bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preclinical Results: Canine Phase I Safety Study of CM-101, a Tumor Capillary Specific Streptococcal Polysaccharide Toxin, for application in Spontaneous Canine Cancer
Authors: Stout Rhett W , Boudreaux Bonnie , Inegulescu I Horia , Laine Roger A 
Published: March 2024

AbstractBackgroundThe study purpose was to evaluate canine safety of CM101, a polysaccharide Group BStreptococcus agalactiaetumor hemorrhagic toxin therapeutic.HypothesisCM101 specifically targets tumor vasculature as published in a human Phase 1 safety study that showed a wide therapeutic window. The hypothesis is that dogs should display a similar safety profile with low side-effects for CM101 canine cancer therapeutics.AnimalsConsidering the previous human safety trial, and in the interest of conserving purpose-bred dogs, on advice of USDA staff, we only used two healthy males, ∼20 months old.MethodsUSDA advice was to administer 10x the unit dose of 7.5µg/kg to 2 dogs and if no side effects, proceed to a pilot phase II. Given the dose was 10X the effective unit dose in humans, a further dose escalation was not considered necessary. Dogs were given 10 units (75 µg/kg) CM101 in normal saline over 22 minutes intravenously. Blood and Urine were collected before infusion, intervals post infusion, and 2 weeks after. Under anesthesia through recovery, rectal temperature, heart rate and indwelling arterial blood pressure vital signs were monitored electronically. Clinical observations recorded through two weeks after infusion.ResultsTotal WBC (white blood cell) counts dropped below normal range two hours post-infusion, after 6-11 hours rising above the normal range, returning to baseline at 52 hours post-infusion. Creatinine kinase was elevated two hours post infusion returning to baseline in 6-72 hours. Urinalysis remained within normal limits.Conclusions and clinical importanceNo adverse effects were observed when healthy dogs were given 10 units CM101. These finding suggest a wide therapeutic window for investigation in canine cancer.
Differential expression and co-expression reveal cell types relevant to rare disease phenotypes
Authors: Alías-Segura Sergio , Pazos Florencio , Chagoyen Monica 
Published: March 2024

AbstractDisease phenotypes, serving as valuable descriptors for delineating the spectrum of human pathologies, play a critical role in understanding disease mechanisms. Integration of these phenotypes with single-cell RNA sequencing (scRNA-seq) data facilitates the elucidation of potential associations between phenotypes and specific cell types underlying them, which sheds light on the underlying physiological processes related to these phenotypes. In this study, we utilized scRNA-seq data to infer potential associations between rare disease phenotypes and cell types. Differential expression and co-expression analyses of genes linked to abnormal phenotypes were employed as metrics to identify the involved cell types. Comparative assessments were made against existing phenotype-cell type associations documented in the literature. Our findings underscore the utility of differential expression and co-expression analyses in identifying significant relationships. Moreover, co-expression analysis unveils cell types potentially linked to abnormal phenotypes not extensively characterized in prior studies.Key points-Cell types underling rare disease phenotypes remain largely unknown-Single-cell RNA-seq data from healthy tissues can be analyzed to reveal these cell types-We employed differential expression and co-expression analysis to identify cell types associated with rare disease phenotypes-We validated our results with known relations described in the literature
Conditional c-MYC activation in catecholaminergic cells drives distinct neuroendocrine tumors: neuroblastoma vs somatostatinoma
Authors: Wang Tingting , Liu Lingling , Fang Jie , Jin Hongjian , Natarajan Sivaraman , Sheppard Heather , Lu Meifen , Turner Gregory , Confer Thomas , Johnson Melissa , Steinberg Jeffrey , Ha Larry , Yadak Nour , Jain Richa , Picketts David J. , Ma Xiaotu , Murphy Andrew , Davidoff Andrew M. , Glazer Evan S. , Easton John , Chen Xiang , Wang Ruoning , Yang Jun 
Published: March 2024

