bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRIB3 silencing promotes the downregulation of Akt pathway and PAX3-FOXO1 in high-risk rhabdomyosarcoma
Authors: Gallo-Oller Gabriel , Pons Guillem , Sansa-Girona Julia , Navarro Natalia , Zarzosa Patricia , García-Gilabert Lia , Cabré Fernandez Paula , Guillén Burrieza Gabriela , Valero-Arrese Lorena , Segura Miguel F. , Lizcano José M. , Sánchez de Toledo José , Moreno Lucas , Gallego Soledad , Roma Josep 
Published: December 2023

AbstractBackgroundRhabdomyosarcoma (RMS), such as other childhood tumors, has witnessed treatment advancements in recent years. However, high-risk patients continue to face poor survival rates, often attributed to the presence of the PAX3/7-FOXO1 fusion proteins, which has been associated with metastasis and treatment resistance. Despite efforts to directly target these chimeric proteins, clinical success remains elusive. In this study, the main aim was to address this challenge by investigating regulators of FOXO1. Specifically, we focused on TRIB3, a potential regulator of the fusion protein in RMS.MethodsTRIB3 expression was examined through the analysis of patient datasets, including gene expression profiling and gene set enrichment analyses. In cell lines, the DepMap dataset for RMS was utilized alongside Western blot analysis to assess TRIB3 expression. The functional significance of TRIB3 in RMS was assessed through constitutive and inducible shRNA-mediated knockdowns. Subsequentin vitroandin vivoanalyses, including orthotopic tumor models in immune-compromised mice, were conducted to delineate the role and underlying molecular mechanisms exerted by TRIB3 in RMSResultsOur findings revealed a prominent TRIB3 expression in RMS tumors, highlighting its correlation with several clinical features. By conducting TRIB3 genetic inhibition experiments, we observed an impairment on cell proliferation. Notably, the knockdown of TRIB3 led to a decrease in PAX3-FOXO1 and its target genes at protein level, accompanied by a reduction in the activity of the Akt signaling pathway. Furthermore, TRIB3 influenced posttranslational modifications, such as phosphorylation together with proteasomal degradation of PAX3-FOXO1 protein. Additionally, inducible silencing of TRIB3 significantly delayed tumor growth and improved overall survivalin vivo.ConclusionsBased on our comprehensive analysis, we propose that TRIB3 holds therapeutic potential for treating the most aggressive subtype of RMS. The findings herein reported contribute to our understanding of the underlying molecular mechanisms driving RMS progression and provide novel insights into the potential use of TRIB3 as a therapeutic intervention for high-risk RMS patients.
Comparative analysis of methodologies for detecting extrachromosomal circular DNA
Authors: Gao Xuyuan , Liu Ke , Luo Songwen , Tang Meifang , Liu Nianping , Jiang Chen , Fang Jingwen , Li Shouzhen , Hou Yanbing , Guo Chuang , Qu Kun 
Published: December 2023

AbstractExtrachromosomal circular DNA (eccDNA) is crucial in oncogene amplification, gene transcription regulation, and intratumor heterogeneity. While various analysis pipelines and experimental methods have been developed for eccDNA identification, their detection efficiencies have not been systematically assessed. To address this, we evaluated the performance of 7 analysis pipelines using three simulated datasets, in terms of accuracy, similarity, duplication rate, and computational resource consumption. We also compared the eccDNA detection efficiency of 7 experimental methods through twenty-one real sequencing datasets. Our results identified Circle-Map and CReSIL as the most effective pipelines for eccDNA detection through short-read and long-read sequencing data, respectively. Moreover, third-generation sequencing-based Circle-Seq showed superior efficiency in detecting copy number-amplified eccDNA over 10 kb in length. These results offer valuable insights for researchers in choosing the most suitable methods for eccDNA research.
Early Pastoralism in Central European Forests: Insights from Ancient Environmental Genomics
Authors: Zampirolo Giulia , Holman Luke E. , Sawafuji Rikai , Ptáková Michaela , Kovačiková Lenka , Šída Petr , Pokorný Petr , Pedersen Mikkel Winther , Walls Matthew 
Published: December 2023

