Biology subjects

Yang, X.

Publications and source records attributed to Yang, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Successor representation supports structural learning of syllable sequences

Humans efficiently learn the temporal structure of speech, yet the underlying cognitive mechanisms remain unclear. Recent research in visuospatial sequential memory has proposed the successor representation (SR), important in reinforcement learning, which encodes multi-step transitional relationships. To test whether SR also supports the structural learning of rapidly changing speech syllable sequences, we adapted a pyramid-structured sequential learning paradigm using syllable streams presented at a natural speech rate (~ 4 Hz). Participants exhibited robust structural learning, evidenced by asymmetric memory performance modulated by adjacent transitional probabilities. Notably, the SR model captured recognition performance for non-adjacent syllable pairs. Moreover, SR-based learning effects generalized across all syllable sequences, regardless of adjacency. Furthermore, the effectiveness of SR learning was associated with cognitive flexibility and working memory capacity. Together, these findings suggest that humans rely on effortful SR-like mechanisms for the structural learning of syllable sequences, highlighting a modality-general computational principle for sequential learning across various temporal modulation scales.

neuroscience↗

bioRxiv2026

Panic at the Discordance: the Asparagaceae Phylogenetic Backbone

The Asparagaceae is an economically and ecologically important angiosperm (monocot) clade, containing iconic garden plants such as asparagus, hyacinth and agave, and arid-adapted keystone species like Joshua tree and dragon blood tree. The approximately 2,500 species in the family are spread across seven subfamilies: Agavoideae, Aphyllanthoideae, Asparagoideae, Brodiaeoideae, Lomandroideae, Nolinoideae and Scilloideae. Relationships among the seven subfamilies are generally unresolved and the sources of gene tree-species tree discordance are largely unknown. Investigating the biology underlying such discordance requires a robust sampling of both taxa and molecular markers, due to the extremely short branches that form the backbone of the Asparagaceae phylogeny. Using targeted sequencing of 1,726 low-copy nuclear genes, and a nearly complete sampling of genera, we interrogate relationships among all seven Asparagaceae subfamilies and investigate the underlying sources of discordance across the phylogeny. Analyses using different phylogenomic approaches (multispecies coalescence vs. nuclear gene supermatrix vs. chloroplast gene supermatrix) each revealed extensive discordance across the Asparagaceae backbone, which may be associated with rapid lineage diversifications that occurred in Africa shortly following the origin of the family ~49 Ma. Specifically, we found that two branches, representing ancestors of Aphyllanthoideae and Nolinoideae, may be responsible for much of the backbone discordance. The placement of Aphyllanthoideae, represented by one extant taxon (Aphyllanthes monspeliensis), is controversial with discordant topologies across many studies. However, multispecies coalescence-based analyses from this study strongly support a sister relationship between Aphyllanthoideae and a larger Agavoideae + Scilloideae + Brodiaeoideae clade. According to gene tree quartet frequencies and ABBA-BABA tests, we cannot reject incomplete lineage sorting (ILS) as the main source of discordance for the placement of Aphyllanthoideae; our results leave open the possibility of an ancient reticulation involving an ancestor of Aphyllanthoideae and an extinct basal Asparagaceae lineage. Regarding Nolinoideae, we found that conflicting support for two possible bifurcating clades (Asparagoideae + Nolinoideae vs. Asparagoideae + Lomandroideae) was associated with skewed support for alternative gene tree topologies, suggesting that phenomena other than ILS may explain the observed discordance. A quartet-based ABBA-BABA analysis, used to test for signatures of introgression, revealed a putative ancient hybridization event between two divergent, ancestral lineages which may have contributed to the origin of the Nolinoideae clade in Africa ~45 Ma. In sum, this study elucidates the long-troublesome backbone of the Asparagaceae phylogeny and advances our understanding of the evolutionary and biogeographical origins of all extant subfamilies. More broadly, this study expands our understanding of the various sources of gene tree discordance that may arise from natural processes associated with rapid lineage radiations across the tree of life.

evolutionary biology↗

bioRxiv2026

Platform-specific count-matrix preprocessing workflows for spatial transcriptomics data analysis