AbstractThe MYC proto-oncogenes (c-MYC,MYCN,MYCL) are among the most deregulated oncogenic drivers in human malignancies including high-risk neuroblastoma, 50% of which areMYCN-amplified. Genetically engineered mouse models (GEMMs) based on theMYCNtransgene have greatly expanded the understanding of neuroblastoma biology and are powerful tools for testing new therapies. However, a lack of c-MYC–driven GEMMs has hampered the ability to better understand mechanisms of neuroblastoma oncogenesis and therapy development given that c-MYC is also an important driver of many high-risk neuroblastomas. In this study, we report two transgenic murine neuroendocrine models driven by conditional c-MYC induction in tyrosine hydroxylase (Th) and dopamine β-hydroxylase (Dbh)-expressing cells. c-MYC induction in Th-expressing cells leads to a preponderance of Pdx1+somatostatinomas, a type of pancreatic neuroendocrine tumor (PNET), resembling human somatostatinoma with highly expressed gene signatures of δ cells and potassium channels. In contrast, c-MYC induction in Dbh-expressing cells leads to onset of neuroblastomas, showing a better transforming capacity than MYCN in a comparable C57BL/6 genetic background. The c-MYC murine neuroblastoma tumors recapitulate the pathologic and genetic features of human neuroblastoma, express GD2, and respond to anti-GD2 immunotherapy. This model also responds to DFMO, an FDA-approved inhibitor targeting ODC1, which is a known MYC transcriptional target. Thus, establishing c-MYC–overexpressing GEMMs resulted in different but related tumor types depending on the targeted cell and provide useful tools for testing immunotherapies and targeted therapies for these diseases.
DNA replication initiation drives focal mutagenesis and rearrangements in human cancers
Authors: Murat Pierre , Guilbaud Guillaume , Sale Julian E. 
Published: March 2024

AbstractThe rate and pattern of mutagenesis in cancer genomes is significantly influenced by DNA accessibility and active biological processes. Here we show that efficient sites of replication initiation drive and modulate specific mutational processes in cancer. Sites of replication initiation impede nucleotide excision repair in melanoma and are off-targets for activation-induced deaminase (AICDA) activity in lymphomas. Using ductal pancreatic adenocarcinoma as a cancer model, we demonstrate that the initiation of DNA synthesis is error-prone at G-quadruplex-forming sequences in tumours displaying markers of replication stress, resulting in a previously recognised but uncharacterised mutational signature. Finally, we demonstrate that replication origins serve as hotspots for genomic rearrangements, including structural and copy number variations. These findings reveal replication origins as functional regulators of tumour biology and demonstrate that replication initiation both passively and actively drives focal mutagenesis in cancer genomes.
PARP14 inhibits the inflammatory response of macrophages through the NF-κB pathway
Authors: Guo Xuefei , Zhao Yang 
Published: March 2024

AbstractThe poly-ADP-ribose polymerase (PARP) superfamily consists of 17 members, which regulate many biological processes in physiological or pathological conditions, such as DNA damage repair, anti-viral responses, and development of adaptive immune cells. Among them, PARP14 is the biggest member, containing two RNA recognition motifs at the N-terminal, three macro-domains, one WWE domain, and one PARP domain at the C-terminal, which was reported to regulate IL4/STAT6 signaling in adaptive immune cells. However, whether PARP14 participates in regulating host inflammatory response remains unclear. In a previous study, we observed that virus infection and LPS treatment induced the transcription ofParp14. By comparing the primary macrophages derived fromParp14KO and WT mice, we found that some inflammatory cytokines were significantly induced in KO macrophages. Still, the expression ofIfnb1had no significant difference compared to the WT macrophages. RNA-seq analysis showed that the KO group had a more robust inflammatory response but a weaker innate immune response upon stimulation. We validated these results by performing a knockdown ofParp14in RAW 264.7 cells. Moreover, the survival time of the KO mice was much shorter than that of the WT group upon LPS injection. Transcription factor enrichment analysis indicated that nuclear factor-kappaB1 (NF-κB1) may be the main reason for increasing the production of these inflammatory cytokines. As expected, the up-regulation was deleted upon the treatment of the inhibitor of NF-κB, JSH23. These data imply that PARP14 regulates inflammatory responses through the NF-κB pathway.
The pivotal role of Drgx in survival, wiring and identity of T4/T5 neurons
Authors: Gizler Laura , Schneider Katharina , Steigleder Sarah , Benmaamar Simon , Schneuwly Stephan , Rass Mathias 
Published: March 2024

