Biology subjects

Zhang, T.

Publications and source records attributed to Zhang, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Relative reward memories retain multidimensional information in bumblebees

Previously, we showed that bumblebees encode reward value relative to local alternatives and, when comparing options learned in separate contexts, retrieve only their ordinal rank rather than absolute reward magnitude (Solvi et al., 2022). However, that study, like related work across species, varied reward along a single dimension. Natural rewards such as nectar are multidimensional, yet how such rewards are represented in relative memory remains unknown. We tested this by training bumblebees in separate contexts with rewards varying in two intrinsic dimensions, sucrose concentration and NaCl content, and then comparing options never encountered together. When only sucrose concentration varied, bees showed no preference between options that had each been locally better, despite differing in absolute concentration. With multidimensional rewards, however, this equivalence no longer held: bees preferred an option that had been locally better on both sucrose and NaCl over one better on only sucrose or only NaCl. A two-dimensional advantage also produced a stronger preference than a one-dimensional advantage 48 h after training. Thus, the ordinal rank we previously identified captures only part of the relative reward representation: with multidimensional rewards, bumblebees also retain information about the dimensions on which an option had been locally better.

animal behavior and cognition↗

bioRxiv2026

Recombinant Ehrlichia TRP75 Rescues Molting Failure of Ticks Infected with TRP75 Mutant Ehrlichia

Ehrlichia species are obligatory intracellular bacteria that exist in nature through a cycle of infection and transmission between ticks and their mammalian hosts, potentially causing a severe febrile illness called ehrlichiosis in humans and animals. Roles of Ehrlichia molecules in tick-mammal Ehrlichia transmission are mostly unknown. Tandem repeat protein (TRP) 75 is a lipoprotein conserved among Ehrlichia species. We identified and cloned a Himar1 transposon insertional mutant of Ehrlichia japonica that lacks C-terminal intrinsically disordered region of TRP75 (TRP75{Delta}C). This mutant was competent in infecting and replicating in both mammalian and tick cells in culture, and causing fatal illness similar to wild-type (WT) E. japonica. Upon feeding on TRP75{Delta}C and WT Ehrlichia-infected mice, both larval- and nymphal-stage of Ixodes scapularis ticks ingested similar amounts of blood meal as those fed on uninfected mice, and acquired similar levels of infection. However, most of TRP75{Delta}C Ehrlichia-infected ticks failed to complete molting, in contrast to successful molting of WT Ehrlichia-infected and uninfected ticks by 10 weeks post-feeding. In both WT Ehrlichia-infected and uninfected ticks, ~1,000-fold exponential increase in ecdysone receptor (EcR) mRNA occurred at 15 days post-feeding, whereas EcR mRNA was not upregulated in TRP75{Delta}C Ehrlichia-infected ticks. Upon microinjection of recombinant full-length TRP75 protein into engorged ticks infected with TRP75{Delta}C Ehrlichia, molting efficiency was ~90% restored, and there was significantly increased EcR mRNA compared with solvent microinjection control. This suggests that the endoparasitic bacterial molecule TRP75 manipulates the molting success of infected ticks and EcR mRNA levels for the survival of bacteria-hosted ticks and transstadial transmission.

microbiology↗

bioRxiv2026

N-Acetylglucosamine ameliorates knee osteoarthritis by enhancing UDP-GlcNAc conversion and chondrocyte DNA repair capacity

Background: Knee osteoarthritis (KOA) is a degenerative joint disease characterized by progressive cartilage degradation and synovial inflammation, while current therapies offer only symptomatic relief. This study aimed to determine whether N-acetylglucosamine (GlcNAc) is superior to glucosamine hydrochloride (GlcN{middle dot}HCl) in slowing the progression of KOA and to elucidate the underlying mechanisms involved. Methods: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed to assess serum concentrations of UDP-GlcNAc to conduct a comprehensive evaluation of the pharmacokinetics and pharmacodynamics associated with both GlcNAc and GlcN{middle dot}HCl. Using a destabilization of the medial meniscus (DMM) rat model, we performed micro-computed tomography and histopathological assessments to evaluate structural changes in the joint tissues. Additionally, we conducted bulk RNA sequencing, flow cytometry and ELISA to validate the efficacy of GlcNAc in anti-inflammatory immunoregulation and DNA repair in knee cartilage. Results: GlcNAc achieved higher peak serum concentrations and more efficient conversion to UDP-GlcNAc than GlcN{middle dot}HCl, with UDP-GlcNAc levels 4.57 times higher at 9 hours after administration. GlcNAc significantly attenuated KOA-like pathological changes, downregulated catabolic markers Mmp3 and Adamts4, decreased pain-related neural markers Pgp9.5 and Ngf, and alleviated pain sensitivity. RNA-seq identified 4,395 downregulated DEGs in DMM rats, of which GlcNAc upregulated 2,808 compared to only 391 by GlcN{middle dot}HCl. GlcNAc promoted DNA repair and adaptive immune cell differentiation pathways, and decreased serum IL-1{beta}, IL-6, and IL-17. Four candidate DNA repair genes, Hist1h2an, Poli, Ube2t, and Hells, were identified as significantly upregulated by GlcNAc, with GSEA confirming homologous recombination repair pathway enrichment. Conclusion: This study shows GlcNAc outperforms GlcN{middle dot}HCl in rat DMM knee osteoarthritis via multiple mechanisms, including 4.57-fold higher UDP-GlcNAc conversion, reduced cartilage degeneration, immune rebalancing, and DNA repair activation, supporting GlcNAc as a promising KOA candidate warranting further clinical study.

