bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted engagement of β-catenin-Ikaros complexes in refractory B-cell malignancies
Authors: Cosgun Kadriye Nehir , Jumaa Huda , Robinson Mark E. , Kistner Klaus M. , Xu Liang , Xiao Gang , Chan Lai N. , Lee Jaewoong , Kume Kohei , Leveille Etienne , Fonseca-Arce David , Khanduja Dhruv , Ng Han Leng , Feldhahn Niklas , Song Joo , Chan Wing-Chung , Chen Jianjun , Taketo M. Mark , Kothari Shalin , Davids Matthew S. , Schjerven Hilde , Jellusova Julia , Müschen Markus 
Published: March 2023

ABSTRACTIn most cell types, nuclear β-catenin functions as prominent oncogenic driver and pairs with TCF7-family factors for transcriptionalactivationof MYC. Surprisingly, B-lymphoid malignancies not only lacked expression and activating lesions of β-catenin but critically depended on GSK3β for effective β-catenin degradation. Our interactome studies in B-lymphoid tumors revealed that β-catenin formed repressive complexes with lymphoid-specific Ikaros factors at the expense of TCF7. Instead of MYC-activation, β-catenin was essential to enable Ikaros-mediated recruitment of nucleosome remodeling and deacetylation (NuRD) complexes for transcriptionalrepressionof MYC.To leverage this previously unrecognized vulnerability of B-cell-specific repressive β-catenin-Ikaros-complexes in refractory B-cell malignancies, we examined GSK3β small molecule inhibitors to subvert β-catenin degradation. Clinically approved GSK3β-inhibitors that achieved favorable safety prof les at micromolar concentrations in clinical trials for neurological disorders and solid tumors were effective at low nanomolar concentrations in B-cell malignancies, induced massive accumulation of β-catenin, repression of MYC and acute cell death. Preclinicalin vivotreatment experiments in patient-derived xenografts validated small molecule GSK3β-inhibitors for targeted engagement of lymphoid-specific β-catenin-Ikaros complexes as a novel strategy to overcome conventional mechanisms of drug-resistance in refractory malignancies.HIGHLIGHTSUnlike other cell lineages, B-cells express nuclear β-catenin protein at low baseline levels and depend on GSK3β for its degradation.In B-cells, β-catenin forms unique complexes with lymphoid-specific Ikaros factors and is required for Ikaros-mediated tumor suppression and assembly of repressive NuRD complexes.CRISPR-based knockin mutation of a single Ikaros-binding motif in a lymphoidMYCsuperenhancer region reversed β-catenin-dependent Myc repression and induction of cell death.The discovery of GSK3β-dependent degradation of β-catenin as unique B-lymphoid vulnerability provides a rationale to repurpose clinically approved GSK3β-inhibitors for the treatment of refractory B-cell malignancies.GRAPHICAL ABSTRACTAbundant nuclear β-cateninβ-catenin pairs with TCF7 factors for transcriptional activation of MYCB-cells rely on efficient degradation of β-catenin by GSK3βB-cell-specific expression of Ikaros factorsUnique vulnerability in B-cell tumors:GSK3β-inhibitors induce nuclear accumulation of β-catenin.β-catenin pairs with B-cell-specific Ikaros factors for transcriptional repression of MYC
Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome
Authors: Venkatraman Kailash , Lee Christopher T. , Garcia Guadalupe C. , Mahapatra Arijit , Milshteyn Daniel , Perkins Guy , Kim Keun-Young , Pasolli H. Amalia , Phan Sebastien , Lippincott-Schwartz Jennifer , Ellisman Mark H. , Rangamani Padmini , Budin Itay 
Published: March 2023