AbstractThe development ofDrosophila melanogaster’sT4/T5 motion-sensing neurons has been extensively studied. Despite identifying many genes, important developmental steps remain unknown. This study investigates the Paired-like homeobox transcription factor Dorsal root ganglia homeobox (Drgx) in T4/T5 neuron development.Drgxexpression initiates in T4/T5 neuroblasts and persists in mature neurons. Knockdowns using T4/T5-specific drivers yield distinct phenotypes in the optic lobe, including dendrite mistargeting and reduced lobular plate size due to apoptosis in early knockdowns. Late knockdowns exhibit only extensive mistargeting. Therefore, Drgx plays a dual role, initially inhibiting apoptosis and later on establishing T4/T5 neuron identity and circuit formation. Targeted DamID (TaDa) and RNA-sequencing (RNA-seq) identify Drgx target genes involved in apoptosis and neuron projection development. Therefore, Drgx orchestrates vital stages in T4/T5 neuron development, influencing survival, identity, and circuitry and connects to the previously identified transcription factorSox102Fas a target of Drgx.Summary statementThe Paired-like homeobox transcription factor Drgx is essential for the correct establishment of the identity of a specific type of motion vision neurons inDrosophila.
Development of MHC Class I Blocking Peptides to Target Metabolic Dysfunction-Associated Steatohepatitis CD8+T Cell Activation
Authors: Adams Victoria , Sarma Sudeep , Hall Carol K. , Kennedy Arion 
Published: March 2024

ABSTRACTMHC class I molecules play a crucial role in the immune system by presenting peptides derived from intracellular proteins to cytotoxic T lymphocytes (CTLs). This process is essential for immune surveillance and eliminating infected or malignant cells. In some diseases, the immune system fails to recognize and eliminate abnormal cells, leading to disease progression. Under conditions of metabolic dysfunction-associated steatohepatitis (MASH), subsets of CD8+T cells have been identified as pathogenic, leading to inflammation and fibrosis. Therefore, explicitly targeting factors responsible for T cell activation may be necessary to prevent the onset of MASH and future complications such as cirrhosis or hepatocellular carcinoma. We have identified a specific MHC class I antigen that activates hepatic and splenic CD8+T cells isolated from MASH mice. To specifically target the antigen, we developed two MHC H2-Kbblocking peptides, MHCP3 and MHCP5, that competitively inhibit the Ncf2 peptide from binding to H2-Kband reduce activation and proliferation of CD8+T cells. By inhibiting the recognition of specific antigens, these blocking peptides may prevent the activation of CD8+T cells and progression of MASH.
A multi-modal image fusion workflow incorporating MALDI imaging mass spectrometry and microscopy for the study of small pharmaceutical compounds
Authors: Liang Zhongling , Guo Yingchan , Sharma Abhisheak , McCurdy Christopher R. , Prentice Boone M. 
Published: March 2024

