Biology subjects

Fu, J.

Publications and source records attributed to Fu, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Sex stratified analyses enable new genetic insights into brain imaging phenotypes

Sex differences are commonly observed in neuroimaging phenotypes and in the risk of brain diseases, yet the underlying genetic mechanisms remain poorly understood. We investigated sex differences in the genetic architecture of 805 neuroimaging phenotypes in 22,950 males and 22,950 females matched for sample size and covariates, and systematically compared sex-stratified with sex-combined genetic analyses. We found eight variant-trait associations with significant sex differences, 235 fine-mapped sex-dominant causal associations, 457 sex-dominant colocalizations with sex hormones, and 96 sex-dominant colocalizations with schizophrenia. Compared with sex-combined analysis, sex-stratified analysis identified 47 new genetic associations, 170 new fine-mapped causal associations, 1,019 new colocalizations with sex hormones, and 191 new colocalizations with schizophrenia. Additionally, sex-stratified analysis improved global heritability and genetic-correlation estimates and enhanced polygenic prediction for certain phenotypes. This work highlights the need to routinely perform sex-stratified genetic association analyses to elucidate sex-specific and sex-shared genetic control of neuroimaging phenotypes and related disorders.

genetics↗

bioRxiv2026

Cell-nanoplastics association impacts cell proliferationand motility

Detection of micro- and nanoplastics (MNPs) in human tissues has raised growing concern about their biological effects on tissue and cell function. While previous studies have examined MNP-cell interaction, most focused on limited cell and plastic types. Here, we present a comprehensive, quantitative investigation into how different types of nanoplastics (NPs) associate with and affect diverse cell types under physiologically relevant conditions. Using microfluidic-calibrated fluorescence microscopy, we quantify NP accumulation in cells in vitro and match cellular NP concentrations to levels reported in human tissues. While cell-associated NPs could be gradually released in vitro, they persist in vivo for over one month without detectable reduction in a mouse model. We discover that NP exposure at these levels broadly impairs cell proliferation across epithelial, endothelial, fibroblast, and immune cells, with cell type-dependent sensitivity. NP exposure also reduces motility in T cells and fibroblasts, with more complex effects observed in macrophages. Mechanistically, NP-cell association and trans-epithelial transport involved not only classical endocytic regulators but also pathways related to ion and water transport. Notably, NP association and release were highly sensitive to the extracellular fluid environment within the physiological range. By testing inhibitors of these pathways, we identified molecules that reduce NP-cell association and promote release. We further compared common NPs found in human samples and widely used in research: polystyrene (PS), polyethylene (PE), and polypropylene (PP). Although these NPs similarly impaired proliferation and motility, they showed markedly different cellular association and release dynamics. These findings reveal the impact of NPs on tissue cell functions and uncover novel regulatory pathways, establishing a quantitative framework for studying NP-cell interactions in biologically relevant conditions.

cell biology↗

bioRxiv2026

Impact of Kernel Dimensionality on the Generalizability and Efficiency of Convolutional Neural Networks to Decode Neural Drive from High-density Electromyography Signal

Convolutional neural networks (CNNs) have been widely used to estimate neural drive from high-density surface electromyography (HD-sEMG) signals in neural machine interfaces owing to their real-time capability. Depending on kernel dimensionality (1D, 2D, or 3D), CNNs can extract temporal, spatial, or spatiotemporal features. Given that motor unit action potentials propagate across both space and time, architectures that exploit spatial features may offer advantages for neural drive estimation. Despite the potential importance of kernel dimensionality, its influence on neural drive estimation remains poorly understood. Existing studies have mainly evaluated CNN generalizability across participants, contraction intensities, or muscles within the same HD-sEMG dataset, while computational efficiency has seldom been considered. As a result, it remains unclear whether different kernel dimensionalities affect cross-dataset generalizability and computational efficiency. In this study, we implemented three CNN architectures--differing only in kernel dimensionality-- to investigate whether exploiting the spatial and spatiotemporal features of motor unit action potentials improves the generalizability and computational efficiency of neural drive estimation from HD-sEMG recorded during lower-limb isometric contractions. We trained the CNNs on one HD-sEMG dataset and evaluated them, without retraining, on two independent, unseen datasets recorded from different participants, sessions, and protocols--one spanning three contraction intensities and the other three muscles. All three architectures are generalized to both unseen datasets. The 2D and 3D CNNs marginally outperformed the 1D CNN with a 0.2% increase in R, while the 3D CNN showed no advantage over the 2D CNN. Computational efficiency depended on kernel dimensionality in a platform-dependent manner. On the CPU, the 3D CNN showed the slowest inference time, which was 2x slower than the 2D and 1D CNN, owing to the higher arithmetic cost of its spatiotemporal convolutions. On the GPU, all three architectures achieved similar inference times of about 1.36 ms/sample. These findings indicate that increased architectural complexity of CNN does not improve generalizability for neural drive estimation, and that a 2D CNN offers the best balance of accuracy and efficiency for a reliable, deployable CNN-based neural drive estimator--particularly on CPU-only or resource-constrained platforms.

