bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct Mechanisms of Type 3 Secretion System Recognition Control LTB4Synthesis in Neutrophils versus Macrophages
Authors: Brady Amanda , Mora-Martinez Leonardo C. , Hammond Benjamin , Haribabu Bodduluri , Uriarte Silvia M. , Lawrenz Matthew B. 
Published: July 2024

AbstractLeukotriene B4 (LTB4) is critical for initiating the inflammatory cascade in response to infection. However,Yersinia pestiscolonizes the host by inhibiting the timely synthesis of LTB4and inflammation. Here, we show that the bacterial type 3 secretion system (T3SS) is the primary pathogen associated molecular pattern (PAMP) responsible for LTB4production by leukocytes in response toYersiniaandSalmonella, but synthesis is inhibited by the Yop effectors duringYersiniainteractions. Moreover, we unexpectedly discovered that T3SS-mediated LTB4synthesis by neutrophils and macrophages require two distinct host signaling pathways. We show that the SKAP2/PLC signaling pathway is essential for LTB4production by neutrophils but not macrophages. Instead, phagocytosis and the NLRP3/CASP1 inflammasome are needed for LTB4synthesis by macrophages. Finally, while recognition of the T3SS is required for LTB4production, we also discovered a second unrelated PAMP-mediated signal independently activates the MAP kinase pathway needed for LTB4synthesis. Together, these data demonstrate significant differences in the signaling pathways required by macrophages and neutrophils to quickly respond to bacterial infections.SignificanceThe production of inflammatory lipid mediators by the host is essential for timely inflammation in response to invasion by bacterial pathogens. Therefore, defining how immune cells recognize pathogens and rapidly produce these lipids is essential for us to understand how our immune system effectively controls infection. In this study, we discovered that the host signaling pathways required for leukotriene B4 (LTB4) synthesis differ between neutrophils and macrophages, highlighting important differences in how immune cells respond to infection. Together, these data represent a significant improvement in our understanding of how neutrophils and macrophages rapidly react to bacteria and provide new insights into howYersinia pestismanipulates leukocytes to evade immune recognition to cause disease.
Kingdom-specific lipid unsaturation shapes up sequence evolution in membrane arm subunits of eukaryotic respiratory complexes
Authors: Gupta Pooja , Chakroborty Sristi , Rathod Arun K. , Bhat Shreya , Ghosh Suparna , Rao T Pallavi , Nagaraj R , Manna Moutusi , Raychaudhuri Swasti 
Published: July 2024

AbstractSequence evolution of protein complexes (PCs) is constrained by protein-protein interactions (PPIs). PPI-interfaces are predominantly conserved and hotspots for disease-related mutations. How lipid-protein interactions (LPIs) constrain sequence evolution of membrane- PCs? We explore Respiratory Complexes (RCs) as a case study as these allow to compare sequence evolution in subunits exposed to both lipid-rich inner-mitochondrial membrane (IMM) and aqueous matrix. We find that lipid-exposed surfaces of the IMM-subunits but not of the matrix subunits are populated with non-PPI disease-causing mutations signifying LPIs in stabilizing RCs. Further, IMM-subunits including their exposed surfaces show high intra- kingdom sequence conservation but remarkably diverge beyond. Molecular Dynamics simulation suggests contrasting LPIs of structurally superimposable but sequence-wise diverged IMM-exposed helices of Complex I (CI) subunit Ndufa1 from human andArabidopsisdepending on kingdom-specific unsaturation of cardiolipin fatty acyl chains.in celluloassays consolidate inter-kingdom incompatibility of Ndufa1-helices due to the lipid- exposed amino acids. Plant-specific unsaturated fatty acids in human cells also trigger CI- instability. Taken together, we posit that altered LPIs calibrate sequence evolution at the IMM-arms of eukaryotic RCs.
DNA methylation database for gynecological cancer detection, classification and assay development
Authors: Boers Joachim , Boers Ruben , Sakoltchik Jan , Dasgupta Shatavisha , Martens Lotte , Tadema Kirke C.D. , Prevoo Frederique , van IJcken Wilfred F.J. , van den Munckhof Henk , Quint Wim , van Beekhuizen Heleen J. , Quint Wim H. , van Kemenade Folkert J. , Gribnau Joost 
Published: July 2024

