bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lack of detectable neoantigen depletion in treatment-naïve cancers
Authors: Slagter Maarten , Fanchi Lorenzo F. , van Buuren Marit M. , Velds Arno , Bounova Gergana , Wessels Lodewyk F.A. , Schumacher Ton N. 
Published: June 2023

SummaryWhile neoantigen depletion, a form of immunoediting due to Darwinian pressure exerted by the T cell based immune system during tumor evolution, has been clearly described in murine models, its prevalence in treatment-naive, developing human tumors remains controversial. We developed two novel methodologies to test for depletion of predicted neoantigens in patient cohorts, which both compare patients in terms of their expected number of neoantigens per mutational event. Application of these strategies to TCGA patient cohorts showed that neither basic nor more extensive versions of the methodologies, controlling for confounding factors such as genomic loss of the HLA locus, provided statistically significant evidence for neoantigen depletion. In the subset of analyses that did show a trend towards neoantigen depletion, statistical significance was not reached and depletion was not consistently observed across HLA alleles. Our results challenge the notion that neoantigen depletion is detectable in cohorts of unmatched patient samples using HLA binding prediction-based methodology.
Multimodule imaging of the hierarchical equine hoof wall porosity and structure
Authors: Mahrous Mahmoud A. , Chadha Charul , Robins Pei L. , Bonney Christian , Boateng Kingsley A. , Meyers Marc , Jasiuk Iwona 
Published: June 2023

AbstractThe equine hoof wall has a complex, hierarchical structure that can inspire designs of impact-resistant materials. In this study, we utilized micro-computed tomography (μ-CT) and serial block-face scanning electron microscopy (SBF-SEM) to image the microstructure and nanostructure of the hoof wall. We quantified the morphology of tubular medullary cavities by measuring equivalent diameter, surface area, volume, and sphericity. High-resolution μ-CT revealed that tubules are partially or fully filled with tissue near the exterior surface and become progressively empty towards the inner part of the hoof wall. Thin bridges were detected within the medullary cavity, starting in the middle section of the hoof wall and increasing in density and thickness towards the inner part. Porosity was measured using three-dimensional (3D) μ-CT, two-dimensional (2D) μ-CT, and a helium pycnometer, with the highest porosity obtained using the helium pycnometer (8.07%), followed by 3D (3.47%) and 2D (2.98%) μ-CT. SBF-SEM captured the 3D structure of the hoof wall at the nanoscale, showing that the tubule wall is not solid, but has nano-sized pores, which explains the higher porosity obtained using the helium pycnometer. The results of this investigation provide morphological information on the hoof wall for the future development of hoof-inspired materials and offer a novel perspective on how various measurement methods can influence the quantification of porosity.
The neural basis of resting-state fMRI functional connectivity in fronto-limbic circuits revealed by chemogenetic manipulation
Authors: Elorette Catherine , Fujimoto Atsushi , Stoll Frederic M. , Fujimoto Satoka H. , Fleysher Lazar , Bienkowska Niranjana , Russ Brian E. , Rudebeck Peter H. 
Published: June 2023

ABSTRACTMeasures of fMRI resting-state functional connectivity (rs-FC) are an essential tool for basic and clinical investigations of fronto-limbic circuits. Understanding the relationship between rs-FC and neural activity in these circuits is therefore vital. Here we introduced inhibitory designer receptors exclusively activated by designer drugs (DREADDs) into the macaque amygdala and activated them with a highly selective and potent DREADD agonist, deschloroclozapine. We evaluated the causal effect of activating the DREADD receptors on rs-FC and neural activity within circuits connecting amygdala and frontal cortex. Interestingly, activating the inhibitory DREADD increased rs-FC between amygdala and ventrolateral prefrontal cortex. Neurophysiological recordings revealed that the DREADD-induced increase in fMRI rs-FC was associated with increased local field potential coherency in the alpha band (6.5-14.5Hz) between amygdala and ventrolateral prefrontal cortex. Thus, our multi-disciplinary approach reveals the specific signature of neuronal activity that underlies rs-FC in fronto-limbic circuits.
Culture conditions greatly impact the levels of vesicular and extravesicular Ago2 and RNA in extracellular vesicle preparations
Authors: Jimenez Lizandra , Barman Bahnisikha , Jung Youn Jae , Cocozza Lauren , Krystofiak Evan , Saffold Cherie , Vickers Kasey C. , Wilson John T. , Dawson T. Renee , Weaver Alissa M. 
Published: June 2023

