bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroRNA-34a suppresses KLF2 to promote pathological angiogenesis through the CXCR4/CXCL12 pathway in age-related macular degeneration
Authors: Colasanti Jason J. , Lin Joseph B. , Terao Ryo , Lee Tae Jun , Santeford Andrea , Apte Rajendra S. 
Published: February 2025

AbstractAge-related macular degeneration (AMD), characterized by pathologic choroidal neovascularization (CNV), is a leading cause of vision loss in the elderly. Vascular endothelial growth factor A (VEGFa) antagonists can prevent acute vision loss, but high treatment burden and loss of efficacy with chronic therapy highlight the need to explore alternative mechanisms. Recently, microRNA-34a (miR-34a) has emerged as a key regulator in aging and age-related diseases, but its role in neovascular AMD is unclear. In an injury-induced murine CNV model, we discovered miR-34a promoted pathological angiogenesis, without altering expression of Vegfa or its receptor Kdr, the canonical regulators of CNV. Mechanistically, miR-34a directly targets and inhibits the transcription factor KLF2 thereby upregulating the pro-angiogenic factors CXCR4 and CXCL12. Finally, we show miR-34a exacerbates CNV in aged mice and is expressed in CNV lesions excised from wet AMD patients. These findings establish a causal link between the age-related miR-34a and neovascularization in AMD.TeaserIdentification of a molecular mechanism involved in the pathogenesis of a prevalent and debilitating age-related ocular disease.
Wnt-dependent spatiotemporal reprogramming of bone marrow niches drives fibrosis
Authors: Banjanin Bella , Nagai James , Mun YeVin , Fuchs Stijn , Snoeren Inge , Boers Joachim , Ruiz Tejada Segura Mayra L. , Mora Hector Tejeda , Galyga Anna Katharina , Benabid Adam , Sarkis Rita , Naveiras Olaia , Rizk Marta , Wolf Michael , Craveiro Rogerio B. , Peisker Fabian , Stalmann Ursula , Pritchard Jessica E. , Ryou Hosuk , Alham Nasullah Khalid , Weiler Marek , Kiessling Fabian , Lammers Twan , Migliaccio Anna Rita , Sivaraj Kishor Kumar , Adams Ralf H. , Bindels Eric , Gribnau Joost , Royston Daniel , Gleitz Hélène F.E , Kramann Rafael , Nombela-Arrieta César , Costa Ivan G. , Schneider Rebekka K. 
Published: February 2025

AbstractBone marrow fibrosis is the most extensive matrix remodeling of the microenvironment and can includede novoformation of bone (osteosclerosis). Spatiotemporal information on the contribution of distinct bone marrow niche populations to this process is incomplete. We demonstrate that fibrosis-inducing hematopoietic cells cause profibrotic reprogramming of perivascular CXCL12 abundant reticular (CAR) progenitor cells resulting in loss of their hematopoiesis-support and upregulation of osteogenic and pro-apoptotic programs. In turn, peritrabecular osteolineage cells (OLCs) are activated in an injury-specific, Wnt-dependent manner, comparable to skeletal repair. OLCs fuel bone marrow fibrosis through their expansion and skewed differentiation, resulting in osteosclerosis and expansion of Ly6a+ fibroblasts. NCAM1 expression marks peritrabecular OLCs and their expansion into the central marrow is specific for fibrosis in mice and patients. Peritrabecular stromal b-catenin expression is linked to fibrosis in patients and inhibition of Wnt signaling reduces bone marrow fibrosis and osteosclerosis, possibly being a clinically relevant therapeutic target.
Evaluation of the Safety and Efficacy of the Respiratory Syncytial Virus FG Chimeric Vaccine KD-409 in Rodent Models for Maternal and Pediatric Vaccination
Authors: Yamaue Ryo , Terashima Madoka , Soejima Kenji , Torikai Masaharu 
Published: February 2025

