bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein Kinase C positively regulates peroxisome biogenesis by promoting peroxisome-endoplasmic reticulum interaction
Authors: Borisyuk Anya , Howman Charlotte , Pattabiraman Sundararaghavan , Kaganovich Daniel , Amen Triana
Published: January 2025

Peroxisomes carry out a diverse set of metabolic functions, including oxidation of very long-chained fatty acids, degradation of D-amino acids and hydrogen peroxide, and bile acid production. Many of these functions are upregulated on demand, therefore cells control peroxisome abundance, and by extension peroxisome function, in response to environmental and developmental cues. The mechanisms upregulating peroxisomes in mammalian cells have remained unclear. Here we identify a signaling regulatory network and a mechanism that coordinate cellular demand for peroxisomes and peroxisome abundance by regulating peroxisome proliferation. We show that protein kinase C (PKC) promotes peroxisome PEX11b-dependent formation. PKC activation leads to an increase in peroxisome formation, promoting peroxisome-ER contact site formation through inactivation of GSK3β. We show that removal of VAPA and VAPB impairs peroxisome biogenesis and PKC regulation. Inhibition of PKC reduces peroxisome-ER interactions, leading to a decrease in peroxisome abundance. During neuronal differentiation, active PKC leads to a significant increase in peroxisome formation. We propose that peroxisomal regulation by transient active PKC signaling enables rapid and fine-tuned responses to the need for peroxisomal activity.
The effect of surface properties on the interactions of particles and marine mucous filters
Authors: Jacobi Yuval , Epstein José A. , Paz Ariella , Shavit Uri , Yahel Gitai , Ramon Guy Z.
Published: January 2025

Free-living suspended cells form the foundation of marine food webs, making suspension feeding a key mode in aquatic ecosystems. Suspension feeders across phyla use diverse filtration mechanisms, often relying on mucus and low-pressure pumps with high filtration efficiencies and self-cleaning capabilities. Traditionally, particle capture was thought to depend on size alone, but recent evidence highlights the importance of physicochemical surface interactions between prey cells and filtration apparatuses. In this study, we investigated the capture of 0.3-3 µm particles by ascidians and found that coating particles with amphiphilic polymers altered their mobility within the mucous filter, affecting capture efficiency. Surface interactions, such as steric repulsion, significantly influence particle mobility and inversely correlate with capture success. Furthermore, we discovered that the mucous filter in ascidians is much thicker (∼5 µm) than previously believed, functioning as a continuous sheet. These findings suggest a need to reevaluate suspension feeding models, with implications for marine ecosystems and filtration technology development.
Macromolecular Diamidobenzimidazole Conjugates Activate STING
Authors: Arora Karan , Sheehy Taylor L. , Schulman Jacob A. , Kimmel Blaise R. , McAtee Caitlin , Bharti Vijaya , Weaver Alissa M. , Wilson John T.
Published: January 2025

Pharmacologic activation of the stimulator of interferon genes (STING) pathway has broad potential applications, including the treatment of cancer and viral infections, which has motivated the synthesis and testing of a diversity of STING agonists as next generation immunotherapeutics. A promising class of STING agonists are the non-nucleotide, small molecule, dimeric-amidobenzimidazoles (diABZI), which have been recently used in the synthesis of polymer- and antibody-drug conjugates to improve pharmacokinetics, modulate biodistribution, and to confer other favorable properties for specific disease applications. These approaches have leveraged diABZI variants functionalized with reactive handles and enzyme-cleavable linkers at the 7-position of the benzimidazole for conjugation to and tunable drug release from carriers. However, since this position does not interact with STING and is exposed from the binding pocket when bound in an “open lid” configuration, we sought to evaluate the activity of macromolecular diABZI conjugates that lack enzymatic release and are instead conjugated to polymers via a stable linker. By covalently ligating diABZI to 5 or 20 kDa mPEG chains via an amide bond, we surprisingly found that these conjugates could activate STINGin vitro.To further evaluate this phenomenon, we designed a diABZI-functionalized RAFT chain transfer agent that provided an enabling tool for synthesis of large, hydrophilic, dimethylacrylamide (DMA) polymers directly from a single agonist and we found that these conjugates also elicited STING activationin vitrowith similar kinetics to highly potent small molecule analogs. We further demonstrated thein vivoactivity of these macromolecular diABZI platforms, which inhibited tumor growth to a similar extent as small molecule variants. Using flow cytometry and fluorescence microscopy to evaluate intracellular uptake and distribution of Cy5-labeled analogs, our data indicate that although diABZI-DMA conjugates enter cells via endocytosis, they can still colocalize with the ER, suggesting that intracellular trafficking processes can promote delivery of endocytosed macromolecular diABZI compounds to STING. In conclusion, we have described new chemical strategies for the synthesis of stable macromolecular diABZI conjugates with unexpectedly high immunostimulatory potency, findings with potential implications for the design of polymer-drug conjugates for STING agonist delivery that also further motivate investigation of endosomal and intracellular trafficking as an alternative route for achieving STING activation.
A hydrophobic core in the coiled-coil domain essential for NRC resistosome function
Authors: Wang Hung-Yu , Lee Kim-Teng , Goh Foong-Jing , Bozkurt Tolga O. , Wu Chih-Hang
Published: January 2025

