bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diverse microtubule-destabilizing drugs induce equivalent molecular pathway responses in endothelial cells
Authors: Horin Lillian J. , Sonnett Matthew , Li Boyan , Mitchison Timothy J. 
Published: January 2025

AbstractDrugs that modulate microtubule (MT) dynamics are well-characterized at the molecular level, yet the mechanisms linking these molecular effects to their distinct clinical outcomes remain unclear. Several MT-destabilizing drugs, including vinblastine, combretastatin A4, and plinabulin, are widely used, or are under evaluation for cancer treatment. Although all three depolymerize MTs, they do so through distinct biochemical mechanisms. Furthermore, their clinical profiles and therapeutic uses differ considerably. To investigate whether differential modulation of molecular pathways might account for clinical differences, we compared gene expression and signaling pathway responses in human pulmonary microvascular endothelial cells (HPMECs), alongside the MT-stabilizing drug docetaxel and the pro-inflammatory cytokine TNF-α. RNA-sequencing and phosphoproteomics revealed that all three MT destabilizers triggered equivalent molecular responses. The substantial changes in gene expression caused by MT destabilization were completely dependent on Rho family GTPase activation. These findings suggest that the distinct clinical profiles of the destabilizing drugs depend on differences in pharmacokinetics (PK) and tissue distribution rather than molecular actions. The washout rate of the three drugs differed, which likely translates to PK differences. Our data provide insights into how MT destabilization triggers signaling changes, potentially explaining how these drugs induce cell cycle re-entry in quiescent cells and how plinabulin ameliorates chemotherapy-induced neutropenia.Significance StatementMicrotubule (MT)-destabilizing drugs, despite their potential for toxicity, are used to treat a surprising range of diseases, including cancers, inflammatory disorders, and parasitic infections. To investigate how drugs with apparently similar actions on MTs achieve diverse clinical effects, we compared the molecular pathways that are activated by three drugs with different clinical profiles, vinblastine, combretastatin A4, and plinabulin. All three elicited similar gene expression responses via Rho GTPase activation. This finding suggests that their distinct clinical effects are not caused by different effects on MTs, but rather by differences in drug transport, pharmacokinetics or tubulin isotype affinity. Our findings provide insights into how plinabulin might protect the bone marrow and may help medicinal chemists design MT drugs for new applications.
Structures of the 26S proteasome in complex with the Hsp70 cochaperone Bag1 reveal a novel mechanism of ubiquitin-independent proteasomal degradation
Authors: Maestro-López Moisés , Cheung Cheng Tat , Muntaner Jimena , Menéndez Margarita , Alonso Melissa , Schweitzer Andreas , Cuéllar Jorge , Valpuesta José María , Sakata Eri 
Published: January 2025

AbstractThe 26S proteasome primarily degrades proteins marked by polyubiquitin chains. Although ubiquitin-independent pathways for proteasomal degradation exist, the mechanisms involved remain poorly understood. Bag1 links the Hsp70 chaperone to the 26S proteasome, recruiting Hsp70-bound aberrant proteins for degradation. Here, we present high-resolution cryo-EM structures of the Bag1-bound 26S proteasome, which reveal unprecedented conformational changes within the 19S regulatory particle. Bag1 binding to the Rpn1 subunit induces a dramatic reconfiguration of AAA+ ATPase subunits, disrupting the canonical spiral staircase conformation and remodeling the central channel architecture. This creates a large cavity above the substrate entry gate of the 20S core particle, enabling the direct entry of Hsp70 clients into the proteolytic chamber. Thus, in this ubiquitin-independent degradation pathway, unfolded proteins can bypass the need for both client ubiquitination and ATP hydrolysis for degradation.
The E2F4 transcriptional repressor is a key mechanistic regulator of colon cancer resistance toirinotecan(CPT-11)
Authors: Matsubara Junichi , Li Yong Fuga , Koul Sanjay , Mukohyama Junko , Valencia Salazar Luis E. , Isobe Taichi , Qian Dalong , Clarke Michael F. , Sahoo Debashis , Altman Russ B. , Dalerba Piero 
Published: January 2025