neuroscience↗

bioRxiv2026

Nutrishield Beta-Carotene Attenuates LPS-Induced Systemic Inflammation and Oxidative Stress in Murine Model

{beta}-Carotene is a strong antioxidant and immunomodulator, but it breaks down in the presence of oxygen and isnt readily bioavailable. Nutrishield(R) {beta}-Carotene is a special starch-based microencapsulation system designed to protect {beta}-carotene from oxidation, make it easier to spread in the gastrointestinal environment, and improve its effectiveness. This study reported Nutrishield(R) as a formulation platform by using {beta}-carotene as a model compound. We compared how well it worked in vitro and in vivo with {beta}-carotene that wasnt encapsulated. We randomly put thirty-two male BALB/c mice into four groups (n=8): Control, LPS, LPS + {beta}-Carotene (10 mg/kg/day), and LPS + Nutrishield(R) (the same dose of {beta}-Carotene). After an intraperitoneal injection of LPS (1 mg/kg, twice weekly), the treatments were administered orally for 28 days. LPS administration significantly elevated TNF- (142 {+/-} 8 pg/mL), IL-6 (118 {+/-} 7 pg/mL), and serum 8-OHdG (5.4 {+/-} 0.3 ng/mL) in comparison to controls (TNF- = 62 {+/-} 5 pg/mL; IL-6 = 51 {+/-} 4 pg/mL; 8-OHdG = 2.1 {+/-} 0.2 ng/mL). Nutrishield(R) {beta}-Carotene supplementation significantly normalized cytokine profiles (TNF- = 69 {+/-} 4 pg/mL; IL-6 = 56 {+/-} 3 pg/mL; IL-10 increased from 38 {+/-} 2 to 76 {+/-} 3 pg/mL; p < 0.001 vs. LPS). Histological analysis demonstrated reduced hepatocellular vacuolation and renal tubular degeneration in the Nutrishield(R) {beta}-Carotene group relative to the {beta}-carotene and LPS groups. These findings demonstrate that Nutrishield(R) microencapsulation significantly enhances the functional antioxidant and anti-inflammatory efficacy of {beta}-carotene in a murine model of systemic inflammation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/711625v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@184b37forg.highwire.dtl.DTLVardef@124680aorg.highwire.dtl.DTLVardef@12a704aorg.highwire.dtl.DTLVardef@1321a42_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Pregnancy and Early-Life Gut Virome in the Lifelines NEXT cohort:Origin, Persistence, Influencing Factors and Health Implications

The human gut virome is a key modulator of gut microbial ecology and function, yet its role in early gut ecosystem development remains poorly understood. Here, we profiled the DNA virome from 4,523 fecal and 91 breastmilk metagenomes from 714 mother-infant pairs in the Dutch birth cohort Lifelines NEXT. This analysis generated a catalog of 31,205 unique vOTUs, with 31,019 detected in fecal and 248 in breastmilk samples, including 16,540 not previously reported in other databases. We find that the maternal virome is largely stable, in contrast to the infant viromes rapid diversification over time. We also identify delivery and feeding modes as major drivers of infant virome developmental trajectories, with additional influences of maternal parity, infections during pregnancy, socioeconomic factors, gestational age and infant birth weight. Notably, increased viral diversity was associated with the infant developing a food allergy. Strain-level virome profiling confirmed the maternal gut as the primary source of viruses for the infant gut, with increased sharing rates in vaginally delivered infants and with breastmilk as a secondary reservoir. We demonstrate that temperate phages frequently co-transmit with their bacterial hosts and identify multiple protein families associated with anti-defense functions enriched among maternally shared viruses. Finally, we show that DNA adenine N6-methyltransferase hin1523, together with widely active diversity-generating retroelements, promote long-term viral persistence in the infant and maternal gut. Together, these findings establish the origin, dynamics and modulating factors of the infant gut virome, along with the genetic strategies supporting its persistence in the gut ecosystem.