The NRC (Nucleotide-binding leucine-rich repeat protein (NLR)-required for cell death) family represents a group of helper NLRs that are required by sensor NLRs to execute cell death during pathogen infection. NRC proteins are classified as CNL, which contain a coiled-coil (CC) domain in their N-terminal region. Previous studies highlighted the importance of the MADA motif in the first alpha helix of the CC domain for NRC-mediated defense responses. However, how other alpha helices in the CC domain contribute to NRC function remains unclear. In this study, we identified a novel hydrophobic feature localized in the CC domain barrel that contributes to NRC-mediated immunity. We screened the conserved hydrophobic residues among NRCs and identified seven required for NRC4-mediated cell death. Structural analysis revealed that four of these residues form a hydrophobic center in the CC domain. We further demonstrated that this hydrophobic core is important for NRC4 subcellular localization, oligomerization, and phospholipid association, but not for NRC4 focal accumulation on the extra-haustorial membrane duringPhytophthora infestansinfection. By comparing sequences of multiple NLRs in the NRC superclade, we found that the residues of the hydrophobic core in sensor NLRs exhibit greater diversity than those in helper NLRs. Cell death assays indicated that the function of the hydrophobic core has degenerated in certain sensor NLRs but remains essential in NRCs and ZAR1. Overall, our study highlights a novel hydrophobic feature in the CC domain of the NRC and its contribution to NLR-mediated immunity.

Significance

Plant intracellular immune receptors known as NRCs (NLR-required for cell death) form resistosome complexes to activate pathogen defense, yet the contributions of coiled-coil (CC) domain features beyond the MADA motif remain unclear. Here, we uncover a novel hydrophobic core in the CC domain of NRC4 that is critical for subcellular localization, oligomerization, and phospholipid association, and thus for effective immune signaling. Intriguingly, while this hydrophobic feature is highly conserved among helper NRCs and singleton NLR ZAR1, the corresponding amino acid residues show greater sequence diversity or has been functionally degenerated in most other sensor NLRs, suggesting a divergence in sequences and in function. Our findings highlight the importance of this previously uncharacterized structural element for NRC-mediated cell death.
Spatial profiling identifies regionally distinct microenvironments and targetable immunosuppressive mechanisms in pediatric osteosarcoma pulmonary metastases
Authors: Eigenbrood Jason , Wong Nathan , Mallory Paul , Pereira Janice , Morris Douglass W , Beck Jessica A , Cronk James C , Sayers Carly M , Mendez Monica , Kaiser Linus , Galindo Julie , Singh Jatinder , Cardamone Ashley , Pore Milind , Kelly Michael , LeBlanc Amy K , Cotter Jennifer , Kaplan Rosandra N , McEachron Troy A
Published: January 2025