SummaryChanges in the genome wide DNA methylation landscape are hallmarks of cancer cells and precursor lesions of cancers. To capitalize on utilizing DNA methylation for detection and classification of cancer, we generated a DNA methylation database of gynecological cancers and associated healthy tissues using Methylated DNA sequencing (MeD-seq). We show that target cell enrichment to generate the database is crucial for marker discovery and report a wide range of novel biomarkers for classification and tissue of origin determination of gynecological cancers. We developed a subset of these novel biomarkers, both intragenic and intergenic, into a qMSP assays that detect all gynecological cancers at once or specific gynecological cancer subtypes, as well as cancers that are not part of our database. The database generated in this study not only provides the foundation for cancer detection, classification and biomarker discovery, but also for treatment monitoring of cancers using MeD-seq on liquid biopsies.
1.94 Å structure of synthetic α-synuclein fibrils seeding MSA neuropathology
Authors: Burger Domenic , Kashyrina Marianna , Lewis Amanda J. , De Nuccio Francesco , Mohammed Inayathulla , de La Seiglière Hortense , van den Heuvel Lukas , Verchère Jérémy , Feuillie Cécile , Berbon Mélanie , Arotçarena Marie-Laure , Retailleau Aude , Bezard Erwan , Laferrière Florent , Loquet Antoine , Bousset Luc , Baron Thierry , Lofrumento Dario Domenico , De Giorgi Francesca , Stahlberg Henning , Ichas François 
Published: July 2024

AbstractMultiple system atrophy (MSA) is a rapidly progressive neurodegenerative disease of unknown etiology, typically affecting individuals aged 50-60 and leading to patient death within a decade1–3. Characterized by the presence of oligodendroglial intracellular aggregates (GCIs) primarily composed of fibrillar alpha-synuclein (aSyn)4–8, formation of MSA neuropathology presents similarities to prion propagation9,10. While previous investigations have scrutinized fibrils extracted from MSA brains11, their “protein-only” replication was questioned12and their capacity to induce GCIs in animal models was not explored. Conversely, the synthetic fibril strain 1B13,14assembled from recombinant human aSyn self-replicates autonomouslyin vitroand induces GCIs in mice15, suggesting relevance to MSA. Here we report the high-resolution structural analysis of the 1B fibrils revealing similarities with human brain extracted MSA aSyn filaments, particularly the lack of a specific Thioflavin T (ThT) binding pocket16. In addition, 1B causes sustained intracerebral GCI spread over the years, prompt lethality in transgenic mice, and transmission of inclusion pathology to wild-type animals after crude brain homogenate inoculation. This points to an underlying prion-like seeding process which we demonstratein situusing correlative light-electron microscopy. Our findings underscore structural features of aSyn fibrils pivotal for MSA pathogenesis and provide insights for therapeutic development.
CRISPR targeting of FOXL2 c.402C>G mutation reduces malignant phenotype in granulosa tumor cells and identifies anti-tumoral compounds
Authors: Amarilla-Quintana Sandra , Navarro Paloma , Ramos Alejandra , Montero-Calle Ana , Cabezas-Sainz Pablo , Barrero Maria J , Megías Diego , Vilaplana-Martí Borja , Epifano Carolina , Gómez-Domínguez Déborah , Hernández Iván , Monzón Sara , Cuesta Isabel , Sánchez Laura , Barderas Rodrigo , García-Donas Jesús , Martín Alberto , Pérez de Castro Ignacio 
Published: July 2024

