bluuebunny/crossref_metadata_2025_split huggingface dataset:
The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate
Authors: Marin Harold , Simental Eric , Allen Charlie , Martin Eric , Panning Barbara , Al-Sady Bassem , Buchwalter Abigail 
Published: July 2024

AbstractHeterochromatic loci marked by histone H3 lysine 9 dimethylation (H3K9me2) are enriched at the nuclear periphery in metazoans, but the effect of spatial position on heterochromatin function has not been defined. Here, we remove three nuclear lamins and lamin B receptor (LBR) in mouse embryonic stem cells (mESCs) and show that heterochromatin detaches from the nuclear periphery. Mutant mESCs sustain naïve pluripotency and maintain H3K9me2 across the genome but cannot repress H3K9me2-marked genes or transposons. Further, mutant cells fail to differentiate into epiblast-like cells (EpiLCs), a transition that requires the expansion of H3K9me2 across the genome. Mutant EpiLCs can silence naïve pluripotency genes and activate epiblast-stage genes. However, H3K9me2 cannot repress markers of alternative fates, including primitive endoderm. We conclude that the nuclear periphery controls the spatial position, dynamic remodeling, and repressive capacity of H3K9me2-marked heterochromatin to shape cell fate decisions.
Optically Mapped Black Genomes: Distinct Structures and 22q11.2 Deletion Syndrome Mechanisms
Authors: Pastor Steven , Tran Oanh , Lapointe Ryan , Olali Arnold Z. , Wallace Douglas C. , Morrow Bernice , Zackai Elaine H. , McDonald-McGinn Donna M. , Emanuel Beverly S. 
Published: July 2024

AbstractThe genomic architecture of 22q11.2 Deletion Syndrome (22q11.2DS) has focused on analysis of white genomes. However, Black individuals appear to have a lower prevalence of 22q11.2DS compared to whites. To improve the understanding of different populations in relation to 22q11.2DS, optical mapping data from 106 genomes across various Black and white genomes were used to determine the organization of 22q11.2 genomic structures. This revealed extensive variability between the groups regarding copy number and orientation changes of the elements comprising the 22q11.2 low copy repeats (LCR22s). Several novel CNVs and whole haplotype configurations, private and of different prevalence to each group were detected. The diversity of CNVs within Black genomes compared to white genomes was especially striking. To determine the impact of this variability, Black families withde novo22q11.2DS probands were compared to white families. The highly variable configurations of Black and white haplotypes led to several unique non-allelic homologous recombination (NAHR) scenarios with recombinations at different loci. In particular, Black families had unique recombinations yet to be observed. Thus, the unique and highly variable haplotype configurations of LCR22s in Black individuals may play a role in their decreased incidence of 22q11.2DS.
Behavioral and anatomical effects of complex rearing after day 7 neonatal frontal lesions vary with sex
Authors: Gibb Robbin , Kolb Bryan 
Published: July 2024

AbstractRats received medial frontal lesions, or sham surgery, on postnatal day 7 (P7), and were placed in complex environments or standard lab housing at weaning. Three months later the animals were tested in a spatial learning task and in a skilled reaching task. Rats with P7 lesions had smaller deficits in spatial learning than similar adult operates, and males performed better than females. Complex housing further improved the performance of male, but not female, lesion rats. The opposite was seen in motor performance as female lesion rats performed better than males and benefited from experience whereas males did not. There was a correlation between behavior and dendritic change as complex housing reversed lesion-induced dendritic atrophy, an effect that was greater in males. P7 frontal males, but not females, showed an increase in spine density that was reversed by complex housing. Experience thus can affect functional and anatomical outcome after early brain injury, but the effects vary with sex.
Acute rapamycin treatment reveals novel mechanisms of behavioral, physiological, and functional dysfunction in a maternal inflammation mouse model of autism and sensory over-responsivity
Authors: Le Belle JE , Condro M , Cepeda C , Oikonomou KD , Tessema K , Dudley L , Schoenfield J , Kawaguchi R , Geschwind D , Silva AJ , Zhang Z , Shokat K , Harris NG , Kornblum HI 
Published: July 2024