ABSTRACTRespiratory syncytial virus (RSV) causes severe infection in neonates and infants. However, a suitable RSV vaccine for children has yet to be approved. We developed an effective and safe RSV vaccine for newborns and children. Accordingly, we evaluated the safety and efficacy of the RSV FG chimeric protein KD-409, which incorporates a highly conserved region of the RSV G protein into the RSV F protein, in several rodent models. We confirmed the effect of our vaccine-induced antibody transfer using a guinea pig model. Subsequently, we evaluated the exacerbation of infection in a BALB/c mouse model of passive immunity, which was designed to mimic the vaccination of pregnant women. Notably, KD-409 in the presence of alum did not exacerbate infection, which occurred upon administering pre-F with alum. Our active immunization model of BALB/c mice, which simulated vaccination with a pediatric vaccine, suggested that KD-409 with alum was less likely to exacerbate inflammation than FI-RSV or pre-F with alum. The efficacy was evaluated in a cotton rat model, in which KD-409 demonstrated better protection against infection than pre-F without adjuvant, the only currently approved formulation for immunizing pregnant women. Collectively, antibody transfer in pregnant guinea pigs during immunization, safety in mice during passive and active immunization, and efficacy in cotton rats demonstrate the high potential of KD-409 as a novel vaccine candidate. Our results provide insights into the potential of KD-409 as a safe and effective next-generation RSV vaccine that can cover the neonatal-to-pediatric age range.IMPORTANCEThe safety and efficacy of KD-409, an RSV FG chimeric protein, were evaluated in appropriate rodents. We found that KD-409 was less likely to exacerbate infections and symptoms, and exhibited superior safety and efficacy to pre-F without adjuvant, which is the only approved vaccine for pregnant women. Thus, KD-409 represents a valuable immunization modality for maternal and pediatric immunization.
Putative interfollicular stem cells of skin epidermis possess a specific mechanical signature that evolves during aging
Authors: Miny Sarah , Runel Gaël , Chlasta Julien , Lapart Jean-André , Bonod Christelle 
Published: February 2025

AbstractSkin homeostasis and self-renewal are partially maintained by interfollicular stem cells (ISCs), located in the basal layer above the dermal papillae of the dermo-epidermal junction (DEJ). Aging leads to a decline in skin renewal and a concurrent reduction in stem cell potential. It is also marked by disorganization of the extracellular matrix in both the DEJ and dermis, and flattening of the DEJ. To better understand ISC aging, new methods are needed to characterize ISCs and their environment. Since mechanical properties of cells and their substrate influence cell fate, we employed atomic force microscopy to explore whether ICSs niches and the DEJ exhibit distinct mechanical properties. Our findings reveal that ISCs possess greater stiffness than other basal cells, a mechanical signature that diminishes with age. Additionally, the DEJ beneath ISCs shows higher stiffness than under other basal cells, providing ISCs with a specific mechanical environment, which also deteriorates during aging.In vitro, sorting of ISCs based on MCSP expression effectively isolates ISCs beneath the dermal papillae, allowing the measurement of their mechanical signature and stemness potential under varying mechanical conditions. The study of ISC mechanical signatures offers a promising approach for characterizing 3D skin models and understanding defects in skin renewal and wound healing.
The response of mitochondrial position to glucose stimulation in a model system of the pancreatic beta cell
Authors: Perez Luis , Ng Xue Wen , Piston David W. , Mukherji Shankar 
Published: February 2025

AbstractThe compartmentalization of eukaryotic cells into membrane-bound organelles with specific subcellular positioning enables precise spatial and temporal control of cellular functions. While functionally significant mitochondrial localization has been demonstrated in cells such as neurons, it remains unclear how general these cell principles are. Here, we examine the spatial organization of mitochondria within MIN6 pancreatic beta cells under variable glucose conditions. We observe glucose-dependent redistributions of mitochondria, favoring peripheral localization at elevated glucose levels when insulin secretion is also elevated. Our results suggest that active mitochondrial transport along microtubules and calcium activity, but not ATP synthesis, are critical regulators of this redistribution. We derived a mathematical model that reveals a putative affinity of the mitochondria for cellular membranes competes with mitochondrial microtubule attachment to play an important role in establishing the mitochondrial spatial patterns we observe. These results suggest that mitochondrial positioning may contribute to optimizing energy delivery in response to local demand, potentially representing a general regulatory mechanism across various cell types.
Small and large extracellular vesicles from human preovulatory follicular fluid display distinct ncRNA cargo profile and differential effect on granulosa cell line KGN
Authors: Varik Inge , Saretok Katariina Johanna , Rosenberg Kristine , Quintero Ileana , Puhka Maija , Volkova Nataliia , Trošin Aleksander , Guazzi Paolo , Velthut-Meikas Agne 
Published: February 2025