AbstractFOXL2 is a transcription factor essential for sex determination and ovary development and maintenance. Mutations in this gene are implicated in syndromes involving premature ovarian failure and granulosa cell tumors (GCTs). This rare cancer accounts for less than 5% of diagnosed ovarian cancers and is causally associated with the FOXL2 c.402C>G, p.C134W mutation in 97% of the adult cases (AGCTs). In this study, we employed CRISPR technology to specifically eliminate the FOXL2 c.402C>G mutation in granulosa tumor cells. Our results show that this Cas9-mediated strategy selectively targets the mutation without affecting the wild-type allele. Granulosa cells lacking the FOXL2 c.402C>G exhibit a reduced malignant phenotype, with significant changes in cell proliferation, invasion, and cell death. Furthermore, these modified cells are more susceptible to Dasatinib and Ketoconazole. Transcriptomic and proteomic analyses reveal that CRISPR-modified granulosa tumor cells shift their expression profiles towards a wild-type like phenotype. Additionally, this altered expression signature has led to the identification of new compounds with antiproliferative and pro-apoptotic effects on granulosa tumor cells. Our findings demonstrate the potential of CRISPR technology for the specific targeting and elimination of a mutation causing granulosa cell tumors, highlighting its therapeutic promise for treating this rare ovarian cancer.Simple SummaryAdult granulosa cell tumors (AGCTs), characterized by a specific point mutation (C134W) in the gene FOXL2, are less than 5% of all the diagnosed ovarian cancers. Surgery is the cornerstone treatment for AGCT even at relapse, with systemic therapy showing poor results. The aim of our study is to explore the potential therapeutic effect of the elimination of the C134W mutation. To achieve our goal, we have eliminated the mutant allele using CRISPR technology. Our results demonstrate that CRISPR-mediated elimination of FOXL2-C134W reduces the malignant phenotype of granulosa tumor cells, which change their transcriptional, proteomic, and cellular phenotype to a wild type like, granulosa type. Moreover, the induced changes allowed us to find new compounds with antitumoral activity. This work highlights the therapeutic potential of CRISPR mediated technology for the treatment of AGCT.
PhoPQ-mediated lipopolysaccharide modification regulates intrinsic resistance to tetracycline and glycylcycline antibiotics inEscherichia coli
Authors: Choi Byoung Jun , Choi Umji , Ryu Dae-Beom , Lee Chang-Ro 
Published: July 2024

ABSTRACTTetracyclines and glycylcycline are among the last-resort antibiotics used to combat infections caused by multidrug-resistant Gram-negative pathogens. Despite the clinical importance of these antibiotics, their mechanisms of resistance remain unclear. In this study, we elucidated a novel mechanism of resistance to tetracycline and glycylcycline antibiotics via lipopolysaccharide (LPS) modification. Disruption of theEscherichia coliPhoPQ two-component system, which regulates the transcription of various genes involved in magnesium transport and LPS modification, leads to increased susceptibility to tetracycline, minocycline, doxycycline, and tigecycline. These phenotypes are caused by enhanced expression of phosphoethanolamine transferase EptB, which catalyzes the modification of the inner core sugar of LPS. PhoPQ-mediated regulation of EptB expression appears to affect the intracellular transportation of doxycycline. Disruption of EptB increases resistance to tetracycline and glycylcycline antibiotics, whereas the other two phosphoethanolamine transferases, EptA and EptC, that participate in the modification of other LPS residues, are not associated with resistance to tetracyclines and glycylcycline. Overall, our results demonstrated that PhoPQ-mediated modification of a specific residue of LPS by phosphoethanolamine transferase EptB regulates resistance to tetracycline and glycylcycline antibiotics.ImportanceElucidating the resistance mechanisms of clinically important antibiotics helps in maintaining the clinical efficacy of antibiotics and in the prescription of adequate antibiotic therapy. Although tetracycline and glycylcycline antibiotics are clinically important in combating multidrug-resistant Gram-negative bacterial infections, their mechanisms of resistance are not fully understood. Our research demonstrates that theEscherichia colitwo-component system PhoPQ regulates resistance to tetracycline and glycylcycline antibiotics by controlling the expression of phosphoethanolamine transferase EptB, which catalyzes the modification of the inner core residue of lipopolysaccharide (LPS). Therefore, our findings highlight a novel resistance mechanism to tetracycline and glycylcycline antibiotics and the physiological significance of LPS core modification inE. coli.One sentence summaryLipopolysaccharide modification-mediated tigecycline resistance
Bridging the Gap in Health Literacy: Harnessing the Power of Large Language Models to Generate Plain Language Summaries from Biomedical Texts
Authors: Salazar-Lara Carolina , Arias Russi Andrés Felipe , Manrique Rubén 
Published: July 2024

