bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative analysis reveals a macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer
Authors: Zuljan Erika , von der Emde Benjamin , Piwonski Iris , Afonseca Pestana Ana Cristina , Klinghammer Konrad , Mock Andreas , Horak Peter , Heining Christoph , Klauschen Frederick , Pretzell Ina , Boerries Melanie , Brandts Christian H , Kreutzfeldt Simon , Teleanu Maria-Veronica , Hübschmann Daniel , Morris Luc G T , Keller Ulrich , Glimm Hanno , Fröhling Stefan , Ochsenreither Sebastian , Keilholz Ulrich , Blanc Eric , Beule Dieter , Rieke Damian T 
Published: June 2024

ABSTRACTBackgroundSalivary gland cancers (SGC) are rare and heterogeneous malignant tumors. Advanced SGC lack established treatment options and show poor response to immunotherapy. Here, an integrative multi-omics analysis in a large cohort of advanced SGC revealed insights into the tumor immune microenvironment (TIM) and distinct mechanisms of immune evasion.MethodsA total of 104 patients with recurrent/metastatic SGC from the DKTK MASTER program were included in this study. Whole-exome or whole-genome sequencing and RNA-sequencing was performed on fresh frozen tumor tissue. The tumor immune microenvironment was analyzed using CIBERSORT deconvolution analysis and immune gene expression scores in bulk RNA-sequencing data. Single-nuclei sequencing and immunohistochemistry analyses were performed in selected samples. Results were validated in bulk RNA-sequencing data of a previously published independent dataset.ResultsBulk transcriptome analysis revealed an immune-deserted TIM in the majority of advanced SGC samples. Immune exclusion was most prominent in adenoid cystic carcinoma (ACC) subgroup 1 exhibiting a downregulation of the antigen processing machinery. Only a small subset of advanced SGC, including few adenoid cystic carcinoma, exhibited T-cell inflammation, which was correlated with tumor mutational burden in Non-ACC samples. Subtype specific expression of immune checkpoints as well as cancer testis antigens were identified with prominent expression of VTCN1 in luminal cells within ACC. Single-cell RNA-sequencing and bulk RNA-seq deconvolution analysis validated immune cell exclusion and revealed a TIM that was dominated by M2 macrophages across SGC subtypes. Among evaluable patients treated with immune checkpoint inhibitors, a high T-cell to macrophage ratio was associated with clinical benefit.ConclusionsThese data support biomarker-based development of immune-checkpoint inhibition and the development of novel immune-checkpoint inhibitors and cellular therapies in SGC.Trial RegistrationRetrospectively registered,NCT05852522
DeepSEA: an alignment-free deep learning tool for functional annotation of antimicrobial resistance proteins
Authors: Borelli Tiago Cabral , Paschoal Alexandre Rossi , da Silva Ricardo Roberto 
Published: June 2024

AbstractSurveying antimicrobial resistance (AMR) is essential to track its evolution and spread. Alignment-based annotation tools use strict identity (>80%) cutoffs to distinguish between non-resistant (NRP) and resistant proteins (ARP) only annotating proteins similar to those in their databases. Deep learning and Hidden Markov Models (HMM) based tools also depend on protein alignment at some level. DeepARG filters input data to select the um SNP ARG-like proteins and HMMs are built on multi-sequence alignment (MSA) specific for the protein in a given family or group. Therefore, there is a need to remove the alignment dependency of AMR annotation tools to identify proteins with remote homology Here we present DeepSEA, an alignment-free tool fitted on antimicrobial-resistant sets of aligned and unaligned ARPs and NRP. DeepSEA outperforms the current multi-class AMR classifiers DeepARG, RGI and AMRfinder. Furthermore, DeepSEA trained weights cluster AMR by resistant mechanisms, indicating that the model’s latent variables successfully captured distinguishing features of antibiotic resistance. Our tool annotated functionally validated tetracycline destructases (TDases) and confirmed the identification of a novel TDase found by HMM.
MYC and HSF1 Cooperate to Drive PLK1 inhibitor Sensitivity in High Grade Serous Ovarian Cancer
Authors: Williams Imade , DeHart Haddie , O’Malley Matthew , Walker Bobby , Ulhaskumar Vrushabh , Ray Haimanti , Delaney Joe R. , Nephew Kenneth P. , Carpenter Richard L. 
Published: June 2024