ABSTRACTMulti-modal imaging analyses of dosed tissue samples can provide more comprehensive insight into the effects of a therapeutically active compound on a target tissue compared to single-modal imaging. For example, simultaneous spatial mapping of pharmaceutical compounds and endogenous macromolecule receptors is difficult to achieve in a single imaging experiment. Herein, we present a multi-modal workflow combining imaging mass spectrometry with immunohistochemistry (IHC) fluorescence imaging and brightfield microscopy imaging. Imaging mass spectrometry enables direct mapping of pharmaceutical compounds and metabolites, IHC fluorescence imaging can visualize large proteins, and brightfield microscopy imaging provides tissue morphology information. Single-cell resolution images are generally difficult to acquire using imaging mass spectrometry, but are readily acquired with IHC fluorescence and brightfield microscopy imaging. Spatial sharpening of mass spectrometry images would thus allow for higher fidelity co-registration with higher resolution microscopy images. Imaging mass spectrometry spatial resolution can be predicted to a finer value via a computational image fusion workflow, which models the relationship between the intensity values in the mass spectrometry image and the features of a high spatial resolution microscopy image. As a proof of concept, our multi-modal workflow was applied to brain tissue extracted from a Sprague Dawley rat dosed with a kratom alkaloid, corynantheidine. Four candidate mathematical models including linear regression, partial least squares regression (PLS), random forest regression, and two-dimensional convolutional neural network (2-D CNN), were tested. The random forest and 2-D CNN models most accurately predicted the intensity values at each pixel as well as the overall patterns of the mass spectrometry images, while also providing the best spatial resolution enhancements. Herein, image fusion enabled predicted mass spectrometry images of corynantheidine, GABA, and glutamine to approximately 2.5 μm spatial resolutions, a significant improvement compared to the original images acquired at 25 μm spatial resolution. The predicted mass spectrometry images were then co-registered with an H&E image and IHC fluorescence image of the μ- opioid receptor to assess co-localization of corynantheidine with brain cells. Our study also provides insight into the different evaluation parameters to consider when utilizing image fusion for biological applications.
SuperResNET GUI: model-free single molecule network analysis software achieves molecular resolution of Nup96
Authors: Li Y. Lydia , Khater Ismail M. , Hallgrimson Christian , Cardoen Ben , Wong Timothy H. , Hamarneh Ghassan , Nabi Ivan R. 
Published: March 2024

ABSTRACTSuperResNET is an integrated machine learning-based analysis software for visualizing and quantifying 3D point cloud data acquired by single molecule localization microscopy (SMLM). The computational modules of SuperResNET include correction for multiple blinking of a single fluorophore, denoising, segmentation (clustering), and feature extraction, which are then used for cluster group identification, modularity analysis, blob retrieval and visualization in 2D and 3D. Using publicly available dSTORM data, we apply a graphical user interface (GUI) version of SuperResNET to nucleoporin Nup96 structures, that present a highly organized octagon structure comprised of eight corners. SuperResNET GUI effectively segments nuclear pores and Nup96 corners based on differential proximity threshold analysis. SuperResNET GUI quantitatively analyzes features from segmented nuclear pore structures, including complete structures with 8-fold symmetry, and from segmented corners. SuperResNET GUI modularity analysis of segmented corners distinguishes two modules at 11.1 nm distance, corresponding to two individual Nup96 molecules. SuperResNET GUI is therefore a model-free tool that can reconstruct network architecture and molecular distribution of subcellular structures without the bias of a specified prior model, attaining molecular resolution from dSTORM data. SuperResNET GUI provides flexibility to report on structural diversity in situ within the cell without model-fitting, providing opportunities for biological discovery.
Molecular signatures and associated regulators of the pea leaf response to sulfur deficiency and water deficit as revealed by multi-omics analyses
Authors: Bonnot Titouan , Henriet Charlotte , Aimé Delphine , Kreplak Jonathan , Térézol Morgane , Balliau Thierry , Ourry Alain , Zivy Michel , Vernoud Vanessa , Gallardo Karine 
Published: March 2024