Osteosarcoma is the most common malignant bone tumor in young patients and remains a significant clinical challenge, particularly in the context of metastatic disease. Despite extensive documentation of genomic alterations in osteosarcoma, studies detailing the immunosuppressive mechanisms within the metastatic osteosarcoma microenvironment are lacking. Our objective was to characterize the spatial transcriptional landscape of metastatic osteosarcoma to reveal these immunosuppressive mechanisms and identify promising therapeutic targets. Here, we performed spatial transcriptional profiling on a cohort of osteosarcoma pulmonary metastases from pediatric patients. We reveal a conserved spatial gene expression pattern resembling a foreign body granuloma, characterized by peripheral inflammatory signaling, fibrocollagenous encapsulation, lymphocyte exclusion, and peritumoral macrophage accumulation. We also show that the intratumoral microenvironment of these lesions lack inflammatory signaling. Additionally, we identified CXCR4 as an actionable immunomodulatory target that bridges both the intratumoral and extratumoral microenvironments and highlights the spatial heterogeneity and complexity of this pathway. Collectively, this study reveals that metastatic osteosarcoma specimens are comprised of multiple regionally distinct immunosuppressive microenvironments.
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

Drugs 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 Statement

Microtubule (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

The 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

Background.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

Current 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

Recent 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

We 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

We 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

Spinocerebellar 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

Over 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

Droughts 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 Managers

Australia 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

Transposable 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

Starvation 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.
Region-specific mean field models enhance simulations of local and global brain dynamics
Authors: Lorenzi Roberta Maria , Palesi Fulvia , Casellato Claudia , Gandini Wheeler-Kingshott Claudia A.M. , D’Angelo Egidio
Published: January 2025

Brain dynamics can be simulated using virtual brain models, in which a standard mathematical representation of oscillatory activity is usually adopted for all cortical and subcortical regions. However, some brain regions have specific microcircuit properties that are not recapitulated by standard oscillators. Moreover, magnetic resonance imaging (MRI)-based connectomes may not be able to capture local circuit connectivity. Region-specific models incorporating computational properties of local neurons and microcircuits have recently been generated using the mean field (MF) approach and proposed to impact large-scale brain dynamics. Here we have used a MF of the cerebellar cortex to generate a mesoscopic model of the whole cerebellum featuring a prewired connectivity of multiple cerebellar cortical areas with deep cerebellar nuclei. This multi-node cerebellar mean field model was then used to substitute the corresponding standard oscillators and build up a cerebellar mean field virtual brain (cMF-TVB), for a group of healthy human subjects. Simulations revealed that electrophysiological and fMRI signals generated by the cMF-TVB significantly improved the fitness of local and global dynamics with respect to a homogeneous model made solely of standard oscillators. The cMF-TVB reproduced the rhythmic oscillations and coherence typical of the cerebellar circuit and allowed to correlate electrophysiological and functional MRI signals to specific neuronal populations. In aggregate, region-specific models based on MF technology and pre-wired circuit connectivity can significantly improve virtual brain simulations fostering the generation of effective brain digital twins that could be used for physiological studies and clinical applications.
Computationally designed stem-epitope mimetics elicit broadly reactive antibodies
Authors: Wehrle Sarah , Scheck Andreas , Reusch Laura , Matassoli Flavio , Georgeon Sandrine , Castro Karla M. , Cramer Johannes , Harshbarger Wayne , Rosset Stéphane , Andrews Sarah F. , Schön Karin , Bouzya Badiaa , Rouxel Ronan , Blais Normand , Malito Enrico , McDermott Adrian , Krey Thomas , Mallett Corey P. , Vassilev Ventzislav , Angeletti Davide , Correia Bruno E.
Published: January 2025

Broad protection against diverse influenza viruses can be conferred by broadly neutralizing antibodies (bnAbs) targeting a conserved site on the hemagglutinin (HA) stem domain. However, the low immunogenicity of this antigenic region hinders the robust induction of such antibodies. Here, we showcase a structure-based immunogen design strategy focusing on the surface mimicry of antigenic sites. By leveraging the structural definition of a stem epitope, we apply computational protein design to develop epitope mimetics to focus the immune response against this site of viral vulnerability. The structurally complex antigenic site is displayed on heterologous protein scaffolds, retaining excellent binding towards known HA stem-specific bnAbs. Our epitope-mimetic induces stem-specific antibodies against highly divergent group 1 and 2 subtypes. The results provide a general framework for the design of novel immunogens eliciting focused immune responses which may be a valuable tool in the development of effective vaccine candidates against other variable pathogens.
Oxidative stress leads to Fur-mediated activation offtnAinEscherichia coliindependently of OxyR/SoxRS regulators
Authors: Matveeva Valeriia O. , Grebennikova Anna D. , Sakharov Daniil I. , Fomin Vadim V. , Manukhov Ilya V. , Bazhenov Sergey V.
Published: January 2025