AbstractExtracellular vesicle (EV)-carried miRNAs can influence gene expression and functional phenotypes in recipient cells. Argonaute 2 (Ago2) is a key miRNA-binding protein that has been identified in EVs and could influence RNA silencing. However, Ago2 is in a non-vesicular form in serum and can be an EV contaminant. In addition, RNA-binding proteins (RBPs), including Ago2, and RNAs are often minor EV components whose sorting into EVs may be regulated by cell signaling state. To determine the conditions that influence detection of RBPs and RNAs in EVs, we evaluated the effect of growth factors, oncogene signaling, serum, and cell density on the vesicular and nonvesicular content of Ago2, other RBPs, and RNA in small EV (SEV) preparations. Media components affected both the intravesicular and extravesicular levels of RBPs and miRNAs in EVs, with serum contributing strongly to extravesicular miRNA contamination. Furthermore, isolation of EVs from hollow fiber bioreactors revealed complex preparations, with multiple EV-containing peaks and a large amount of extravesicular Ago2/RBPs. Finally, KRAS mutation impacts the detection of intra- and extra-vesicular Ago2. These data indicate that multiple cell culture conditions and cell states impact the presence of RBPs in EV preparations, some of which can be attributed to serum contamination.
Purinergic Preconditioning Induces Epigenomic and Transcriptomic Changes Resembling Epilepsy-associated Microglial States
Authors: Martins-Ferreira Ricardo , Calafell-Segura Josep , Chaves João , Ciudad Laura , Martins da Silva António , Pinho e Costa Paulo , Leal Bárbara , Ballestar Esteban 
Published: June 2023

ABSTRACTMicroglia, as the main immune effector cells in the central nervous system (CNS), play a crucial role in a diverse range of neuropathological conditions through their exacerbated activation. Microglial inflammatory responses can be influenced by prior exposures to noxious stimuli, such as increased levels of extracellular adenosine and ATP. These conditions are characteristic of brain insults like epileptic seizures and could potentially shape subsequent responses through epigenetic regulation. In this study, we investigated DNA methylation and expression changes in microglia-like cells differentiated from monocytes following ATP-mediated preconditioning. First, during differentiation, we demonstrate that microglia-like cells acquire standard microglial features, including whole transcriptomes and methylomes likein vivoprofiles. We show a predominant DNA demethylation in genomic sequences enriched in binding motifs of microglia lineage transcription factors like PU.1, consistent with the relevance of this factor inin vivomicroglia. TLR-mediated activation, after a first exposure to ATP, promotes exacerbated pro-inflammatory activation compared to cells not pre-exposed to ATP. These changes are accompanied by DNA methylation and transcriptional reprogramming associated with the acquisition of trained immunity and altered immune-related functions such as with antigen presentation, phagocytosis and cytokine signaling. Finally, the reprogramming associated with ATP-mediated preconditioning leads to profiles found in microglial subsets linked to epilepsy. Purine-driven microglia immune preconditioning drives epigenetic and transcriptional changes that could contribute to altered functions of microglia during seizure development and progression, particularly associated with neuroinflammation.
BrainProt(™) 3.0: Understanding Human Brain Diseases using comprehensively curated & Integrated OMICS datasets
Authors: Biswas Deeptarup , Shenoy Sanjyot Vinayak , Chauhan Aparna , Halder Ankit , Ghosh Biplab , Padhye Advait , Auromahima Shreeman , Yadav Deeksha , Sasmal Souvik , Dutta Sampurna , Kumari Neha , Bhavaskar Hiren , Mukherjee Ayan Prasad , Kumar Tunuguntla Rishi , Srivastava Sanjeeva 
Published: June 2023