microbiology↗

bioRxiv2026

Nucleoli as drivers of nuclear remodelling in cardiomyocytes during Heart Failure

Cardiomyocyte mechanotransduction has traditionally focused on the sarcomere and cytoskeleton, yet emerging evidence highlights the nucleus as an active mechanical responder. To adapt to the dynamic mechanical environment, the nucleus forms nuclear invaginations (NIs), double-membrane folds that provide structural support to chromatin and incorporate nuclear pore complexes to facilitate nucleo-cytoplasmic transport, including Ca2+ transport. However, how these structures are formed is not yet understood. We leveraged advances in high-resolution microscopy, mechanical stimulation, rat models and human samples, to study the formation, function and remodelling of cardiac NIs in Heart Failure (HF). Here, we demonstrate that the formation of NI in cardiomyocytes is regulated by both, cytoskeleton such as actin and detyrosinated microtubules as well as intranuclear nucleolar interactions with NI disruption resulting in elevated baseline nuclear Ca2+. In a 16-week post-Myocardial Infarction (MI) end-stage HF rat model, as well as in human Dilated Cardiomyopathy samples, a marked reduction in NIs was observed. Importantly, NI loss was already evident at 8 weeks post-MI, preceding detectable cytoskeletal stiffening. At this stage, we observed increased DNA damage in the peri-nucleolar region, accompanied by nucleolar remodelling and a shift in nucleolar biomechanical properties. In conclusion, preserving nucleolar integrity emerges as a potential target for intervention.

cell biology↗

bioRxiv2026

JanusX: an integrated and high-performance platform for scalable genome-wide association studies and genomic selection

As genomic datasets expand in both sample size and marker density, genome-wide association studies (GWAS) and genomic selection (GS) require workflows that remain statistically rigorous, computationally efficient, and reproducible across the full analysis path, from genotype matrix to decision-relevant outputs. Here we present JanusX, an integrated high-performance framework that provides a streamlined, user-oriented workflow for GWAS and GS by unifying data handling, model execution, and visualization. Across simulated and real datasets, JanusX maintained high concordance with established baselines while substantially reducing runtime and memory usage. In GWAS, JanusX achieved up to a 19-fold speedup over GEMMA in linear mixed model (LMM) inference, and implemented additional LMM inference based on a sparse genomic relationship matrix with GRAMMAR-Gamma calibration, alleviating computational and memory bottlenecks in large-scale cohorts. JanusX also provides a FarmCPU implementation within its GWAS module, achieving a median 11.4-fold runtime improvement and reducing peak memory usage by 84.9% relative to rMVP. In GS, JanusX integrates an optimized best linear unbiased prediction (BLUP) backend that adaptively selects sample- and SNP-space solvers and incorporates a Preconditioned Conjugate Gradient (PCG) solver. This implementation efficiently completes five-fold cross-validation of 500k individuals x 500k single-nucleotide polymorphisms (SNPs) in 35.1 minutes with only 14.3 gibibyte (GiB) of peak memory. Beyond BLUP, JanusX integrates Bayesian and machine-learning predictors under a single interface with compact automatic tuning to ensure robust cross-model performance. JanusX therefore enables efficient locus discovery and genomic prediction under consistent analytical assumptions, even in large-scale cohorts.

bioinformatics↗

bioRxiv2026

Cardiomyocyte mechanical activity counteracts intraluminal calcium depletion in the transverse-axial tubular system during fast electrical stimulation