AbstractMaternal inflammatory response (MIR) during early gestation in mice induces a cascade of physiological and behavioral changes that have been associated with autism spectrum disorder (ASD). In a prior study and the current one, we find that mild MIR results in chronic systemic and neuro-inflammation, mTOR pathway activation, mild brain overgrowth followed by regionally specific volumetric changes, sensory processing dysregulation, and social and repetitive behavior abnormalities. Prior studies of rapamycin treatment in autism models have focused on chronic treatments that might be expected to alter or prevent physical brain changes. Here, we have focused on the acute effects of rapamycin to uncover novel mechanisms of dysfunction and related to mTOR pathway signaling. We find that within 2 hours, rapamycin treatment could rapidly rescue neuronal hyper-excitability, seizure susceptibility, functional network connectivity and brain community structure, and repetitive behaviors and sensory over-responsivity in adult offspring with persistent brain overgrowth. These CNS-mediated effects are also associated with alteration of the expression of several ASD-,ion channel-, and epilepsy-associated genes, in the same time frame. Our findings suggest that mTOR dysregulation in MIR offspring is a key contributor to various levels of brain dysfunction, including neuronal excitability, altered gene expression in multiple cell types, sensory functional network connectivity, and modulation of information flow. However, we demonstrate that the adult MIR brain is also amenable to rapid normalization of these functional changes which results in the rescue of both core and comorbid ASD behaviors in adult animals without requiring long-term physical alterations to the brain. Thus, restoring excitatory/inhibitory imbalance and sensory functional network modularity may be important targets for therapeutically addressing both primary sensory and social behavior phenotypes, and compensatory repetitive behavior phenotypes.
Endogenous FGFs drive ERK-dependent cell fate patterning in 2D human gastruloids
Authors: Jo Kyoung , Liu Zong-Yuan , Patel Gauri , Yu Zhiyuan , Yao LiAng , Teague Seth , Johnson Craig , Spence Jason , Heemskerk Idse 
Published: July 2024

AbstractThe role of FGF is the least understood of the morphogens driving mammalian gastrulation. Here we investigated the function of FGF in a stem cell model for human gastrulation known as a 2D gastruloid. We found a ring of FGF-dependent ERK activity that closely follows the emergence of primitive streak (PS)-like cells but expands further inward. We showed that this ERK activity pattern is required for PS-like differentiation and that loss of PS-like cells upon FGF receptor inhibition can be rescued by directly activating ERK. We further demonstrated that the ERK-ring depends on localized activation of basally localized FGF receptors (FGFR) by endogenous FGF gradients. We confirm and extend previous studies in analyzing expression of FGF pathway components, showing the main receptor to be FGFR1 and the key ligands FGF2/4/17, similar to the human and monkey embryo but different from the mouse. In situ hybridization and scRNA-seq revealed thatFGF4andFGF17expression colocalize with the PS marker TBXT but onlyFGF17is maintained in nascent mesoderm and endoderm. FGF4 and FGF17 reduction both reduced ERK activity and differentiation to PS-like cells and their derivatives, indicating overlapping function. Thus, we have identified a previously unknown role for FGF-dependent ERK signaling in 2D gastruloids and possibly the human embryo, driven by a mechanism where FGF4 and FGF17 signal through basally localized FGFR1 to induce PS-like cells.
Ketogenesis supports hepatic polyunsaturated fatty acid homeostasis via fatty acid elongation
Authors: Queathem Eric D. , Moazzami Zahra , Stagg David B , Nelson Alisa B. , Fulghum Kyle , Hayir Abdirahman , Seay Alisha , Gillingham Jacob R. , d’Avignon D. Andre , Han Xianlin , Ruan Hai-Bin , Crawford Peter A. , Puchalska Patrycja 
Published: July 2024

SummaryTherapeutic interventions targeting hepatic lipid metabolism in metabolic dysfunction-associated steatotic liver disease (MASLD) and steatohepatitis (MASH) remain elusive. Using mass spectrometry-based stable isotope tracing and shotgun lipidomics, we established a novel link between ketogenesis and MASLD pathophysiology. Our findings show that mouse liver and primary hepatocytes consume ketone bodies to support fatty acid (FA) biosynthesis via both de novo lipogenesis (DNL) and FA elongation. Analysis of13C-labeled FAs in hepatocytes lacking mitochondrial D-β-hydroxybutyrate dehydrogenase (BDH1) revealed a partial reliance on mitochondrial conversion of D-βOHB to acetoacetate (AcAc) for cytoplasmic DNL contribution, whereas FA elongation from ketone bodies was fully dependent on cytosolic acetoacetyl-CoA synthetase (AACS). Ketone bodies were essential for polyunsaturated FA (PUFA) homeostasis in hepatocytes, as loss of AACS diminished both free and esterified PUFAs. Ketogenic insufficiency depleted liver PUFAs and increased triacylglycerols, mimicking human MASLD, suggesting that ketogenesis supports PUFA homeostasis, and may mitigate MASLD-MASH progression in humans.
Repeated extrinsic and anisotropic mechanical inputs promote polarized adherens junction elongation
Authors: Yang Xinyi , Ferraro Teresa , Molnar Kelly , Pontabry Julien , Malanda Sam-Rayden , Maghelli Nicola , Royer Loïc , Grill Stephan W. , Myers Gene , Grigolon Silvia , Labouesse Michel 
Published: July 2024