ABSTRACTBrainProt 3.0 is an integrative and simplified omics-based knowledge base of the human brain and its associated diseases. The current version of BrainProt includes six domains, which provide simplified, robust, and comprehensive data visualization to understand the human brain and its diseases/disorders based on proteomics, transcriptomics, public data curation, and integration strategies. Firstly, the HBDA (Human Brain Disease Atlas), index and navigator of BrainProt provides a resource table for 56 brain diseases. Secondly, Brain Disease Marker Curator (BDMC) and Brain Disease Drug Finder (BDDF) include a total of 20,202 diseases associated genes, more than 1,30,000 Chemical Target interactions, and around 2,145 Clinical Trial Information for more than 50 Brain Diseases. Thirdly, Brain Disease Transcriptome Map (BDTM) and Brain Disease Proteome Map (BDPM) integrate multi-omics data for 11 and 6 alarming brain diseases respectively. Currently, these two domains feature an expressional profile of 52 datasets, information of 1,868 samples, 3,657 DEPs, and 6,256 DEGs. Lastly, BrainProt also modifies and integrates the proteome and phosphoproteome data of the Inter-hemispheric Brain Proteome Map (IBPM). Overall, BrainProt is the first knowledgebase that connects different omics level information of brain diseases and provides a powerful scoring-based ranking platform to select and identify brain disease-associated markers, along with exploration of clinical trials, and drugs/chemical compounds to accelerate the identification of new disease markers and novel therapeutic strategies. The objectives of BrainProt are to support and follow the footsteps of the HBPP (Human Brain Proteome Project) by integrating different datasets to unravel the complexity of Human Brain and its associated diseases.
Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities
Authors: Giordano Nils , Gaudin Marinna , Trottier Camille , Delage Erwan , Nef Charlotte , Bowler Chris , Chaffron Samuel 
Published: June 2023

AbstractMarine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integratedTaraOceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across large phylogenetic distances. Identified co-active communities included species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling revealed a higher potential for interaction within co-active communities and pointed towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach indicates genome streamlining and metabolic auxotrophies as central joint mechanisms shaping bacterioplankton community assembly in the surface global ocean.
Co-linear Chaining on Pangenome Graphs
Authors: Rajput Jyotshna , Chandra Ghanshyam , Jain Chirag 
Published: June 2023

AbstractPangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to these graphs with complex topology and cycles can be challenging. The seed-chain-extend based alignment algorithms use co-linear chaining as a standard technique to identify a good cluster of exact seed matches that can be combined to form an alignment. Recent works show how the co-linear chaining problem can be efficiently solved for acyclic pangenome graphs by exploiting their small width [Makinenet al., TALG’19] and how incorporating gap cost in the scoring function improves alignment accuracy [Chandra and Jain, RECOMB’23]. However, it remains open on how to effectively generalize these techniques for general pangenome graphs which contain cycles. Here we present the first practical formulation and an exact algorithm for co-linear chaining on cyclic pangenome graphs. We rigorously prove the correctness and computational complexity of the proposed algorithm. We evaluate the empirical performance of our algorithm by aligning simulated long reads from the human genome to a cyclic pangenome graph constructed from 95 publicly available haplotype-resolved human genome assemblies. While the existing heuristic-based algorithms are faster, the proposed algorithm provides a significant advantage in terms of accuracy.Implementationhttps://github.com/at-cg/PanAligner
TRPML1 activation ameliorates lysosomal phenotypes in CLN3 deficient retinal pigment epithelial cells
Authors: Wünkhaus D. , Tang R. , Nyame K. , Laqtom N. N. , Schweizer M. , Rosato A. Scotto , Krogsæter E. K. , Wollnik C. , Abu-Remaileh M. , Grimm C. , Hermey G. , Kuhn R. , Gruber-Schoffnegger D. , Markmann S. 
Published: June 2023