Preprocessing of spatial transcriptomics (ST) count matrices is critical for removing technical variation while preserving biological signals, but optimal strategies remain unclear across diverse platforms. We systematically benchmarked 371 preprocessing workflows across 45 data spanning 11 mainstream ST platforms, evaluating their performance using specifically designed complementary metrics. To further assess preprocessing factors upstream of count-matrix generation, we additionally evaluated image preprocessing, including cell segmentation and post-segmentation transcript processing, across representative imaging-based ST platforms. We found that no universal count-matrix preprocessing workflow performed optimally across all platforms, while data from the same platforms exhibited striking consistency in optimal count-matrix preprocessing workflows. We identified the key data structure characteristics and count-matrix preprocessing steps that critically influence preprocessing performance. We developed platform-specific and data structure-guided recommendations to assist users in selecting the optimal count-matrix preprocessing workflow, validated across a broader range of downstream tasks. We demonstrated that our data-driven recommendations uncover subtle biologically meaningful spatial patterns in new data that were obscured by suboptimal count-matrix preprocessing. Our findings suggest best practices for ST data count-matrix preprocessing.

bioinformatics↗

bioRxiv2026

Refinement of the Pathogenic T Cell Receptor Motif Suggests Type 17 CD8+ T Cells Initiate HLA-B*27-associated Autoimmunity

Human leukocyte antigen B*27 (HLA-B*27) is a major risk factor for autoimmune diseases such as axial spondyloarthritis (axSpA), acute anterior uveitis (AAU), and psoriatic arthritis (PsA). HLA-B*27 presents bacterial and self-antigens to disease-associated CD8+ T cells, however, how this leads to a pathogenic IL-17-mediated disease remains unclear. We performed mutational experiments in an established disease-associated TCR and demonstrated that the pathogenic motif encompasses a wider range of TCR sequences than previously appreciated. We next leveraged computational pairing of alpha/beta TCR sequencing (TCR-seq) to demonstrate that the broadened pathogenic motif distinguishes axSpA and AAU patients from healthy controls. Paired single-cell RNA sequencing and single-cell TCR sequencing datasets demonstrated that the pathogenic cells have a distinct transcriptional signature. We find a coupling of pathogenic TCRs to this transcriptional signature in public datasets from axSpA and PsA joint fluid and AAU ocular fluid. Finally, we detect the pathogenic CD8+ T cells in the gut and demonstrate that they express a Type 17 program. Our findings suggest that HLA-B*27+ axSpA, AAU, and PsA are initiated by HLA-B*27-restricted pathogenic CD8+ T cells that undergo Type 17 differentiation in response to intestinal antigens.

immunology↗

bioRxiv2026

TopoFlow: Evolutionarily Conditioned Flow Matching for Protein Conformational Ensemble Generation

Proteins function through dynamic conformational ensembles rather than a single static structure, yet accurately modeling these ensembles remains challenging. Here, we introduce TopoFlow, an evolutionarily conditioned flow-matching framework for protein conformational ensemble generation. TopoFlow uses evolutionary representations from multiple sequence alignments (MSAs) to encode global conformational heterogeneity. It combines this with structural variables from a variational autoencoder (VAE) to capture local flexibility. These complementary representations are then adaptively fused through a conditional modulation module to construct unified conditioning features that guide protein conformational ensemble generation. On the ATLAS molecular dynamics (MD) benchmark, TopoFlow improved the Jensen Shannon metrics for pairwise distances (JS-PwD), radius of gyration (JS-Rg), and time-lagged independent components (JS-TIC) by 10.73%, 5.78% and 7.75%, respectively, relative to BioEmu. Notably, this performance generalizes to experiment-based evaluation, where TopoFlow exhibits strong agreement with experimental observables, including chemical shifts (CS) and small-angle X-ray scattering (SAXS). Ablation analyses further indicated that the evolutionary representations and structural latent variables contributed complementary information to ensemble generation. Our results suggest that TopoFlow, through its integration of evolutionary and structural latent information, offers a promising strategy for generating structurally plausible and conformationally informative protein ensembles.

