Biology subjects

Lee, M.

Publications and source records attributed to Lee, M..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Mechanisms of disrupted neurodevelopment after Zika virus infection in infancy

Congenital and early-life Zika virus (ZIKV) infection can result in neurologic deficits. Precise mechanisms of injury, especially in the more subtle presentation of postnatal infection, are not fully elucidated. Here, we defined the effects of ZIKV on the developing brain using single cell transcriptomics, histopathology and design-based stereology, diffusion MRI, and neurobehavioral assessments in infant rhesus macaques. ZIKV upregulated interferon-stimulated genes in activated microglia and cell death pathways in neurons and downregulated metabolism and differentiation genes in mature oligodendrocytes. Abnormal micro-organization of the corpus collosum and limbic white matter tracts was seen on diffusion weighted imaging. A curated gene set associated with autism spectrum disorder risk was negatively enriched in inhibitory and excitatory neurons from ZIKV-infected infants, with increased emotional reactivity already evident two weeks following infection. From single cells to organism-level behaviors, these results define the pathways and processes disrupted by early-life ZIKV infection.

neuroscience↗

bioRxiv2026

Ecology of mosquitoes in Scottish wetlands and confirmation of Culex molestus and hybrids in Scotland

BackgroundThe recent spread of mosquito-borne pathogens and their vectors within Europe highlights the impact of climate change on vector-borne disease (VBD) distributions. Mosquito surveillance has been implemented in many European countries to monitor expansion of vector populations and VBDs, but ability to predict disease risk is constrained by geographic data gaps, particularly in northern areas. In the United Kingdom, wetland mosquito surveillance has been conducted extensively in England, with a knowledge deficit for Scotland. Here, we addressed this gap through a nationwide survey of mosquitoes at Scottish wetlands, with aims of 1) confirming the geographic distribution and environmental drivers of mosquito occurrence and abundance, and 2) identifying the presence of vector species of epidemiological concern, including the Culex pipiens molestus biotype, an important vector of emerging VBDs in mainland Europe. MethodsMonthly mosquito sampling was conducted between June and October 2023 at 22 sites across Scotland comprising six wetland types: coastal saltmarsh, wet grassland, wet woodland, reedbeds, ponds and blanket bog. Adult and larval populations were sampled using Biogents BG-Pro traps and larval dipping respectively. Microclimatic and hydrological variables were recorded at collection sites and used in generalised linear mixed models to identify predictors of mosquito presence and abundance. Results1951 adults (17 species/ groups) and 860 larvae (six species/ groups) were collected from wetlands over 183 and 164 sampling events respectively. Mosquitoes were widely distributed across the Scottish mainland including up to the northern coast, being found at all but one site. Several potential vector species including Culex pipiens s.l. and Anopheles claviger were common. Amongst the adult Culex pipiens s.l. specimens, approximately 8% were Culex pipiens biotype molestus or hybrid forms. Total mosquito abundance and that of key vector species were positively associated with temperature and rainfall. ConclusionsWe report the widespread distribution of mosquitoes in wetlands throughout Scotland, including potential vector species previously unconfirmed in Scotland. Predicted associations between mosquito abundance, rainfall and temperature indicate that climate change could favour mosquito populations in Scotland. Our results provide the first comprehensive description of mosquito ecology in Scotland, as required to update assessment of VBD risk under climate change.

ecology↗

bioRxiv2026

Monounsaturated fatty acid biosynthesis is critical for streptococcal envelope homeostasis and stress tolerance

AbstractThe genus Streptococcus contains some of the most important commensals and pathogens of the human microbiome. To obtain the fatty acids required for cell membranes, Streptococcus either produce fatty acids de novo through the fatty acid biosynthesis (fab) pathway or uptake host fatty acids through the fatty acid kinase (fak) pathway. Although both the fab and fak pathways represent potential therapeutic targets to prevent or treat infection, progress is limited because of an incomplete understanding of taxon-to-taxon variability in streptococcal lipid metabolism. Here, we examined the role of de novo monounsaturated fatty acid (MUFA) synthesis in physiology and virulence-associated traits in Streptococcus mutans, Streptococcus pyogenes, and Streptococcus pneumoniae, three major pathogens that cause disease at distinct body sites. In all three species, deletion of fabM abolished MUFA production and caused severe growth defects, decreased stress tolerance, increased antibiotic susceptibility, and defects in cell viability, morphology, and division. In S. mutans, loss of fabM also markedly reduced competence signaling and production of the mutacin IV bacteriocin. Deletion of fabM increased susceptibility to killing by human neutrophils in S. mutans and S. pneumoniae, but not S. pyogenes. Together, these findings illustrate that MUFA synthesis is broadly important for streptococcal physiology and cell membrane homeostasis, while its contribution to pathogenesis is strongly species- and context-dependent, providing leads to guide development of novel therapeutic and/or preventative strategies.