ABSTRACTFollicular fluid extracellular vesicles (FF EVs) facilitate communication between oocytes and somatic cells within the ovarian follicle, playing a pivotal role in follicular development. This study highlights the molecular and functional distinctions between small (SEV) and large (LEV) FF EV subpopulations, revealing their specialized regulatory roles in granulosa cell (GC) biology and their consequential impact on ovarian function. Single-EV profiling uncovered distinct tetraspanin distributions, with LEVs containing a lower proportion of CD9/CD63/CD81-positive particles compared to SEVs. Functionally, SEVs reduced estradiol secretion by GCs, whereas LEVs enhanced progesterone production, demonstrating their differential effects on steroidogenesis. Transcriptomic analysis revealed extensive SEV-induced changes in GC gene expression, affecting pathways involved in transcription, TGF-β signaling, extracellular matrix (ECM) remodeling, and cell cycle regulation. In contrast, LEVs elicited minimal transcriptional changes, primarily modulating genes associated with immune regulation and oxidative stress defense. Small RNA sequencing further revealed distinct non-coding RNA (ncRNA) profiles, with SEVs enriched in miRNAs targeting pathways critical for GC differentiation, while LEVs carried higher levels of piRNAs implicated in maintaining genomic stability. These findings advance our understanding of FF EV-mediated intercellular communication and underscore the importance of investigating EV subpopulations independently.
TRPV2 and TRPM2 channels facilitate pulmonary endothelial barrier recovery after ROS-induced permeability
Authors: Schaller Lena , Gudermann Thomas , Dietrich Alexander 
Published: February 2025

ABSTRACTReactive oxygen species (ROS), such as hydrogen peroxide (H2O2), are known signaling molecules that increase endothelial barrier permeability. In this study, we investigated the roles of two redox-sensitive transient receptor potential (TRP) ion channels, TRPM2 and TRPV2, in H2O2- induced endothelial barrier dysfunction. Using primary human pulmonary microvascular endothelial cells (HPMEC), we employed impedance-based resistance measurements, Western blot, and immunofluorescence staining to assess the effects of H2O2on the endothelial barrier. Exposure to sublytic concentrations of H2O2caused an acute loss of endothelial barrier integrity, accompanied by the cleavage of vascular endothelial cadherin (VE-cadherin), which was also apparent after application of the TRPV2 activator cannabidiol. The inhibition of either TRPV2 with tranilast or a disintegrin and metalloprotease domain-containing protein 10 (ADAM10) with GI254023X significantly reduced H2O2-induced VE-cadherin cleavage, while TRPM2 inhibition by econazole significantly increased H2O2-driven VE-cadherin cleavage. Although inhibition of either TRP channel did not prevent the initial loss of barrier resistance upon H2O2exposure, both were essential for the subsequent recovery of barrier integrity. Time-course immunofluorescence stainings revealed that HPMEC barrier recovery involved a transient localization of N-cadherin proteins at cell-cell junctions, which were replaced by VE-cadherin within 90 minutes. This process of cadherin-switching did not occur upon inhibition of TRPV2 or ADAM10. Our results highlight complementary roles for TRPM2 and TRPV2 as redox sensitive ion channels in the microvascular endothelium and provide insight into the mechanisms underlying pulmonary microvascular endothelial barrier recovery.Graphical Abstract: See text for more details
Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
Authors: Xian Wenfei , Carbonell-Bejerano Pablo , Rabanal Fernando A. , Bezrukov Ilja , Reymond Philippe , Weigel Detlef 
Published: February 2025