bioinformatics↗

bioRxiv2026

Loss of TCA cycle turning promotes stem cell function

The citric acid cycle (TCA cycle) is the common terminal pathway for the oxidation of all nutrients. Citrate oxidation to oxaloacetate produces CO2, and citrate synthase (CS) uses nutrient-derived acetyl groups to regenerate citrate and fuel cycle turning. However, the essentiality of cycle fueling and turning in vivo remains unclear. Here we use hematopoiesis, the most proliferative system in the body, as a model to show that, contrary to common assumptions, TCA cycle turning is dispensable for respiration, survival, and proliferation of stem and progenitor cells in vivo, and its loss promotes stem cell function. Hematopoietic-specific Cs deletion in adult mice blocked citrate cycling without reducing the frequency of hematopoietic stem (HSC) and progenitor cells. HSCs and progenitor cells adapted to TCA cycle loss by markedly increasing nutrient consumption and biosynthesis. Disruption of cycle turning increased HSC regeneration, myeloid progenitor proliferation, and myelopoiesis in vivo. HSCs without a turning TCA cycle outcompeted wild-type HSCs within the same environment. The effect of CS deletion on HSC function was not phenocopied by genetic ablation of cytosolic citrate use and was rescued by ablation of glutamine use in biosynthesis. Therefore, TCA cycle turning restrains nutrient uptake, biosynthesis, cell proliferation, and stem cell function. These results suggest an explanation for the reduction in cycle activity observed in many normal proliferating cells and cancer cells.

biochemistry↗

bioRxiv2026

A multi-electrode array and immunofluorescence workflow to characterize impacts of HHV-6 infection in induced pluripotent stems cells differentiated to mixed neuronal endpoints

Roseoloviruses, notably human herpesviruses 6A and 6B (HHV-6A and HHV-6B), are neurotropic viruses implicated as agents in neurological disorders, including: epilepsy, multiple sclerosis, and chronic fatigue syndrome. However, the effects of roseolovirus infection on neuronal signaling and network activity are not characterized. This is, in part, due to the complexities of monitoring electrical activity in individual neurons and across neuronal connections during viral infection. This protocol describes a human induced pluripotent stem cell (iPSC)-derived neuronal culture system that employs multi-electrode array (MEA) recordings to study neurophysiological changes during viral infection. Two culture platforms are described: (a) NGN2-induced forebrain neuronal cultures; and, (b) progenitor cell-derived neuron-astrocyte mixed cultures. Cell composition in cultures is validated by immunofluorescence staining using neuronal, glial, and viral markers. Functional activity is assessed using extracellular recordings detected via the MEA2100 system. Mean firing rate, inter-spike interval, single-electrode bursting, and network burst activity are characterized between roseolovirus-infected versus uninfected (control) states. Pharmacological treatment with bicuculline, gabazine, and nicotine in conjunction with immunofluorescence is used to confirm functional responsiveness of defined neuronal neurotransmitter chemotypes. Here, we show that HHV-6A infection changes neuronal firing compared to uninfected controls. The methods/workflows described provide a strategy to study how virus infection alters neuronal excitability and may be adapted to compare the effects of different viruses on nerve cell function, infection time courses, different multiplicities of infection (MOI), and therapeutic interventions.

microbiology↗

bioRxiv2026

In Utero Alcohol Exposure Reprograms Mammary Gland Development and Stem/Progenitor Cell Activity in a Non-Tumorigenic Mouse Model

In utero alcohol exposure (IUE) can alter mammary development and increase mammary tumor susceptibility in experimental models. However, most previous studies have relied on carcinogen-induced or genetically tumor-prone models, leaving it unresolved whether prenatal alcohol exposure produces mammary developmental and molecular changes before the introduction of an oncogenic challenge. Here, we addressed this question using non-tumorigenic C57BL/6 mice. Pregnant dams received a Lieber-DeCarli liquid diet containing 1.7% (v/v) ethanol or an isocaloric control diet from gestational day 11 to 19, and mammary glands from female offspring were examined during puberty (postnatal day 40, PND40) and young adulthood (PND70). At PND40, IUE enhanced mammary ductal morphogenesis, increased terminal end bud numbers, and elevated epithelial proliferation. These developmental alterations persisted at PND70, with increased lateral branching and proliferative activity. IUE also altered mammary epithelial composition, expanding the basal/myoepithelial compartment and the CD24highCD49fhigh mammary repopulating unit/stem cell-enriched population. Mammary epithelial cells from IUE-exposed offspring exhibited increased colony-forming cells (CFCs), mammosphere formation, and 3D Matrigel growth, indicating enhanced stem/progenitor-associated activity. At the molecular level, IUE increased ER; expression and phosphorylation together with Cyclin D1, c-Myc, E2F1, and Bcl-2, and enhanced AKT, ERK, and STAT3 phosphorylation, IL-6 expression, and SOX2 at PND40. Importantly, major components of this signaling phenotype remained altered at PND70, including ER;-associated signaling, AKT/ERK activation, and IL-6/STAT3 signaling, whereas the pubertal increase in SOX2 was not sustained. Together, these findings demonstrate that prenatal alcohol exposure induces profound and persistent histomorphological, cellular, and signaling alterations in the mammary gland in the absence of a carcinogenic challenge or genetically introduced oncogenic driver. These results identify intrinsic developmental reprogramming of normal mammary tissue as a potential basis through which prenatal alcohol exposure may modify subsequent responses to tumor-promoting or other environmental challenges.