AbstractOvarian cancer is a deadly female cancer with high rates of recurrence. The primary treatment strategy for patients is platinum-based therapy regimens that almost universally develop resistance. Consequently, new therapeutic avenues are needed to overcome the plateau that current therapies have on patient outcomes. We describe a gene amplification involving both HSF1 and MYC, wherein these two genes on chromosome 8q are co-amplified in over 7% of human tumors that is enriched to over 30% of patients with ovarian cancer. We further found that HSF1 and MYC transcriptional activity is correlated in human tumors and ovarian cancer cell lines, suggesting they may cooperate in ovarian cancer cells. CUT&RUN for HSF1 and MYC in co-amplified ovarian cancer cells revealed that HSF1 and MYC have overlapping binding at a substantial number of locations throughout the genome where their binding peaks are near identical. Consistent with these data, a protein-protein interaction between HSF1 and MYC was detected in ovarian cancer cells, implying these two transcription factors have a molecular cooperation. Further supporting their cooperation, growth of HSF1-MYC co-amplified ovarian cancer cells were found to be dependent on both HSF1 and MYC. In an attempt to identify a therapeutic target that could take advantage of this dependency on both HSF1 and MYC, PLK1 was identified as being correlated with HSF1 and MYC in primary human tumor specimens, consistent with a previously established effect of PLK1 on HSF1 and MYC protein levels. Targeting PLK1 with the compound volasertib (BI-6727) revealed a greater than 200-fold increased potency of volasertib in HSF1-MYC co-amplified ovarian cancer cells compared to ovarian cancer cells wild-type HSF1 and MYC copy number, which extended to several growth assays, including spheroid growth. Volasertib, and other PLK1 inhibitors, have not shown great success in clinical trials and this study suggests that targeting PLK1 may be viable in a precision medicine approach using HSF1-MYC co-amplification as a biomarker for response.
Elevated phagocytic capacity directs innate spinal cord repair
Authors: Shaw Dana Klatt , Saraswathy Vishnu Muraleedharan , McAdow Anthony R. , Zhou Lili , Park Dongkook , Mote Ridim , Johnson Aaron N. , Mokalled Mayssa H. 
Published: June 2024

ABSTRACTImmune cells elicit a continuum of transcriptional and functional states after spinal cord injury (SCI). In mammals, inefficient debris clearance and chronic inflammation impede recovery and overshadow pro-regenerative immune functions. We found that, unlike mammals, zebrafish SCI elicits transient immune activation and efficient debris clearance, without causing chronic inflammation. Single-cell transcriptomics and inducible genetic ablation showed zebrafish macrophages are highly phagocytic and required for regeneration. Cross-species comparisons between zebrafish and mammalian macrophages identifiedtranscription and immune response regulator(tcim) as a macrophage-enriched zebrafish gene. Genetic deletion of zebrafishtcimimpairs phagocytosis and regeneration, causes aberrant and chronic immune activation, and can be rescued by transplanting wild-type immune precursors intotcimmutants. Conversely, genetic expression of humanTCIMaccelerates debris clearance and regeneration by reprogramming myeloid precursors into activated phagocytes. This study establishes a central requirement for elevated phagocytic capacity to achieve innate spinal cord repair.
Rickettsia β-peptide Reactivity with Immune IgM
Authors: Fuller Lee , Ordanza Susan , Reyna Julia 
Published: June 2024

AbstractSpotted Fever Group (SFG) Rickettsia species maintain an s-layer with two major outer membrane proteins (OmpA and OmpB) aligned within a lipopolysaccharide (LPS) matrix external to the bacterial outer membrane. While the two typhus group species (R. typhi and R. prowazekii) maintain a similar s-layer containing only OmpB with its own specific form of LPS. A major component of these two types of OmpB is a specific and highly conserved beta peptide (β-peptide) non-covalently attached to the respective OmpB passenger domain. This β-peptide is initially translated as the c-terminus of the 168 kDa polypeptide and initially forms a membrane pore to allow the larger passenger domain to exit the bacterial cytoplasm through the outer membrane. Prior to the full exit of this passenger domain from the cytoplasm the long polypeptide chain is cleaved by a peptidase, leaving the c-terminus remaining as a beta-folded membrane pore and the N-terminal passenger domain exiting to the space between the bacterial membrane and the s-layer. The fate of this pore structure and the attachment of β-peptide to the OmpB continues to be examined and will be discussed as another protective component of the Rickettsia. An EIA IgM assay has been developed to utilize this antigen for clinical diagnostic use to accurately detect acute rickettsial infection in testing labs and lead to the availability of rapid test (lateral flow) formats for more immediate testing.
Protein-ligand co-design: a case for improving binding affinity between Type II NADH:quinone oxidoreductase and quinones
Authors: Porokhin Vladimir , Brown Anne M. , Hassoun Soha 
Published: June 2024