Ferritin FtnA is the main scavenger of Fe2+and storage of Fe3+in bacterial cells, together with Dps and Bfr preventing the Fenton reaction and thus protecting the cell from iron-induced oxidative stress. However, until now, it was not known how its expression is regulated under conditions of oxidative stress, and the available evidence was contradictory. To study the regulation ofE. coli ftnAexpression in response to oxidative stress, PftnA-luxCDABEtranscriptional fusion in different strains was used. It has been shown that PftnAis induced after the addition of oxidative stress inducers. The maximum amplitude of this activation did not depend on the presence of functional genesoxyRandsoxRin the cell, but completely disappeared in the absence offur. The response is amplified in theftnAmutant and is diminished in the FtnA-overproducing strain, which indicates that iron sequestration blocks the response. Exposure of a cell to H2O2initially inactivates Fur and a number of iron-utilizing proteins, and derepresses iron uptake. This results in an increase in the cellular iron content with the consequent Fur reactivation, which leads to the induction offtnAexpression. Thus, oxidative stress leads to PftnAactivation, which is mediated by Fur and time-delayed in comparison with OxyR-response.
A pan-cancer atlas of T cell targets
Authors: Li Guangyuan , Guzman-Bringas Omar Uriel , Sharma Aman , Harpaz Zachary , Tardio Ethan , Natarajan Aswin , Liu Xinya , Taylor Darren , Yamin Rachel , Dellacherie Maxence , Krogsgaard Michelle , Cruz C. Russell Y. , Yarmarkovich Mark
Published: January 2025

T-cell-based immunotherapies have revolutionized cancer treatment, yet only a minority of patients respond to these approaches, significantly constrained by the limited knowledge of tumor-specific antigens. Here we present a comprehensive map of T cell targets across 21 cancer types, revealing actionable tumor-specific targets in 86% of tumors. To define the repertoire of actionable T cell targets, we conducted a comprehensive pan-cancer analysis integrating data from 7,473 RNA-Seq datasets, 1,564 immunopeptidomes and 208 cancer single-cell datasets, comparing these against 17,384 normal samples covering 51 tissues. Our analysis uncovered 88 viable surface protein targets and 15,079 tumor-specific HLA-presented antigens, deriving from 11 distinct molecular events, across 21 tumor types, providing a comprehensive resource for T-cell-based immunotherapy development. We highlight 128 promising new tumor targets and validate 20 targets across five antigen classes. Among the antigens uncovered, we highlight 339 previously uncharacterized neoantigens, a new PMEL splicing peptide that we expect to be a superior antigen to the clinical target, novel self-antigens, peptides derived from ORFs previously unknown to encode proteins, and novel tumor-specific microbial targets. These findings significantly expand the therapeutic landscape of T cell therapies. To catalyze therapeutic development, we have made our pan-cancer target atlas and accompanying toolkit available to the scientific community and expect these resources will pave the way for immunotherapies across multiple cancers.

Significance

We identified 88 viable membrane proteins and 15,079 tumor-specific HLA-presented antigens across 21 cancer types through a pan-cancer analysis of RNA-Seq, immunopeptidomes, and normal tissues. This comprehensive atlas highlights diverse antigen classes and key HLA presentation factors, providing a vital resource to catalyze T-cell based immunotherapy development and enhance understanding of antigen presentation and tumor biology.
Ultra-deep sequencing of somatic mutations induced by a maize transposon
Authors: Scherer Justin , Hinczewski Michael , Nelms Brad
Published: January 2025