developmental biology↗

bioRxiv2026

Transcriptomic Analysis of the Newborn Mammary Gland Identifies Prenatal Ethanol-Induced Remodeling of Insulin Signaling and Enhanced Proliferative Programming

Prenatal alcohol exposure (PAE) can produce persistent alterations in mammary development and increase susceptibility to mammary tumorigenesis, but the early molecular events underlying these effects remain poorly understood. Here, we examined whether PAE alters the molecular program of the mammary gland at birth. Pregnant MMTV-ErbB2 mice received control or ethanol-containing liquid diets during gestation, and mammary tissues were collected from newborn female offspring. RNA sequencing revealed exposure-level-dependent transcriptional reprogramming, with substantially broader alterations following moderate compared with lower ethanol exposure. Pathway analyses identified prominent changes in metabolic and growth-regulatory networks, including insulin signaling, with coordinated alterations in components of the insulin/IGF-IRS-PI3K/AKT pathway. Biochemical analyses further demonstrated exposure-dependent changes in IGFBP expression and IRS1 abundance and phosphorylation, supporting remodeling of insulin/IGF-associated signaling. Transcriptomic analyses also revealed enrichment of RNA metabolic and translational processes and, particularly following moderate exposure, enhanced DNA-replication, cell-cycle, and mitotic programs. These molecular signatures were accompanied by increased proliferative features in newborn mammary tissue. Together, these findings demonstrate that PAE establishes substantial molecular reprogramming of the mammary gland by birth and identify altered insulin/metabolic signaling and proliferative programming as prominent features of this early developmental response.

developmental biology↗

bioRxiv2026

Rising water is an underappreciated driver of forest mortality

Forests are known to burn and desiccate under a changing climate; less appreciated is that they also drown. Across much of the globe, a warming atmosphere is amplifying the length and intensity of both droughts and floods. Whereas massive die-offs from drought and fire are widely studied as consequences of climate change on forests, inundation-induced mortality remains poorly quantified. Using approximately 1 m resolution aerial imagery and deep learning, we tracked over 260 million dead trees across the United States' Great Lakes and ocean coastlines from 2012 to 2023. Within 10 km of the coasts, more than half of mapped mortality was concentrated in just 10% of forests, primarily in high-elevation inland wetlands and low-lying forests prone to inundation. Mortality rates doubled within a decade around expanding freshwater lakes and in inland wetlands experiencing intensifying regional-scale precipitation, while tripling in low-lying coastal forests where salinization compounded inundation in sea-level rise hotspots. Our findings identify rising waters as a widespread, underappreciated driver of forest die-off that can extend far inland, underscoring the need to reassess the impacts of climate change on the functioning, demography, and carbon-methane budgets amongst the world's most carbon-rich forests as seas rise and hydroclimate shifts globally.

ecology↗

bioRxiv2026

Chronic Alcohol Exposure Induces Persistent DNA Damage Response Signaling and Sensitizes Breast Epithelial Cells to PARP Inhibition