AbstractBiological engineering aims to enhance biological systems by designing proteins with improved catalytic properties or ligands with enhanced function. Typically, applications permit designing proteins, e.g., an enzyme in a biodegradation reaction, or ligands e.g., a drug for a target receptor, but not both. Yet, some applications can benefit from a more flexible approach where both the protein and ligand can be designed or modified together to enhance a desired property. To meet the need for this co-design capability, we introduce a novel co-design paradigm and demon- strate its application to Ndh2-quinone pairings to enhance their binding affinity. Ndh2, type-II NADH dehydrogenase, is an enzyme found in certain bacteria that facilities extracellular electron transfer (EET) when interacting with exogenous quinone mediators. This interaction leads to the generation of a detectable electric current that can be used for biosensing applications. Our results demonstrate the benefits of the co-design paradigm in realizing Ndh2-quinone pairings with enhanced binding affinities, therefore highlighting the importance of considering protein-ligand engineering from a holistic co-design perspective.
ClpS directs degradation of primary N-end rule substrates inMycolicibacterium smegmatis
Authors: Presloid Christopher J. , Jiang Jialiu , Kandel Pratistha , Anderson Henry R. , Beardslee Patrick C. , Swayne Thomas M. , Schmitz Karl R. 
Published: June 2024

ABSTRACTDrug-resistant tuberculosis infections are a major threat to global public health. The essential mycobacterial ClpC1P1P2 protease has received attention as a prospective target for novel antibacterial therapeutics. However, efforts to probe its function in cells are constrained by our limited knowledge of its physiological proteolytic repertoire. Here, we interrogate the role of mycobacterial ClpS in directing N-end rule proteolysis by ClpC1P1P2 inMycolicibacterium smegmatis. Binding assays demonstrate that mycobacterial ClpS binds canonical primary N-degrons (Leu, Phe, Tyr, Trp) with moderate affinity. N-degron binding restricts the conformational flexibility of a loop adjacent to the ClpS N-degron binding pocket and strengthens ClpS•ClpC1 binding affinity ∼30-fold, providing a mechanism for cells to prioritize N-end rule proteolysis when substrates are abundant. Proteolytic reporter assays inM. smegmatisconfirm degradation of substrates bearing primary N-degrons, but suggest that secondary N-degrons are absence in mycobacteria. This work expands our understanding of the mycobacterial N-end rule pathway and identifies ClpS as a critical component for substrate specificity, providing insights that may support the development of improved Clp protease inhibitors.
An optimized method to visualize lipid droplets in brain tissue demonstrates their substantial accumulation in aged brains
Authors: Petrelli Francesco , Rey Alicia , Panfilova Diana , Madsen Sofia , Héritier Noéline , Knobloch Marlen 
Published: June 2024

AbstractLipid droplets (LDs) are cellular stores for lipids. These organelles have recently gained interest in neuroscience because they accumulate in various cell types in neurodegenerative diseases. However, their role under physiological conditions is still not fully understood. Classical LD staining methods, which use lipophilic dyes like BODIPY 493/503 (BD493) or antibodies against LD coat proteins, show very few LDs in healthy brain tissue. Our recently developed novel endogenous LD reporter mouse challenges this view. We have been able to detect numerous LDs in healthy brain tissue from both adult and developing mice without staining. To understand why classical staining and endogenous labeling yield different results, we thoroughly investigated the effects of tissue preparation and detergent used in LD detection. We found that BD493 works poorly in brain tissue, while other lipophilic dyes visualize many LDs. We also found that antibody-based LD detection depends on tissue pretreatment and detergent concentration but can reveal a similar number of LDs as observed with the endogenous LD reporter mouse. Taken together, we here present an optimized procedure for LD detection in brain tissue using commercially available dyes and antibodies. Using these methods, we demonstrate that LDs are numerous in healthy brain tissue and substantially accumulate in aged brains in various cell types, including neurons.
Contribution of neurons that expressfruitlessandClocktranscription factors to behavioral rhythms and courtship
Authors: Deluca Anthony , Bascom Brooke , Key Planas Daniela A , Kocher Matthew A , Torres Marielise , Arbeitman Michelle N 
Published: June 2024