AbstractCristae are high curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae-shaping proteins have been defined, analogous mechanisms for lipids have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the IMM against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein-mediated curvatures. The model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that CL is essential in low oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of CL is dependent on the surrounding lipid and protein components of the IMM.Synopsiscritical lipidic breakpoint for yeast mitochondria phenocopies the loss of cristae-shaping proteins in the IMM.saturation controls membrane mechanical properties and modulates ATP synthase oligomerization.mitochondrial-specific lipid cardiolipin can functionally compensate for increased phospholipid saturation and is required for cristae formation in low oxygen environments.mathematical model for cristae membrane tubules predicts a snapthrough instability mediated by both protein and lipid-encoded curvatures.Synopsis Figure
Modelling collagen fibril self-assembly from extracellular medium in embryonic tendon
Authors: Revell Christopher K. , Herrera Jeremy A. , Lawless Craig , Lu Yinhui , Kadler Karl E. , Chang Joan , Jensen Oliver E. 
Published: March 2023

AbstractCollagen is a key structural component of multicellular organisms and is arranged in a highly organised manner. In structural tissues such as tendons, collagen forms bundles of parallel fibres between cells, which appear within a 24 hour window between E13.5 and E14.5 during mouse embryonic development. Current models assume that the organised structure of collagen requires direct cellular control, whereby cells actively lay down collagen fibrils from cell surfaces. However, such models appear incompatible with the time- and length-scales of fibril formation. We propose a phase-transition model to account for the rapid development of ordered fibrils in embryonic tendon, reducing reliance on active cellular processes. We develop phase-field crystal simulations of collagen fibrillogenesis in domains derived from electron micrographs of inter-cellular spaces in embryonic tendon and compare results qualitatively and quantitatively to observed patterns of fibril formation. To test the prediction of this phase-transition model that free protomeric collagen should exist in the intercellular spaces prior to the formation of observable fibrils, we use laser-capture microdissection, coupled with mass spectrometry, which demonstrates steadily increasing free collagen in intercellular spaces up to E13.5, followed by a rapid reduction of free collagen that coincides with the appearance of less soluble collagen fibrils. The model and measurements together provide evidence for extracellular self-assembly of collagen fibrils in embryonic mouse tendon, supporting an additional mechanism for rapid collagen fibril formation during embryonic development.
Stroke-related gene expression profiles across species: A meta-analysis
Authors: Rust Ruslan 
Published: March 2023

AbstractStroke patients are often left with permanent disabilities with no regenerative treatment options. Unbiased RNA sequencing studies decoding the transcriptional signature of stroked tissue hold promise to identify new potential targets and pathways directed to improve treatment for stroke patients. Here, gene expression profiles of stroked tissue across different time points, species, and stroke models were compared using NCBI GEO database. In total, 32 datasets from mice, rats, humans, and primates were included, exploring gene expression differences in healthy and stroked brain tissue. Distinct changes in gene expression and pathway enrichment revealed the heterogenicity of the stroke pathology in stroke-related pathways e.g., inflammatory responses, vascular repair, remodelling and cell proliferation and adhesion but also in diverse general, stroke-unrelated pathways that have to be carefully considered when evaluating new promising therapeutic targets.
Molecular bases for strong phenotypic effects of single-site synonymous substitutions in theE.coli ccdBtoxin gene
Authors: Bajaj Priyanka , Bhasin Munmun , Varadarajan Raghavan 
Published: March 2023