Cells accumulate mutations throughout development, contributing to cancer, aging, and evolution. Quantitative data on the abundance ofde novomutations within plants or animals are limited, as new mutations are often rare within a tissue and fall below the limits of current sequencing depths and error rates. Here, we show that mutations induced by the maize Mutator (Mu) transposon can be reliably quantified down to a detection limit of 1 part in 12,000. We measured the abundance of millions ofde novoMu insertions across four tissue types. Within a tissue, the distribution ofde novoMu allele frequencies was highly reproducible between plants, showing that, despite the stochastic nature of mutation, repeated statistical patterns of mutation abundance emerge. In contrast, there were significant differences in the allele frequency distribution between tissues. At the extremes, root was dominated by a small number of highly abundantde novoinsertions, while endosperm was characterized by thousands of insertions at low allele frequencies. Finally, we used the measured pollen allele frequencies to reinterpret a classic genetic experiment, showing that evidence for late Mu activity in pollen are better explained by cell division statistics. These results provide insight into the complexity of mutation accumulation in multicellular organisms and a system to interrogate the factors that shape mutation abundance.
A framework for constructing insect steering circuits
Authors: Mitchell Robert , Webb Barbara
Published: January 2025

Insects perform a variety of goal-directed navigation behaviours, each of which requires a comparison between their current and desired heading direction. Recent work has uncovered such a steering circuit in the fruit flyDrosophila melanogaster. We used the available neuroanatomical and physiological descriptions to derive six general rules which can be used to construct a class of steering circuits which operate in the same way. These rules are surprisingly permissive, suggesting that across insect species, steering circuits may have differing wiring while remaining functionally identical. We simulate an extreme example and demonstrate that it is functionally identical to the reported fruit fly circuit. Further, we argue that the principled approach we apply here could be applied more generally in performing comparative analyses across different insect species.
Regulation of B cell tolerance and autoimmunity by miR-130b
Authors: Herrero-Fernández Beatriz , González-Molina María del Pilar , Gámez-Reche Laura , Prieto-Muñoz Ana M , Sanz Javier , Gonzalo Tania , Moreno Alba , Nemazee David , Xiao Changchun , Mañas Laura , González-Martín Alicia
Published: January 2025

Autoimmune diseases represent a timely health challenge due to their increasing incidence and lack of definitive cures. Autoreactive B cells play essential roles in several autoimmune diseases, including lupus erythematosus, rheumatoid arthritis and multiple sclerosis. However, the molecular mechanisms regulating these cells remain largely unknown. In this study, we identified miR-130b as a critical regulator of B cell tolerance through an unbiased bioinformatic motif enrichment analysis of lymphocyte-expressed miRNAs. Elevated levels of miR-130b impaired the elimination of autoreactive B cells during their development, enabling their escape to peripheral tissues. Mechanistically, miR-130b hindered clonal deletion by suppressing the expression of its targets Estrogen receptor alpha (ERα) and PTEN. Notably, ERα deficiency alone was sufficient to compromise B cell tolerance, allowing autoreactive B cells to reach the periphery, where they can contribute to the development and progression of autoimmune diseases. Overall, this study advances our understanding of B cell tolerance and provides new insights into the gender differences frequently observed in autoimmunity. The identification of miR-130b and ERα as regulators of B cell tolerance opens new avenues to improve the diagnosis and treatment of autoimmune diseases.
Single-molecule tweezers decoding hidden dimerization patterns of membrane proteins within lipid bilayers
Authors: Sadongo Victor W. , Kim Eojin , Kim Seoyoon , Wijesinghe W.C. Bhashini , Lee Tae Seung , Choi Jeong-Mo , Min Duyoung
Published: January 2025

Dimerization of transmembrane (TM) proteins is an essential biological process within cellular membranes, playing a key role in diverse pathophysiological pathways and serving as a promising therapeutic target. Although often simplified as a two-state transition from freely diffusing monomers to fully formed dimers, the dimerization process after monomer diffusion—the post-diffusion dimerization—is likely more complex due to intricate inter-residue interactions. Here, we introduce a single-molecule tweezer platform to map detailed profiles of the post-diffusion transitions in TM protein dimerization. This approach captures reversible dimerization events of a single TM dimer, revealing hidden intermediate states that emerge following the quiescent phase of monomer diffusion. Profiling the post-diffusion intermediates, kinetics, and energy landscapes—integrated with molecular dynamics simulations—uncovers the dimerization pathway, the effects of residue interactions and lipid bilayers, and the kinetic and energetic contributions of distinct dimerization domains. Furthermore, this platform characterizes selective and localized modulations via peptide binding, underscoring its potential to elucidate the mechanisms of action of TM dimer-targeting drugs at single-molecule resolution.