ABSTRACTBackground.Colorectal carcinomas(CRCs) are seldom eradicated by cytotoxic chemotherapy. Cancer cells with stem-like functional properties, often referred to as“cancer stem cells”(CSCs), display preferential resistance to several anti-tumor agents used in cancer chemotherapy, but the molecular mechanisms underpinning their selective survival remain only partially understood.Methods.In this study, we usedTranscription Factor Target Genes(TFTG) enrichment analysis to identify transcriptional regulators (activators or repressors) that undergo preferential activation by chemotherapy in CRC cells with a“bottom-of-the-crypt”phenotype (EPCAM+/CD44+/CD166+; CSC-enriched) as compared to CRC cells with a“top-of-the-crypt”phenotype (EPCAM+/CD44neg/CD166neg; CSC-depleted). The two cell populations were purified in parallel byfluorescence-activated cell sorting(FACS) from apatient-derived xenograft(PDX) line representative of a moderately differentiated human CRC, followingin vivochemotherapy withirinotecan(CPT-11). The transcriptional regulators identified as differentially activated were tested for differential expression in normal vs. cancer tissues, and in cell populations enriched in stem/progenitor cell-types as compared to differentiated lineages (goblet cells, enterocytes) in the mouse colon epithelium. Finally, the top candidate was tested for mechanistic contribution to drug-resistance by selective down-regulation usingshort-hairpin RNAs(shRNAs).Results.Our analysis identified E2F4 and TFDP1, two core components of the DREAM transcriptional repression complex, as transcriptional modulators preferentially activated byirinotecanin EPCAM+/CD44+/CD166+as compared to EPCAM+/CD44neg/CD166negcancer cells. The expression levels of both genes (E2F4,TFDP1) were found up-regulated in CRCs as compared to human normal colon tissues, and in a sub-population of mouse colon epithelial cells enriched in stem/progenitor elements (Epcam+/Cd44+/Cd66alow/Kitneg) as compared to other sub-populations enriched in either goblet cells (Epcam+/Cd44+/Cd66alow/Kit+) or enterocytes (Epcam+/Cd44neg/Cd66ahigh). Most importantly, E2F4 down-regulation using shRNAs dramatically enhanced the sensitivity of human CRCs toin vivotreatment withirinotecan, across three independent PDX models.Conclusions.Our data identified E2F4 and the DREAM repressor complex as critical regulators of human CRC resistance toirinotecan, and as candidate targets for the development of chemo-sensitizing agents.
Bi-specific CAR-iNKT cell immunotherapy for high-risk KMT2A-rearranged leukemia outperforms CAR-T in an NKG2D-dependent manner and eradicates leptomeningeal disease
Authors: Ren Hongwei , Elliott Natalina , Lye Bryan , Sharif Shohan Mohammad Umer , Cross Joe W , Field Lucy , Ponnusamy Kanagaraju , Rice Siobhan , Jackson Thomas , Leontari Ilia , Ouazzani Nouhad El , Thomas Rebecca , Inglott Sarah , Bartram Jack , Smith Owen , Bond Jonathan , Roberts Irene AG , Halsey Christina , Bashford-Rogers Rachael , Milne Thomas A , Roy Anindita , Karadimitris Anastasios 
Published: January 2025

AbstractCurrent therapies, including autologous CAR-T immunotherapy, fail to cure half of infants withKMT2A-rearranged acute lymphoblastic leukemia (KMT2Ar-ALL). Here we deploy allogeneic iNKT cells, ‘innately’ more powerful effectors than T cells, and equip them with CD19- and/or CD133-targeting CARs. Compared to mono-specific counterparts and bi-specific CAR-T, CD19-CD133 bi-specific CAR-iNKT have more potent anti-leukemia activity, they effectively target CAR antigen-low leukemia, eradicate medullary and leptomeningeal leukemia and induce sustained remissions without discernible hematologic toxicity. Mechanistically, dynamic CAR- and CAR antigen-dependent upregulation of the activating innate receptor NKG2D and its engagement by corresponding ligands on KMT2Ar-ALL cells lead to more potent anti-leukemia effect of CAR-iNKT over CAR-T cells, including against CAR antigen-negative leukemia. Thus, by engaging with two different types of leukemia-associated targets, CAR-iNKT provide a powerful platform for the treatment of KMT2Ar-ALL. This approach can be readily adapted for other high-risk malignancies, including those with otherwise difficult to target leptomeningeal involvement.
Molecular Insights into Fungal Innate Immunity Using theNeurospora crassa - Pseudomonas syringaeModel
Authors: Stark Frances Grace , Torii-Karch Mari , Yuvaraj Sudyut , Bonometti Lucas , Gladieux Pierre , Glass N. Louise , Krasileva Ksenia 
Published: January 2025