ABSTRACTSingle-site synonymous mutations typically have only minor or no effects on gene function. Here, we estimate the effects on cell growth of ~200 single-site synonymous mutations in an operonic context by mutating each position ofccdB, the 101-residue long cytotoxin of theccdABToxin-Antitoxin (TA) operon to all possible degenerate codons. Phenotypes were assayed by transforming the mutant library into CcdB sensitive and resistantE. colistrains, isolating plasmid pools, and subjecting them to deep sequencing. Since autoregulation is a hallmark of TA operons, phenotypes obtained forccdBsynonymous mutants after transformation in a RelE toxin reporter strain followed by deep sequencing provided information on the amount of CcdAB complex formed. Synonymous mutations in the N-terminal region involved in translation initiation showed the strongest non-neutral phenotypic effects. We observe an interplay of numerous factors, namely, location of the codon, codon usage, t-RNA abundance, formation of anti-Shine Dalgarno sequences, transcript secondary structure, and evolutionary conservation in determining phenotypic effects ofccdBsynonymous mutations. Incorporation of an N-terminal, hyperactive synonymous mutation, in the background of the single-site synonymous mutant library sufficiently increased translation initiation, such that mutational effects on either folding or termination of translation became more apparent. Introduction of putative pause sites not only affects the translational rate but might also alter the folding kinetics of the proteinin vivo. This information is useful in optimizing heterologous gene expression inE. coliand understanding the molecular bases for alteration in gene expression that arise due to synonymous mutations.SIGNIFICANCE STATEMENTSynonymous mutations which do not change amino-acid identity, typically have only minor or no effects on gene function. Using sensitive genetic screens in the context of theccdABbacterial toxin-antitoxin operon, we demonstrate that many single-site synonymous mutations of theccdBtoxin gene display significant phenotypic effects in an operonic context. The largest effects were seen for synonymous mutations in the N-terminal region involved in translation initiation. Synonymous mutations that affected either folding or translation termination were also identified. Lack of translational pausing due to synonymous mutations in hydrophobic residue stretches, was found to decrease the amount of properly folded CcdB protein. In summary the study provides novel insights into diverse mechanisms by which synonymous mutations modulate gene function.
Left ventricular global longitudinal strain as a parameter of mild myocardial dysfunction in athletes after COVID-19
Authors: Schellenberg J , Ahathaller M , Matits L , Kirsten J , Kersten J , Steinacker JM 
Published: March 2023

AbstractBackgroundWhether impaired left ventricular (LV) function contributes to persistent cardiopulmonary symptoms or decreased exercise capacity after COVID-19 remains unclear. The aim of this prospective study was to determine differences in LV global longitudinal strain (GLS) between athletes who did not have a history of LV dysfunction but had a positive COVID-19 test (PCAt) and healthy control (CON) athletes and relate them to symptoms during COVID-19.MethodsWe performed 151 transthoracic echocardiographies in our high-performance laboratory. GLS was determined in four-, two-, and three-chamber views and assessed offline by a blinded investigator in 88 PCAt (35% women) at a median of two months after COVID-19 who trained at least three times per week with more than 20 MET per week and 52 CONs from the German national squad (38% women).ResultsGLS was significantly lower (GLS -18.53±1.94% vs. -19.94±1.42%, p<0.001) and diastolic function significantly reduced (E/A 1.54±0.52 vs. 1.66±0.43, p=0.020; E’l 0.15±0.04 vs. 0.17±0.04, p=0.009; E/E’l 5.74±1.74 vs. 5.22±1.36, p=0.024) in PCAt. There was no association between GLS and acute symptoms like resting dyspnea, exertional dyspnea during or after COVID-19, palpitations, chest pain or increased resting heart rate. However, there was a trend toward lower GLS in PCAt with subjectively perceived performance limitation (p=0.054).ConclusionsIn a cohort of athletes at a median two months after COVID-19, significantly lower GLS and diastolic function were observed, suggesting mild myocardial dysfunction. GLS could be used as a screening element during return-to-sport examinations.
Association of radiological severity with inflammatory biomarkers for prognostic prediction in patients with COVID-19
Authors: Zouine Y. , Benzalim M. , Alj S. 
Published: March 2023