SummaryAnimals need to integrate information across neuronal networks that direct reproductive behaviors and circadian rhythms. In Drosophila, the master regulatory transcription factors that direct courtship behaviors and circadian rhythms are co-expressed in a small set of neurons. In this study we investigate the role of these neurons in both males and females. We find sex-differences in the number of thesefruitlessandClock-expressing neurons (fru∩Clkneurons) that is regulated by male-specific Fru. We assign thefru∩Clkneurons to the electron microscopy connectome that provides high resolution structural information. We also discover sex-differences in the number offru-expressing neurons that are post-synaptic targets ofClk-expressing neurons, with more post-synaptic targets in males. Whenfru∩Clkneurons are activated or silenced, males have a shorter period length. Activation offru∩Clkneurons also changes the rate a courtship behavior is performed. We find that activation and silencingfru∩Clkneurons impacts the molecular clock in the sLNv master pacemaker neurons, in a cell-nonautonomous manner. These results reveal how neurons that subserve the two processes, reproduction and circadian rhythms, can impact behavioral outcomes in a sex-specific manner.
Miniscope Recording Calcium Signals at Hippocampus of Mice Navigating an Odor Plume
Authors: Simoes de Souza Fabio M. , Williamson Ryan , McCullough Connor , Teel Alec , Futia Gregory , Ma Ming , True Aaron , Crimaldi John. P. , Gibson Emily , Restrepo Diego 
Published: June 2024

ABSTRACTMice navigate an odor plume with a complex spatiotemporal structure in the dark to find the source of odorants. This article describes a protocol to monitor behavior and record Ca2+transients in dorsal CA1 stratum pyramidale neurons in hippocampus (dCA1) in mice navigating an odor plume in a 50 cm x 50 cm x 25 cm odor arena. An epifluorescence miniscope focused through a GRIN lens imaged Ca2+transients in dCA1 neurons expressing the calcium sensor GCaMP6f in Thy1-GCaMP6f mice. The paper describes the behavioral protocol to train the mice to perform this odor plume navigation task in an automated odor arena. The methods include a step-by-step procedure for the surgery for GRIN lens implantation and baseplate placement for imaging GCaMP6f in CA1. The article provides information on real-time tracking of the mouse position to automate the start of the trials and delivery of a sugar water reward. In addition, the protocol includes information on using of an interface board to synchronize metadata describing the automation of the odor navigation task and frame times for the miniscope and a digital camera tracking mouse position. Moreover, the methods delineate the pipeline used to process GCaMP6f fluorescence movies by motion correction using NorMCorre followed by identification of regions of interest with EXTRACT. Finally, the paper describes an artificial neural network approach to decode spatial paths from CA1 neural ensemble activity to predict mouse navigation of the odor plume.SUMMARYThis protocol describes how to investigate the brain-behavior relationship in hippocampal CA1 in mice navigating an odor plume. This article provides a step-by-step protocol, including the surgery to access imaging of the hippocampus, behavioral training, miniscope GCaMP6f recording and processing of the brain and behavioral data to decode the mouse position from ROI neural activity.
Sex-biased gene expression precedes sexual dimorphism in the agonadal annelidPlatynereis dumerilii
Authors: Ribeiro Rannyele P. , Null Ryan W. , Özpolat B. Duygu 
Published: June 2024

AbstractGametogenesis is the process by which germ cells differentiate into mature sperm and oocytes, cells essential for sexual reproduction. The sex-specific molecular programs that drive spermatogenesis and oogenesis can also serve as sex identification markers.Platynereis dumeriliiis a research organism that has been studied in many areas of developmental biology. However investigations often disregard sex, asP. dumeriliijuveniles lack sexual dimorphism. The molecular mechanisms of gametogenesis in the segmented wormP. dumeriliiare also largely unknown. In this study, we used RNA sequencing to investigate the transcriptomic profiles of gametogenesis inP. dumeriliijuveniles. Our analysis revealed that sex-biased gene expression becomes increasingly pronounced during the advanced developmental stages, particularly during the meiotic phases of gametogenesis. We identified conserved genes associated with spermatogenesis, such asdmrt1, and a novel genepsmt, that is associated with oogenesis. Additionally, putative long non-coding RNAs were upregulated in both male and female gametogenic programs. This study provides a foundational resource for germ cell research inP. dumerilii,markers for sex identification, and offers comparative data to enhance our understanding of the evolution of gametogenesis mechanisms across species.Summary statementThis study provides insights into the mechanisms of gametogenesis inPlatynereis dumeriliithrough comparative transcriptomics, unveiling sex-biased genes, including conserved and novel genes, governing this largely unexplored process.
Polygenic risk score portability for common diseases across genetically diverse populations
Authors: Moreno-Grau Sonia , Vernekar Manvi , Lopez-Pineda Arturo , Mas-Montserrat Daniel , Barrabes-Torrella Miriam , Quinto-Cortés Consuelo D. , Moatamed Babak , Lee Ming Ta ’Michael’ , Yu Zhenning , Numakura Kensuke , Matsuda Yuta , Wall Jeffrey D. , Ioannidis Alexander , Katsanis Nicholas , Takano Tomohiro , Bustamante Carlos D 
Published: June 2024

