bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell extrusion - a novel mechanism driving neural crest cell delamination
Authors: Moore Emma , Zhao Ruonan , McKinney Mary C , Yi Kexi , Wood Christopher , Trainor Paul 
Published: March 2024

AbstractNeural crest cells (NCC) comprise a heterogeneous population of cells with variable potency, that contribute to nearly every tissue and organ system throughout the body. Considered unique to vertebrates, NCC are transiently generated within the dorsolateral region of the neural plate or neural tube, during neurulation. Their delamination and migration are crucial events in embryo development as the differentiation of NCC is heavily influenced by their final resting locations. Previous work in avian and aquatic species has shown that NCC delaminate via an epithelial-mesenchymal transition (EMT), which transforms these stem and progenitor cells from static polarized epithelial cells into migratory mesenchymal cells with fluid front and back polarity. However, the cellular and molecular drivers facilitating NCC delamination in mammals are poorly understood. We performed live timelapse imaging of NCC delamination in mouse embryos and discovered a group of cells that exit the neuroepithelium as isolated round cells, which then halt for a short period prior to acquiring the mesenchymal migratory morphology classically associated with most delaminating NCC. High magnification imaging and protein localization analyses of the cytoskeleton, together with measurements of pressure and tension of delaminating NCC and neighboring neuroepithelial cells, revealed these round NCC are extruded from the neuroepithelium prior to completion of EMT. Furthermore, we demonstrate that cranial NCC are extruded through activation of the mechanosensitive ion channel, PIEZO1, a key regulator of the live cell extrusion pathway, revealing a new role for PIEZO1 in neural crest cell development. Our results elucidating the cellular and molecular dynamics orchestrating NCC delamination support a model in which high pressure and tension in the neuroepithelium results in activation of the live cell extrusion pathway and delamination of a subpopulation of NCC in parallel with EMT. This model has broad implications for our understanding of cell delamination in development and disease.
Structural and biophysical characterisation of ubiquitin variants that specifically inhibit the ubiquitin conjugating enzyme Ube2d2
Authors: McAlpine Jeffery M.R.B. , Zhu Jingyi , Pudjihartono Nicholas , Teyra Joan , Currie Michael J. , Dobson Renwick C.J. , Sidhu Sachdev S. , Day Catherine L. , Middleton Adam J. 
Published: March 2024

AbstractThe ubiquitin conjugating E2 enzymes play a central role in ubiquitin transfer. Disruptions to the ubiquitin system are implicated in multiple diseases and as a result, molecules that modulate the activity of the ubiquitin system are of interest. E2 enzyme function is reliant on interactions with partner proteins and disruption of these is an effective way of modulating activity. Here, we report the discovery of ubiquitin variants (UbVs) that inhibit the E2 enzyme, Ube2d2 (UbcH5b). The six UbVs identified inhibit ubiquitin chain building, and structural and biophysical characterisation of two of these demonstrate they bind to Ube2d2 with low micromolar affinity and high specificity within the Ube2d family of E2 enzymes. Both characterised UbVs bind at a site that overlaps with E1 binding, while the more inhibitory UbV blocks a critical non-covalent ubiquitin binding site on the E2 enzyme. The discovery of novel protein-based ubiquitin derivatives that inhibit protein-protein interactions is an important step towards discovery of small molecules that inhibit the activity of E2 enzymes. Furthermore, the specificity of the UbVs within the Ube2d family suggests that it may be possible to develop tools to selectively inhibit highly related E2 enzymes.
Fertilization-induced synergid cell death by RALF12-triggered ROS production and ethylene signaling
Authors: Chen Junyi , Wang Huan , Wang Jinlin , Zheng Xixi , Qu Wantong , Fang Huijian , Wang Shuang , He Le , Hao Shuang , Dresselhaus Thomas 
Published: March 2024