Chronic alcohol consumption is associated with increased breast cancer risk; however, the long-term effects of alcohol exposure on DNA damage response (DDR) signaling and therapeutic vulnerability in breast epithelial cells remain incompletely understood. In the present study, we established a chronic alcohol exposure model using immortalized human breast epithelial MCF-10A cells to investigate persistent alterations in DNA damage signaling and sensitivity to poly (ADP-ribose) polymerase (PARP) inhibition. MCF-10A cells that chronically exposed to 0.2% alcohol for 20 weeks and then withdrew alcohol treatment for 4 weeks still retained elevated {gamma}H2AX levels and sustained activation of ATM/ATR-associated DDR pathways. Chronic alcohol-exposed cells also exhibited increased sensitivity to the PARP inhibitors olaparib and veliparib, as demonstrated by reduced cell viability, decreased clonogenic survival, and enhanced apoptosis. Mechanistically, olaparib induced greater G2/M checkpoint activation and replication-associated DNA damage in chronic alcohol-exposed cells compared with control cells. In addition, chronic alcohol exposure increased PARP expression and enhanced activation of DDR signaling following PARP inhibition. These findings demonstrate that chronic alcohol exposure induces persistent DNA repair stress and sensitizes breast epithelial cells to PARP inhibition. Our study suggests that chronic alcohol-associated genomic stress may create potential vulnerability to PARP inhibition.

cell biology↗

bioRxiv2026

Alcohol Promotes ER+ Breast Cancer Cell Proliferation and Invasion Through the Upregulation of Neuregulin 1-Mediated ER-ErbB3 Crosstalk

Alcohol consumption is an established risk factor for breast cancer, with a particularly strong association with estrogen receptor-positive (ER+) disease. Although the estrogenic activity of alcohol is well recognized, how alcohol-induced ER signaling is coupled to growth factor receptor pathways that promote tumor cell growth and progression remains incompletely understood. Here, we identify neuregulin-1 (NRG1) as a functional mediator, linking alcohol-induced ER activity to ErbB3 receptor tyrosine kinase signaling in ER+ breast cancer cells. Under estrogen-depleted conditions, alcohol induced proliferation, clonogenic growth, and S-phase progression in MCF-7 and T47D cells. Alcohol concurrently increased ER phosphorylation and transcriptional activity, including enhanced ER occupancy at the endogenous TFF1/pS2 regulatory region, and activated ErbB3 and downstream Akt, ERK, and p38 signaling. Notably, alcohol induced NRG1 expression in both cell lines. Pharmacological inhibition of ER signaling with ICI 182,780 (fulvestrant) substantially attenuated NRG1 induction, ErbB3/RTK activation, and alcohol-promoted growth, indicating that NRG1 induction and engagement of RTK signaling are strongly dependent on functional ER signaling. Conversely, shRNA-mediated NRG1 depletion suppressed alcohol-induced proliferation, clonogenic growth, and cell-cycle progression and markedly reduced alcohol-induced migratory and invasive phenotypes. NRG1 depletion also attenuated ErbB3/Akt/ERK signaling while reducing ER activation and ERE-dependent transcription, demonstrating a functional contribution of NRG1 to both arms of the signaling response. Together, these findings support a reciprocal ER-NRG1-ErbB3 signaling circuit in which alcohol-induced ER activity promotes NRG1 expression, while NRG1-dependent ErbB3 signaling reinforces ER activity and tumor-promoting phenotypes. Our study identifies NRG1 as a previously unrecognized molecular link between the estrogenic activity of alcohol and growth factor receptor signaling and provides a mechanistic framework for understanding alcohol-associated promotion of ER+ breast cancer.

cell biology↗

bioRxiv2026

ALDH2 Knockout Induces Dysregulation of Arginine biosynthesis in SKBR-3 Breast Cancer Cells

Background/Objectives: Aldehyde dehydrogenase 2 (ALDH2), a mitochondrial enzyme, mitigates cellular stress by detoxifying reactive aldehydes produced during alcohol exposure and endogenous metabolic processes. ALDH2*2 polymorphism, which results in deficient catalytic activity, is prevalent in East Asian populations and is associated with an increased risk of cancer and other diseases. While the effects of ALDH2 deficiency on cellular stress responses are well documented, the specific metabolic dysregulations arising from this deficiency require further investigation. Methods; An ALDH2 knockout subline of SKBR-3 cells was established using CRISPR/Cas9 strategy. The metabolomic profiles of control (SKBR-3/C) and ALDH2 knockout (SKBR-3/ADKO) cells were evaluated via ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS). Results: ALDH2 knockout in SKBR-3 cells resulted in increased cellular stress, evidenced by elevated levels of 8-OHdG, reactive oxygen species (ROS), and malondialdehyde (MDA). Metabolomic analysis of the paired cell lines assigned a total of 5,033 signals, of which 281 were significantly different (fold change [≥] 2, p-value <0.05) between the two groups. Pathway analysis with MetaboAnalyst identified significant metabolic pathways associated with ALDH2 deficiency, particularly those involving arginine biosynthesis, and arginine and proline metabolism. ALDH2 deficiency reprogramed arginine metabolism toward polyamine pathways while suppressing the urea cycle. Network analysis further revealed alterations in amino acid and lipid metabolism in ALDH2-deficient cells. Conclusions; This study provides a novel insight into the role of ALDH2 in cancer metabolism and may have broader implication for cancer biology.