The transverse-axial tubular system (TATS) enables close structural and functional coupling between plasma membrane and sarcoplasmic reticulum of cardiomyocytes. It supports fast and efficient Ca2+-induced Ca2+ release upon cell depolarisation, crucial for excitation-contraction coupling in the heart. Due to the small diameter and tortuosity of individual tubules, the TATS forms a domain of restricted diffusive transport. It has previously been suggested that, as a consequence of an uneven distribution of Ca2+ influx and efflux pathways in TATS compared to outer surface plasma membrane domains of cardiomyocytes, cyclic electrical activity may lead to a gradual depletion of Ca2+ in the TATS. Here, we show experimentally that in mechanically uncoupled rabbit ventricular cardiomyocytes, electrical stimulation does indeed lead to an L-type Ca2+ channel-dependent gradual depletion of Ca2+ inside TATS, an effect that scales with pacing frequency. Ca2+ depletion was absent in freely contracting cardiomyocytes, presumably as a result of cyclic TATS deformation during cell shortening. This squeezes transverse TATS tubules and adds an advective contribution to, and thereby accelerates the, intra-TATS content exchange with bulk extracellular fluid. Our results reveal a novel mechanism of cardiac mechano-dependent auto-regulation, where the increased propensity for development of intra-TATS Ca2+ gradients at high electrical stimulation rates is mitigated by the coinciding mechanically induced TATS deformation, twice on each cycle in the heart (during diastolic stretch and systolic shortening), which accelerates luminal content exchange. Our study provides first insight into a novel facet of cardiac mechano-biology, whose auto-regulatory benefit may be reduced by TATS remodelling in disease.

cell biology↗

bioRxiv2026

An ER-Inner Membrane Complex Bridge via VAP-VPS13A-DAT1 Drives Daughter Budding in Toxoplasma gondii

All alveolates including apicomplexa parasites contain an inner membrane complex (IMC) underneath the plasma membrane. The IMC is synthesized de novo during the daughter cell budding (endodyogeny) within the mother cell and serves as a crucial scaffold for supporting cytoskeletal structures and the glideosome machinery for the parasite locomotion. However, the mechanism(s) underlying the membrane biogenesis in the IMC are not well understood. Using clinically-relevant and globally-prevalent pathogenic protist model, Toxoplasma gondii, we identified the TgVAP-TgVPS13A-TgDAT1 complex bridging the IMC to the endoplasmic reticulum (ER) - the major site of phospholipid synthesis. Individual components of this complex play a crucial role in the IMC biogenesis, where the multi-modular TgVPS13A protein interacts with the lipid scramblase TgDAT1 in the IMC via its C-terminal VAB domain, and with the ER-resident TgVAP through its N-terminal region. DAT1 is recruited for the progeny formation sites during the early stages of budding. Conditional depletion of TgVPS13A, TgDAT1 or TgVAP results in collapse of the inner membrane complex, leading to parasite death, as visualized by endodyogeny-specific organelle markers. LactC2-GFP, a biosensor of phosphatidylserine and phosphatidylthreonine lipids made in the ER and enriched in the IMC, also mislocalizes upon protein depletion. In conclusion, we propose that TgVAP-TgVPS13A-TgDAT1 bridge the ER and IMC and mediate the inter-organelle transport of lipids, thus contributing to the organelle biogenesis and daughter budding in T. gondii. Author SummaryThe inner membrane complex (IMC) in apicomplexan parasites is essential for maintaining the structural stability of the parasite, as well as for its budding and motility. The IMC is composed of flattened vesicles, alveolins, and microtubules. However, the mechanism behind the biogenesis of these flattened vesicles remains unclear. In this study, we provide evidence that a protein complex formed by TgVAP, TgVPS13A, and TgDAT1 exists between the endoplasmic reticulum (ER) and the IMC. Phenotypic analysis indicates that the absence of any individual component of this protein complex disrupts the biogenesis of daughter IMCs, which in turn affects the budding of daughter parasites. We also demonstrated that TgDAT1 functions as a scramblase. Based on our findings, we propose a model in which the TgVAP-TgVPS13A-TgDAT1 complex mediates lipid transport from the ER to the nascent IMC, driving the expansion of the IMC membrane and the budding of daughter parasites in T. gondii. Furthermore, TgDAT1 may facilitate the transfer of lipids from the outer leaflet to the inner leaflet of the IMC sacs, promoting a balanced composition of the IMC membrane components.

microbiology↗

bioRxiv2025

Anionic Lipid Trafficking and Cell Mechanics RegulateMembrane Electrical Potential in Non-Excitable Tissue Cells

