bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oncogenic Mutant p53 Sensitizes Non-Small Cell Lung Cancer Cells to Proteasome Inhibition via Oxidative Stress-Dependent Induction of Mitochondrial Apoptosis
Authors: Chougoni Kranthi Kumar , Neely Victoria , Ding Boxiao , Oduah Eziafa , Lam Vianna , Hu Bin , Koblinski Jennifer E. , Windle Bradford E. , Deb Swati Palit , Deb Sumitra , Radhakrishnan Senthil K. , Harada Hisashi , Grossman Steven R. 
Published: February 2024

AbstractNon-small cell lung cancer (NSCLC) cells with oncogenic mutant p53 alleles (Onc-p53) exhibit significantly higher levels of proteasome activity, indicating that Onc-p53 induces proteotoxic stress which may be leveraged as a therapeutic vulnerability. Proteasome inhibitors (PIs), such as bortezomib (BTZ), can induce toxic levels of oxidative stress in cancer cells and thus we investigated whether PIs exhibit preferential cytotoxicity in Onc-p53 NSCLC cells. Indeed, BTZ and other PIs exhibited the IC506-7-fold lower in Onc-p53 cells vs. wild-type (WT) p53 cells. BTZ cytotoxic effects in Onc-p53 cells were nearly completely rescued by antioxidants such as N-acetyl cysteine, indicating that oxidative stress is the critical driver of BTZ-dependent cytotoxic effects in Onc-p53 cells. Importantly, we observed oxidative stress-dependent transcriptional induction of the pro-apoptotic NOXA with downstream cleaved caspase-3, consistent with apoptotic cell death in Onc-p53 but not in WT p53 cells treated with BTZ, and BTZ-generated oxidative stress was linked to nuclear translocation of NRF2 and transcriptional activation of ATF3, which in turn was required for NOXA induction. Validating BTZ’s translational potential in Onc-p53 NSCLC, BTZ and carboplatin or the BH3-mimetic navitoclax were synergistically cytotoxic in Onc-p53 but not WT p53 cellsin vitro,and BTZ effectively limited growth of Onc-p53 NSCLC xenografts when combined with either carboplatin or navitoclaxin vivo. Our data therefore support further investigation of the therapeutic utility of PIs combined with carboplatin or BH3-mimetics in Onc-p53 human NSCLC as novel therapeutic strategies.SignificanceNon-small cell lung cancer (NSCLC) is the leading cause of cancer death due, in part, to a lack of active therapies in advanced disease. We demonstrate that proteasome inhibitor/BH3-mimetic combination therapy is an active precision therapy in NSCLC cells and tumors expressing oncogenic mutant p53 alleles (Onc-p53).
Environmental drivers of the decline of the fen orchid, Liparis loeselii
Authors: Andersen Dagmar Kappel , Ejrnæs Rasmus , Minter Martine , Riis Tenna , Vinther Erik , Bruun Hans Henrik 
Published: February 2024

AbstractBackgroundLiparis loeseliiis a rare and declining orchid species restricted to rich fens in the Northern Hemisphere. Habitat destruction, eutrophication, drainage and scrub encroachment have been suggested as reasons for the decline. However, which factors are most important is not well understood.AimsBased on vegetation and environmental properties from extant, potential and historicalL. loeseliisites, we i) developed habitat suitability models from either Ellenberg Indicator Values or field-measured environmental properties, and ii) identified the primary reasons for the observed decline ofL. loeselii.ResultsNutrient status was the most important predictor forL. loeseliioccurrence, followed by hydrology proxies (Ellenberg reaction and Ellenberg moisture). Vegetation height and Ellenberg light were of minor importance.ConclusionEffect partitioning based on sites, from whichL. loeseliihas gone locally extinct, pinpointed eutrophication and drainage to be the most likely primary drivers of the species’ demise. Phosphorus limitation induced by discharge of Calcium-rich groundwater seems to be crucial forL. loeseliito sustain populations in landscapes dominated by intensive agricultural.
The Apurinic/Apyrimidinic Endodeoxyribonuclease 1 is an RNA G-quadruplex binding protein and regulates miR-92b expression in cancer cells
Authors: Bellina Alessia , Malfatti Matilde Clarissa , Salgado Gilmar , Fleming Aaron M. , Antoniali Giulia , Gualandi Nicolò , La Manna Sara , Marasco Daniela , Dassi Erik , Burrows Cynthia J. , Tell Gianluca 
Published: February 2024

