bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive pharmacological survey across heterogeneous patient-derived GBM stem cell models
Authors: Elliott Richard J.R. , Nagle Peter , Furqan Muhammad , Dawson John C. , McCarthy Aoife , Munro Alison F , Drake Camilla , Morrison Gillian M , Marand Michael , Ebner Daniel , Pollard Steven M. , Brunton Valerie G , Frame Margaret C , Carragher Neil O. 
Published: December 2024

AbstractDespite substantial drug discovery investments, the lack of any significant therapeutic advancement in the treatment of glioblastoma (GBM) over the past two decades calls for more innovation in the identification of effective treatments. The inter-and intra-patient heterogeneity of GBM presents significant obstacles to effective clinical progression of novel treatments by contributing to tumour plasticity and rapid drug resistance that confounds contemporary target directed drug discovery strategies. Phenotypic drug screening is ideally suited to heterogeneous diseases, where targeting specific oncogenic drivers have been broadly ineffective. Our hypothesis is that a modern phenotypic led approach using disease relevant patient derived GBM stem cell systems will be the most productive approach to identifying new therapeutic targets, drug classes and future drug combinations that target the heterogeneity of GBM. In this study we incorporate a panel of patient derived GBM stem cell lines into an automated and unbiased ‘Cell Painting’ assay to quantify multiple GBM stem cell phenotypes. By screening several compound libraries at multiple concentrations across a panel of patient-derived GBM stem cells we provide the first comprehensive survey of distinct pharmacological classes and known druggable targets, including all clinically approved drug classes and oncology drug candidates upon multiple GBM stem cell phenotypes linked to cell proliferation, survival and differentiation. Our data set representing, 3866 compounds, 2.2million images and 64000 datapoints is the largest phenotypic screen carried out to date on a panel of patient-derived GBM stem cell models that we are aware off. We seek to identify agents and targets classes which engender potent activity across heterogenous GBM genotypes and phenotypes, in this study we further characterize two validated target classes, histone deacetylase inhibitors and cyclin dependent kinases that exert broad and potent effects on the phenotypic and transcriptomic profiles of GBM stem cells. Here we present all validated hit compounds and their target assignments for the GBM community to explore.
Towards Spectral Variation Analysis: A Data Quality Framework for Non-Targeted Methods
Authors: Nichani Kapil , Uhlig Steffen , San Martin Victor , Colson Bertrand , Hettwer Karina , Steinacker Ulrike , Kaspar Heike , Gowik Petra , Kemmlein Sabine 
Published: December 2024

AbstractNon-targeted methods (NTM) require robust methods for comparing spectral data for reliable classification and identification. Traditional approaches using match factors reduce complex spectral relationships to single values, limiting their utility in quality assurance. This study presents an evaluation of spectral comparison methodologies, contrasting classical Mahalanobis distance (MD) with neural network approaches, namely, neural classification distance (NCD). Using matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry data from bacterial isolates, we systematically assessed these methods across varying levels of spectral variability. The MD approach exhibited consistent performance under controlled conditions but showed limitations with increasing spectral complexity. In contrast, the NCD demonstrated adaptability across all scenarios, revealing its capability in handling complex spectral relationships. Through this exemplary example, we present the mathematical framework for quantifying spectral variations and establish criteria for method selection in different analytical scenarios. This work provides a foundation for proposing data quality metrics in NTMs and offers practical implementations for routine quality assurance. The methodology developed here extends beyond mass spectrometry applications and contributes to the broader field of analytical quality control in complex spectral analysis.
Loss of chromogranin A and catestatin affect pancreatic islet homeostasis, endocrine function, and neurotransmitters
Authors: Muntjewerff Elke M. , Epremidze Dali , Nezhyva Mariya , Bootsma Marleen , Mannaa Atef , Ikebuchi Hiromi , Nilsson Anna , Andrén Per E. , Jansson Erik , Mahata Sushil K. , Christoffersson Gustaf 
Published: December 2024