AbstractSomatic mutations are particularly relevant for long-lived organisms. Sources of somatic mutations include imperfect DNA repair, replication errors, and exogenous damage such as ultraviolet radiation. A previous study estimated a surprisingly low number of somatic mutations in a 234-year-old individual of the pedunculate oak (Quercus robur), known as the Napoleon Oak. It has been suggested that the true number of somatic mutations was underestimated due to gaps in the reference genome and too conservative filtering of potential mutations. We therefore generated new high-fidelity long-read data for the Napoleon Oak (n= 12) to produce both a pseudo-haploid genome assembly and a partially phased diploid assembly. The high heterozygosity allowed for complete reconstruction of phased and gapless centromeres for 22 of the 24 chromosomes. On the other hand, the high heterozygosity posed challenges for short-read alignments. Use of only the pseudo-haploid assembly as a reference led to potential misalignments, while use of only the diploid assembly reduced variant detection sensitivity. Since most somatic mutations are layer-specific, the observed frequency is expected relatively low, even where all cells in a single layer contain a specific mutation. To address this challenge, we employed a read assignment strategy, selecting the appropriate reference sequence (pseudo-haploid or diploid) based on alignment score and mapping quality. Ultimately, we identified 198 high-confidence somatic mutations, compared with 17 somatic mutations identified before with the same set of short reads. Our approach thus increased the total estimated annual mutation rate by a factor of five.
Depolarizing afterpotentials in rodent mEC layer II neurons vary gradually across all principal cell types
Authors: Kümpfbeck Franziska S. , Nagele Johannes , Felmy Felix , Herz Andreas V.M. 
Published: February 2025

AbstractPrincipal cells in Layer II (LII) of the rodent medial entorhinal cortex (mEC) often discharge in short burst episodes, whose biophysical mechanism and biological function are not fully understood. As shown byin vitrorecordings in rats andin vivorecordings in mice, action potentials of stellate cells (SCs) and pyramidal cells (PCs) in mEC LII can trigger depolarizing afterpotentials (DAPs) that facilitate spike doublets and burst firing.In vitrorecordings in mice confirm these findings for SCs and two additional cell types intermediate between SCs and PCs but suggest that mouse PCs generate minute DAPs only. To better understand the diversity and physiology of the intermediate LII mEC cell types, we performed slice experiments in Long Evans rats of both sexes and analyzed the data using clustering techniques. The analysis suggests four distinct cell clusters, reminiscent of previous observations in mice. On purpose, DAP properties were not used for the cluster analysis so that they could be studied post-hoc in an unbiased manner. Our results show that characteristic features of DAPs and other physiological markers are broadly distributed within each cell class and vary gradually from cluster to cluster, forming a continuum of biophysical properties.
Dynamic and Biphasic Regulation of Cell Migration by Ras
Authors: Lin Yiyan , Parajón Eleana , Yuan Qinling , Ye Siyu , Qin Guanghui , Deng Yu , Borleis Jane , Koyfman Ariel , Iglesias Pablo A. , Konstantopoulos Konstantinos , Robinson Douglas N. , Devreotes Peter N. 
Published: February 2025

AbstractRas has traditionally been regarded as a positive regulator and therapeutic target due to its role in cell proliferation, but recent findings indicate a more nuanced role in cell migration, where suppressed Ras activity can unexpectedly promote migration. To clarify this complexity, we systematically modulate Ras activity using various RasGEF and RasGAP proteins and assess their effects on migration dynamics. Leveraging optogenetics, we assess the immediate, non-transcriptional effects of Ras signaling on migration. Local RasGEF recruitment to the plasma membrane induces protrusions and new fronts to effectively guide migration, even in the absence of GPCR/G-protein signaling whereas global recruitment causes immediate cell spreading halting cell migration. Local RasGAP recruitment suppresses protrusions, generates new backs, and repels cells whereas global relocation either eliminates all protrusions to inhibit migration or preserves a single protrusion to maintain polarity. Consistent local and global increases or decreases in signal transduction and cytoskeletal activities accompany these morphological changes. Additionally, we performed cortical tension measurements and found that RasGEFs generally increase cortical tension while RasGAPs decrease it. Our results reveal a biphasic relationship between Ras activity and cellular dynamics, reinforcing our previous findings that optimal Ras activity and cortical tension are critical for efficient migration.SignificanceThis study challenges the traditional view of Ras as solely a positive regulator of cell functions by controlling of gene expression. Using optogenetics to rapidly modulate Ras activity inDictyostelium, we demonstrate a biphasic relationship between Ras activity and migration: both excessive and insufficient Ras activity impair cell movement. Importantly, these effects occur rapidly, independent of transcriptional changes, revealing the mechanism by which Ras controls cell migration. The findings suggest that optimal Ras activity and cortical tension are crucial for efficient migration, and that targeting Ras in cancer therapy should consider the cell’s initial state, aiming to push Ras activity outside the optimal range for migration. This nuanced understanding of the role of Ras in migration has significant implications for developing more effective cancer treatments, as simply inhibiting Ras might inadvertently promote metastasis in certain contexts.
Mrx6 binds the Lon protease Pim1 N-terminal domain to confer selective substrate specificity and regulate mtDNA copy number
Authors: Schrott Simon , Gerle Charlotte , Bibinger Sebastian , Bertgen Lea , Marino Giada , Schwenkert Serena , Rathberger Romina , Herrmann Johannes M. , Osman Christof 
Published: February 2025

