potent cytopathic effects in a panel of cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC) cell lines. In addition, high intranasal doses of MORV were not associated with significant adverse effects and were well tolerated in mice bearing liver tumor xenografts and syngeneic liver cancers. Furthermore, single intratumoral treatments with MORV (1 x 107TCID50) triggered a robust antitumor immune response leading to substantial tumor regression and disease control in a syngeneic CCA model, using 10-fold lower dose compared to VSV (1 x 108TCID50). In addition, MORV and VSV both induced prominent tumor growth delay in immunodeficient mice bearing Hep3B hepatocellular carcinoma (HCC) but not in mice bearing HuCCT-1 CCA xenografts. Our findings indicate that wild-type MORV is safe and can induce potent tumor regression in HCC and CCA animal models without adverse events via immune-mediated and immune-independent mechanisms. Further development and clinical translation of MORV as virotherapy for liver cancers are warranted.
Organization of thalamocortical structural covariance and a corresponding 3D atlas of the mouse thalamus
Authors: Yee Yohan , Ellegood Jacob , French Leon , Lerch Jason P. 
Published: March 2022

AbstractFor information from sensory organs to be processed by the brain, it is usually passed to appropriate areas of the cerebral cortex. Almost all of this information passes through the thalamus, a relay structure that reciprocally connects to the vast majority of the cortex. The thalamus facilitates this information transfer through a set of thalamocortical connections that vary in cellular structure, molecular profiles, innervation patterns, and firing rates. Additionally, corticothalamic connections allow for intracortical information transfer through the thalamus. These efferent and afferent connections between the thalamus and cortex have been the focus of many studies, and the importance of cortical connectivity in defining thalamus anatomy is demonstrated by multiple studies that parcellate the thalamus based on cortical connectivity profiles.Here, we examine correlated morphological variation between the thalamus and cortex, or thalamocortical structural covariance. For each voxel in the thalamus as a seed, we construct a cortical structural covariance map that represents correlated cortical volume variation, and examine whether high structural covariance is observed in cortical areas that are functionally relevant to the seed. Then, using these cortical structural covariance maps as features, we subdivide the thalamus into six non-overlapping regions (clusters of voxels), and assess whether cortical structural covariance is associated with cortical connectivity that specifically originates from these regions.We show that cortical structural covariance is high in areas of the cortex that are functionally related to the seed voxel, cortical structural covariance varies along cortical depth, and sharp transitions in cortical structural covariance profiles are observed when varying seed locations in the thalamus. Subdividing the thalamus based on structural covariance, we additionally demonstrate that the six thalamic clusters of voxels stratify cortical structural covariance along the dorsal-ventral, medial-lateral, and anterior-posterior axes. These cluster-associated structural covariance patterns are prominently detected in cortical regions innervated by fibers projecting out of their related thalamic subdivisions.Together, these results advance our understanding of how the thalamus and the cortex couple in their volumes. Our results indicate that these volume correlations reflect functional organization and structural connectivity, and further provides a novel segmentation of the mouse thalamus that can be used to examine thalamic structural variation and thalamocortical structural covariation in disease models.
Calcium-induced environmental adaptability of the blood protein vitronectin
Authors: Tian Ye , Shin Kyungsoo , Aleshin Alexander E. , Im Wonpil , Marassi Francesca M. 
Published: March 2022