microbiology↗

bioRxiv2026

Genomic Insights into a Multispecies Bacterial Pathogen Complex Driving Bacterial Blotch in White Button Mushrooms.

Bacterial blotch remains a major constraint to global white button mushroom (Agaricus bisporus) industry, yet its etiological complexity has been underestimated. Through a genome resolved, polyphasic approach applied to symptomatic mushrooms collected from United States, we uncovered an unexpectedly diverse complex of Pseudomonas species driving blotch disease. Beyond classical pathogens (P. tolaasii, P. gingeri, P. agarici, and P. "reactans", P. yamanorum, Pseudomonas sp. NC02), our analyses revealed a striking prevalence of P. azotoformans, a species not previously associated with mushroom pathology, alongside P. pergaminensis, P. monsensis, P. tensinigenes, P. simiae, Pseudomonas sp. Irchel 3A7, Pseudomonas sp. REP124 and two putatively novel lineages. Comparative genomics demonstrated pronounced heterogeneity in accessory genome content, with P. azotoformans exhibiting exceptional genomic plasticity indicative of broad ecological adaptability. Secondary metabolite profiling and white line assays further delineated species-specific chemotaxonomic signatures, underscoring the multifactorial nature of virulence. Collectively, this study provides the most comprehensive genomic and phenotypic characterization of blotch-associated Pseudomonas in Northern America, overturning the long-held paradigm of a single dominant pathogen. By establishing that bacterial blotch is multispecies disease complex, our findings redefine its epidemiology and lay the foundation for improved diagnostics strategies in mushroom production systems. The emergence and high prevalence of P. azotoformans underscore the limitations of diagnostic protocols focused exclusively on classical blotch pathogens and highlight the need for broader, genomics informed detection strategies. Collectively, this work offers actionable insights to strengthen production resilience and support the sustainability of white button mushroom cultivation as the worlds most economically important specialty food crop.

microbiology↗

bioRxiv2025

Profiling tyrosine kinase substrate recognition using bacterial peptide display and deep sequencing

Tyrosine kinases control a wide range of cell signaling pathways that are central to human physiology, and they are dysregulated in a variety of human diseases, most notably cancers. Our understanding of tyrosine kinase biology hinges upon a clear delineation of their protein substrates. Thus, much effort has been invested into defining the substrate specificities of tyrosine kinases, which is partly driven by recognition of the amino acid sequences surrounding the phospho-acceptor tyrosine residues. Numerous methods have been developed to profile tyrosine kinase sequence recognition, and these approaches have collectively demonstrated that different tyrosine kinases have distinct substrate sequence preferences. Here, we describe one such method that combines bacterial peptide display and deep sequencing to study tyrosine kinase substrate preferences. Our approach enables rapid measurement of relative phosphorylation efficiencies for thousands of peptides simultaneously. The genetically-encoded nature of the peptide libraries used with this method allows for facile and cheap construction of libraries tailored to answer a variety questions. Notably, our approach is compatible with genetic code expansion via Amber codon suppression, which allows for the construction and screening of libraries containing non-canonical amino acids. Importantly, results from this assay correlate strongly with quantitative measurements of enzyme kinetics, they corroborate previously reported tyrosine kinase substrate preferences, and they can reveal new insights into tyrosine kinase substrate specificity.

biochemistry↗

bioRxiv2025

Multivalent Nanobodies for Potent and Broad Neutralization of Staphylococcus aureus Toxins