AbstractCentral European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5 – 6.0 kyr BP). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter, in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder, have clear representation by the Late Neolithic, around 6.0 kyr BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1 – 3.0 kyr BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the Anthropocene.
Mitochondrial Apolipoprotein MIC26 is a metabolic rheostat regulating central cellular fuel pathways
Authors: Lubeck Melissa , Naha Ritam , Schaumkessel Yulia , Westhoff Philipp , Stefanski Anja , Petzsch Patrick , Stühler Kai , Köhrer Karl , Weber Andreas P. M. , Anand Ruchika , Reichert Andreas S. , Kondadi Arun Kumar 
Published: December 2023

SummaryMitochondria play central roles in metabolism and metabolic disorders such as type 2 diabetes. MIC26, a MICOS complex subunit, was linked to diabetes and modulation of lipid metabolism. Yet, the functional role of MIC26 in regulating metabolism under hyperglycemia is not understood. We employed a multi-omics approach combined with functional assays using WT andMIC26KO cells cultured in normoglycemia or hyperglycemia, mimicking altered nutrient availability. We show that MIC26 has an inhibitory role in glycolysis and cholesterol/lipid metabolism under normoglycemic conditions. Under hyperglycemia, this inhibitory role is reversed demonstrating that MIC26 is critical for metabolic adaptations. This is partially mediated by alterations of mitochondrial metabolite transporters. Furthermore,MIC26deletion led to a major metabolic rewiring of glutamine utilization as well as oxidative phosphorylation. We propose that MIC26 acts as a metabolic ‘rheostat’, that modulates mitochondrial metabolite exchange via regulating mitochondrial cristae, allowing cells to cope with nutrient overload.
Antigenic and genetic diversity of H1 and H3 influenza A viruses in swine in Brazil
Authors: Lopes Sara , Anderson Tavis K. , Schaefer Rejane , Tochetto Caroline , Gava Danielle , Cantao Mauricio E. , Ciacci-Zanella Janice R. , Vincent Baker Amy L. , Lewis Nicola S. 
Published: December 2023

AbstractBackgroundInfluenza A virus (IAV) circulates within human and swine populations, and pigs are considered intermediate hosts for the generation of IAV with pandemic potential. Surveillance and characterization of IAVs circulating in pig populations are crucial to strain match vaccines to control IAV transmission in pigs and quantify pandemic potential to humans.MethodsHere, we characterized the genetic and antigenic diversity of IAVs circulating in Brazilian swine between 2010-2018. Phylogenetic maximum-likelihood trees were generated for 84 Brazilian hemagglutinin (HA) gene segments. Hemagglutination inhibition (HI) assay data was used with antigenic cartography to quantify the antigenic differences among representative H1 and H3 swine viruses and relative cross-reactivity between these viruses and human seasonal vaccine strains.ResultsWe identified two genetic lineages of H1 viruses derived from separate human-to-swine transmission events (H1 1B lineage, clades 1B.2.3 and 1B.2.4), an H3 lineage that has diversified into two genetic clades (H3 1990.5.1 and 1990.5.2), and HA genes associated with the 2009 H1N1 pandemic. There was limited cross-reactivity between circulating swine lineages and significant antigenic variation within lineage.ConclusionsThe antigenic diversity among endemic IAV in swine indicates a need for regional strain-specific vaccination strategies in Brazil. Our data supports the need for systematic genomic surveillance and characterization in Brazil to improve the efficacy of swine vaccines and quantify the pandemic potential of endemic swine influenza A viruses.
Mechanical positive feedback and biochemical negative feedback combine to generate complex contractile oscillations in cytokinesis
Authors: Werner Michael E. , Ray Dylan D. , Breen Coleman , Staddon Michael F. , Jug Florian , Banerjee Shiladitya , Maddox Amy Shaub 
Published: December 2023