1The membrane potential of eukaryotic cells, classically described by the Goldman-Hodgkin-Katz model, is conventionally attributed to the steady-state balance of transmembrane ionic fluxes. Here, we demonstrate that non-excitable cells maintain stable, spatially heterogeneous membrane voltage gradients. Using the ratiometric voltage indicator JEDI-2P-cyOFP1, we quantitatively map membrane potential in live cells and find that cellular protrusions are consistently depolarized, whereas lateral membrane regions are hyperpolarized. These voltage gradients strongly correlate with anisotropic distributions of anionic lipids, including phosphatidylserine (PS) and phosphatidylinositol 3,4,5-trisphosphate (PIP3). Perturbation of cytoskeletal integrity, the ion exchanger NHE1, or vesicular trafficking disrupts both voltage anisotropy and lipid polarization, revealing an uncharacterized electromechanical regulatory mechanism. Moreover, membrane potential dynamically responds to cell shape, substrate stiffness, external electric fields, and cell cycle progression. To account for these phenomena, we develop a quantitative model that integrates ionic fluxes and lipid charge distributions, thereby explaining the emergence of voltage gradients. This framework establishes that membrane potential is governed not solely by ionic currents but also by lipid dynamics and mechanical signaling. Collectively, these findings identify membrane voltage as a global integrator of electrochemical and mechanical cues in eukaryotic cells.

biophysics↗

bioRxiv2025

Optimization of fermentation conditions for Metarhizium robertsii and its effect on rice growth

Metarhizium robertsii is an important entomopathogenic fungus and plant endophyte, possessing dual functionality as both an insecticide and a plant growth promoter, which has led to its widespread application in agriculture. However, the effects and underlying mechanisms of M. robertsii (MAA)in promoting rice growth remain poorly understood. This study confirmed the growth-promoting effects of MAA and its fermentation supernatant on rice. Based on single-factor and response surface methodology experiments, the fermentation conditions of MAA were subsequently optimized using rice root length as a key indicator, and the potential mechanisms behind this growth promotion were preliminarily investigated. The results demonstrated that both MAA and its fermentation supernatant exerted significant growth-promoting effects on rice. Sucrose and peptone were identified as the optimal carbon and nitrogen sources, respectively. The most pronounced effect was observed when the fermentation supernatant, produced under the conditions of pH 6.0, 0.2% {beta}-Ala, and 100 mol/L Al2(SO4)3, was applied, resulting in a 21.7% increase in rice root length compared to the control group. Furthermore, significant enhancements in chlorophyll content and denser root hairs were recorded in rice treated with the MAA fermentation supernatant, with the chlorophyll content increasing by 28.17% compared to the control. These findings provide a theoretical basis for the development and application of green and efficient bio-inoculants. IMPORTANCEMetarhizium robertsii is an endogenous plant fungus that can be effective for efficient insect control, but the plant-promoting effect of this fungus and its related studies are less reported. The colonization ability and growth promotion effect of Metarhizium robertsii on different crops vary. In this study, a sterile hydroponic system for rice was established. The research found that Metarhizium robertsii can colonize the root system of rice, significantly promoting rice growth, and its growtion-promoting effect is affected by the differences in its fermentation products. After the optimization of the response surface of the fermentation conditions of Metarhizium robertsii, its growth-promoting ability increased by 21.7%. Developing microbial biofertilizers/biopesticides as a basis for reducing chemical inputs in rice cultivation.

microbiology↗

bioRxiv2025

Deep learning reveals a microprotein atlas in maize and uncovers novel regulators of seed amino acid metabolism

Microproteins represent a vast and functionally important class of genes that remain largely unexplored in plant genomes. Here, we developed DeepMp, a deep learning framework that integrated multi-omics evidence and built the most comprehensive plant microprotein atlas to date, identifying 18,338 high-confidence candidates in maize. The majority of these appear to have originated de novo from regions previously annotated as noncoding, and they show hallmarks of rapid, lineage-specific evolution and pronounced tissue specificity. These novel microproteins were found integrated into core regulatory networks, particularly in organ development and nutrient storage. Focusing on the maize kernel, population-scale analyses linked microprotein expression to natural variation in amino acid content. We functionally validated three grain-filling-specific candidates originating from noncoding regions by CRISPR-Cas9 knockouts, which confirmed their roles as precise modulators of arginine, aspartate, and methionine levels, without pleiotropic effects on kernel morphology. Our study provides a foundational resource and analytical framework, establishes microproteins as a new and functionally important coding layer in maize, and uncovers a previously untapped source of targets for crop improvement.

genomics↗

bioRxiv2025

Spatially-resolved Photoproximity Profiling of MYC Identifies a MYC-BAF Liability in Cancer Cells