AbstractSulfur availability in soils affects both yield and seed quality in major crops, and the plant capacity to tolerate environmental constraints. Under stress combination, plants often show specific responses at the molecular level. To dissect the molecular responses to sulfur deficiency in interaction or not with water deficit, a multi-omics approach was used focusing on the leaves of pea (Pisum sativum), at several days during the early reproductive phase. Using ionomics, transcriptomics, proteomics and gene network analyses, we identified a module of genes strongly driven by sulfur availability. This includes known and putative new players of plant responses to sulfur-deprived conditions. Conserved profiles between proteins and mRNAs were specifically observed within this module, suggesting transcriptional regulation. While moderate water deficit had little impact when occurring alone, it thoroughly perturbed plant growth and the leaf transcriptome and proteome when combined with sulfur deficiency. Under this stress combination, molecular responses were amplified, notably at the transcriptome level, in a time-specific manner. Genes with specific or greater responses under this condition were identified, and transcriptional regulators of the highlighted genes and pathways were predicted, which may represent interesting targets to develop crops tolerant to multi-stress conditions.
SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery
Authors: Kremling Viviane , Falke Sven , Fernández-García Yaiza , Ehrt Christiane , Kiene Antonia , Klopprogge Bjarne , Scheer Emilie , Barthels Fabian , Middendorf Philipp , Kühn Sebastian , Günther Stephan , Rarey Matthias , Chapman Henry N. , Oberthür Dominik , Sprenger Janina 
Published: March 2024

AbstractNon-structural protein 10 (nsp10) and non-structural protein 16 (nsp16) are part of the RNA synthesis complex, which is crucial for the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nsp16 exhibits 2’-O-methyltransferase activity during viral messenger RNA capping and is active in a heterodimeric complex with enzymatically inactive nsp10. It has been shown that inactivation of the nsp10-16 protein complex interferes severely with viral replication, making it a highly promising drug target. As information on ligands binding to the nsp10-16 complex (nsp10-16) is still scarce, we screened the active site for potential binding of drug-like and fragment-like compounds using X-ray crystallography. The screened set of 234 compounds consists of derivatives of the natural substrateS-adenosyl methionine (SAM) and adenine derivatives, of which some have been described previously as methyltransferase inhibitors and nsp16 binders. A docking study guided the selection of many of these compounds. Here we report structures of binders to the SAM site of nsp10-16 and for two of them, toyocamycin and sangivamycin, we present additional crystal structures in the presence of a second substrate, Cap0-analog/Cap0-RNA. The identified hits were tested for binding to nsp10-16 in solution and antiviral activity in cell culture. Our data provide important structural information on various molecules that bind to the SAM substrate site which can be used as novel starting points for selective methyltransferase inhibitor designs.
Visualizing histone H4K20me1 in knock-in mice expressing the mCherry-tagged modification-specific intracellular antibody
Authors: Sato Yuko , Takenoshita Maoko , Ueoka Miku , Ueda Jun , Yamagata Kazuo , Kimura Hiroshi 
Published: March 2024

AbstractDuring development and differentiation, histone modifications dynamically change locally and globally, associated with transcriptional regulation, DNA replication and repair, and chromosome condensation. The level of histone H4 Lys20 monomethylation (H4K20me1) increases during the G2 to M phases of the cell cycle and is enriched in facultative heterochromatin, such as inactive X chromosomes in cycling cells. To track the dynamic changes of H4K20me1 in living cells, we have developed a genetically encoded modification-specific intracellular antibody (mintbody) probe that specifically binds to the modification. Here, we report the generation of knock-in mice in which the coding sequence of the mCherry-tagged version of the H4K20me1-mintbody is inserted into theRosa26locus. The knock-in mice, which ubiquitously expressed the H4K20me1-mintbody, developed normally and were fertile, indicating that the expression of the probe does not disturb the cell growth, development, or differentiation. Various tissues isolated from the knock-in mice exhibited nuclear fluorescence without the need for fixation. The H4K20me1-mintbody was enriched in inactive X-chromosomes in developing embryos and in XY bodies during spermatogenesis. The knock-in mice will be useful for the histochemical analysis of H4K20me1 in any cell types.