AbstractIn the last decade, several novel functions of the mammalian Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APE1) have been discovered, going far beyond its canonical function as a DNA repair enzyme, unveiling its potential roles in cancer development. Indeed, it was shown to be involved in DNA G-quadruplex biology and RNA metabolism, most importantly in the miRNA maturation pathway and the decay of oxidized- or abasic-miRNAs during oxidative stress conditions. Furthermore, in recent years several non-canonical pathways of miRNA biogenesis have been described, with a specific focus on guanosine-rich precursors that can form RNA G-quadruplex (rG4) structures. In this study, we show that several miRNA precursors, dysregulated upon APE1-depletion, contain an rG4 motif and that their corresponding target genes are upregulated after APE1-depletion. We also show, both byin vitroassays and by using a HeLa cell model, that APE1 can bind and regulate the folding of an rG4 structure contained in pre-miR92b, with a mechanism strictly dependent on critical lysine residues present in the N-terminal disordered region. Furthermore, APE1 depletion in HeLa cells alters the maturation process of miR-92b, mainly affecting the shuttling between the nucleus and cytosol. Lastly, bioinformatic analysis of APE1-regulated rG4-containing miRNAs supports the relevance of our findings for cancer biology. Specifically, these miRNAs exhibit high prognostic significance in lung, cervical, and liver cancer, as suggested by their involvement in several cancer-related pathways.Significance StatementWe highlight an undescribed non-canonical role of the mammalian Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APE1) in the context of RNA G-quadruplexes (rG4), specifically in the alternative pathway of miRNA maturation of guanosine-rich miRNA precursors. Specifically, APE1 binds these structures and modulates their folding, mainly through its N-terminal region and some residues in its catalytic domain. Moreover, we showed an interesting new role of APE1 in regulating the shuttling and accumulation of miR-92b between the nuclear and cytosolic compartments, opening new perspectives on how APE1 may exercise its role in the miRNA maturation pathway and function. Moreover, APE1-depleted dysregulated miRNAs with rG4 motifs in their precursors have significant prognostic value in lung, cervical, and liver tumors, suggesting potential targets for cancer therapy.
Escape from X inactivation is directly modulated by levels of Xist non-coding RNA
Authors: Hauth Antonia , Panten Jasper , Kneuss Emma , Picard Christel , Servant Nicolas , Rall Isabell , Pérez-Rico Yuvia A. , Clerquin Lena , Servaas Nila , Villacorta Laura , Jung Ferris , Luong Christy , Chang Howard Y. , Zaugg Judith B. , Stegle Oliver , Odom Duncan T. , Loda Agnese , Heard Edith 
Published: February 2024

ABSTRACTIn placental females, one copy of the two X chromosomes is largely silenced during a narrow developmental time window, in a process mediated by the non-coding RNA Xist1. Here, we demonstrate that Xist can initiate X-chromosome inactivation (XCI) well beyond early embryogenesis. By modifying its endogenous level, we show that Xist has the capacity to actively silence genes that escape XCI both in neuronal progenitor cells (NPCs) andin vivo, in mouse embryos. We also show that Xist plays a direct role in eliminating TAD-like structures associated with clusters of escapee genes on the inactive X chromosome, and that this is dependent on Xist’s XCI initiation partner, SPEN2. We further demonstrate that Xist’s function in suppressing gene expression of escapees and topological domain formation is reversible for up to seven days post-induction, but that sustained Xist up-regulation leads to progressively irreversible silencing and CpG island DNA methylation of facultative escapees. Thus, the distinctive transcriptional and regulatory topologies of the silenced X chromosome is actively, directly - and reversibly - controlled by Xist RNA throughout life.
Septin-associated PIPKIγ splice variants drive centralspindlin association with the midbody via PI(4,5)P2
Authors: Russo Giulia , Hümpfer Nadja , Jaensch Nina , Restel Steffen , Schmied Christopher , Heyd Florian , Lehmann Martin , Haucke Volker , Ewers Helge , Krauss Michael 
Published: February 2024