The c-MYC transcription factor is aberrantly expressed in most human cancers to enhance expression of proliferative gene programs. Owing to its pseudo-ordered structure and reliance on extensive and dynamic protein-protein interactions in distinct transcriptional regulatory complexes, defining context-specific MYC interactors has remained challenging. Therefore, mapping MYC-centered complex topologies in disease relevant models could identify components critical for its function which may serve as therapeutic targets in MYC-driven cancers. Here, we present a matched pair of photoproximity probes coupled with quantitative proteomics which enable context-dependent mapping of protein complex topology inside cells. We applied this spatially resolved, intracellular photoproximity (siPROX) profiling workflow to map MYC interactomes across temporal, spatial and disease-relevant contexts. Basal and inhibitor-treated profiles confirmed interactions with a wide range of known chromatin-associated transcriptional regulatory factors that define the extended MYC transcriptional bubble in live cells. Time-resolved mapping of inhibitor treated cells identified dynamic remodeling of numerous transcriptional regulatory factors and identified several BAF complex members (e.g., PBRM1 and SMARCC1)1 that persist in the presence of bromodomain inhibition. Furthermore, spatial MYC topology maps in small cell lung cancer cells confirmed the presence of BAF complex members under conditions where MYC induced target gene expression, altered cell morphology and enhanced proliferation. Lastly, loss of BAF function via inhibition of SMARCA2/4 ATPase activity resulted in rapid loss of chromatin-bound and nuclear MYC levels, downregulation of MYC-dependent transcripts and MYC-specific cell growth in several cancer cell models. Together, these data highlight the potential for siPROX to identify spatially resolved, dynamic TF interactors and highlight MYC-proximal BAF interactions as a targetable liability to regulate MYC-dependent transcription and proliferation.

cancer biology↗

bioRxiv2025

GECSI: Large-scale chromatin state imputation from gene expression

Compendiums of chromatin state annotations based on integrating maps of multiple epigenetic marks such as from ChromHMM have become a powerful resource. While these compendiums have coverage of many biological samples, there are many additional biological samples that have gene expression data but lack epigenetic mark data and chromatin state annotations. The EpiAtlas resource of the International Human Epigenome Consortium (IHEC) contains a large compendium of chromatin state annotations for which many samples have matched gene expression data, which provides the opportunity to use it to train models to predict chromatin state annotations in additional biological samples with only gene expression data available. To address this, we develop Gene Expression-based Chromatin State Imputation (GECSI), which uses a multi-class logistic regression model trained using a large compendium of gene expression and chromatin state annotations, and apply it to IHEC data. Using cross-validation, we find that GECSI accurately predicts chromatin state assignments and generates probability estimates that are predictive of observed chromatin states, overall outperforming multiple other alternative and baseline methods. GECSI-predicted chromatin states reflect relationships among biological samples and show similar transcription factor and gene annotation enrichments as observed chromatin states. Using available IHEC gene expression data, we apply GECSI to predict chromatin state annotations for 449 additional epigenomes. We expect these predicted annotations and the GECSI software will be a useful resource for chromatin state analyses in many additional biological samples.

bioinformatics↗

bioRxiv2025

Pseudomonas aeruginosa uses kinases NahK and RetS to control the motile-biofilm switch

The multidrug-resistant bacterium Pseudomonas aeruginosa (Pa) poses a significant threat to public health. This Gram-negative bacterium establishes pathogenicity through formation of multicellular communities, known as biofilms, that result in significant resistance to antibiotics and host immune systems. In Pa, the motile-to-biofilm transition is regulated through an interconnected signaling network known as the Gac Multikinase Network (Gac-MKN). This network comprises two regulatory branches: the HptB signaling network and GacS/A signaling network. In the Gac-MKN, several histidine kinases converge to regulate the activity of the post-transcriptional regulator protein, RsmA. Although previous studies have assessed the role of individual kinases in this network, the role of each Gac-MKN kinase in regulating RsmA activity has not been quantitatively characterized and compared in side-by-side experiments in the same reference strain, which is presented here. In this study, we show that kinases NahK and RetS are the predominant regulators of the Gac-MKN. Through controlled testing of RsmA-dependent phenotypes, we demonstrate loss of nahK or retS leads to complete inactivation of RsmA, triggering biofilm formation. Our results support previous findings that RetS regulates RsmA through the GacS/A network but present the new finding that NahK is the central kinase involved in HptB phosphorylation; previous studies have attributed HptB phosphorylation to PA1611 and SagS. Our findings demonstrate that NahK signaling controls RsmA activity to rapidly transition between the motile and biofilm states. We anticipate the results of this study will facilitate the use of targeting the Gac-MKN to trigger biofilm dispersal for improved antibiotic treatment.