AbstractHealth literacy is essential for individuals to navigate the healthcare system and make informed decisions about their health. Low health literacy levels have been associated with negative health outcomes, particularly among older populations and those financially restricted or with lower educational attainment. Plain language summaries (PLS) are an effective tool to bridge the gap in health literacy by simplifying content found in biomedical and clinical documents, in turn, allowing the general audience to truly understand health-related documentation. However, translating biomedical texts to PLS is time-consuming and challenging, for which they are rarely accessible by those who need them. We assessed the performance of Natural Language Processing (NLP) for systematizing plain language identification and Large Language Models (LLMs), Generative Pre-trained Transformer (GPT) 3.5 and GPT 4, for automating PLS generation from biomedical texts. The classification model achieved high precision (97·2%) in identifying if a text is written in plain language. GPT 4, a state-of-the-art LLM, successfully generated PLS that were semantically equivalent to those generated by domain experts and which were rated high in accuracy, readability, completeness, and usefulness. Our findings demonstrate the value of using LLMs and NLP to translate biomedical texts into plain language summaries, and their potential to be used as a supporting tool for healthcare stakeholders to empower patients and the general audience to understand healthcare information and make informed healthcare decisions.
Epilepsy Socioeconomic Impact in a Tertiary Center in Brazil From the Patient Perspective
Authors: Romão Tayla , da Silva Everton Nunes , Kayo Monica , Mansilla Raíssa , Ferraz Lucas , D’Andrea Isabella 
Published: July 2024

AbstractBackgroundThis study aimed to evaluate the direct and indirect annual costs of epilepsy from the perspective of patients with epilepsy treated at a public tertiary center situated in Rio de Janeiro, Brazil.MethodsA cross-sectional cost-of-illness study was conducted, using a bottom-up approach based on interviews and records of 166 outpatients with confirmed diagnoses of epilepsy. Direct costs included expenses related to treatment, and transportation, while indirect costs encompassed productivity losses due to morbidity and mortality, assessed through the human capital approach and caregivers.ResultsThe majority of patients in the sample had refractory epilepsy (68.1%) and were on polytherapy (43.98%). The average per capita income of the sample was USD 434,90 per month, and 28.3% of the individuals were unemployed. The total costs amounted to USD 8,243.10 per patient per year, with 76.95% attributed to indirect costs, 23.05% to direct medical costs, and 2.31% to non-medical costs. The primary cost contributors included unemployment (30.42%), caregiver expenses (22.41%), and antiseizure medications (20.30%). The majority of patients reported purchasing all their medications (62.43%). The total out-of-pocket health expenses amounted to USD 2,090.10 per patient per year, with medications accounting for 90.89% of the expenses and transportation for 9.11%.ConclusionsIn addition to unemployment as the main cost driver, the patients incurred catastrophic spending on medications. Even though treated in a public service, out-of- pocket health expenses made up 40.04% of the average per capita income of the sample and 12.85% of the Brazilian GDP per capita in 2021. The significant patient expenditures may contribute to poor adherence to epilepsy treatment, which can exacerbate the disease and lead to increased seizure frequency. This, in turn, reduces their ability to earn income, contributing to the rise in indirect and intangible costs.
Polyamines regulate cell fate by altering the activity of histone-modifying enzymes
Authors: Emmons-Bell Maya , Forsyth Grace , Sundquist Abby , Oldeman Sylvie , Gardikioti Angeliki , de Souza Roshni , Coene Jonathan , Kamel Maryam H. , Ayyapan Shine , Fuchs Harrison A. , Verhelst Steven , Smeeton Joanna , Musselman Catherine A. , Schvartzman Juan-Manuel 
Published: July 2024