cell biology↗

bioRxiv2026

Functional niche attributes shape species interaction roles in ecological networks

Identifying how species interact in ecological networks is key to understanding species' contributions to ecosystem functioning, but can be difficult to establish in species-rich communities. Functional niches, which capture broader ecological strategies, are often easier to assess and could help approximate species' interaction roles. We tested this by integrating species interaction and leaf functional trait data of tree species and leaf-associated interaction types from a large-scale forest biodiversity experiment. We found that identity, variability, and similarities of functional niches shaped corresponding aspects of interaction roles. Interestingly, however, this association inversed in the case of functional niche variability, which decreased instead of increased the variability of species interactions. This suggests a potential trade-off between processes that determine variability in functional and interaction space. Furthermore, effects were not constrained within aspects, with similarities of interactions being particularly responsive to most tested niche aspects, indicating that interaction-based competition among plants is particularly sensitive to functional niche differences. Moreover, many effects of functional niches depended on tree species biomass and tree species richness, highlighting the importance of the larger ecological context for determining species interaction roles. Together, our findings show that species' interaction roles, while clearly altered by, are not simply a consequence of functional niches. Instead, interaction roles integrate multiple aspects of functional niches depending on species performances and community composition and can therefore be crucial for anticipating ecosystem change.

ecology↗

bioRxiv2026

Risk-Window Palbociclib Exposure Delays ErbB2-Driven Mammary Tumorigenesis and Suppresses Mammary Epithelial Cell Stemness

ErbB2 overexpression occurs in 15-20% of invasive breast cancer (BC) and inactivation of Cyclin D1-CDK4/6 axis reduce mammary stem/progenitor cells in ErbB2-driven tumorigenesis. Here, we explored the preventive role of short-term palbociclib intervention in MMTV-ErbB2 mice. Palbociclib significantly inhibited the proliferation and stemness of ErbB2-overexpressed BC cells in vitro and in vivo. Furthermore, short-term palbociclib exposure during the early premalignant risk window significantly delayed mammary tumor development and reduced tumor multiplicity, accompanied by the suppression of epithelial proliferation and ductal/alveolar morphogenesis in premalignant tissues, as well as prolonged tumor-free survival compared with controls. Importantly, palbociclib reduced the luminal epithelial (CD24high/CD49flow), mammary reconstitution unit-enriched (CD24high/CD49fhigh) subpopulations, and luminal progenitor/TIC-enriched (CD61high/CD49fmid) subpopulations. These changes were accompanied by diminished mammary epithelial cell stemness functions, including colony-forming, mammosphere-forming, and 3D growth activities of mammary epithelial cells. Mechanistically, palbociclib-treated tissues showed inhibition of the Cyclin D1-CDK4/6-RB-E2F axis and coordinated attenuation of ER-, ErbB2- and Wnt/{beta}-catenin-associated signaling. Together, we demonstrate that short-term CDK4/6 inhibition during a premalignant risk window produces a sustained delay in ErbB2-driven mammary tumorigenesis, associated with remodeling of the mammary epithelial hierarchy and suppression of proliferative and stem/progenitor-associated activity, suggesting CDK4/6 inhibition as a strategy for ErbB2-positive BC prevention.

cancer biology↗

bioRxiv2026

Glutamine-regulated VCP acetylation creates a proteostasis vulnerability in RB1-deficient tumor