microbiology↗

bioRxiv2025

APOE Tumor-Associated Macrophages and CD4-DOCK4 T Cells Reveal Distinct Microenvironmental Features in HER2-Low and HER2-0 Hormone Receptor-Positive Breast Cancer

Novel anti-HER2 antibody-drug conjugates (ADCs), such as trastuzumab deruxtecan (T-DXd), have shown efficacy in tumors with varying HER2 expression, including HER2-low and even tumors with minimal HER2 presence. This has sparked interest in the biology underlying the HER2 expression spectrum. Using molecular and multiplexed imaging, we revealed distinct immune and stromal features in treatment-naive, hormone receptor-positive (HR+) HER2-low versus HER2-0 tumors. HER2-0 tumors exhibit inflammatory and tissue remodeling gene signatures, with enrichment of APOE tumor-associated macrophages (TAMs) and DOCK4 CD4 T cells. In contrast, HER2-low tumors are more immunosuppressed, with elevated cell cycle, metabolic, and estrogen signaling pathways, suggesting increased proliferative activity. These findings underscore key biological differences between HR+ HER2-low and HER2-0 breast cancers, and may inform more tailored therapeutic strategies. Statement of significanceThis study revealed the distinct biological profiles of HR+ HER2-low and HER2-0 breast tumors. HER2-0 tumors exhibit inflammatory and tissue remodeling signatures, whereas HER2-low tumors have elevated cell cycle, metabolic, and estrogen signaling. These insights may help refine therapeutic approaches to improve outcomes for breast cancer patients.

cancer biology↗

bioRxiv2025

Neural Progenitors as a Novel Pathogenic Mechanism in Microcephaly

Despite their significance, the genetic and molecular bases of neurodevelopmental disorders remain poorly understood. In this study, using human brain organoids and mouse models, we show that loss of NDE1, a gene closely associated with microcephaly, disrupts progenitor identity, prolongs mitosis, and alters regional patterning in the forebrain. NDE1 knockout leads to a caudal identity shift of neural progenitor cells in the organoids and mouse brains, coinciding with aberrant ERK signaling. Notably, downstream activation of the ERK pathway restored rostral PAX6 expression in human brain organoids. Parallel analyses of Nde1 knockout mice confirmed disrupted regional patterning of the forebrain. Together, our data establish NDE1 as a critical regulator of early human brain regionalization and elucidate molecular mechanisms underlying the structural abnormalities observed in NDE1-associated microcephaly.

developmental biology↗

bioRxiv2025

APOE knockout attenuates vascular graft fibrosis by limiting profibrotic macrophage formation through low-density lipoprotein receptor related protein 1

Vascular graft fibrosis can cause a decrease in cellular infiltration and capillary ingrowth in vascular walls and vascular stiffening. As such, there are still no vascular grafts that can be used in blood vessels where their diameters are less than 6 mm in patients. Although various approaches have been evaluated to mitigate implant-associated fibrosis, effective treatments remain quite limited. In this study, we demonstrated that APOE was significantly increased during vascular regeneration after graft implantation in vivo. APOE knockout (KO) increased compliance of regenerated aortas and reduced extracellular matrix (ECM) deposition in adventitia of the regenerated aortas. Using single cell RNA sequencing (scRNA-seq), a subset of profibrotic macrophages was found to be involved in graft fibrosis and APOE KO limited the formation of profibrotic macrophage formation during vascular regeneration. The interaction between APOE and low-density lipoprotein receptor related protein 1 (LRP1) partially mediated fibrotic differentiation of the macrophages. Profibrotic macrophages promoted graft fibrosis mainly through secretion of insulin-like growth factor-1 (IGF-1) that could support proliferation of fibroblasts. Finally, we showed that APOE knockdown in vivo using adeno-associated virus (AAV) improved the compliance of regenerated aortas and reduced ECM deposited in the adventitial areas by limiting formation of profibrotic macrophages. Collectively, these data indicate that APOE promotes the profibrotic transition of macrophages partially through LRP1, and the profibrotic macrophages increase the proliferation of fibroblasts via IGF-1. Inhibition of APOE by AAV can alleviate graft fibrosis occurring during vascular regeneration.

bioengineering↗