BackgroundCovid – 19 caused by SARS-CoV2 has become a pandemic. It has a rapid disease progression and causes severe and fatal complications. Associating radiological severity with effective biomarkers like CRP, leucocytes, lymphocytes, D – Dimer, would be helpful in screening, categorizing patient, preventing serious complications.Aims and ObjectivesThe aim of the study was to investigate association between levels of inflammatory biomarkers and correlate it with HRCT chest finding to identify patients at risk of fatal complications.Materials and MethodsIt was a retrospective monocentric observational study undertaken at Ibn Tofail hospital COVID-19 dedicated center. 177 Patients>18 year of age who were admitted from september 1, 2020 up to november 30,2020 with laboratory confirmed diagnosis of Covid – 19 were included in the study. Data was collected on demography, disease severity, laboratory measurements, radiology imaging retrospectively from records of patients. The disease severity was classified into light, mild to severe and critic based on CT Severity scoring. HRCT Chest and inflammatory biomarkers were sent in every patient at the time of admission and the outcome was recorded.ResultsThere were 116 male patients, 61 female patients in our study. Average age of patients having severe lung involvement is 61.9years, whereas Average age of patients having non-severe lung involvement is 56.8 years and showed significant association with severity of lung involvement (p value : 0.017). Severity of lung involvement according to HRCT chest findings was greater in patients with both raised values of CRP <0.001), D – Dimer (P value 0.032) and low values of lymphocytes (P value : 0.001). Capillary oxygen SATURATION was also found to be significantly associated with radiological severity among covid-19 patients. Compared with CRP, leukocytes, lymphocytes, and D-Dimeres levels, the CT severity score had higher sensitivity, specificity, and overall accuracy in predicting severe, critical cases, and short-term mortality.Conclusionthe severity of Covid – 19 disease is correlated with radiological severity andinflammatory markers thereby it will help in immediate categorization of patients into different risk groups following diagnosis, to ensure optimal resource allocation.
Targeted repression of DNA topoisomerase I by CRISPRi reveals a critical function for it in theChlamydia trachomatisdevelopmental cycle
Authors: Shen Li , Gao Leiqiong , Swoboda Abigail R. , Ouellette Scot P. 
Published: March 2023

AbstractChlamydia trachomatisis an obligate intracellular bacterium that is responsible for the most prevalent bacterial sexually transmitted infections. Changes in DNA topology in this pathogen have been linked to its pathogenicity-associated developmental cycle. Here, evidence is provided that the balanced activity of DNA topoisomerases (Topos) contributes toChlamydiadevelopmental processes. Utilizing catalytically inactivated Cas12 (dCas12) based-clustered regularly interspaced short palindromic repeats interference (CRISPRi) technology, we demonstrate targeted knockdown of chromosomaltopAtranscription inC. trachomatiswithout detected toxicity of dCas12. Repression oftopAimpaired the growth ofC. trachomatismostly through disruption of its differentiation from a replicative form to an infectious form. Consistent with this, expression of late developmental genes ofC. trachomatiswas downregulated while early genes maintained their expression. Importantly, the growth defect associated withtopAknockdown was rescued by overexpressingtopAat an appropriate degree and time, directly linking the growth patterns to the levels oftopAexpression. Interestingly,topAknockdown had pleiotropic effects on DNA gyrase expression, indicating a potential compensatory mechanism for survival to offset TopA deficiency.C. trachomatiswithtopAknocked down displayed hypersensitivity to moxifloxacin that targets DNA gyrase in comparison with the wild type. These data underscore the requirement of integrated topoisomerase actions to support the essential development and transcriptional processes ofC. trachomatis.ImportanceWe used genetic and chemical tools to demonstrate the relationship of topoisomerase activities and their obligatory role for the chlamydial developmental cycle. Successfully targeting the essential genetopAwith a CRISPRi approach, using dCas12, inC. trachomatisindicates that this method will facilitate the characterization of the essential genome. These findings have an important impact on our understanding of the mechanism(s) by which well-balanced topoisomerase activities enableC. trachomatisto adapt to unfavorable growth conditions imposed by antibiotics.
Deep physico-chemical characterization of the serum antibody response using a dual-titration microspot assay
Authors: Kovács Ágnes , Hérincs Zoltán , Papp Krisztián , Kaczmarek Jakub Zbigniew , Larsen Daniel Nyberg , Stage Pernille , Bereczki László , Ujhelyi Eszter , Pfeil Tamás , Prechl József 
Published: March 2023