SummaryMammalian cytokinesis critically depends on the phospholipid phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] which serves as docking site for crucial components of the cytokinetic machinery at the plasma membrane. PI(4,5)P2supports several stages of cytokinesis, including actomyosin ring assembly and constriction, membrane tethering of spindle microtubules, and midbody organization. How these various activities of PI(4,5)P2and the underlying mechanisms of local PI(4,5)P2synthesis are orchestrated in space and time has remained elusive. Here, we identify a pivotal role of septin-binding splice variants of PIPKIγ that couple nanoscale PI(4,5)P2synthesis at the ingressing cleavage furrow to late midbody formation. Depletion of PIPKIγ isoforms causes multinucleation and perturbs anillin and septin deposition at the intercellular bridge and at the midbody. These defects are rescued by wild-type kinase, but not by septin binding-deficient or catalytically inactive PIPKIγ variants. We further show that both, septins and PIPKIγ form a complex with centralspindlin, and thereby facilitate the recruitment of centralspindlin to the midbody. Taken together, our findings establish septin-associated PIPKIγ isoforms as key regulators of midbody organization that act through generating a local pool of PI4,5P2required for centralspindlin recruitment and maintenance at the midbody, and for septin association with microtubules.
Human MX1 orchestrates the cytoplasmic sequestration of neo-synthesized influenza A virus vRNPs
Authors: McKellar Joe , García de Gracia Francisco , Aubé Corentin , Chaves Valadão Ana Luiza , Tauziet Marine , Arnaud-Arnould Mary , Rebendenne Antoine , Neyret Aymeric , Labaronne Emmanuel , Ricci Emiliano , Delaval Bénédicte , Gaudin Raphaël , Naffakh Nadia , Gallois-Montbrun Sarah , Moncorgé Olivier , Goujon Caroline 
Published: February 2024

AbstractInterferon-inducible Myxovirus resistance 1 (MX1) proteins are well-known to restrict influenza A virus (IAV) at early stages during viral replication, impairing the viral transcription/replication process. Herein, we show that this early restriction was only partial against human IAVs, whereas a strong inhibition of viral production was observed. Indeed, relatively high levels of IAV mRNAs and proteins were observed in the presence of human (Hs) and mouse (Mm) MX1 proteins but additional inhibition processes occurred at later stages of IAV life cycle. Hence, MmMx1 induced an abnormal nuclear accumulation of the viral nucleoprotein (NP) at late time points post-infection. This block was also observed, albeit to a much lower extent, with HsMX1. In most HsMX1-expressing cells, vRNPs could be exported from the nucleus to the cytoplasm however a potent defect in subsequent vRNP cytoplasmic trafficking was observed. Indeed, vRNPs were found sequestrated together with cellular co-factors YBX1 and Rab11a in large clusters in the vicinity of the microtubule organization center (MTOC). Live imaging experiments revealed that the transient association of HsMX1 with Rab11a-associated vRNPs favoured their dynein-dependant retrograde transport along microtubules towards the MTOC. Importantly, dynein inhibition prevented the vRNP sequestration and significantly rescued infectious viral production in the presence of HsMX1, showing a significant contribution of these abnormal vRNP clusters in HsMX1 antiviral activity. In conclusion, this study provides the first evidence of IAV vRNPs being re-routed and accumulated away from the plasma membrane, through the coordinated action of HsMX1 restriction factor, dynein and the microtubule network.
Genotypic variation in blueberry flower morphology and nectar reward content affects pollinator attraction in a diverse breeding population
Authors: Cromie Juliana , Ternest John J. , Komatz Andrew P. , Adunola Paul M. , Azevedo Camila , Mallinger Rachel E. , Muñoz Patricio R. 
Published: February 2024

ABSTRACTPollination is crucial to obtain optimal blueberry yield and fruit quality. Despite substantial investments in seasonal beekeeping services, blueberry producers consistently report suboptimal pollinator visitation and fruit set in some cultivars. Flower morphology and floral rewards are among the key factors that have shown to contribute to pollinator attraction, however little is known about their relative importance for improving yield in the context of plant breeding. Clarifying the relationships between flower morphology, nectar reward content, pollinator recruitment, and pollination outcomes, as well as their genetic components, can inform breeding priorities for enhancing yield. In the present study, we measured ten flower and nectar traits and indices of successful pollination, including fruit set, seed count, and fruit weight in 38 southern highbush blueberry genotypes. Additionally, we assessed pollinator visitation frequency and foraging behavior over two growing seasons. Several statistical models were tested to optimize the prediction of pollinator visitation and pollination success, including partial least squares, BayesB, ridge-regression, and random forest. Random forest models obtained high predictive abilities for pollinator visitation frequency, with values of 0.54, 0.52, and 0.66 for honey bee, bumble bee, and total pollinator visits, respectively. The BayesB model provided the most consistent prediction of fruit set, fruit weight, and seed set, with predictive abilities of 0.07, -0.08, and 0.42, respectively. Variable importance analysis revealed that genotypic differences in nectar volume had the greatest impact on honey bee and bumble bee recruitment, although preferences for flower morphological traits varied depending on the foraging task. Flower density was a major driving factor attracting nectar-foraging honey bees and bumble bees, while pollen-foraging bumble bees were most influenced by flower accessibility, specifically corolla length and the length-to-width ratio. Corolla length and the length-to-width ratio were also identified as the main predictors of fruit set, fruit weight, and seed count, suggesting that bumble bees and their foraging preferences may play a pivotal role in fruit production. Moderate to high narrow-sense heritability values (ranging from 0.30 to 0.77) were obtained for all floral traits, indicating that selective breeding efforts may enhance cultivar attractiveness to pollinators.
Rational protein engineering to enhance MHC-independent T cell receptors
Authors: Chang Ju-Fang , Landmann Jack H. , Chang Tien-Ching , Tenzin Yangdon , Warrington John M. , Selli Mehmet Emrah , Ritchey Julie , Hsu Yu-Sung , Slade Michael , Gupta Deepesh Kumar , DiPersio John F. , Singh Nathan 
Published: February 2024