AbstractThe adaptability of proteins to their work environments is fundamental for cellular life. Here we describe how the hemopexin-like (HX) domain of the multifunctional blood glycoprotein vitronectin (Vn) binds Ca2+ to adapt to excursions of temperature and shear stress. Using X-ray crystallography and molecular dynamics (MD) simulations, nuclear magnetic resonance (NMR) and differential scanning calorimetry (DSF), we describe how Ca2+ and its flexible hydration shell enable the protein to perform conformational changes, that relay beyond the Ca2+ binding site to alter the number of polar contacts and confer conformational stability. By means of mutagenesis, we identify key residues that cooperate with Ca2+ to promote protein stability, and we show that Ca2+ association confers protection against shear stress, a property that provides conformational advantage for proteins that circulate in the vasculature like Vn. The data reveal a mechanism of adaptation.Significance StatementThe protein vitronectin (Vn) plays important roles in cell adhesion and migration, bone remodeling and immunity. It circulates in blood, but it is also found in the extracellular matrix, and it accumulates with plaques associated with age-related macular degeneration, Alzheimer’s disease, atherosclerosis and other degenerative disorders. Vn is a calcium-binding protein, and here, we show that calcium helps Vn alter its structure in response to diverse environmental conditions. The results shed light on the way in which Vn adapts to its surroundings. This structural knowledge is important for the development of diagnostic, preventive or therapeutic approaches.
Thermodynamic stabilization of the von Willebrand Factor A1 domain due to loss-of-function disease-related mutations
Authors: Sandoval-Pérez Angélica , Mejía-Restrepo Valeria , Aponte-Santamaría Camilo 
Published: March 2022

AbstractThe von Willebrand disease (vWD) is the most common hereditary bleeding disorder, caused by defects of the von Willebrand Factor (vWF), a large extracellular protein in charge of adhering platelets at sites of vascular lesion. vWF carries out this essential homeostatic task, via the specific protein-protein interaction between the vWF A1 domain and the platelet receptor, the glycoprotein Ib alpha (GPIBα). Upon the vWF activation triggered by the shear of the flowing blood. The two naturally occurring mutations G1324A and G1324S at the A1 domain, near the GPIBα binding site, result in a dramatic decrease of platelets adhesion, a bleeding disorder classified as type 2M vWD. However, it remained unclear how these two supposedly minor modifications lead to this drastic phenotypic response. We addressed this question using a combination of equilibrium-molecular dynamics (MD) and non-equilibrium MD-based free energy simulations. Our data confirm that both mutations maintain the highly stable Rossmann fold of the vWF A1 domain. These mutations locally diminished the flexibility of the binding site to GPIBα and induced a conformational change that affected the nearby secondary structure elements. Furthermore, we observed two significant changes in the vWF A1 domain upon mutation, the global redistribution of the internal mechanical stress and the increased thermodynamic stability of the A1 domain. These observations are consistent with previously-reported mutation-augmented melting temperatures. Overall, our results support the idea of thermodynamic conformational restriction of A1— before the binding to GPIBα—as a crucial factor determining the loss-of-function of the G1324A(S) vWD mutants.
Prokaryotic genome design is ruled by the mechanical properties and complexity of the DNA sequence
Authors: Tatsuke Tsuneyuki 
Published: March 2022

AbstractAlthough we represent the genetic code using four letters, namely A, T, G, and C, it is a chemical entity with sequence-dependent physical properties and a spatial extent. In other words, it can be said that genetic information is compressed and recorded in the genomic DNA as a storage medium with a spatial spread. This study analyzed prokaryotic genomes in terms of their physical properties and complexity. The findings clearly indicated that a mathematic equation can be used to express the relationship between the length of a genome and the upper limit of its rigidity. Furthermore, many prokaryotes have been shown to maximize DNA complexity under various physical constraints. Here, this relationship between rigidity and complexity was found to be shaped like an entropy function. It was also clarified that codon usage tendencies are affected by the physical properties and complexity of the DNA sequence. Moreover, the analysis of codons encoding two consecutive synonymous amino acids suggests that many prokaryotic codon combinations tend to increase genomic DNA complexity. This study revealed the macro-level rules for packing genomic DNA into prokaryotic cells.
Programming bacteria for multiplexed DNA detection
Authors: Cheng Yu-Yu , Chen Zhengyi , Cao Xinyun , Ross Tyler D. , Falbel Tanya G. , Burton Briana M. , Venturelli Ophelia S. 
Published: March 2022