AbstractRecent comparative genomics and mechanistic analyses support the existence of a fungal immune system. Fungi encode genes with features similar to non-self recognition systems in plants, animals, and bacteria. However, limited functional or mechanistic evidence exists for the surveillance-system recognition of heterologous microbes in fungi. We found thatNeurosporaspecies coexist withPseudomonasin their natural environment. We leveraged two model organisms,Neurospora crassaandPseudomonas syringaeDC3000 (PSTDC3000) to observe immediate fungal responses to bacteria. PSTDC3000 preferentially surroundsN. crassacells on a solid surface, causing environmental dependent growth responses, bacterial proliferation and varying fungal fitness. Specifically, the Type III secretion system (T3SS) ΔhrcC mutant of PSTDC3000 colonizedN. crassahyphae less well. To dissect initial cellular signaling events within the population of germinated asexual spores (germlings), we performed transcriptomics onN. crassaafter PSTDC3000 inoculation. Upon contact with live bacteria, a subpopulation of fungal germlings initiate a response as early as ten minutes post-contact revealing transcriptional differentiation of Reactive Oxygen Species (ROS) mechanisms, trace metal warfare, cell wall remodeling dynamics, multidrug-efflux transporters, secondary metabolite synthesis, and excretion. We dissected mutants of plausible receptors, signaling pathways, and responses thatN. crassauses to detect and mount a defense against PSTDC3000 and found seven genes that influence resistant and susceptibility phenotypes ofN. crassato bacterial colonization. Mutants in genes encoding a ctr copper transporter (tcu-1), ferric reductase (fer-1), superoxide reductase (sod-2), multidrug resistance transporter (mdr-6), a secreted lysozyme-Glycoside hydrolase (lyz) and the Woronin body tether leashin (NCU02793,lah-1andlah-2) showed a significant reduction of growth in the presence of bacteria, allowing the bacteria to fully take over the fungal mycelium faster than wildtype. In this study we provide a bacterial-fungal model system within Dikarya that allows us to begin to dissect signaling pathways of the putative fungal immune system.
A high-quality reference genome for the Ural Owl (Strix uralensis) enables investigations of cell cultures as a genomic resource for endangered species
Authors: Chrysostomakis Ioannis , Mozer Annika , Bruno Di-Nizo Camilla , Fischer Dominik , Sargheini Nafiseh , von der Mark Laura , Huettel Bruno , Astrin Jonas J. , Töpfer Till , Böhne Astrid 
Published: January 2025

AbstractWe generated a reference genome for the Ural Owl (Strix uralensis) based on high-fidelity (HiFi) long reads and chromosome conformation capture (Hi-C) data. The primary assembly had a size of 1.38 gigabase pairs (Gb), while the alternative assembly (i.e., the second haplotype) had a size of 1.3 Gb. The corresponding N50 was 90.1 Mb for the primary assembly and 17.0 Mb for the alternate assembly. The primary assembly achieved a compleasm BUSCO completeness of 99.94%, indicative of a high-quality genome. In addition, cell culture of progressive passages was evaluated as a tool for genetic resources. To this aim, a cell culture of the same Ural Owl individual was established from skin tissue. At passages 5 and 10, cells were harvested and investigated for possible nucleotide variants by analysing the karyotype and single nucleotide polymorphisms (SNPs) to investigate the effect of cell culture on mutation. Karyotyping confirmed the number of chromosomes and no large variants were observed, while SNP analysis revealed a minor presence of short variants over cell passages. The established reference genome is a valuable resource for ongoing conservation efforts but also generally for avian genomics research. Cell culture, on the other hand, requires more research to determine if progressive passages can be safely used in genomic research.
Lipid Nanoparticles for the Delivery of CRISPR/Cas9 Machinery to Enable Site-Specific Integration of CFTR and Mutation-Agnostic Disease Rescue
Authors: Foley Ruth A. , Ayoub Paul G. , Sinha Vrishti , Juett Colin , Sanoyca Alicia , Duggan Emily C. , Lathrop Lindsay E. , Bhatt Priyanka , Coote Kevin , Illek Beate , Gomperts Brigitte N. , Kohn Donald B. , Jonas Steven J. 
Published: January 2025