AbstractFertilization-dependent elimination of the persistent synergid cell is essential to block supernumerary pollen tubes and thus to avoid polyspermy in flowering plants. Little is known about the molecular mechanisms ensuring timely induction and execution of synergid cell death. We analysed manually isolated maize synergid cells along their degeneration and show that they are gland cells expressing batteries of genes encoding small secreted proteins under control of the MYB98 transcription factor. This network is down-regulated after fertilization, while genes involved in reactive oxygen species (ROS) production, ethylene biosynthesis and response, senescence, and oxidative stress regulation are induced before synergid elimination and its ultimate fusion with the endosperm. We further show that fertilization-induced RALF12 peptide specifically triggers mitochondrial ROS and apoptosis, while ethylene promotes synergid degeneration. In conclusion, this study sheds light on developmental programmed cell death (dPCD) in plants and provides a unique resource to discover novel PCD regulators.
Tipping-point transition from transient to persistent inflammation in pancreatic islets
Authors: Holst-Hansen Thomas , Yde Pernille , Jensen Mogens H. , Mandrup-Poulsen Thomas , Trusina Ala 
Published: March 2024

ABSTRACTType 2 diabetes (T2D) is associated with a systemic increase in the pro-inflammatory cytokine IL-1β. While transient exposure to low IL-1β concentrations improves insulin secretion and β-cell proliferation in pancreatic islets, prolonged exposure leads to impaired insulin secretion and collective β-cell death. IL-1 is secreted locally by islet-resident macrophages and β-cells; however it is unknown if and how the two opposing modes may emerge at single islet level.We investigated the duality of IL-1β with a quantitative in-silico model of the IL-1 regulatory network in pancreatic islets. We find that the network can produce either transient or persistent IL-1 responses, when induced by pro-inflammatory and metabolic cues. This suggests that the duality of IL-1 may be regulated at the single islet level. We use two core feedbacks in the IL-1 regulation to explain both modes: First, a fast positive feedback in which IL-1 induces its own production through IL-1R/IKK/NF-κB pathway. Second, a slow negative feedback where NFκ-κB upregulates inhibitors acting at different levels along the IL-1R/IKK/NF-κB pathway – IL-1 receptor antagonist and A20 among others. A transient response ensues when the two feedbacks are balanced. When positive feedback is dominating over the negative islets transit into the persistent inflammation mode. Consistent with several observations, where the size of islets was implicated in its inflammatory state, we find that large islets and islets with high density of IL-1β amplifying cells are more prone to transit into persistent IL-1β mode.Our results are likely not limited to IL-1β but general for the combined effect of multiple pro-inflammatory cytokines and chemokines. Generalizing complex regulations in terms of two feedbacks of opposing nature and acting on different time scales provides a number of testable predictions, which call for dynamic monitoring of pro-inflammatory cytokines at the single islet level.AUTHOR SUMMARYDifferent expression or activity dynamics of the same proteins or signaling molecules can lead to opposing fates in cells and tissues. While it is known that brief and prolonged exposure to pro-inflammatory cytokine IL-1β have opposing effects on the functionality and viability of pancreatic β-cells, it is unclear if and how these differences in dynamics may arise at the single islet level. We use a mathematical model of the core feedback loops in the IL-1β regulatory network to show that transient and persistent responses are the two characteristic dynamic modes of the IL-1β response. The likelihood of each mode depends on systemic inflammation and elevated glycaemia and free fatty acids levels. We find that large islets are more prone to transit into the persistent mode, which may provide an explanation for why large islets are underrepresented in type 2 diabetes patients.
Cytokine and Chemokine Receptor Profiles in Adipose Tissue Vasculature Unravel Endothelial Cell Responses in HIV
Authors: Obare Laventa M. , Priest Stephen , Ismael Anas , Mashayekhi Mona , Zhang Xiuqi , Stolze Lindsey K. , Sheng Quanhu , Vue Zer , Neikirk Kit , Beasley Heather , Gabriel Curtis , Temu Tecla , Gianella Sara , Mallal Simon , Koethe John R. , Hinton Antentor , Bailin Samuel , Wanjalla Celestine N. 
Published: March 2024