ABSTRACTDNA is a universal and programmable signal of living organisms. Here we developed cell-based DNA sensors by engineering the naturally competent bacteriumBacillus subtilis(B. subtilis) to detect specific DNA sequences in the environment. The DNA sensor strains can identify diverse bacterial species including major human pathogens with high specificity and sensitivity. Multiplexed detection of genomic DNA from different species in complex samples can be achieved by coupling the sensing mechanism to orthogonal fluorescent reporters. We also demonstrate that the DNA sensors can detect the presence of species in the complex samples without requiring DNA extraction. The modularity of the living cell-based DNA sensing mechanism and simple detection procedure could enable programmable DNA sensing for broad applications.
Quantitative Systems Pharmacology Modeling Framework of Autophagy in Tuberculosis: Application to Adjunctive Metformin Host-Directed Therapy
Authors: Mehta Krina , Guo Tingjie , Wallis Robert , van der Graaf Piet H. , van Hasselt J.G. Coen 
Published: March 2022

AbstractBackgroundQuantitative systems pharmacology (QSP) modeling of the host-immune response against Mtb can inform rational design of host-directed therapies (HDTs). We aimed to develop a QSP framework to evaluate the effects of metformin-associated autophagy-induction in combination with antibiotics.MethodsA QSP framework for autophagy was developed by extending a model for host-immune response to include AMPK-mTOR-autophagy signalling. This model was combined with pharmacokinetic-pharmacodynamic models for metformin and antibiotics against Mtb. We compared the model predictions to mice infection experiments, and derived predictions for pathogen and host-associated dynamics in humans treated with metformin in combination with antibiotics.ResultsThe model adequately captured the observed bacterial load dynamics in mice Mtb infection models treated with metformin. Simulations for adjunctive metformin therapy in newly diagnosed patients suggested a limited yet dose-dependent effect of metformin on reducing the intracellular bacterial load and selected pro-inflammatory cytokines. Our predictions suggest that metformin may provide beneficiary effects when overall bacterial load, or extracellular-to-intracellular bacterial ratio is low, either early after infection or late during antibiotic treatment.ConclusionsWe present the first QSP framework for HDTs against Mtb, linking cellular-level autophagy effects to disease progression. This framework may be extended to guide design of HDTs against Mtb.
Bartonella taylorii: A model organism for studying Bartonella infection in vitro and in vivo
Authors: Fromm Katja , Boegli Alexandra , Ortelli Monica , Wagner Alexander , Bohn Erwin , Malmsheimer Silke , Wagner Samuel , Dehio Christoph 
Published: March 2022

AbstractBartonella spp. are Gram-negative facultative intracellular pathogens that infect diverse mammals and cause a long-lasting intra-erythrocytic bacteremia in their natural host. These bacteria translocate Bartonella effector proteins (Beps) into host cells via their VirB/VirD4 type 4 secretion system (T4SS) in order to subvert host cellular functions, thereby leading to the downregulation of innate immune responses. Most studies on the functional analysis of the VirB/VirD4 T4SS and the Beps were performed with the major zoonotic pathogen Bartonella henselae for which efficient in vitro infection protocols have been established. However, its natural host, the cat, is unsuitable as an experimental infection model. In vivo studies were mostly confined to rodent models using rodent-specific Bartonella species, while the in vitro infection protocols devised for B. henselae are not transferable for those pathogens. The disparities of in vitro and in vivo studies in different species has hampered progress in our understanding of Bartonella pathogenesis. Here we describe the murine-specific strain B. taylorii IBS296 as a new model organism facilitating the study of bacterial pathogenesis both in vitro in cell cultures and in vivo in laboratory mice. We implemented the split NanoLuc luciferase-based translocation assay to study BepD translocation through the VirB/VirD4 T4SS. We found increased effector-translocation into host cells if the bacteria were grown on tryptic soy agar (TSA) plates and experienced a temperature shift immediately before infection. The improved infectivity in vitro could be correlated to an upregulation of the VirB/VirD4 T4SS. Using our adapted infection protocols, we showed BepD-dependent immunomodulatory phenotypes in vitro. In mice, the implemented growth conditions enabled infection by a massively reduced inoculum without having an impact on the course of the intra-erythrocytic bacteremia. The established model opens new avenues to study the role of the VirB/VirD4 T4SS and the translocated Bep effectors in vitro and in vivo.
Cellular stress in brain organoids is limited to a distinct and bioinformatically removable subpopulation
Authors: Vértesy Ábel , Eichmueller Oliver L. , Naas Julia , Novatchkova Maria , Esk Christopher , Balmaña Meritxell , Ladstaetter Sabrina , Bock Christoph , Haeseler Arndt von , Knoblich Juergen A. 
Published: March 2022