AbstractChimeric antigen receptor (CAR)-based therapies have pioneered synthetic cellular immunity against cancer, however remain limited in their scope and long-term efficacy. Emerging data suggest that dysregulated CAR-driven T cell activation causes T cell dysfunction and therapeutic failure. To re-engage the endogenous T cell response, we designed hybrid MHC-independent T cell receptors (miTCRs) by linking antibody variable domains to TCR constant domains. While functional, we observed stark differences in miTCR-driven T cell function that were dependent on receptor orientation. Using predictive structural modeling, we observed significant biochemical conflicts at the hybrid variable-constant domain interface. To overcome this, we performed iterative sequence modifications and structural modeling to design a panel of miTCR variants predicted to have improved interface stability. Functional screening nominated a variant with superior efficacy to all other miTCRs as well as a standard CAR against high burdens of leukemia.Statement of SignificanceImproving the durability of engineered T cell immunotherapies is critical to enhancing efficacy. We used structure-informed design to evolve MHC-independent T cell receptors that drive improved tumor control. This work underscores the central role of synthetic receptor structure on T cell function and provides a framework for improved receptor engineering.
Elucidating TolC Protein Dynamics: Structural Shifts Facilitate Efflux Mediated β-lactam Resistance
Authors: Kantarcioglu Isik , Gaszek Ilona K. , Guclu Tandac F. , Yildiz M. Sadik , Atilgan Ali Rana , Toprak Erdal , Atilgan Canan 
Published: February 2024

ABSTRACTEfflux-mediated β-lactam resistance represents a significant public health challenge, limiting the efficacy of various β-lactam antibiotics against numerous clinically relevant pathogenic bacteria. Structural and functional analyses have revealed that the efflux protein TolC in several Gram-negative bacteria serves as a conduit for antibiotics, bacteriocins, and phages, affecting bacterial susceptibility and virulence. In this study, we conducted a comprehensive examination of the efflux of β-lactam drugs mediated by TolC, employing extensive experimental and computational analyses. Our computational investigations into the molecular dynamics of drug-free TolC revealed critical unidirectional movements of the trimeric TolC and identified residues significantly involved in TolC opening. To corroborate these findings, we performed a whole-gene-saturation mutagenesis assay, systematically mutating each residue of TolC to 19 other amino acids and measuring the fitness effects of these mutations under β-lactam-induced selection. The β-lactams oxacillin, piperacillin, and carbenicillin were selected for this study because they are effluxed by the AcrAB-TolC complex with varying efficiencies. This approach clarified the similarities and differences in the efflux processes of the three β-lactam antibiotics through the trimeric TolC. Further analysis of TolC’s efflux mechanism for these β-lactam antibiotics via steered molecular dynamics simulations revealed the existence of general and drug-specific mechanisms employed by TolC. We identified key positions at the periplasmic entry of TolC whose altered dynamics influence long-range efflux motions as allosteric modulators. Our findings provide valuable insights into the structural dynamics of TolC, establishing a foundation for understanding the key mechanisms behind multidrug resistance and principles for designing new antibiotics and antibiotic derivatives capable of circumventing the bacterial efflux mechanism.
Nova-ST: Nano-Patterned Ultra-Dense platform for spatial transcriptomics
Authors: Poovathingal Suresh , Davie Kristofer , Vandepoel Roel , Poulvellarie Nicholas , Verfaillie Annelien , Corthout Nikky , Aerts Stein 
Published: February 2024