AbstractWe report the engineering of lipid nanoparticles (LNPs) to transport CRISPR/Cas9 payloads, including double-stranded DNA (dsDNA) donor templates, designed for homology directed repair (HDR)-mediated site-specific insertion of the cystic fibrosis transmembrane conductance regulator (CFTR) gene to correct cystic fibrosis (CF) in diseased airway epithelium. We screened various nanoparticle formulations, adjusting ratios of Cas9-encoding mRNA, single guide RNAs (sgRNAs), and dsDNA donor templates to optimize gene editing using human bronchial epithelial cells (16HBE14o-) harboring a CF-causing mutation (G542X). Populations of G542X cells editedviaLNP delivery ofCFTRdonors achieved 3 – 3.5% gene integration and yielded comparable CFTR protein expression compared to normal 16HBE14o- controls. These edited populations exhibit restoration of CFTR-dependent Cl- current toca.80% of values measured in normal 16HBE14o- cell monolayers. This LNP platform adds capabilities for transporting large gene editing machinery to airway epithelial cells for genomic integration of entire genes, enabling therapeutic solutions that achieve correction of any CF-causing mutation.
Allosteric Modulation of Pathological Ataxin-3 Aggregation: A Path to Spinocerebellar Ataxia Type-3 Therapies
Authors: Silva Alexandra , Duarte-Silva Sara , Martins Pedro M. , Rodrigues Beatriz , Serrenho Débora , Vilasboas-Campos Daniela , Teixeira-Castro Andreia , Vieyto-Nuñez Julio , Mieres-Perez Joel , Figueiredo Francisco , Fraga Joana , Noble James , Lantz Carter , Sepanj Niki , Monteiro-Fernandes Daniela , Guerreiro Sara , Neves-Carvalho Andreia , Pereira-Sousa Joana , Klärner Frank-Gerrit , Schrader Thomas , Loo Joseph A. , Pastore Annalisa , Sanchez-Garcia Elsa , Bitan Gal , Carvalho Ana Luísa , Maciel Patrícia , Macedo-Ribeiro Sandra 
Published: January 2025

AbstractSpinocerebellar ataxia type 3 (SCA3) is a rare inherited neurodegenerative disease caused by the expansion of a polyglutamine repeat in the protease ataxin-3 (Atx3). Despite extensive knowledge of the downstream pathophysiology, no disease-modifying therapies are currently available to halt disease progression. The accumulation of protein inclusions enriched in the polyQ-expanded Atx3 in neurons suggests that inhibiting its self-assembly may yield targeted therapeutic approaches. Here it is shown that a supramolecular tweezer, CLR01, binds to a lysine residue on a positively charged surface patch of the Atx3 catalytic Josephin domain. At this site, the binding of CLR01 decreases the conformational fluctuations of the distal flexible hairpin. This results in reduced exposure of the nearby aggregation-prone region, which overlaps with the substrate ubiquitin binding site and primes Atx3 self-assembly, ultimately delaying Atx3 amyloid fibril formation and reducing the secondary nucleation rate, a process linked to fibril proliferation and toxicity. These effects translate into the reversal of synapse loss in a SCA3 cultured cortical neuron model, an improved locomotor function in a C. elegans SCA3 model, and a delay in disease onset, accompanied by reduced severity of motor symptoms in a SCA3 mouse model. This study provides critical insights into Atx3 self-assembly, revealing a novel allosteric site for designing CLR01-inspired therapies targeting pathological aggregation pathways while sparing essential functional sites. These findings emphasize that targeting allosteric sites in amyloid-forming proteins may offer unique opportunities to develop safe therapeutic strategies for various protein misfolding disorders.
Extensive genome evolution distinguishes maize within a stable tribe of grasses
Authors: Stitzer Michelle C. , Seetharam Arun S. , Scheben Armin , Hsu Sheng-Kai , Schulz Aimee J. , AuBuchon-Elder Taylor M. , El-Walid Mohamed , Ferebee Taylor H. , Hale Charles O. , La Thuy , Liu Zong-Yan , McMorrow Sarah J. , Minx Patrick , Phillips Alyssa R. , Syring Michael L. , Wrightsman Travis , Zhai Jingjing , Pasquet Rémy , McAllister Christine A. , Malcomber Simon T. , Traiperm Paweena , Layton Daniel J. , Zhong Jinshun , Costich Denise E. , Dawe R. Kelly , Fengler Kevin , Harris Charlotte , Irelan Zach , Llaca Victor , Parakkal Praveena , Zastrow-Hayes Gina , Woodhouse Margaret R. , Cannon Ethalinda K. , Portwood John L. , Andorf Carson M. , Albert Patrice S. , Birchler James A. , Siepel Adam , Ross-Ibarra Jeffrey , Romay M. Cinta , Kellogg Elizabeth A. , Buckler Edward S. , Hufford Matthew B. 
Published: January 2025