AbstractThe pro-hormone chromogranin A (CgA) and its cleavage product, the neuropeptide catestatin (CST) are linked to various cardiovascular and autoimmune diseases (T1D, IBD, RA) as biomarkers for disease severity. In these diseases, CgA and CST seem to affect inflammation, nerve communication, insulin resistance and hypertension. Since we found various CgA cleavage products leading towards CST in the pancreatic islet, we investigated how CgA and CST may modulate the pancreatic islet microenvironment and function. We show that CgA-KO and CST-KO mice have fewer insulin producing cells per islet and altered physiological islet function. To map the neurotransmitter microenvironment in the pancreatic islet and exocrine tissue we used spatial mass spectrometry that allowed us to identify neurotransmitter levels in and outside of the islets. Using this method, we show that endocrine cell homeostasis and insulin regulating pathways are disturbed in the pancreatic islets upon CgA or CST deletion. Thus, absence of CgA or CST in mice affects the endocrine composition and microenvironment of the pancreatic islet. Our findings contribute to understanding the role of CgA and CST in the pancreas with possible implications for the pathology of both type 1 and type 2 diabetes.
Passage through micro-sprayer increases functional activity – implications for activity assays in time-resolved cryo-EM
Authors: Garg Priyanka , Feng Xiangsong , De Swastik , Frank Joachim 
Published: December 2024

AbstractThis study examines the validity of an assay that is used to report on the retainment of functional competence by ribosomes as they pass a micro-sprayer. We find a reproducibleincrease, rather than the expecteddecreasein GFP production as monitored by fluorescence, which suggests heterogeneity or partial aggregation of ribosomes in solution. An even larger increase in functional activity is observed when sonication is used, pointing to mechanical agitation as the decisive factor in both scenarios. The results have a bearing on the design and interpretation of validation experiments in time-resolved cryo-EM based on microfluidic chips.
Morphological map of under- and over-expression of genes in human cells
Authors: Chandrasekaran Srinivas Niranj , Alix Eric , Arevalo John , Borowa Adriana , Byrne Patrick J. , Charles William G. , Chen Zitong S. , Cimini Beth A. , Deng Boxiong , Doench John G. , Ewald Jessica D. , Fritchman Briana , Fuller Colin J. , Gaetz Jedidiah , Goodale Amy , Haghighi Marzieh , Han Yu , Hanifehlou Zahra , Hennig Holger , Hernandez Desiree , Jacob Christina B. , James Tim , Jetka Tomasz , Kalinin Alexandr A. , Komalo Ben , Kost-Alimova Maria , Krawiec Tomasz , Marion Brittany A. , Martin Glynn , McCarthy Nicola Jane , Miller Lisa , Monsees Arne , Moshkov Nikita , Muñoz Alán F. , Ogier Arnaud , Otrocka Magdalena , Rataj Krzysztof , Root David E. , Rubbo Francesco , Scrace Simon , Selinger Douglas W. , Senft Rebecca A. , Sommer Peter , Thibaudeau Amandine , Trisorus Sarah , Veettil Rahul Valiya , Van Trump William J. , Wang Sui , Warchoł Michał , Weisbart Erin , Weiss Amélie , Wiest Michael , Zaremba Agata , Zinovyev Andrei , Singh Shantanu , Carpenter Anne E. 
Published: December 2024

AbstractCell Painting images offer valuable insights into a cell’s state and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUMP (Joint Undertaking in Morphological Profiling) Cell Painting Consortium perturbed roughly 75% of the protein-coding genome in human U-2 OS cells, generating a rich resource of single-cell images and extracted features. These profiles capture the phenotypic impacts of perturbing 15,243 human genes, including overexpressing 12,609 genes (using open reading frames, ORFs) and knocking out 7,975 genes (using CRISPR-Cas9). We mitigated technical artifacts by rigorously evaluating data processing options and validated the dataset’s robustness and biological relevance. Analysis of phenotypic profiles revealed novel gene clusters and functional relationships, including those associated with mitochondrial function, cancer, and neural processes. The JUMP Cell Painting genetic dataset is a valuable resource for exploring gene relationships and uncovering novel functions.
Structural polymorphism ofα-synuclein fibrils alters pathway of Hsc70 mediated disaggregation
Authors: Jäger Svenja , Tittelmeier Jessica , Dang Thi Lieu , Bellande Tracy , Redeker Virginie , Buell Alexander K. , Melki Ronald , Nussbaum-Krammer Carmen , Bukau Bernd , Wentink Anne S. 
Published: December 2024