AbstractSpatial transcriptomics workflows using barcoded capture arrays are commonly used for resolving gene expression in tissues. However, existing techniques are either limited by capture array density or are cost prohibitive for large scale atlasing. We present Nova-ST, a dense nano-patterned spatial transcriptomics technique derived from randomly barcoded Illumina sequencing flow cells. Nova-ST enables customized, low cost, flexible, and high-resolution spatial profiling of large tissue sections. Benchmarking on mouse brain sections demonstrates significantly higher sensitivity compared to existing methods, at reduced cost.MotivationSpatial transcriptomics analysis is becoming exceedingly important in biomedical and clinical research. Several platforms for spatial transcriptomics are currently available, but most of these technologies are commercialized making them inflexible and cost prohibitive. The motivation for this work was to establish an open source, flexible and sensitive sequencing-based spatial transcriptomics platform that can provide a considerable cost advantage for performing large scale spatial profiling. We provide thorough and in-depth guidance and resources both for the experimental and computational components of the workflow, to facilitate easy implementation of Nova-ST.
Androgens modulate the immune profile in a mouse model of polycystic ovary syndrome
Authors: Torstensson Sara , Ascani Angelo , Risal Sanjiv , Lu Haojiang , Zhao Allan , Espinosa Alexander , Lindgren Eva , Johansson Maria H. , Eriksson Gustaw , Barakat Maya , Karlsson Mikael C.I. , Svensson Camilla , Benrick Anna , Stener-Victorin Elisabet 
Published: February 2024

AbstractPolycystic ovary syndrome (PCOS) is associated with a low-grade inflammation, but it is unknown how hyperandrogenism, the hallmark of PCOS, affects the immune system. Using a well-established PCOS-like mouse model, we demonstrate that androgen exposure affects immune cell populations in reproductive, metabolic, and immunological tissues differently in a site-specific manner. Co-treatment with flutamide, an androgen receptor antagonist, prevents most of these alterations, demonstrating that these effects are mediated through androgen receptor activation. Dihydrotestosterone (DHT)-exposed mice display a drastically reduced eosinophil population in uterus compared to controls, coupled with lower levels of eotaxin (CCL11), suggesting a reduced recruitment from blood. Decreased frequencies of eosinophils were also seen in visceral adipose tissue (VAT). A higher expression level of CD69, a marker of activation or tissue residency, was consistently found on natural killer (NK) cells in all analyzed tissues. However, a higher frequency of NK cells and elevated levels of IFN-γ and TNF-α were only seen in uteri of androgen-exposed mice, while NK cell frequencies were unaffected in all other analyzed compartments. Distinct alterations of macrophages in ovaries, uterus and VAT were also found in DHT-exposed mice and could potentially be linked to PCOS-like traits of the model. Indeed, androgen-exposed mice were insulin resistant and displayed an aberrant immune profile in VAT, albeit unaltered fat mass. Collectively, we demonstrate that hyperandrogenism causes tissue-specific alterations of immune cells in reproductive organs and VAT, which could have considerable implications on tissue function and contribute to the reduced fertility and metabolic comorbidities associated with PCOS.
Comparison of gnotobiotic communities reveals unexpected amino acid metabolism by the pre-weaning microbiome
Authors: Lubin Jean-Bernard , Silverman Michael A. , Planet Paul J. 
Published: February 2024

AbstractThe intestinal microbiome during infancy and childhood has distinct compositions and metabolic functions to that of adults. We recently published a gnotobiotic mouse model of the pre-weaning microbiome (PedsCom), which retains a pre-weaning configuration during the transition from a milk-based diet to solid foods and leads to a stunted immune system and susceptibility to enteric infection. Here we compared the phylogenetic and metabolic relationship of the PedsCom consortium to the adult-derived gnotobiotic communities, Altered Schaedler Flora and Oligo-MM12. We find that PedsCom contains several unique functions relative to adult-derived mouse consortia. In particular, amino acid degradation metabolic modules are more prevalent among PedsCom isolates, which is in line with the ready availability of these nutrients in milk. Indeed, metabolomic analysis showed significantly lower levels of free amino acids in the intestinal contents of adult PedsCom colonized mice versus Oligo-MM12 controls. Thus, enhanced amino acid metabolism is a prominent feature of the pre-weaning microbiome that may facilitate design of early life microbiome interventions.