AbstractChronic systemic inflammation contributes to a substantially elevated risk of myocardial infarction in people living with HIV (PLWH). Endothelial cell dysfunction disrupts vascular homeostasis regulation, increasing the risk of vasoconstriction, inflammation, and thrombosis that contribute to cardiovascular disease. Our objective was to study the effects of plasma from PLWH on endothelial cell (EC) function, with the hypothesis that cytokines and chemokines are major drivers of EC activation. We first broadly phenotyped chemokine and cytokine receptor expression on arterial ECs, capillary ECs, venous ECs, and vascular smooth muscle cells (VSMCs) in adipose tissue in the subcutaneous adipose tissue of 59 PLWH using single cell transcriptomic analysis. We used CellChat to predict cell-cell interactions between ECs and other cells in the adipose tissue and Spearman correlation to measure the association between ECs and plasma cytokines. Finally, we cultured human arterial ECs (HAECs) in plasma-conditioned media from PLWH and performed bulk sequencing to study the direct effects ex-vivo. We observed that arterial and capillary ECs expressed higher interferon and tumor necrosis factor (TNF) receptors. Venous ECs had more interleukin (IL)-1R1 and ACKR1 receptors, and VSMCs had high significant IL-6R expression. CellChat predicted ligand-receptor interactions between adipose tissue immune cells as senders and capillary ECs as recipients in TNF-TNFRSF1A/B interactions. Chemokines expressed largely by capillary ECs were predicted to bind ACKR1 receptors on venous ECs. Beyond the adipose tissue, the proportion of venous ECs and VSMCs were positively plasma IL-6. In ex-vivo experiments, HAECs cultured with plasma-conditioned media from PLWH expressed transcripts that enriched for the TNF-α and reactive oxidative phosphorylation pathways. In conclusion, ECs demonstrate heterogeneity in cytokine and chemokine receptor expression. Further research is needed to fully elucidate the role of cytokines and chemokines in EC dysfunction and to develop effective therapeutic strategies.
Mechanistic insights into transport models of the sphingolipid transport protein, Spinster homolog 2 (Spns2), using MD simulations
Authors: Sharp Amanda K. , LoPresti Marion Q. , Brown Anne M. 
Published: March 2024

AbstractSphingosine-1-phosphate (S1P) is a sphingolipid signaling molecule that when elevated results in multiple disease states including metastatic cancers. Modulating the extracellular concentrations of S1P has been an evolving strategy in drug development for metastatic cancers due to its role in angiogenesis and cell migration. Research has shown that Spns2, the S1P transport protein, is an important microenvironment regulatory gene in metastatic lung cancer colonization and has demonstrated that Spns2 inhibition is a powerful suppressor of metastatic cancers. Spns2 transports and regulates cellular levels of S1P but has unresolved aspects related to mechanism of transport. Here, molecular modeling strategies including, homology modeling and molecular dynamics (MD) simulations, were used to determine structural mechanisms of action related to S1P transport and exploitable for inhibition. Results indicate Spns2 contains a unique salt-bridge network essential for structural stability that is disrupted by the R119A mutation. Additionally, we observe that Spns2 follows a rocker-switch transport model and that S1P translocation is initialized by interacting with residues such as Thr216, Arg227, and Met230. This work provides initial insight into structural morphologies sampled by Spns2, the role of a complex salt bridge network, and residues engaged in structural state transition that can be targeted with inhibitors to control extracellular concentrations of S1P.
SARS-CoV-2 Omicron BA.2.87.1 Exhibits Higher Susceptibility to Serum Neutralization Than EG.5.1 and JN.1
Authors: Wang Qian , Guo Yicheng , Schwanz Logan T. , Mellis Ian A. , Sun Yiwei , Qu Yiming , Urtecho Guillaume , Valdez Riccardo , Stoneman Emily , Gordon Aubree , Wang Harris H. , Liu Lihong , Ho David D. 
Published: March 2024

AbstractAs SARS-CoV-2 continues to spread and mutate, tracking the viral evolutionary trajectory and understanding the functional consequences of its mutations remain crucial. Here, we characterized the antibody evasion, ACE2 receptor engagement, and viral infectivity of the highly mutated SARS-CoV-2 Omicron subvariant BA.2.87.1. Compared with other Omicron subvariants, including EG.5.1 and the current predominant JN.1, BA.2.87.1 exhibits less immune evasion, reduced viral receptor engagement, and comparable infectivity in Calu-3 lung cells. Intriguingly, two large deletions (Δ15-26 and Δ136-146) in the N-terminal domain (NTD) of the spike protein facilitate subtly increased antibody evasion but significantly diminish viral infectivity. Collectively, our data support the announcement by the USA CDC that the public health risk posed by BA.2.87.1 appears to be low.
cGAS-STING is responsible for aging of telomerase deficient zebrafish
Authors: Şerifoğlu Naz , Allavena Giulia , Bastos-Lopes Bruno , Marzullo Marta , Bousounis Pavlos , Trompouki Eirini , Ferreira Miguel Godinho 
Published: March 2024