AbstractPolyamines are polycationic alkyl-amines abundant in proliferating stem and cancer cells. How these metabolites influence numerous cellular functions remains unclear. Here we show that polyamine levels decrease during differentiation and that inhibiting polyamine synthesis leads to a differentiated-like cell state. Polyamines concentrate in the nucleus and are further enriched in the nucleoli of cells in culture andin vivo. Loss of polyamines drives changes in chromatin accessibility that correlate with altered histone post-translational modifications. Polyamines interact electrostatically with DNA on the nucleosome core, stabilizing histone tails in conformations accessible to modifying enzymes. These data reveal a mechanism by which an abundant metabolite influences chromatin structure and function in a non-sequence specific manner, facilitating chromatin remodeling during reprogramming and limiting it during fate commitment.
Delineation of a thrombin receptor-stimulated vascular smooth muscle cell transition generating cells in the plaque-stabilising fibrous cap
Authors: Taylor James CK , Worssam Matthew D , Oc Sebnem , Lambert Jordi , Mahbubani Krishnaa T , Foote Kirsty , Finigan Allie , Chan Yee-Hung , Figg Nichola , Clarke Murray C H , Bennett Martin R , Jørgensen Helle F 
Published: July 2024

AbstractAimsVascular smooth muscle cells (VSMCs) accumulate in atherosclerotic plaques and exhibit remarkable phenotypic plasticity, contributing to both plaque growth and stability. The plaque-stabilising fibrous cap is rich in VSMC-derived cells, yet the cellular transitions and regulatory mechanisms governing fibrous cap formation remain unclear. We aimed to delineate the VSMC phenotypic transitions associated with this critical process.Methods and ResultsMapping of lineage-traced VSMCs during plaque development revealed investment of VSMCs prior to fibrous cap formation. Using single-cell RNA-sequencing (scRNA-seq) profiles of lineage-traced VSMCs from atherosclerotic and acutely injured mouse arteries, we identified a disease-specific VSMC state co-expressing contractile genes with extracellular matrix (ECM) components (including fibrillar collagens and elastin) and NOTCH3, which are associated with fibrous cap formation. Computational trajectory analysis predicted that this proposed fibrous cap-related VSMC (fcVSMC) state arises from a previously described plastic, intermediate VSMC population expressing SCA1 and VCAM1. Clonal analysis further showed that NOTCH3+fcVSMCs derive from intermediate VSMCs in both atherosclerosis and an acute vascular injury model, suggesting a conserved disease-relevant mechanism. The fcVSMCs were enriched in plaque fibrous caps compared to lesion cores, consistent with a role in fibrous cap formation. By combining scRNA-seq trajectory analysis and spatial transcriptomics of human atherosclerotic plaques, we identified protease-activated receptor-1 (PAR1) as a candidate regulator of fcVSMC generation. PAR1 was expressed by VSMCs in human plaque fibrous caps and, PAR1 activation by thrombin induced expression of contractile genes and ECM components associated with the fcVSMC state in human VSMCs.ConclusionsOur findings identify a VSMC transition linked to fibrous cap formation in atherosclerosis and show this is modelled by vascular injury. We identify VSMC-expressed PAR1 as a potential therapeutic target for promoting plaque stability by driving the transition to the matrix-producing, fibrous cap-associated VSMC state.
Nanoscale cluster mapping of molecular complexes with pixel-based correlations
Authors: Kiuchi Tai , Kobayashi Ryouhei , Ogawa Shuichiro , Elverston Louis L. H. , Watanabe Naoki 
Published: July 2024

AbstractSuper-resolution microscopy achieves a few nanometers resolution, but protein quantification and colocalization is limited by its labeling density. Here we present a method to map molecular complexes using the multiplexed data of IRIS super- resolution imaging. We developed antiserum-derived Fab IRIS probes for high- density labeling of endogenous targets, and image analysis, Protein Cluster coloring (PC-coloring), which employs pixel-based principal component analysis and clustering. PC-coloring was first used to map regions of distinct ratios of targets on the image. The molecular complex formation was then evaluated by correlation between all combinations of two proteins in each PC-colored region. We elucidate receptor recruitment and the complex formation in a clathrin-coated structure (CCS) which is pre-assembled prior to endocytosis. Upon EGF stimulation, EGFR-, EGFR-Grb2-complex- and Grb2-dominant regions lined up from the CCS rim. Along the interior of Grb2-dominant regions, Eps15, FCHo1/2 and intersectin-1 formed a complex with Grb2. The interior of Eps15-FCHo1/2 complexes was lined with Eps15-intersectin-1 complexes. The results reveal a laminar complex formation of EGFR, Grb2 and CCS components at the recruitment sites.