AbstractContractile force generation by the cortical actomyosin cytoskeleton is essential for a multitude of biological processes. The actomyosin cortex behaves as an active material that drives local and large-scale shape changes via cytoskeletal remodeling in response to biochemical cues and feedback loops. Cytokinesis is the essential cell division event during which a cortical actomyosin ring generates contractile force to change cell shape and separate two daughter cells. Our recent work with active gel theory predicts that actomyosin systems under the control of a biochemical oscillator and experiencing mechanical strain will exhibit complex spatiotemporal behavior, but cytokinetic contractility was thought to be kinetically simple. To test whether active materialsin vivoexhibit spatiotemporally complex kinetics, we used 4-dimensional imaging with unprecedented temporal resolution and discovered sections of the cytokinetic cortex undergo periodic phases of acceleration and deceleration. Quantification of ingression speed oscillations revealed wide ranges of oscillation period and amplitude. In the cytokinetic ring, activity of the master regulator RhoA pulsed with a timescale of approximately 20 seconds, shorter than that reported for any other biological context. Contractility oscillated with 20-second periodicity and with much longer periods. A combination ofin vivoandin silicoapproaches to modify mechanical feedback revealed that the period of contractile oscillation is prolonged as a function of the intensity of mechanical feedback. Effective local ring ingression is characterized by slower speed oscillations, likely due to increased local stresses and therefore mechanical feedback. Fast ingression also occurs where material turnover is high,in vivoandin silico. We propose that downstream of initiation by pulsed RhoA activity, mechanical positive feedback, including but not limited to material advection, extends the timescale of contractility beyond that of biochemical input and therefore makes it robust to fluctuations in activation. Circumferential propagation of contractility likely allows sustained contractility despite cytoskeletal remodeling necessary to recover from compaction. Our work demonstrates that while biochemical feedback loops afford systems responsiveness and robustness, mechanical feedback must also be considered to describe and understand the behaviors of active materialsin vivo.
Artificial intelligence-assisted stimulated Raman molecular cytology enables accurate and rapid intraoperative assessment of the surgical margin in pancreatic ductal adenocarcinoma
Authors: Fang Tinghe , Liu Daoning , Chen Xun , Zhou Keji , Hao Chunyi , Yue Shuhua 
Published: December 2023

ABSTRACTPancreatic ductal adenocarcinoma (PDAC) is a highly mortal cancer with surgical resection the only potentially curative treatment. The accurate intraoperative assessment of PDAC surgical margins is significant in guaranteeing resection adequacy and improving the patient’s survival. However, the commonly used frozen-section pancreatic biopsy is limited by its strict requirement of practitioners and lack of objectivity. Here, we developed the multi-instance cytology with learned Raman embedding (MICLEAR), a label-free cytology based on chemical information reflected by Raman spectra. First, 4085 cells collected from 41 patients were imaged with stimulated Raman scattering (SRS) microscopy. Then, a contrastive learning (CL)-based cell embedding model was obtained to represent each cell with a concise vector that contained its morphological and componential information. Finally, a multi-instance learning (MIL)-based diagnosis model using cell vectors predicted the probability that the margin was positive. MICLEAR reached 80% sensitivity, 94.1% specificity, and 0.86 AUC on the pancreatic neck margin (PNM) samples from 27 patients. It holds promise for rapid and accurate assessment of PDAC surgical margins.
Towards ultra-low-cost smartphone microscopy
Authors: Zhang Haoran , Zhang Weiyi , Zuo Zirui , Yang Jianlong 
Published: December 2023

AbstractThe outbreak of COVID-19 exposed the inadequacy of our technical tools for home health surveillance, and recent studies have shown the potential of smartphones as a universal optical microscopic imaging platform for such applications. However, most of them use laboratory-grade optomechanical components and transmitted illuminations to ensure focus tuning capability and imaging quality, which keeps the cost of the equipment high. Here we propose an ultra-low-cost solution for smartphone microscopy. To realize focus tunability, we designed a seesaw-like structure capable of converting large displacements on one side into small displacements on the other (reduced to ∼9.1%), which leverages the intrinsic flexibility of 3D printing materials. We achieved a focus-tuning accuracy of ∼ 5µm, which is 40 times higher than the machining accuracy of the 3D-printed lens holder itself. For microscopic imaging, we use an off-the-shelf smartphone camera lens as the objective and the built-in flashlight as the illumination. To compensate for the resulting image quality degradation, we developed a learning-based image enhancement method. We use the CycleGAN architecture to establish the mapping from smartphone microscope images to benchtop microscope images without pairing. We verified the imaging performance on different biomedical samples. Except for the smartphone, we kept the full costs of the device under 4 USD. We think these efforts to lower the costs of smartphone microscopes will benefit their applications in various scenarios, such as point-of-care testing, on-site diagnosis, and home health surveillance.Research highlightsWe propose a solution for ultra-low-cost smartphone microscopy. Utilizing the flexibility of 3D-printed material, we can achieve focusing accuracy of ∼ 5µm. Such a low-cost device will benefit point-of-care diagnosis and home health surveillance.
In situlipidomics ofStaphylococcus aureusosteomyelitis using imaging mass spectrometry
Authors: Good Christopher J. , Butrico Casey E. , Colley Madeline E. , Gibson-Corley Katherine N. , Cassat James E. , Spraggins Jeffrey M. , Caprioli Richard M. 
Published: December 2023