ABSTRACTA key challenge in development is understanding how complex organisms physically coordinate the morphogenesis of multiple tissues. Here, using biophysical approaches, we investigate how muscles under the epidermis specifically stimulate the extension of anterior-posterior (AP-oriented) epidermal adherens junctions during lateC. elegansembryonic elongation. First, light-sheet imaging shows that asynchronous patterns of muscle contractions drive embryo rotations. In turn, junctions between the lateral and dorso-ventral epidermis repeatedly oscillate between a folded, hypotensed state, and an extended, hypertensed state. Second, FRAP (Fluorescence Recovery After Photobleaching) analysis of an E-cadherin::GFP construct shows that muscle contractions stimulate E-cadherin turnover. Moreover, a mechano-chemical model backed by genetic tests suggests that E-cadherin trafficking modulates junction elongation due to lower line tension. Altogether, our results illustrate how muscle contractions fluidize epidermal adherens junctions, which, combined with anisotropic tension in the epidermis, drives their polarized extension.
Septins function in exocytosis via physical interactions with the exocyst complex in fission yeast cytokinesis
Authors: Singh Davinder , Liu Yajun , Zhu Yi-Hua , Zhang Sha , Naegele Shelby , Wu Jian-Qiu 
Published: July 2024

AbstractSeptins can function as scaffolds for protein recruitment, membrane-bound diffusion barriers, or membrane curvature sensors. Septins are important for cytokinesis, but their exact roles are still obscure. In fission yeast, four septins (Spn1 to Spn4) accumulate at the rim of the division plane as rings. The octameric exocyst complex, which tethers exocytic vesicles to the plasma membrane, exhibits a similar localization and is essential for plasma membrane deposition during cytokinesis. Without septins, the exocyst spreads across the division plane but absent from the rim during septum formation. These results suggest that septins and the exocyst physically interact for proper localization. Indeed, we predicted six pairs of direct interactions between septin and exocyst subunits by AlphaFold2 ColabFold, most of them are confirmed by co-immunoprecipitation and yeast two-hybrid assays. Exocyst mislocalization results in mistargeting of secretory vesicles and their cargos, which leads to cell-separation delay in septin mutants. Our results indicate that septins guide the targeting of exocyst complex on the plasma membrane for vesicle tethering during cytokinesis through direct physical interactions.
Physical interaction with Ephrin B1 promotes CXCR4 intracellular localization and oncogenic potential
Authors: Rabbito Alessandro , Otun Omolade , Fumagalli Amos , Séveno Martial , Galant Sonya , Counson Manuel , Durroux Thierry , Bechara Cherine , Smit Martine J , Granier Sébastien , Szpakowska Martyna , Chevigné Andy , Chaumont-Dubel Séverine , Marin Philippe 
Published: July 2024

AbstractChemokine receptor 4 (CXCR4) is a member of the chemokine receptor exclusively activated by the chemokine CXCL12. While CXCR4 regulates numerous physiological processes associated with cell migration and embryogenesis, its overexpression has been involved in various cancer types. Studies suggest that intracellular CXCR4 expression rather than CXCR4-operated signaling underlies its pro-tumorigenic functions. Given the role of GPCR interacting proteins in their trafficking and subcellular localization, we characterized the CXCR4 interactome using an affinity purification coupled to mass spectrometry (AP-MS) strategy. The most abundant protein identified in the CXCR4 interactome is Ephrin B1, a member of the Ephrin protein family that shares several functions with CXCR4, such as the regulation of cell migration and proliferation. Further studies showed that interaction between CXCR4 and Ephrin B1 is direct and enhanced by treating cell with CXCL12. They also indicated that Ephrin B1 prevents CXCR4 N-glycosylation, decreases CXCR4 cell surface expression and consistently inhibits CXCL12-induced CXCR4 coupling to Gαi1-3and the recruitment of β-arrestins 1 and 2. Conversely, Ephrin B1 signals to Erk1,2 through CXCR4 activation and mediates the decrease in Death Receptor 5 expression elicited by intracellular CXCR4. Collectively, these findings identify Ephrin B1 as a key mediator of CXCR4 tumorigenic signaling.
Dual inhibition of ATR and DNA-PKcs radiosensitizes ATM-mutant prostate cancer
Authors: Hofstad Mia , Woods Andrea , Parra Karla , Sychev Zoi E. , Mazzagatti Alice , Yu Lan , Gilbreath Collin , Ly Peter , Drake Justin M. , Kittler Ralf 
Published: July 2024