AbstractTelomere shortening occurs in multiple tissues throughout aging. When telomeres become critically short, they trigger DNA damage responses and p53 stabilization, leading to apoptosis or replicative senescence.In vitro, cells with short telomeres activate the cGAS-STING innate immune pathway resulting in type I interferon inflammation and senescence. However, the consequences of these events to the organism are not yet understood. Here, we show thatstingis responsible for premature aging of telomerase-deficient zebrafish. We generatedsting-/- tert-/-double mutants and observed a thorough rescue oftert-/-phenotypes. At the cellular level, lack of cGAS-STING inter tmutants resulted in reduced senescence, increased cell proliferation, and low inflammation despite similar short telomeres. Critically, absence ofstingfunction resulted in dampening of the DNA damage response and low p53 levels. At the organism level,sting-/- tert-/-zebrafish regained fertility, delayed cachexia, and cancer incidence, resulting in increased healthspan and lifespan of telomerase mutants.
Helicobacter pyloriγ-glutamyltransferase relates to proteomic adaptions important for gastric colonization
Authors: Fuchs Sonja , Fiedler Michaela K. , Heiduk Nicole , Wanisch Andreas , Debowski Aleksandra W. , Marshall Barry J. , Sieber Stephan A. , Gerhard Markus , Mejías-Luque Raquel 
Published: March 2024

AbstractHelicobacter pyloriγ-glutamyltransferase (gGT) is a virulence factor that promotes bacterial colonization and immune tolerance. Although some studies addressed potential functional mechanisms, the supportive role of gGT forin-vivocolonization remains unclear. Additionally, it is unknown how different gGT expression levels may lead to compensatory mechanisms ensuring infection and persistence. Hence, it is crucial to unravel thein-vivofunction of gGT. We assessed acid survival under conditions mimicking the human gastric fluid and elevated the pH in the murine stomach prior toH. pyloriinfection to link gGT-mediated acid resistance to colonization. By comparing proteomes of gGT-proficient and -deficient isolates before and after infecting mice, we investigated proteomic adaptations of gGT-deficient bacteria during infection. Our data indicate that gGT is crucial to sustain urease activity in acidic environments, thereby supporting survival and successful colonization. Absence of gGT triggers expression of proteins involved in the nitrogen and iron metabolism and boosts the expression of adhesins and flagellar proteins during infection, resulting in increased motility and adhesion capacity. In summary, gGT-dependent mechanisms confer a growth advantage to the bacterium in the gastric environment, which renders gGT a valuable target for the development of new treatments againstH. pyloriinfection.Author SummaryH. pyloriγ-glutamyltransferase (gGT) is a virulence factor that strongly supports bacterial colonization. Despite considerable research on the function of gGT, the exact role of this enzyme in ensuringin-vivoinfection remained elusive. We developed a novel system that allowed us to selectively inhibit gGT-activity and used this model to assess the function of gGT in the gastric environment. We found that gGT sustains urease activity in acidic environments thereby facilitating survival and effective colonization. In addition, we identified several compensatory mechanisms triggered by the loss of gGT which ensure colonization and persistence. These mechanisms included increased flagellar motility, adhesion capacity and expression of proteins involved in the nitrogen and iron metabolism. These findings unraveled novel functional roles of gGT important for bacterial colonization and thereby confirmed gGT as a promising target for novel treatments againstH. pyloriinfection. By comprehensively addressing the compensatory mechanisms resulting from the loss of gGT-activity, the success of such new treatments can be improved.
miR-644a is a tumor cell-intrinsic mediator of sex bias in glioblastoma
Authors: Hong Ellen S. , Wang Sabrina Z. , Ponti András K. , Hajdari Nicole , Lee Juyeun , Mulkearns-Hubert Erin E. , Volovetz Josephine , Kay Kristen E. , Lathia Justin D. , Dhawan Andrew 
Published: March 2024