AbstractThe pathological aggregation ofα-synuclein into amyloid fibrils is a hallmark of synucleinopathies including Parkinson’s disease. Despite this commonality, synucleinopathies display divergent disease phenotypes that have been attributed to disease specific three-dimensional structures ofα-synuclein fibrils, each with a unique toxic gain-of-function profile. The Hsc70 chaperone is remarkable in its ability to disassemble pre-existing amyloid fibrils of different proteins in an ATP and co-chaperone dependent manner. We find however, using six well-defined conformational polymorphs ofα-synuclein fibrils, that the activity of the Hsc70 disaggregase machinery is sensitive to differences in the amyloid conformation, confirming that fibril polymorphism directly affects interactions with the proteostasis network. Amyloid conformation influences not only how efficiently fibrils are cleared by the Hsc70 machinery but also the preferred pathway of disaggregation. We further show that,in vitro, the active processing of fibrils by the Hsc70 machinery inadvertently produces seeding competent species that further promote protein aggregation. Amyloid conformation thus is an important feature that can tilt the balance between beneficial or detrimental protein quality control activities in the context of disease.
Unveiling Cell Wall Structure and Echinocandin Response inCandida aurisandCandida albicansvia Solid-State NMR
Authors: Widanage Malitha C. Dickwella , Singh Kalpana , Li Jizhou , Yarava Jayasubba Reddy , Scott Faith J. , Xu Yifan , Gow Neil A.R. , Mentink-Vigier Frederic , Wang Ping , Lamoth Frederic , Wang Tuo 
Published: December 2024

ABSTRACTInvasive candidiasis affects 1.6 million people annually, implicating high mortality and morbidity in immunocompromised and hospitalized patients. Echinocandins, inhibitors of β-1,3-glucan synthesis, are used as a first-line treatment; however, their efficacy is increasingly compromised by resistance and tolerance. To understand how echinocandins remodelCandidacell wall structures, thereby reducing drug effectiveness, this study compares the effects of echinocandin exposure on the cell walls of the prevalent pathogenCandida albicansand the recently emerged multidrug-resistant superbugCandida auris. High-resolution solid-state NMR analysis revealed a conserved cell wall structure in both species, with a rigid inner layer composed of closely associated chitin microfibrils and β-1,3-glucans, supported by a flexible network of β-1,6-glucans and additional β-1,3-glucans. Despite the presence ofN-mannan fibrils in the outer layer, mannan components are mobile and rely on α-1,2-linked mannoside sidechains to maintain contact with chitin and β-1,3-glucans. Caspofungin treatment rigidifies certain mannan sidechains and β-1, 6-glucans to reinforce the cell wall in response to the depletion of most β-1,3-glucans. While caspofungin treatment reduced water permeability in both species, onlyC. albicansresponded by inducing cell wall thickening and changes in chitin and β-1,3-glucan dynamics. Furthermore, the deletion ofKRE6genes encoding β-1,6-glucan synthase reduced the echinocandin susceptibility ofC. auris,and the impaired β-1,6-glucan biosynthesis were offset by compensatory upregulation of this wall component due to caspofungin treatment. The profound alterations induced by caspofungin inCandidacell wall architecture suggest that cell wall structural contribute substantially to drug resistance and tolerance.
Shifts in Coral Reef Holobiont Communities in the High-CO2Marine Environment of Iōtorishima Island
Authors: Huerlimann Roger , Wee Hin Boo , Alves dos Santos Maria , Kise Hiroki , Mizuyama Masaru , Dudoit ‘Ale’alani , Jamodiong Emmeline , Satoh Nagi , Soong Giun Yee , Kurihara Haruko , Toonen Robert J , Husnik Filip , Iguchi Akira , Ravasi Timothy , Reimer James Davis 
Published: December 2024