RB1 deficiency defines an aggressive tumor state with limited therapeutic options. Osteosarcoma represents a clinically relevant model of RB1 deficient malignancy, as RB1 alterations are among the most frequent genomic events in this tumor type. However, the non cell cycle vulnerabilities created by RB1 loss remain incompletely understood. We therefore used osteosarcoma to identify therapeutic dependencies associated with RB1 deficiency. Through high-throughput compound screening, we identified a selective vulnerability of RB1-deficient tumor cells to VCP inhibition. NMS-873 and other VCP-targeting compounds preferentially suppressed RB1 deficient cells across two-dimensional cultures, three-dimensional spheroids, patient-derived organoids, and in vivo tumor models. Mechanistically, VCP inhibition exacerbated proteostasis stress and activated endoplasmic reticulum stress responses in RB1-deficient cells. We further found that VCP function was regulated by glutamine-dependent acetylation, with lysine 615 serving as a dominant acetylation site that modulated sensitivity to VCP inhibition. Glutamine restriction phenocopied, whereas glutamine supplementation partially rescued, the effects of NMS-873 on VCP acetylation and tumor cell growth. Clinical and transcriptomic analyses further linked VCP expression and protein-folding stress programs to aggressive disease features. Together, these findings identify glutamine regulated VCP acetylation as a metabolic proteostasis dependency in RB1-deficient tumors and nominate VCP inhibition as a therapeutic strategy for this difficult-to-target tumor state.

cell biology↗

bioRxiv2026

PromptBio: An Agentic Platform for End-to-End Computational Biomedical Research

Modern biomedical research increasingly depends on complex computational analyses, yet translating a scientific question into a reliable workflow still requires substantial technical expertise and manual coordination. PromptBio is a multi-agent AI platform available through a web portal at https://promptbio.ai that addresses this challenge. Through natural-language interaction, its agent harness, PromptGenie, translates a research objective into an inspectable plan, executes the required research and analysis, and adapts subsequent steps as evidence and results emerge. PromptBio integrates reasoning with managed execution while preserving human oversight and a traceable record of the research process. It can apply validated methods, construct custom analyses, and incorporate external workflows, enabling researchers to move beyond fixed pipelines while supporting reproducibility. We evaluate the platform through benchmarks of end-to-end bioinformatics analysis and biomedical deep research, validation of representative omics and machine-learning skills, and a hypothesis-driven regulatory-genomics case study. PromptGenie achieved higher analytical accuracy and stronger evidence retrieval and synthesis than the comparison agents, while the evaluated domain skills produced results consistent with established methods. The case study further demonstrates how PromptBio can integrate human-specific genomic and epigenomic features to investigate cortical development. Together, these findings show that PromptBio can coordinate complex biomedical analyses under researcher oversight, offering an accessible approach for accelerating scientific iteration and transforming research questions into transparent, reusable computational workflows.

bioinformatics↗

bioRxiv2026

Catalytic and inhibitory architecture of comammox ammonia monooxygenase

Complete ammonia oxidizers (comammox) are widespread nitrifiers that can dominate ammonia oxidation in diverse environments by efficiently converting ammonia to nitrate within a single cell, yet the molecular basis distinguishing their ammonia monooxygenase (AMO) from those of canonical bacterial AMO remains unresolved. Here we report cryo-electron microscopy (cryo-EM) structures of AMO from the comammox Nitrospira inopinata (NiAMO) in inhibitor-free and allylthiourea (ATU)-bound states at 2.47 and 2.68 angstrom, respectively. NiAMO displays distinctive auxiliary-subunit organization, copper-site configuration and hydrophobic-channel architecture. Integrative molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations support a methyl-plastoquinol (methyl-PQH2)-coupled, CuD-centric catalytic model, with CuC potentially facilitating quinone redox cycling. N. inopinata exhibited broad susceptibility to several known nitrification inhibitors, and ATU-bound NiAMO structure localized the inhibitor to the CuC-CuD region, accompanied by constriction of the hydrophobic channel, which is consistent with the competitive role of ATU demonstrated in recovery assays. Multi-omics analyses further revealed an energy-limited stress response to ATU, including induction of urea transport and utilization systems. Collectively, these findings define a methyl-PQ-linked catalytic and inhibitor-responsive architecture of comammox AMO and establish a mechanistic framework for lineage-aware management of nitrification in natural and engineered ecosystems.

biophysics↗