Staphylococcus aureus is a leading cause of lethal bacteremia and pneumonia, which are driven by potent virulence factors such as T-cell superantigens and alpha hemolysin. S. aureus has among the highest rates of antibiotic resistance, yet no vaccines or alternative therapies are available despite decades of research. Here, we developed a repertoire of potent, high affinity nanobodies (Nbs) targeting key toxins in S. aureus infection, including superantigens (SAgs) SEB, SEC, TSST-1, and Hla. Comprehensive cryo-EM and AlphaFold3 analyses of these Nbs, which were elicited with clinical cocktail vaccines, revealed diverse neutralizing epitopes and mechanisms that provide strategic insights for immunotherapy and vaccine design. Guided by these findings, we engineered highly stable, multivalent, and multifunctional Nb constructs. These constructs included an aerosolizable trimeric Nb with enhanced neuralization activity against Hla and SEC, and an ultrapotent decameric Nb-IgG-Fc fusion construct against a wide range of major toxins in S. aureus sepsis (SEB, SEC, TSST-1, and Hla). These multifunctional Nbs demonstrated promising protective activity in murine models of pneumonia and sepsis, underscoring their potential as versatile immunotherapies that address the complex virulence profiles of S. aureus. Our work lays a foundation for precision immunotherapies beyond current treatment options to combat complex bacterial infections with multiple virulence mechanisms. Significance statementS. aureus is among the most common, antibiotic-resistant, and deadly causes of bacterial infections. We developed nanobodies against clinically significant virulence factors in S. aureus sepsis and pneumonia, including superantigens (SAgs) SEB, SEC, and TSST-1 as well as pore forming toxin Hla. These nanobodies displayed complete and potent neutralization of each toxin, exploiting a wide variety neutralizing mechanisms. Structural investigation of these diverse neutralizing nanobodies, which were elicited in llamas using clinically investigated cocktail vaccines, highlighted the importance of disrupting SAg interaction with TCR or MHCII and potential flaws in targeting poorly neutralizing conserved SAg epitopes using vaccine cocktails. Nb leads against each toxin were combined in different multivalent configurations, including an aerosolizable trimeric Nb and a half-life extended decameric Nb IgG Fc fusion construct. This work highlights multivalent nanobodies as a comprehensive yet therapeutically precise drug platform that addresses the complex virulence profiles of bacterial infectious diseases.

microbiology↗

bioRxiv2025

Identifying membrane-bound transcriptional regulatory proteins from rare but evolutionarily conserved domain combinations

Transcriptional regulatory proteins, including transcription factors (TFs) and chromatin modifiers, must act inside cell nuclei, but membrane-bound transcription factors (MBTFs) are first anchored in membranes before nuclear translocation. Known MBTFs are vital for processes from myelin expression (MYRF) to cholesterol homeostasis (SREBP), yet their overall diversity remains uncharted. We hypothesized that additional membrane-bound transcriptional regulators (MBTRs) might exist, so we developed a bioinformatics screen to prioritize membrane proteins that are likely to regulate transcription. Our approach leverages domain composition by positing that surprising domain combinations suggest novel biological functions. We searched for rare but evolutionarily conserved pairings of transmembrane domains with domains likely involved in transcriptional regulation. Our method rediscovered known MBTFs and membrane-bound histone kinases, and identified novel MBTR candidates, including transmembrane histone N-acetyltransferases, a putative new subclass of MBTFs that share MYRFs DNA-binding domain, and the prolactin regulatory element-binding protein PREB (SEC12). Assays using recombinant PREB demonstrated that the transmembrane domain is the determinant of PREB subcellular localization, governing its distribution between the membrane and the nucleus in mouse embryonic stem cells. These findings underscore the utility of our method and provide a framework for investigating MBTRs that likely facilitate the integration of extracellular signals with transcriptional responses. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/695554v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@15c71e9org.highwire.dtl.DTLVardef@3aa8e8org.highwire.dtl.DTLVardef@1272f0eorg.highwire.dtl.DTLVardef@18246e1_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Genetic regulators of neuronal survival across metabolic environments