AbstractAntigen specific humoral immunity can be characterized by the analysis of serum antibodies. While serological assays for the measurement of specific antibody levels are available, these are not quantitative in the biochemical sense. Yet, understanding humoral immune responses quantitatively on the systemic level would need a universal, complete, quantitative, comparable measurement method of antigen specific serum antibodies of selected immunoglobulin classes. Here we describe a fluorescent, dual-titration immunoassay, which provides the physico-chemical parameters that are both necessary and sufficient to quantitatively characterize the humoral immune response. We define the theory of the approach that is based on physical chemistry. For validation of theory, we used recombinant receptor binding domain of SARS-CoV-2 as antigen on microspot arrays and varied the concentration of both the antigen and serum antibodies from infected persons to obtain a measurement matrix of binding data. Both titration curves were simultaneously fitted using an algorithm based on the generalized logistic function and adapted for analyzing thermodynamic variables of binding. We obtained equilibrium affinity constants and chemical potentials for distinct antibody classes. These variables reflect the quality and the effective quantity of serum antibodies, respectively. The proposed fluorescent dual-titration microspot immunoassay can generate truly quantitative serological data that is suitable for immunological, medical and systems biological analysis.
Inhibition of Cellular MEK/ERK Signaling Suppresses Murine Papillomavirus Type 1 Replicative Activities and Promotes Tumor Regression
Authors: Luna Adrian J. , Young Jesse M. , Sterk Rosa T. , Bondu Virginie , Schultz Fred A. , Kusewitt Donna F. , Kang Huining , Ozbun Michelle A. 
Published: March 2023

AbstractHuman papillomaviruses (HPVs) are a significant public health concern due to their widespread transmission, morbidity, and oncogenic potential. Despite efficacious vaccines, millions of unvaccinated individuals and those with existing infections will develop HPV-related diseases for the next two decades. The continuing burden of HPV-related diseases is exacerbated by the lack of effective therapies or cures for most infections, highlighting the need to identify and develop antivirals. The experimental murine papillomavirus type 1 (MmuPV1) model provides opportunities to study papillomavirus pathogenesis in cutaneous epithelium, the oral cavity, and the anogenital tract. However, to date the MmuPV1 infection model has not been used to demonstrate the effectiveness of potential antivirals. We previously reported that inhibitors of cellular MEK/ERK signaling suppress oncogenic HPV early gene expressionin vitro. Herein, we adapted the MmuPV1 infection model to determine whether MEK inhibitors have anti-papillomavirus propertiesin vivo. We demonstrate that oral delivery of a MEK1/2 inhibitor promotes papilloma regression in immunodeficient mice that otherwise would have developed persistent infections. Quantitative histological analyses revealed that inhibition of MEK/ERK signaling reduces E6/E7 mRNAs, MmuPV1 DNA, and L1 protein expression within MmuPV1-induced lesions. These data suggest that MEK1/2 signaling is essential for both early and late MmuPV1 replication events supporting our previous findings with oncogenic HPVs. We also provide evidence that MEK inhibitors protect mice from developing secondary tumors. Thus, our data suggest that MEK inhibitors have potent anti-viral and anti-tumor properties in a preclinical mouse model and merit further investigation as papillomavirus antiviral therapies.Significance StatementPersistent human papillomavirus (HPV) infections cause significant morbidity and oncogenic HPV infections can progress to anogenital and oropharyngeal cancers. Despite the availability of effective prophylactic HPV vaccines, millions of unvaccinated individuals, and those currently infected will develop HPV-related diseases over the next two decades and beyond. Thus, it remains critical to identify effective antivirals against papillomaviruses. Using a mouse papillomavirus model of HPV infection, this study reveals that cellular MEK1/2 signaling supports viral tumorigenesis. The MEK1/2 inhibitor, trametinib, demonstrates potent antiviral activities and promotes tumor regression. This work provides insight into the conserved regulation of papillomavirus gene expression by MEK1/2 signaling and reveals this cellular pathway as a promising therapeutic target for the treatment of papillomavirus diseases.