AbstractMutations in the lysosomal membrane protein CLN3 cause Juvenile Neuronal Ceroid Lipofuscinosis (JNCL). Activation of the lysosomal ion channel TRPML1 has previously been shown to be beneficial in several neurodegenerative disease models. Here, we tested whether TRPML1 activation rescues disease-associated phenotypes in CLN3-deficient retinal pigment epithelial (ARPE-19 CLN3-KO) cells. ARPE-19 CLN3-KO cells accumulate LAMP1 positive organelles and show lysosomal storage of mitochondrial ATPase subunit C (SubC), globotriaosylceramide (Gb3), and glycerophosphodiesters (GPDs), whereas lysosomal bis(monoacylglycero)phosphate (BMP/LBPA) lipid levels were significantly decreased. Activation of TRPML1 reduced lysosomal storage of Gb3 and SubC but failed to restore BMP levels in CLN3-KO cells. TRPML1-mediated decrease of storage was TFEB-independent, and we identified TRPML1-mediated enhanced lysosomal exocytosis as a likely mechanism for clearing storage including GPDs. Therefore, ARPE-19 CLN3-KO cells represent a human cell model for CLN3 disease showing many of the described core lysosomal deficits, some of which can be improved using TRPML1 agonists.
Targeting the conserved active site of splicing machines with specific and selective small molecule modulators
Authors: Silvestri Ilaria , Manigrasso Jacopo , Andreani Alessandro , Brindani Nicoletta , Vivo Marco De , Marcia Marco 
Published: June 2023

AbstractThe self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation studies, we demonstrate how these introns recognize small molecules through their conserved active site. These RNA-binding small molecules selectively inhibit the two steps of splicing by adopting distinctive poses at different stages of catalysis, and by preventing crucial active site conformational changes that are essential for splicing progression. Our data exemplify the enormous power of RNA binders to mechanistically probe vital cellular pathways. Most importantly, by proving that the evolutionarily-conserved RNA core of splicing machines can recognize small molecules specifically, our work puts solid bases for the rational design of splicing modulators not only against bacterial and organellar introns, but also against the human spliceosome, which is a validated drug target for the treatment of congenital diseases and cancers.
The Chicken Chorioallantoic Membrane as a Low-Cost, High-Throughput Model for Cancer Imaging
Authors: Smith Lydia M. , Greenwood Hannah E. , Tyrrell Will E. , Edwards Richard S. , Santis Vittorio de , Baark Friedrich , Firth George , Tanc Muhammet , Terry Samantha Y.A. , Herrmann Anne , Southworth Richard , Witney Timothy H. 
Published: June 2023

ABSTRACTPurposeMouse models are invaluable tools for radiotracer development and validation. They are, however, expensive, low throughput, and are constrained by animal welfare considerations. Here, we assessed the chicken chorioallantoic membrane (CAM) as an alternative to mice for preclinical cancer imaging studies.MethodsGrowth of NCI-H460 Fluc tumors on the CAM was optimized using a range of physical and chemical supports. Tumor-bearing eggs were imaged by dynamic18F-2-fluoro-2-deoxy-D-glucose (18F-FDG) or (4S)-4-(3-18F-fluoropropyl)-L-glutamate (18F-FSPG) PET/CT following intravenous injection, with mice bearing subcutaneous NCI-H460 Fluc xenografts imaged with18F-FDG for comparison. The dependence of the transporter system xc-onin ovo18F-FSPG tumor uptake was determined through treatment with imidazole ketone erastin. Additionally,18F-FSPG PET/CT was used to monitor treatment responsein ovo24 h following external beam radiotherapy.ResultsNCI-H460 Fluc cells grown in Matrigel formed vascularized tumors of reproducible size without compromising embryo viability. By designing a simple method for cannulation it was possible to perform dynamic PET imagingin ovo, producing high tumor-to-background signal for both18F-FDG and18F-FSPG.18F-FDG tumor uptake kinetics were similarin ovoandin vivo, with18F-FSPG providing an early marker of both treatment response and target inhibition in CAM-grown tumors.ConclusionsThe CAM provides a low-cost alternative to tumor xenograft mouse models which may broaden access to PET and SPECT imaging. Rapid tumor growth and high-quality PET images that can be obtained with this model suggest its potential use for early radiotracer screening, pharmacological studies, and monitoring response to therapy.
Separation-of-function mutants reveal the NF-κB-independent involvement of IκBα in the regulation of stem cell and oncogenic programs
Authors: Álvarez-Villanueva Daniel , Galán-Palma Luis , Bertran Joan , Floor Martin , Solé Laura , Lobo-Jarne Teresa , Maqueda María , Rajbhandari Rajani , Marruecos Laura , Villà-Freixa Jordi , Bredel Markus , Bigas Anna , Espinosa Lluís 
Published: June 2023