Cellular energy metabolism and oxygen availability shape neuronal function and vulnerability, yet the genetic regulators of these metabolic processes in human neurons remain incompletely understood. Here, we performed CRISPR interference (CRISPRi) screens in human induced pluripotent stem cell (iPSC)-derived neurons across four distinct metabolic conditions and at three physiologically relevant oxygen tensions. This combinatorial approach enabled systematic interrogation of gene-environment interactions that govern neuronal metabolic adaptation. We identified genes--including genes associated with Leigh syndrome and autism spectrum disorder--whose importance for cell survival is highly sensitive to environmental context, revealing potential mechanisms underlying metabolic specification and selective neuronal vulnerability in neurological disorders. Our screens also uncovered regulators of neuronal glycolysis, including KIAA1429 and MAPT among others, which are previously uncharacterized modulators of neuronal glucose utilization and metabolic flexibility. Our work nominates candidate metabolic interventions and gene targets for enhancing neuronal resilience under hypoxic or nutrient-limited conditions.

systems biology↗

bioRxiv2025

Degraded sensory coding in a mouse model of Scn2a-related disorder and its rescue by CRISPRa gene activation

Heterozygous loss-of-function mutations in SCN2A, a sodium channel gene expressed in cortical pyramidal (PYR) cells, lead to a neurodevelopmental disorder characterized by autism, intellectual disability, and cortical sensory dysfunction. In Scn2a+/- mice, PYR dendritic excitability and synapses are impaired, but cortical information processing deficits are unknown. In the whisker somatosensory cortex, we found strongly degraded somatotopic tuning of PYR cells, profoundly blurred whisker maps, and impaired population coding, despite normal overall firing rates. This constitutes a robust biomarker for Scn2a-related cortical dysfunction. Parvalbumin (PV) interneurons were also unexpectedly hypofunctional. We tested for rescue of coding deficits in post-critical period, young adult mice by viral delivery of CRISPR activation (CRISPRa) reagents that upregulate Scn2a. CRISPRa treatment normalized cortical sensory representations at the single-unit and map levels. This suggests that therapy to increase Scn2a expression may be effective in normalizing cortical function in Scn2a loss-of-function disorder, even in older children or adults.

neuroscience↗

bioRxiv2025

Phenotypic and functional characterization of tumor-reactive T cells in malignant pleural effusions

BackgroundAdoptive cell therapy using tumor-infiltrating lymphocytes (TIL) is approved for the treatment of advanced melanoma but is limited by the need for patients to undergo surgical tumor resection. Malignant pleural effusions (MPE) may represent a more accessible source of tumor-reactive T cells. Here, we characterize the cellular composition as well as the transcriptional and functional properties of T cells from MPE compared with pulmonary metastasis and blood from a patient with melanoma. MethodsThe immune cellular composition was immunophenotyped by high-dimensional flow cytometry from synchronously collected MPE, a lung metastasis, and blood from a patient with metastatic melanoma. Sorted CD3+ T cells were profiled by single-cell RNA sequencing (scRNA-seq) and T cell receptor sequencing (scTCR-seq). TCR reactivity to autologous tumor was evaluated through in vitro activation assays with TCR-transduced Jurkat and autologous cancer cells. The killing capacity of ex vivo expanded T cells of autologous cancer cells was assessed through in vitro cytotoxicity assays. ResultsMPE had higher proportions of CD45+ immune cells and CD3+ T cells (70.5% vs 50%) compared with tumor and was enriched for effector CD8+ T cells, CCR7-CD45RA- effector memory CD4+ T cells, and quiescent CD25highCD127low regulatory CD4+ T cells. MPE T cells exhibited lower levels of co-inhibitory receptors (PD-1, LAG-3, TIGIT, TIM-3) expression relative to tumor. ScRNA-seq showed enrichment of NK-like effector CD8+ T cells in MPE. Pseudotime analysis indicated that MPE T cells were less exhausted than tumor T cells. The clonal repertoire of MPE and tumor highly overlapped, including 62.2% of predicted neoantigen-specific (NeoTCR) clonotypes. Notably, clonally-related NeoTCR T cells in MPE exhibited higher cytotoxic and stemness, and lower exhaustion signatures compared with sister clones in the tumor. Two of four selected NeoTCR clonotypes transduced in Jurkat cells demonstrated MHC class I-restricted reactivity in co-culture with autologous cancer cells. MPE T cells also readily expanded in the presence of high-dose IL-2 and demonstrated MHC class I-dependent killing of autologous cancer cells. ConclusionsMPE harbors polyclonal, tumor-reactive T cells with lower features of terminal exhaustion and higher cytotoxic potential relative to tumor T cells. MPE may therefore serve as a more accessible source for TIL therapy.