ABSTRACTMitochondrial DNA (mtDNA) copy number regulation remains incompletely understood, despite its importance in cellular function. InSaccharomyces cerevisiae, Mrx6 belongs to the Pet20-domain-containing protein family, consisting of Mrx6, Pet20, and Sue1. Notably, absence of Mrx6 leads to increased mtDNA copy number. Here, we identify the C-terminus of Mrx6 as essential for its stability and interaction with the mitochondrial matrix protein Mam33. Deletion of Mam33 mimics the effect of Mrx6 loss, resulting in elevated mtDNA copy number. Bioinformatics, mutational analyses, and immunoprecipitation studies reveal that a subcomplex of Mam33 and Mrx6 trimers interacts with the substrate recognition domain of the conserved mitochondrial Lon protease Pim1 through a bipartite motif in the Pet20 domain of Mrx6. Loss of Mrx6, its paralog Pet20, Mam33, or mutations disrupting the interaction between Mrx6 and Pim1 stabilize key proteins required for mtDNA maintenance, the RNA polymerase Rpo41 and the HMG-box-containing protein Cim1. We propose that Mrx6, alongside Pet20 and Mam33, regulates mtDNA copy number by modulating substrate degradation through Pim1. Additionally, Mrx6 loss alters Cim1’s function, preventing the detrimental effect on mtDNA maintenance observed upon Cim1 overexpression. The presence of three Pet20-domain proteins in yeast implies broader roles of Lon protease substrate recognition beyond mtDNA regulation.
Balancing Act: Groundwater microbiome’s resilience and vulnerability to hydroclimatic extremes
Authors: Wang He , Herrmann Martina , Schroeter Simon A. , Zerfaß Christian , Lehmann Robert , Lehmann Katharina , Ivanova Arina , Pohnert Georg , Gleixner Gerd , Trumbore Susan E. , Totsche Kai Uwe , Küsel Kirsten 
Published: February 2025

AbstractGroundwater health is increasingly threatened by climate change, which alters precipitation patterns, leading to groundwater recharge shifts. These shifts impact subsurface microbial communities, crucial for maintaining ecosystem functions. In this decade-long study of carbonate aquifers, we analyzed 815 bacterial 16S rRNA gene datasets, 226 dissolved organic matter (DOM) profiles, 387 metabolomic datasets, and 174 seepage microbiome sequences. Our findings reveal distinct short- and long-term temporal patterns of groundwater microbiomes driven by environmental fluctuations. Microbiomes of hydrologically connected aquifers exhibit lower temporal stability due to stochastic processes and greater susceptibility to surface disturbances, yet they demonstrate remarkable resilience. Conversely, isolated aquifer microbiomes show resistance to short-term changes, governed by deterministic processes, but exhibit reduced stability under prolonged stress. Variability in seepage-associated microorganisms, DOM, and metabolic diversity further drive microbiome dynamics. These findings highlight the dual vulnerability of groundwater systems to acute and chronic pressures, emphasizing the critical need for sustainable management strategies to mitigate the impacts of hydroclimatic extremes.