AbstractIn advanced castration resistant prostate cancer (CRPC), mutations in the DNA damage response (DDR) geneataxia telangiectasia mutated(ATM) are common. While poly(ADP-ribose) polymerase inhibitors are approved in this context, their clinical efficacy remains limited. Thus, there is a compelling need to identify alternative therapeutic avenues forATMmutant prostate cancer patients. Here, we generated matched ATM-proficient and ATM-deficient CRPC lines to elucidate the impact of ATM loss on DDR in response to DNA damage via irradiation. Through unbiased phosphoproteomic screening, we unveiled that ATM-deficient CRPC lines maintain dependence on downstream ATM targets through activation of ATR and DNA-PKcs kinases. Dual inhibition of ATR and DNA-PKcs effectively inhibited downstream γH2AX foci formation in response to irradiation and radiosensitized ATM-deficient lines to a greater extent than either ATM-proficient controls or single drug treatment. Further, dual inhibition abrogated residual downstream ATM pathway signaling and impaired replication fork dynamics. To circumvent potential toxicity, we leveraged the RUVBL1/2 ATPase inhibitor Compound B, which leads to the degradation of both ATR and DNA-PKcs kinases. Compound B effectively radiosensitized ATM-deficient CRPCin vitroandin vivo, and impacted replication fork dynamics. Overall, dual targeting of both ATR and DNA-PKcs is necessary to block DDR in ATM-deficient CRPC, and Compound B could be utilized as a novel therapy in combination with irradiation in these patients.Graphical Abstract
A multiomic atlas of human early skeletal development
Authors: To Ken , Fei Lijiang , Patrick Pett J. , Roberts Kenny , Polański Krzysztof , Li Tong , Yayon Nadav , He Peng , Xu Chuan , Cranley James , Li Ruoyan , Kanemaru Kazumasa , Huang Ni , Megas Stathis , Richardson Laura , Kapuge Rakesh , Perera Shani , Tuck Elizabeth , Wilbrey-Clark Anna , Mulas Ilaria , Memi Fani , Cakir Batuhan , Predeus Alexander V. , Horsfall David , Murray Simon , Prete Martin , Mazin Pavel , He Xiaoling , Meyer Kerstin B. , Haniffa Muzlifah , Barker Roger A. , Bayraktar Omer , Buckley Christopher D. , Teichmann Sarah A. 
Published: July 2024

AbstractBone and joint formation in the developing skeleton rely on co-ordinated differentiation of progenitors in the nascent developing limbs and joints. The cell states, epigenetic processes and key regulatory factors underlying their lineage commitment to osteogenic and other mesenchymal populations during ossification and joint formation remain poorly understood and are largely unexplored in human studies. Here, we apply paired single-nuclei transcriptional and epigenetic profiling of 336,000 droplets, in addition to spatial transcriptomics, to construct a comprehensive atlas of human bone, cartilage and joint development in the shoulder, hip, knee and cranium from 5 to 11 post-conception weeks. Spatial mapping of cell clusters to our highly multiplexed in situ sequencing (ISS) data using our newly developed tool ISS-Patcher revealed new cellular mechanisms of zonation during bone and joint formation. Combined modelling of chromatin accessibility and RNA expression allowed the identification of the transcriptional and epigenetic regulatory landscapes that drive differentiation of mesenchymal lineages including osteogenic and chondrogenic lineages, and novel chondrocyte cell states. In particular, we define regionally distinct limb and cranial osteoprogenitor populations and trajectories across the fetal skeleton and characterise differential regulatory networks that govern intramembranous and endochondral ossification. We also introduce SNP2Cell, a tool to link cell-type specific regulatory networks to numerous polygenic traits such as osteoarthritis. We also conductin silicoperturbations of genes that cause monogenic craniosynostosis and implicate potential pathogenic cell states and disease mechanisms involved. This work forms a detailed and dynamic regulatory atlas of human fetal skeletal maturation and advances our fundamental understanding of cell fate determination in human skeletal development.
Proteome-Wide Bioinformatic Annotation and Functional Validation of the Monotopic Phosphoglycosyl Transferase Superfamily
Authors: Durand Theo , Dodge Greg J. , Siuda Roxanne P. , Higinbotham Hugh R. , Arbour Christine A. , Ghosh Soumi , Allen Karen N. , Imperiali Barbara 
Published: July 2024