AbstractWe previously demonstrated that the NF-κB inhibitor IκBα binds the chromatin together with PRC2 to regulate a subset of developmental- and stem cell-related genes. This alternative function has been elusive in both physiological and disease conditions because of the predominant role of IκBα as a negative regulator of NF-κB.We here uniquely characterize specific residues of IκBα that allow the generation of separation-of-function (SOF) mutants that are defective for either NF-κB-related (SOFΔNF-κB) or chromatin-related (SOFΔH2A,H4) activities. Expression of IκBα SOFΔNF-κB, but not SOFΔH2A/H4, is sufficient to negatively regulate a specific stemness program in intestinal cells, thus rescuing the differentiation blockage imposed by IκBα deficiency. In contrast, full IκBα activity is required for regulating clonogenic/tumor-initiating activity of colorectal cancer cells.Our data indicate that SOF mutants represent an exclusive tool for studying IκBα functions in physiology and disease, and identified IκBα as a robust prognosis biomarker for human cancer.
A systematic approach identifies p53-DREAM target genes associated with blood or brain abnormalities
Authors: Rakotopare Jeanne , Lejour Vincent , Duval Carla , Eldawra Eliana , Escoffier Hugues , Toledo Franck 
Published: June 2023

Abstractp53 is mainly known as a tumor suppressor, but mouse models revealed that increased p53 activity may cause bone marrow failure, through mechanisms that likely include gene repression mediated by the p53-DREAM pathway. Here we designed a systematic approach to identify p53-DREAM targets whose repression might contribute to abnormal hematopoiesis. We used gene ontology to analyze transcriptomic changes associated with bone marrow cell differentiation and p53 activation, then ChIP-seq data to find promoters bound by the DREAM complex. We next created positional frequency matrices to identify evolutionary conserved sequence elements potentially bound by DREAM. The same approach was developed to find p53-DREAM targets associated with brain abnormalities, also observed in mice with increased p53 activity. Putative DREAM binding sites were found for 151 candidate p53-DREAM target genes, of which 106 are mutated in a blood or brain genetic disorder. Twenty-one DREAM binding sites were tested and found to impact on gene expression in luciferase reporter assays, notably regulating genes mutated in dyskeratosis congenita (Rtel1), Fanconi anemia (Fanca), Diamond-Blackfan anemia (Tsr2), primary microcephaly (Casc5,Ncaph,Wdr62) or pontocerebellar hypoplasia (Toe1). These results provide clues on the role of the p53-DREAM pathway in regulating hematopoiesis and brain development, with implications for tumorigenesis.Author SummaryThe capacity of p53 to activate the transcription of genes important for cell cycle arrest, apoptosis or cellular metabolism has been recognized for decades. By contrast, the potential importance of p53-dependent transcriptional repression emerged more recently. Although p53 frequently appears to repress genes indirectly via the DREAM repressor complex, only a few studies attempted to define p53-DREAM target gene repertoires, often by analyzing cell cycle regulation in fibroblasts. Here we aimed to gain a better appreciation of the clinical relevance of the p53-DREAM pathway by designing a systematic approach for the identification of p53-DREAM targets. Because mouse models with increased p53 activity suffer from bone marrow failure or brain hypoplasia, we relied on transcriptomic changes associated with bone marrow cell differentiation, blood- and brain-related gene ontology terms and RNAseq data from hematopoietic or neural progenitor cells to identify p53-DREAM targets, then created positional frequency matrices to find putative DREAM binding sites. Our study provides a resource of predicted DREAM binding sites for 151 genes associated with blood and/or brain abnormalities, many of which were not previously known to be DREAM targets. Furthermore, our analysis suggests that p53-DREAM alterations may contribute to phenotypic variations in glioblastoma cells.