AbstractOcean acidification (OA), driven by rising atmospheric CO2, presents a serious threat to marine biodiversity, especially within coral reef ecosystems. Natural analogue sites, such as the high-pCO2 seep at Iōtorishima Island in Japan, offer insights into future conditions. This study investigated the holobiont communities of Symbiodiniaceae and bacteria in the zoantharianPalythoa tuberculosaat Iōtorishima and compared them to specimens from control sites in Okinawa and Hawaiʻi.Using amplicon sequencing of the dinoflagellate internal transcribed spacer 2 (ITS2) region of ribosomal DNA and microbial 16S rRNA gene, we detected significant shifts in both Symbiodiniaceae and bacterial communities under high-pCO2conditions at Iōtorishima. Specifically,P. tuberculosaat the seep site had reduced Symbiodiniaceae diversity, predominatly featuringCladocopiumC1 and C3 types. Additionally, its bacterial communities showed lower richness with distinct taxonomic profiles, including increased levels ofMollicutesandVibriospp.These results highlight the potentially adverse effects of OA on hexacoral holobionts and emphasize the need for detailed, high-resolution studies across various holobiont species and geographic locations. The shifts observed specifically in Symbiodiniaceae and bacterial communities at the Iōtorishima Seep suggest that holobionts may exhibit plasticity in response to environmental stress, which has implications for resilience and adaptation of zoantharians and other reef organisms amid climate change. This research provides crucial baseline data for predicting future coral reef compositions in an OA-affected world.
Temporal Configuration as a New Feature of Sound: Psychological and Neurophysiological Evidence, Cross-species Consistency and Underlying Neuronal Mechanisms
Authors: Zhai Yuying , Du Xinyu , Song Peirun , Xu Haoxuan , Ye Hangting , Bao Xuehui , mehmood Ishrat , Tanigawa Hisashi , Niu Wanqiu , Tu Zhiyi , Chen Pei , Zhang Tingting , Zhang Lingling , Zhao Xuan , Yu Xiongjie 
Published: December 2024

AbstractTemporal integration is crucial for auditory perception, yet the mechanisms underlying its role are not fully elucidated. This study examines the perceptual discrimination of click trains with varied temporal configurations to determine if they can be perceived as distinct auditory objects, potentially introducing a novel dimension to sound perception. In humans, psychological experiments using a delayed match-to-sample task revealed that participants could distinctly discriminate between click trains with different temporal configurations, suggesting that temporal configuration significantly influences auditory perception. This was supported by electroencephalogram (EEG) recordings showing robust mismatch negativity (MMN) signals, indicating that the auditory system differentiates standard from deviant sounds based on their temporal characteristics. Parallel electrocorticography (ECoG) studies in rats demonstrated similar discriminatory abilities, suggesting a cross-species consistency. Neuronal recordings showed pronounced stimulus-specific adaptation (SSA) in the primary auditory cortex (A1) but minimal SSA in lower auditory areas such as the inferior colliculus (IC) and medial geniculate body (MGB), indicating that A1 uniquely integrates temporal features and discriminates complex temporal patterns. This research advances our understanding of how temporal configurations are processed in the auditory system and suggests a new feature of sound perception.
PHLPP2 is a pseudophosphatase that lost activity in the metazoan ancestor
Authors: Husremović Tarik , Siess Katharina M. , Antonioli Sumire , Meier Vanessa , Piëch Lucas , Grishkovskaya Irina , Kircheva Nikoleta , Angelova Silvia E. , Brandstätter Andreas , Veis Jiri , Miočić-Stošić Fran , Anrather Dorothea , Hartl Markus , Truebestein Linda , Žagrović Bojan , Hann Stephan , Bock Christoph , Ogris Egon , Dudev Todor , Irwin Nicholas A.T. , Haselbach David , Leonard Thomas A. 
Published: December 2024

AbstractThe phosphoinositide 3-kinase (PI3K) pathway is a major regulator of cell and organismal growth. Consequently, hyperactivation of PI3K and its downstream effector kinase, Akt, is observed in many human cancers. PH domain leucine-rich repeat-containing protein phosphatases (PHLPP), two paralogous members of the metal-dependent protein phosphatase family, have been reported as negative regulators of Akt signaling and, therefore, tumor suppressors. However, the stoichiometry and identity of the bound metal ion(s), mechanism of action, and enzymatic specificity of these proteins are not known. Seeking to fill these gaps in our understanding of PHLPP biology, we unexpectedly discovered that PHLPP2 has no catalytic activity against the regulatory phosphorylation sites of Akt, nor the generic substratepara-nitrophenylphosphate. Instead, we found that PHLPP2 is a pseudophosphatase with a single zinc ion bound in its catalytic center. Furthermore, we found that current cancer genomics data do not support the proposed role of PHLPP1 or PHLPP2 as tumor suppressors. Phylogenetic analyses revealed an ancestral phosphatase that arose more than 1000 Mya, but that lost activity at the base of the metazoan lineage. In summary, our results provide a molecular explanation for the inconclusive results that have hampered research on PHLPP and argue for a new focus on non-catalytic roles of PHLPP1 and PHLPP2.Significance StatementPHLPP1 and PHLPP2 have previously been reported as protein phosphatases that specifically inactivate Akt, a pro-growth and survival kinase hyperactivated in many human cancers. Unexpectedly, we found that purified PHLPP2 has no detectable enzymatic activity in vitro, an observation which can be rationalized by its unusual active site, which has diverged significantly from that of canonical metal-dependent phosphatases. Furthermore, we show that cancer genomics do not support a role for either PHLPP1 or PHLPP2 in cancer. Our findings argue for the exploration of alternative hypotheses regarding the role of PHLPP in Akt signaling and cancer, with a focus on its non-catalytic functions.
Histology-Guided Single-Cell Mass Spectrometry Imaging using Integrated Bright-field and Fluorescence Microscopy
Authors: Potthoff Alexander , Niehaus Marcel , Bessler Sebastian , Schwenzfeier Jan , Hoffmann Emily , Soehnlein Oliver , Höhndorf Jens , Dreisewerd Klaus , Soltwisch Jens 
Published: December 2024