AbstractOver the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy – a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relativesZeaandTripsacum. In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genusZea, 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.
The emerging threat of hot drought in Western Australia
Authors: Mastrantonis Stanley , Bourne Amanda R 
Published: January 2025

SummaryDroughts severely affect our environments, biodiversity, production systems and communities. When assessing droughts, we generally consider deficits in rainfall, subsurface water, water for crops and water for societies, economies and the environment. Due to climate change, increasing temperatures and more frequent and prolonged drought events are occurring in Australia and globally. When droughts and extreme temperatures occur together in the same space and time, it results in hot droughts, a phenomenon that can be devastating for flora, fauna and society. Here, we map hot drought events across Western Australia since 1889. Our results indicate that significant hot droughts have become more frequent, with the most severe hot droughts on record occurring within the last five years. Additionally, hot droughts within the last four decades, and particularly within the last two decades, affected a significantly larger area than the average for the historical record. With 2024 already on track to be the driest and hottest year on record in southwest Western Australia, natural resource managers must prepare for the increasing frequency and severity of hot droughts.Implication for ManagersAustralia and the world are experiencing more frequent and intense droughts and heatwaves. Hot droughts, characterised by simultaneous extreme water scarcity and extreme high temperatures, are particularly devastating.We mapped hot drought events in Western Australia since 1889, revealing a recent surge in occurrence concentrated in the most recent five years. Statistical testing indicates that hot droughts within the most recent 20 and 40 years were significantly larger in extent compared to the historical average.With the first half of 2024 exceptionally dry and hot, proactive strategies are imperative for natural resource managers.
Transposable Elements are Dysregulated in Brains of Individuals with Major Depressive Disorder
Authors: Truby Natalie L. , Smith Corinne , Hamilton Peter J. 
Published: January 2025

AbstractTransposable elements (TEs) are repetitive DNA sequences capable of being transcribed and reintegrated, or transposed, into distinct loci throughout the genome. While thought to be largely transcriptionally silenced in brain, TE transcription is increasingly recognized as dynamic and involved in human health and disease states, including in disorders of the brain. In this study, we annotated TE transcripts in publicly available RNA sequencing (RNAseq) of postmortem human brain tissue to investigate the expression profile of TE transcripts in individuals with Major Depressive Disorder (MDD) compared to healthy controls. Our findings reveal a robust and uniform downregulation of TE transcript expression in the brains of subjects with MDD relative to controls, this occurs most prominently in the orbitofrontal cortex (OFC) brain region, and MDD differentially impacts this TE expression by age and sex. This work points to the aberrant transcription of cortical TEs as a potentially overlooked molecular signature of MDD.
Global loss of responsiveness in key regulator metabolites and elevated enzyme proteins as metabolic dysregulation in skeletal muscle and liver of obese mice during starvation
Authors: Li Dongzi , Morita Keigo , Kokaji Toshiya , Hatano Atsushi , Hirayama Akiyoshi , Soga Tomoyoshi , Suzuki Yutaka , Matsumoto Masaki , Tsuchiya Takaho , Ozaki Haruka , Ohno Satoshi , Inoue Hiroshi , Inaba Yuka , Sugimoto Hikaru , Pan Yifei , Kuroda Shinya 
Published: January 2025

AbstractStarvation induces complex metabolic adaptations in skeletal muscle, a key tissue for maintaining energy homeostasis; however, these adaptations are largely impaired in obesity. How obesity alters global metabolic adaptations to starvation in skeletal muscle remains unclear. Here, we analyzed the metabolic adaptations on a trans-omics scale during starvation in skeletal muscle from wild-type (WT) and leptin-deficient obese (ob/ob) mice. We measured multi-omics data during starvation and constructed global trans-omics networks in WT andob/obmice. We found that starvation induces “responsiveness” in WT mice, characterized by increases or decreases in key regulator metabolites, including ATP and AMP, as well as enzyme proteins, leading to global regulation of metabolic pathways, which was lost inob/obmice. In contrast, during starvation,ob/obmice exhibit “difference” in comparison to WT mice, manifested by the persistently elevated expression of metabolic enzymes. These features were similarly found in liver, another key metabolic organ. Thus, global loss of responsiveness and elevated enzyme proteins are systemic features of metabolic dysregulation inob/obmice.