SUMMARYOsteomyelitis occurs whenStaphylococcus aureusinvades the bone microenvironment, resulting in a bone marrow abscess with a spatially defined architecture of cells and biomolecules. Imaging mass spectrometry and microscopy are invaluable tools that can be employed to interrogate the lipidome ofS. aureus-infected murine femurs to reveal metabolic and signaling consequences of infection. Here, nearly 250 lipids were spatially mapped to healthy and infection-associated morphological features throughout the femur, establishing composition profiles for tissue types. Ether lipids and arachidonoyl lipids were significantly altered between cells and tissue structures in abscesses, suggesting their roles in abscess formation and inflammatory signaling. Sterols, triglycerides, bis(monoacylglycero)phosphates, and gangliosides possessed ring-like distributions throughout the abscess, indicating dysregulated lipid metabolism in a subpopulation of leukocytes that cannot be discerned with traditional microscopy. These data provide chemical insight into the signaling function and metabolism of cells in the fibrotic border of abscesses, likely characteristic of lipid-laden macrophages.
Brain mineralization in postoperative delirium and cognitive decline
Authors: Lammers-Lietz Florian , Borchers Friedrich , Feinkohl Insa , Hetzer Stefan , Kanar Cicek , Lachmann Gunnar , Chien Claudia , Spies Claudia , Winterer Georg , Zaborszky Laszlo , Zacharias Norman , Paul Friedemann 
Published: December 2023

ABSTRACTDelirium is a severe postoperative complication associated with poor overall and especially neurocognitive prognosis. Altered brain mineralization is found in neurodegenerative disorders but has not been studied in postoperative delirium and postoperative cognitive decline. We hypothesized that mineralization-related hypointensity in susceptibility-weighted magnetic resonance imaging (SWI) is associated with postoperative delirium and cognitive decline.We analyzed a subsample of cognitively healthy patients ≥65 years presenting for elective major surgery who underwent SWI before (N=65) and three months after surgery (N=33) as part of a subproject in the BioCog study. We measured relative SWI intensities in basal ganglia, hippocampus, and posterior basal forebrain cholinergic system (pBFCS). A post-hoc analysis of two pBFCS subregions (Ch4, Ch4p) was conducted. Patients were screened for delirium until the seventh postoperative day. Cognitive testing was performed before and three months after surgery.Preoperative relative SWI hypointensities in the basal ganglia and pBFCS were associated with increased risk for postoperative delirium after adjustment for surgery duration. After additional adjustment for age, sex, preoperative MMSE and region volume, only the association of pBFCS hypointensity and postoperative delirium remained significant. Adjusted for surgery duration, perioperative change in relative SWI intensities of the pBFCS was associated with cognitive decline three months after surgery. This association remained at a trend level after adjustments for age, sex, and region volume, but a significant independent association especially with pBFCS-subregion Ch4p was found in a post-hoc analysis.Brain mineralization, particularly in the cerebral cholinergic system, could be a pathomechanism in postoperative delirium and cognitive decline.
The small molecule inhibitor 3PO is a modulator of neutrophil metabolism, ROS production and NET release
Authors: Alarcon Michele Fresneda , Abdullah Genna Ali , Nolan Andy , Linford Christina , Meschis Maria Martina , Cross Andrew L , Sellin Andrew , Phelan Marie M , Wright Helen L 
Published: December 2023