immunology↗

bioRxiv2025

FAK inhibitor treatment systemically regulates the glioblastoma immune environment via blocking monocyte trafficking

Glioblastoma (GBM) is the most common primary malignant brain tumour in adults with dismal survival rates, and current therapies, including most immunotherapies, are not efficacious due to the highly immunosuppressive microenvironment. Studies in other solid cancers report that impairment of the integrin effector pathway involving focal adhesion kinase (FAK) can promote anti-tumour immune responses. Therefore, we set out to address whether, and if so how, suppressing FAK function may influence GBM by using both tumour cell-specific FAK gene deletion and systemic delivery of a clinically relevant FAK kinase inhibitor (FAKi) VS-4718 in an orthotopic murine stem cell model of GBM. We found that treatment with the FAKi, but not tumour cell-specific FAK gene deletion, resulted in GBM clearance and improved survival. This was dependent on adaptive immunity, and tumour-infiltrating T cells in FAKi-treated tumours displayed increased cytotoxic potential and reduced exhaustion. We also found a significant reduction in immuno-suppressive peripherally-derived macrophages and FAKi treatment caused sequestration of inflammatory monocytes within the bone marrow, resulting in impaired monocyte trafficking to tumours as judged by adoptive transfer. This is due to suppression of key adhesion and migration signalling through 4{beta}1 integrin and CX3CR1 in peripheral monocytes. Our work here describes a previously unidentified role for FAK in trafficking of peripheral suppressive macrophages to GBM tumours, reducing T cell exhaustion and promoting anti-tumour immunity. This highlights a new way in which systemic FAK inhibitors can be used to provide a beneficial immune modulatory strategy for the treatment of GBM.

immunology↗

bioRxiv2025

Protectin DX resolves fracture-induced postoperative pain in mice via neuronal signaling and GPR37-activated macrophage efferocytosis

Protectin DX (PDX) is a member of the superfamily of specialized pro-resolving mediators (SPMs) and exerts anti-inflammatory actions in animal models; but the specific signaling pathways involved in its actions have not been fully elucidated. Here we demonstrate the analgesic actions of PDX in a mouse model of tibial fracture-induced postoperative pain (fPOP) via activation of GPR37. Intravenous early-phase and late-phase treatment of PDX (100 ng/mouse) effectively alleviated fPOP. Compared to protectin D1/neuroprotectin D1, DHA, steroid, and meloxicam, PDX produced superior pain relief. While dexamethasone and meloxicam prolonged fPOP, PDX shortened the pain duration. The analgesic effects of PDX were abrogated in Gpr37-/- mice, which displayed deficits in fPOP resolution. PDX binds GPR37 and induces calcium responses in peritoneal macrophages. LC-MS-MS-based lipidomic analysis revealed that endogenous PDX levels were [~]10-fold higher than PD1 in muscle at the fracture site. PDX promotes macrophage polarization via GPR37-dependent phagocytosis and efferocytosis through calcium signaling in vitro, and it further enhances macrophage viability and efferocytosis in vivo via GPR37. Finally, PDX rapidly modulates nociceptor neuron responses by suppressing C-fiber-induced muscle reflex in vivo and calcium responses in DRG neurons ex vivo and reducing TRPA1/TRPV1-induced acute pain and neurogenic inflammation in vivo. Our findings highlight multiple benefits of PDX to manage postoperative pain and promote perioperative recovery.

neuroscience↗

bioRxiv2025

Shared Binding Site but Divergent Resistance Profiles Uncover Novel Resistance Mechanisms in Plasmodium HSP90 Inhibitors