AbstractOrganoids enable disease modeling in complex and structured human tissue,in vitro. Like most 3D models, they lack sufficient oxygen supply, leading to cellular stress. These negative effects are particularly prominent in complex models, like brain organoids, where they can prevent proper lineage commitment. Here, we analyze brain organoid and fetal single cell RNA sequencing (scRNAseq) data from published and new datasets totaling over 190,000 cells. We describe a unique stress signature found in all organoid samples, but not in fetal samples. We demonstrate that cell stress is limited to a defined organoid cell population, and present Gruffi, an algorithm that uses granular functional filtering to identify and remove stressed cells from any organoid scRNAseq dataset in an unbiased manner. Our data show that adverse effects of cell stress can be corrected by bioinformatic analysis, improving developmental trajectories and resemblance to fetal data.
Flotillin-2 regulates EGFR activation, degradation, and cancer growth
Authors: Wisniewski David J. , Liyasova Mariya S. , Korrapati Soumya , Zhang Xu , Ratnayake Shashikala , Chen Qingrong , Gilbert Samuel F. , Catalano Alexis , Voeller Donna , Meerzaman Daoud , Guha Udayan , Porat-Shliom Natalie , Annunziata Christina M. , Lipkowitz Stanley 
Published: March 2022

AbstractEpidermal growth factor receptor (EGFR) signaling is frequently dysregulated in various cancers. The ubiquitin ligase Cbl (Casitas B-lineage lymphoma proto-oncogene) regulates degradation of activated EGFR through ubiquitination and acts as an adaptor to recruit proteins required for trafficking. We used Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) mass spectrometry (MS) to compare Cbl complexes with or without epidermal growth factor (EGF) stimulation. We identified over a hundred novel Cbl interactors, and a secondary siRNA screen found that knockdown of Flotillin-2 (FLOT2) led to increased phosphorylation and degradation of EGFR upon EGF stimulation in HeLa cells. In PC9 and H441 cells, FLOT2 knockdown increased EGF-stimulated EGFR phosphorylation, ubiquitination, and downstream signaling, reversible by the EGFR inhibitor erlotinib. CRISPR knockout (KO) of FLOT2 in HeLa cells confirmed EGFR downregulation, increased signaling, and increased dimerization and trafficking to the early endosome. FLOT2 interacted with both Cbl and EGFR. EGFR downregulation upon FLOT2 loss was Cbl-dependent, as co-knockdown of Cbl and Cbl-b restored EGFR levels. Overexpression of FLOT2 decreased EGFR sjgnaling and growth. Overexpression of wild type (WT) FLOT2, but not the soluble G2A FLOT2 mutant, inhibited EGFR phosphorylation upon EGF stimulation in HEK293T cells. FLOT2 loss induced EGFR-dependent proliferation and anchorage-independent growth. Lastly, FLOT2 KO increased tumor formation and tumor volume in nude mice and NSG mice, respectively. These data demonstrated that FLOT2 negatively regulated EGFR activation and dimerization, as well as its subsequent ubiquitination, endosomal trafficking, and degradation, leading to reduced proliferationin vitroandin vivo.