1.ABSTRACTNeutrophils are key effector leukocytes of the innate immune system and play a pivotal role in defending the host against microbial infections. Recent studies have identified a crucial link between glycolysis and neutrophil cellular functions. Using human neutrophils, we have investigated the intricate relationship between glycolysis, extracellular glucose availability, and the enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3), in the regulation of reactive oxygen species (ROS) and neutrophil extracellular trap (NET) production. We have identified that PFKFB3 is elevated in rheumatoid arthritis (RA) neutrophils and that the small molecule PFKFB3 inhibitor 3PO is a key regulator of neutrophil ROS and NET production. 3PO blocked the production of ROS and NETs in a dose-dependent manner in both RA and healthy (HC) neutrophils (p<0.01), and RA neutrophils were more sensitive to lower concentrations of 3PO. Bacterial killing was only partially inhibited by 3PO, and the proportion of live neutrophils after 24h incubation was unchanged. Using NMR metabolomics, we identified that 3PO increases the concentration of lactate, phenylalanine and L-glutamine in neutrophils, as well as significantly decreasing intracellular glutathione (adj. p-value<0.05). We also demonstrated that RA neutrophils produce ROS and NETs in culture conditions which mimic the low glucose environments encountered in RA synovial joints. Our results also suggest 3PO may have molecular targets beyond PFKFB3. By dissecting the intricate interplay between metabolism and neutrophil effector functions, this study advances the understanding of the molecular mechanisms governing pro-inflammatory neutrophil responses and identifies 3PO as a potential therapeutic for conditions characterized by dysregulated neutrophil activation.
Specific cPRC1 complexes are co-opted to mediate oncogenic gene repression in diffuse midline glioma
Authors: Gannon Dáire , Lagan Eimear , Silva Ademar Jesus , Bibawi Peter , Doherty Anthony M. , Nimmo Darragh , McCole Rachel , Monger Craig , Genesi Giovani , Vanderlinden Dibekeme Aurelie , Innes James A. , Yang Lu , Chen Bryan , van Mierlo Guido , Jansen Pascal W.T.C , Wynne Keiran , Sánchez-Rivera Fran-cisco J. , Soto-Feliciano Yadira M. , Vermeulen Michiel , Oliverio Giorgio , Chen Chun-Wei , Philips Richard E. , Brackenand Adrian P. , Brien Gerard L. 
Published: December 2023

ABSTRACTDiffuse midline glioma (DMG) is a fatal childhood brain tumour characterised primarily by mutant histone H3 (H3K27M). H3K27M causes a global reduction in Polycomb Repressive Complex 2 (PRC2)-mediated H3K27me3 by inhibiting PRC2 enzymatic activity. Paradoxically, PRC2 is essential in DMG tumour cells where residual complex activity is required for oncogenic gene repression, although the molecular mechanisms acting downstream of PRC2 in this context are poorly understood. Here, we’ve discovered this oncogenic gene repression is mediated by specific canonical PRC1 (cPRC1) formations. By combining CRISPR screening, biochemical and chromatin mapping approaches with functional perturbations we show that cPRC1 complexes containing CBX4 and PCGF4 drive oncogenic gene repression downstream of H3K27me3 in DMG cells. Remarkably, the altered H3K27me3 modification landscape characteristic of these tumours rewires the distribution of cPRC1 complexes on chromatin. CBX4 and PCGF4 containing cPRC1 accumulate at sites of H3K27me3 while other cPRC1 formations are displaced. Despite accounting for <5% of cPRC1 complexes in DMG, CBX4/PCGF4-containing complexes predominate as gene repressors. Our findings link the altered distribution of H3K27me3 with imbalanced cPRC1 function, promoting oncogenic gene repression in DMG cells, revealing new disease mechanisms and highlighting potential therapeutic opportunities in this incurable childhood brain tumour.
The Parkinson’s Disease related mutant VPS35 (D620N) amplifies the LRRK2 response to endolysosomal stress
Authors: McCarron Katy R. , Elcocks Hannah , Mortiboys Heather , Urbé Sylvie , Clague Michael J. 
Published: December 2023

AbstractThe identification of multiple genes linked to Parkinson’s Disease invites the question as to how they may cooperate. We have generated isogenic cell lines that inducibly express either wild-type or a mutant form of the retromer component VPS35 (D620N), which has been linked to Parkinson’s Disease. This has enabled us to test proposed effects of this mutation in a setting where the relative expression reflects the physiological occurrence. We confirm that this mutation compromises VPS35 association with the WASH complex, but find no defect in WASH recruitment to endosomes, nor in the distribution of lysosomal receptors, cation-independent mannose-6-phosphate receptor and Sortilin. We show VPS35 (D620N) enhances the activity of the Parkinson’s associated kinase LRRK2 towards RAB12 under basal conditions. Furthermore, VPS35 (D620N) amplifies the LRRK2 response to endolysosomal stress resulting in enhanced phosphorylation of RABs 10 and 12. By comparing different types of endolysosomal stresses such as the ionophore nigericin and the membranolytic agent LLOMe, we are able to dissociate phospho-RAB accumulation from membrane rupture.