AbstractPhosphoglycosyl transferases (PGTs) are membrane proteins that initiate glycoconjugate biosynthesis by transferring a phospho-sugar moiety from a soluble nucleoside diphosphate sugar to a membrane-embedded polyprenol phosphate acceptor. The centrality of PGTs in complex glycan assembly and the current lack of functional information make these enzymes high-value targets for biochemical investigation. In particular, the small monotopic PGT family is exclusively bacterial and represents the minimal functional unit of the monotopic PGT superfamily. Here, we combine a sequence similarity network (SSN) analysis with a generalizable, luminescence-based activity assay to probe the substrate specificity of this family of monoPGTs in a bacterial cell-membrane fraction. This strategy allows us to identify specificity on a far more significant scale than previously achievable and correlate preferred substrate specificities with predicted structural differences within the conserved monoPGT fold. Finally, we present the proof-of-concept for a small-scale inhibitor screen (eight nucleoside analogs) with four monoPGTs of diverse substrate specificity, thus building a foundation for future inhibitor discovery initiatives.SignificanceUncovering the function and specificity of enzymes responsible for glycoconjugate biosynthesis traditionally requires a multi-faceted and individually curated approach. This is especially true for bacterial glycoconjugates due to greater monosaccharide diversity and a paucity of established structural information. Here we leverage bioinformatic and in-vitro tools to predict and validate substrate specificity for a unique, exclusively bacterial family of enzymes responsible for the first step in many of these glycan assembly pathways. We further show that this platform is suitable for enhanced functional annotation and inhibitor testing, paving the way for the development of urgently needed antibiotics.
Opening the digital doorway to sexual healthcare: Recommendations from a Behaviour Change Wheel analysis of barriers and facilitators to seeking online sexual health information and support among underserved populations
Authors: McLeod Julie , Estcourt Claudia S. , MacDonald Jennifer , Gibbs Jo , Woode Owusu Melvina , Mapp Fiona , Gallego Marquez Nuria , McInnes-Dean Amelia , Saunders John , Blandford Ann , Flowers Paul 
Published: July 2024

AbstractBackgroundThe ability to access and navigate online sexual health information and support is increasingly needed in order to engage with wider sexual healthcare. However, people from underserved populations may struggle to pass though this “digital doorway”. Therefore, using a behavioural science approach, we first aimed to identify barriers and facilitators to: i) seeking online sexual health information and ii) seeking online sexual health support. Subsequently, we aimed to generate theory-informed recommendations to improve these access points.MethodsThe PROGRESS framework guided purposive recruitment (October 2021–April 2022) of 35 UK participants from diverse backgrounds, including 51% from the most deprived areas and 26% from minoritised ethnic groups. Semi-structured interviews and thematic analysis identified barriers and facilitators to seeking online sexual health information and support. A Behaviour Change Wheel (BCW) analysis then identified recommendations to better meet the needs of underserved populations.ResultsWe found diverse barriers and facilitators. Barriers included low awareness of and familiarity with online information and support; perceptions that online information and support were unlikely to meet the needs of underserved populations; overwhelming volume of information sources; lack of personal relevancy; chatbots/automated responses; and response wait times. Facilitators included clarity about credibility and quality; inclusive content; and in-person assistance. Recommendations included: Education and Persuasion e.g., online and offline promotion and endorsement by healthcare professionals and peers; Training and Modelling e.g., accessible training to enhance searching skills and credibility appraisal; and Environmental Restructuring and Enablement e.g., modifications to ensure online information and support are simple and easy to use, including video/audio options for content.ConclusionsGiven that access to many sexual health services is now digital, our analyses produced recommendations pivotal to increasing access to wider sexual healthcare among underserved populations. Implementing these recommendations could reduce inequalities associated with accessing and using online sexual health service.