AbstractBackgroundPolygenic risk scores (PRS) derived from European individuals have reduced portability across global populations, limiting their clinical implementation at worldwide scale. Here, we investigate the performance of a wide range of PRS models across four ancestry groups (Africans, Europeans, East Asians, and South Asians) for 14 conditions of high-medical interest.MethodsTo select the best-performing model per trait, we first compared PRS performances for publicly available scores, and constructed new models using different methods (LDpred2, PRS-CSx and SNPnet). We used 285K European individuals from the UK Biobank (UKBB) for training and 18K, including diverse ancestries, for testing. We then evaluated PRS portability for the best models in Europeans and compared their accuracies with respect to the best PRS per ancestry. Finally, we validated the selected PRS models using an independent set of 8,417 individuals from Biobank of the Americas-Genomelink (BBofA-GL); and performed a PRS-Phewas.ResultsWe confirmed a decay in PRS performances relative to Europeans when the evaluation was conducted using the best-PRS model for Europeans (51.3% for South Asians, 46.6% for East Asians and 39.4% for Africans). We observed an improvement in the PRS performances when specifically selecting ancestry specific PRS models (phenotype variance increase: 1.62 for Africans, 1.40 for South Asians and 0.96 for East Asians). Additionally, when we selected the optimal model conditional on ancestry for CAD, HDL-C and LDL-C, hypertension, hypothyroidism and T2D, PRS performance for studied populations was more comparable to what was observed in Europeans. Finally, we were able to independently validate tested models for Europeans, and conducted a PRS-Phewas, identifying cross-trait interplay between cardiometabolic conditions, and between immune-mediated components.ConclusionOur work comprehensively evaluated PRS accuracy across a wide range of phenotypes, reducing the uncertainty with respect to which PRS model to choose and in which ancestry group. This evaluation has let us identify specific conditions where implementing risk-prioritization strategies could have practical utility across diverse ancestral groups, contributing to democratizing the implementation of PRS.
Optimizing costs and sustainability for Gamma Knife Radiosurgery: A cost and breakeven analysis at India’s largest Neurosurgery Centre
Authors: Agrawal Nitin , Sharma Nishant , Jamwal Tilotma , Singh Kshitija , Siddharth Vijaydeep , Satpathy Sidhartha 
Published: June 2024

AbstractBackgroundEstablishing and maintaining gamma knife facility incurs significant costs, mandating healthcare institutions to meticulously assess financial implications for sustainability.MethodsThis study explores the financial implications of setting up and operating a Gamma Knife facility, with an aim to ascertain user charges for achieving breakeven. The study was conducted from January to June 2019 at the largest neurosurgery centre of an Institute of National Importance (INI), in Delhi, India. Applying both Traditional and Time-Driven Activity-Based Costing (TD-ABC) methodologies, capital and operating expenses were calculated. (1US$ = INR 70.4 – Average value for the year 2019)ResultsThe average cost per gamma knife radio surgery procedure was calculated to be US $2,469 ( INR 1,73,832), with major costs attributed to machinery & equipment (43.6%), followed by manpower (32.5%), electricity (9.67%), equipment maintenance (8.61%) etc. The initial investment to establish a Gamma Knife facility is significantly higher with an MRI unit (Model A) at US $ 9,836,423 (INR 69,24,84,164) compared to one without (Model B) at US $7,294,986 (INR 51,35,66,988). Currently, the patient has to pay US $1,065 (INR 75,000) for a gamma knife radio surgery, which poses a challenge for achieving breakeven since the variable cost for the same is US $1,367 (INR 96,239) per procedure.ConclusionThe study serve as a tool for strategic planning, pricing adjustments, and enhancing operational efficiencies, thus ensuring that such high-end technologies can be sustainably integrated into the public healthcare landscape of a developing country like India.