Drug resistance is a widespread problem across therapeutic areas including malaria, but what accounts for resistance propensity remains poorly understood. Here, we reveal that two HSP90 inhibitors targeting the identical ATP-binding site exhibit dramatically different resistance profiles in P. falciparum. Geldanamycin readily selected 10 distinct resistance mutations conferring up to 22-fold resistance, while AUY-922 required 44 weeks to yield a single A41S mutation with only 2-fold resistance to AUY-922 but not to geldanamycin. Resistance mapping in parasites and yeast revealed geldanamycin resistance mutations distributed throughout the binding pocket whereas AUY-922 resistance mutations localized close to the ATP-binding site. Unexpectedly, the A41S mutation enhanced AUY-922 binding affinity without changing geldanamycin binding. In silico analysis suggested this enhancement occurs through additional hydrogen bonding, yet stronger binding correlated with resistance. In yeast, A41S had opposite effects, hypersensitizing cells to all HSP90 inhibitors tested. Additionally, conditional HSP90 knockdown increased geldanamycin sensitivity but left AUY-922 activity unaffected, indicating different target dependencies despite shared binding sites. Based on these data, we propose a multi-target hypothesis where AUY-922s lower resistance risk stems from engaging multiple HSP90 family members. Our findings reveal how enhanced drug-target binding can paradoxically correlate with resistance and demonstrate that resistance risk cannot be predicted from binding site identity alone, providing insights for developing more durable drugs across therapeutic areas.

microbiology↗

bioRxiv2025

Participatory development of innovation and implementation strategy - a practical approach

BackgroundHealthcare and academic institutions face growing challenges in strategic planning due to rapid advances in medicine and technology, alongside fiscal and workforce constraints that limit traditional consultation. Participatory approaches offer a way to integrate diverse stakeholder perspectives under these constraints, generating contextually relevant strategies that can indicate whether current directions are appropriate or whether priorities have been overlooked. MethodsA structured participatory workshop was conducted at the 10th Grampian Research Conference (June 2025). One hundred seventy-eight participants including National Health Service (NHS) staff, academics, industry partners, patients, and public contributors, engaged in 14 parallel roundtable discussions. Contributions were captured using posters and Post-it notes, collecting 148 written annotations. Data were analysed using thematic and content analysis, supplemented by strategic frameworks including Strengths, Weaknesses, Opportunities and Threats (SWOT/TOWS), and Easy Wins, to identify and prioritise actionable strategies. ResultsFive core themes emerged: (1) access to healthcare and services, (2) patient and public involvement and engagement, (3) digital health and service delivery innovation, (4) data access, integration, and governance, and (5) workforce development and culture. SWOT analysis identified strengths in telemedicine, interdisciplinary student training, and patient and public involvement, alongside weaknesses in fragmented data, referral tracking, and workforce pressures. TOWS matrix produced strategy-oriented recommendations such as AI-enabled scheduling, remote monitoring, and transparent referral systems. Easy Wins framework assessment highlighted immediate, low-cost improvements including identifiable NHS caller identification, automated text message reminders, updated informational videos and multilingual materials. ConclusionBy combining participatory outputs with structured strategy tools, this approach demonstrated a resource-efficient model for adaptive planning. The findings align with and extend current national health policy frameworks, offering a replicable approach for institutions aiming to obtain meaningful stakeholder engagement despite fiscal and temporal constraints.

scientific communication and education↗

bioRxiv2025

Regulation of the formin INF2 by actin monomers and calcium-calmodulin

In response to increased intracellular calcium, the formin INF2 polymerizes 20-30% of the total cellular actin pool within 30 sec, suggesting robust regulation. INF2 regulation requires an auto-inhibitory interaction between the N-terminal Diaphanous Inhibitory Domain (DID) and the C-terminal Diaphanous Auto-regulatory Domain (DAD). DID mutations are dominantly linked to two human diseases, and constitutively activate INF2. However, DAD binding to actin monomers competes with DID binding, disrupting regulation. Here, we use a novel cell-free assay for detailed investigation of INF2 regulation. Contrary to our previous findings, INF2 inhibition does not require CAP proteins but does require actin buffering by monomer-binding proteins such as profilin or thymosin. INF2 is activated by calcium-bound calmodulin (CALM) through CALM binding to the N-terminus. In addition, the N-terminus plays an important role in INF2 regulation beyond CALM binding. These findings support a role for actin monomer binding proteins in not only regulating overall actin dynamics but also in specific regulation of an actin polymerization factor. SummaryIn this work, a concerted regulatory mechanism for INF2 is described, in which INF2 is activated by a combination of calcium-calmodulin and free actin monomers. In other words, INF2 senses actin monomers, making monomer binding proteins like profilin and thymosin important for INF2 regulation.