AbstractBackgroundBiological sex is an important risk factor for glioblastoma (GBM), with males having a higher incidence and poorer prognosis. The mechanisms for this sex bias are thought to be both tumor intrinsic and tumor extrinsic. MicroRNAs (miRNAs), key post-transcriptional regulators of gene expression, have been previously linked to sex differences in various cell types and diseases, but their role in the sex bias of GBM remains unknown.MethodsWe leveraged previously published paired miRNA and mRNA sequencing of 39 GBM patients (22 male, 17 female) to identify sex-biased miRNAs. We further interrogated a separate single-cell RNA sequencing dataset of 110 GBM patients to examine whether differences in miRNA target gene expression were tumor cell intrinsic or tumor cell extrinsic. Results were validated in a panel of patient-derived cell models.ResultsWe identified 10 sex-biased miRNAs (adjusted<0.1), of which 3 were more highly expressed in males and 7 more highly expressed in females. Of these, miR-644a was higher in females, and increased expression of miR-644a target genes was significantly associated with decreased overall survival (HR 1.3,p= 0.02). Furthermore, analysis of an independent single-cell RNA sequencing dataset confirmed sex-specific expression of miR-644a target genes in tumor cells (p< 10-15). Among patient derived models, miR-644a was expressed a median of 4.8-fold higher in females compared to males.ConclusionsOur findings implicate miR-644a as a candidate tumor cell-intrinsic regulator of sex-biased gene expression in GBM.Key PointsmiR-644a is more highly expressed in female GBM patients.Lower miR-644a target gene expression is associated with improved overall survival.miR-644a target genes are higher in male GBM cells but not in other cell types.Importance of the StudyMicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression at the post-transcriptional level and were previously linked to glioblastoma (GBM) growth and therapeutic resistance. miRNAs play a role in the sex bias of various cell types and diseases, but how miRNAs contribute to sex differences in GBM is not well elucidated. We show that 10 miRNAs are differentially expressed between males and females and identify miR-644a as more highly expressed in female GBM patients. Using single-cell RNA-seq data, we demonstrate that sex differences in miR-644a target gene expression are tumor cell-intrinsic. Likewise, decreased miR-644a target gene expression is associated with improved overall patient survival. Our findings reveal miR-644a as a novel sex-biased miRNA in GBM, and a possible target for sex-specific precision therapies with limited collateral damage.
Distinct intersecting pathways link homolog pairing to initiation of meiotic chromosome synapsis
Authors: Blazickova Jitka , Trivedi Shalini , Bowman Richard , Geetha Sowmya Sivakumar , Subah Silma , Smolikove Sarit , Jantsch Verena , Zetka Monique , Silva Nicola 
Published: March 2024

ABSTRACTFaithful meiotic segregation requires pairwise alignment of the homologous chromosomes and Synaptonemal Complex assembly (SC) at their interface. Here, we investigate on new factors that promote and coordinate these events duringC. elegansmeiosis. We identify BRA-2 (BMPReceptorAssociated family member2)as an interactor of HIM-17, previously shown to promote double-strand break formation. We found that loss ofbra-2specifically impairs synapsis licensing without affecting homologs recognition, SC maintenance or chromosome movement. Double mutant analysis revealed a previously unrecognized role for HIM-17 in promoting homolog pairing under dysfunctional SC assembly, without perturbing nuclear envelope recruitment of factors required for chromosome movement. We provide evidence thatbra-2andhim-17act in distinct pathways, exerting partially redundant functions in SC licensing, as well as separable roles in regulating homologs pairing. Altogether, our findings unveil novel mechanisms that ensure stabilization of homologous chromosome interaction via SC licensing upon homology assessment.
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping
Authors: Lange Bret , Gil Ricardo G. , Yesselman Joseph D. 
Published: March 2024

AbstractStructured RNAs often contain long-range tertiary contacts that are critical to their function. Despite the importance of tertiary contacts, methods to measure their thermodynamics are low throughput or require specialized instruments. Here, we introduce a new quantitative chemical mapping method (qDMS-MaPseq) to measure Mg2+-induced formation of tertiary contact thermodynamics in a high-throughput manner using standard biochemistry equipment. With qDMS-MaPseq, we measured the ΔG of 98 unique tetraloop/tetraloop receptor (TL/TLR) variants in a one-pot reaction. These results agree well with measurements from specialized instruments (R2=0.64). Furthermore, the DMS reactivity of the TL directly correlates to the stability of the contact (R2=0.68), the first direct evidence that DMS reactivity reports on thermodynamics. Combined with structure prediction, DMS reactivity allowed the development of experimentally accurate 3D models of TLR mutants. These results demonstrate that qDMS-MaPseq is broadly accessible, high-throughput, and directly links DMS reactivity to thermodynamics.