AbstractThe rapidly evolving field of spatial biology revolves around the analysis of cells in their native microenvironment. This analysis can include morphological features, the presence of specific antigens or gene expression. To add another layer of information, recent methodological advances in matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) now enable the untargeted analysis of lipids and metabolites at subcellular resolution. The integration of MALDI-MSI at the single-cell level with established optical modalities, however, relies on an accurate yet intricate co-registration. Here, we describe the integration of bright-field and fluorescence microscopy into a prototype ion source of a state-of-the art MALDI-MSI instrument to obtain lipid and fluorescence microscopy-derived information from the same specimen, hence with intrinsic spatial correlation. We demonstrate the potential of the combined mass spectrometric and optical single-cell analysis on three examples. This includes the visualization of intracellular lipid distributions in macrophages, the introduction of pre-MALDI immunofluorescence staining on the example of murine cerebellum, and the heterogeneity of lipid profiles of tumor infiltrating neutrophils correlated to their individual microenvironments. Overall, the achieved tight correlation of single-cell lipid profiles with morphologic features and protein expression patterns constitutes a powerful resource for cell biology.
A female-specific RdDM-associated element guides de novo DNA methylation during rice gametophyte development
Authors: Kim Taehoon , Resende Marcio F. R. , Zhao Meixia , Begcy Kevin 
Published: December 2024

AbstractDNA methylation is crucial for regulating gene expression and silencing transposons. While the spatiotemporal specificity of DNA methylation controls organ formation and development, the molecular mechanisms underlying locus- or tissue-specific DNA methylation remain unclear. Previously, locus- or tissue-specific DNA methylation was thought to depend solely on the recognition of histone methylations. Here we show that high expression of 24-nucleotide small interfering RNAs (24-nt siRNAs) leads to incremental CHH methylation at specific loci via the RNA-directed DNA methylation (RdDM) pathway during female gametophyte development in rice. We also identify a DNA motif, the Female-specific RdDM-associated Element (FRE), which guides methylation to these loci. Furthermore, we show that the female-preferentially expressed protein OsCLSY3 directly interacts with FRE to regulate CHH methylation specifically in female reproductive tissues. These findings uncover a novel molecular mechanism necessary for tissue- and locus-specific de novo DNA methylation that might be conserved across diverse organisms including animals.
Facilitating Gene Editing in Human Lymphoma Cells Using Murine Ecotropic γ-Retroviruses
Authors: Kumar Manish , Gentner-Göbel Eva , Maity Palash Chandra 
Published: December 2024

AbstractGenetic modifications using CRISPR-Cas9 have revolutionized cancer research and other pre-clinical studies. Exceptionally, these efficient tools are inadequate in a few disease models and cell lines due to the aberrant differentiation states and the accumulation of excessive somatic mutations that compromise the robustness of viral gene delivery and stable transduction. A couple of B lymphoma cell lines fall into this category where lentiviral transfection becomes inefficient and exhibits variable efficiency. Additionally, lentiviral delivery requires high biosafety levels. To address this challenge, we have developed a two-step strategy that supports CRISPR-Cas9 through lentivirus and murine ecotropic γ-retrovirus. By engineering B lymphoma cell lines to express Cas9 and mCat-1, a specific receptor for ecotropic retroviruses, we enable efficient and safe gene editing through ecotropic γ-retrovirus. We demonstrate the efficacy of this method by generating IgM-deficient B lymphoma cell lines. This innovative approach simplifies protocols, enhances accessibility, and paves the way for standardized gene manipulation of B cell lymphoma models for molecular cell biology research.