cell biology↗

bioRxiv2025

The structure of the full catalytic cycle of Vibrio cholerae NFeoB

The acquisition of iron is critical for the survival and the virulence of numerous infectious pathogens, and most bacteria acquire ferrous iron (Fe2+) by utilizing the ferrous iron transport (Feo) system. FeoB is the main component of this system, and its function is regulated by the soluble cytosolic domain, termed NFeoB. We have recently begun to define the structure and the mechanism of the Feo system from the bacterium Vibrio cholerae, the causative agent of the disease cholera. However, major structural gaps in our understanding of the nucleotide-promiscuous V. cholerae NFeoB still exist. In this work, we have determined several new X-ray crystal structures that reveal distinct snapshots of the VcNFeoB domain in uncommon and unprecedented states, ultimately illuminating the full catalytic cycle of this NTPase. This work reveals important functional features of VcNFeoB that may be leveraged and ultimately targeted to prevent the infectivity and the spread of cholera. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/680749v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@180652org.highwire.dtl.DTLVardef@146f5a4org.highwire.dtl.DTLVardef@1a913e0org.highwire.dtl.DTLVardef@1581586_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Reproducible autosomal gene expression changes with loss of typical X and Y complement across tumor types

Although there are known sex differences in cancer incidence, severity, and treatment, the sex chromosomes are typically excluded from genomic analyses because of the unique technical challenges associated with assessing their copy number, sequence variation, and expression. Here we assess sex chromosome complement in three widely-used human genomics datasets from normal (non-cancerous) tissues, primary tumors, and cancer cell lines and study the effects on genome-wide gene expression. Expected sex chromosome complements based on reported patient sex were observed in non-cancerous tissues, but about half of tumors and cancer cell lines showed loss of typical sex chromosome gene expression across tissue types with three categories: loss of chromosome Y (LOY), loss of chromosome X (LOX) and reactivation of the inactive X chromosome (XaXa). Genes consistently differentially expressed in tumors with loss of chromosome X, loss of chromosome Y, or loss of X chromosome inactivation are associated with the hallmarks of cancer and include both sex-linked and autosomal genes from nearly all chromosomes, druggable genes, and genes with molecular functions relevant to cancer signaling, such as kinase activity. Strikingly, tumors that are X0, including tumors from female patients that have lost an X chromosome and tumors from male patients that have lost a Y chromosome, cluster together by gene expression profile. Patients with tumors that have LOX or LOY had poorer survival outcomes compared to those with tumors that had maintained their sex chromosome complement. Further, LOX and LOY eliminates nearly all of the differential gene expression between tumors from different patient sexes, affecting sex chromosomal and autosomal gene expression. Going forward, considering patient sex as well as the entire genome, including assessment of the sex chromosome complement, will provide additional insights into personalized tumor etiology, progression, treatment, and patient outcome. TeaserLoss of typical sex chromosome complement is present in primary tumors and cancer cell lines across tissue types. We identify consistent autosomal gene expression changes across multiple cancers when the sex chromosome complement is altered, and show that loss of sex chromosomes reduces tumor gene expression differences between patient sexes. We show that loss of sex chromosomes is also associated with poorer patient survival.

cancer biology↗

bioRxiv2025

Nanoscopy of Organelle Handoff Portals Reveals Direct Coupling between ER Remodeling and Microtubule-Based Transport

How biosynthetic organelles leave the endoplasmic reticulum (ER) and engage with microtubule tracks remains a central question. Combining interferometric scattering with fluorescence nanoscopy, we tracked nanometer-scale handoff events in living cells. ER-derived organelles undergo biased diffusion along ER tubules toward nearby microtubules. ER three-way junctions function as nanoscopic hubs where cargo pauses, contacts multiple microtubules, and then launches onto a track for long-range travel. Remarkably, the ER maintains a membrane tether to the departing cargo, extending its tubules and forming new junctions, thereby coupling inter-network transfer with membrane morphogenesis. These observations reveal an integrated mechanism that links organelle biogenesis, directional trafficking, and continual ER- and cellular remodeling, underscoring the ERs active role in steering transport and repurposing its own output within the crowded intracellular environment.

cell biology↗