pharmacology and toxicology↗

bioRxiv2026

TFL1 homolog integrates temperature signals to control timing of developmental transitions in woodland strawberry

In overwintering plants of temperate climates, inflorescence and flower buds commonly form in autumn under cool temperatures, while flowering occurs the following spring. However, how cool temperatures regulate inflorescence and flower development remains poorly understood. We used woodland strawberry (Fragaria vesca L.), a perennial Rosaceae herb, to investigate the effects of cool temperature on reproductive development. We characterized temperature-dependent developmental patterns at macroscopic and microscopic scale and combined time- and stage-specific gene expression analyses. We show that cool temperature accelerates floral transition but subsequently slows inflorescence and flower development, causing increased inflorescence branching, higher floral organ numbers, and berry fasciation. These effects were restricted to the apical inflorescence and flower meristems, whereas higher-order meristems remained unaffected. Expression analyses revealed stage- and temperature-dependent changes in the abundance and spatial distribution of TERMINAL FLOWER1 (FvTFL1) encoding the floral repressor. Loss of functional FvTFL1 abolished temperature-dependent differences in floral transition, inflorescence branching, and floral organ numbers. Our results establish FvTFL1 as a major regulator of temperature-responsive reproductive development. The stage-specific activity of FvTFL1 provides a mechanism through which woodland strawberry integrates temperature signals to balance developmental plasticity of the primary growth axis with the robustness of lateral branches.

plant biology↗

bioRxiv2026

Global statistical constraint and local partner-sensitive inference support dynamic, open-ended verbal coordination

Effective verbal communication requires individuals to align their communicative intentions through the precise use of utterances, yet how this is achieved in dynamic, open-ended communication remains unclear. Combining predictive deep language models (DLMs) with cognitive computational modeling, we tested a computational division of labor between context-sensitive global constraint on the utterance space and partner-sensitive local adjustment of selection priorities. We formalized local adjustment using an active inference inspired updating rule within a statistical-pragmatic hybrid model. Thirty dyads performed a dynamic, open-ended collaborative word-generation task during functional near infrared spectroscopy (fNIRS) hyperscanning. Interlocutors converged in their lexical choices, and lexical alignment was best explained by a hybrid model integrating contextual selection priors with interaction-specific local adjustment among the models tested. This hybrid process formed a dynamic hypothesis landscape comprising a global semantic search region and local selection priorities. Critically, interaction did not simply reduce uncertainty: within individuals, the hypothesis space of global semantic search progressively narrowed while local uncertainty among plausible alternatives increased; between partners, both global hypothesis space and local selection became increasingly aligned, with alignment of local selection priorities most strongly predicting subsequent lexical alignment. The contribution of local adjustment was stronger during precise verbal communication than in the control tasks. Neural analyses further identified correlates of the local adjustment process: temporoparietal and anterior temporal regions supported partner-related inference and semantic prediction error, respectively, and their activity during thinking predicted subsequent inferior frontal activity associated with self-updating during speaking. The participant's own hypothesis landscape was also represented in the left inferior parietal-supramarginal cortex. The main findings generalized across language models and an independent Czech dataset. Together, these findings reveal that alignment in open-ended communication emerges from complementary statistical and pragmatic computations, providing a framework for understanding human and human-AI communication.

neuroscience↗

bioRxiv2026

Oligodendrocyte ER-phagy Restricts Excessive Myelination by Degrading Sphingolipid Synthases

Myelination is critical for nervous system function. Numerous signaling pathways have been identified that promote myelin sheath growth, disruption of which can lead to hypomyelination, characterized by a reduction in myelin sheath thickness. However, the negative regulators of myelin sheath expansion remain poorly defined. Here, we identify a cellular brake on central nervous system myelination that restricts myelin sheath thickness during brain development. This brake is mediated by a selective form of autophagy, known as endoplasmic reticulum (ER)-phagy, which degrades the ER and its resident sphingolipid synthases. ER-phagy is highly active in oligodendrocytes during myelin membrane expansion, and its impairment leads to ER accumulation, elevated sphingolipid production, and excessive myelin thickening. Genetic reduction of de novo sphingolipid biosynthesis in the ER rescues the hypermyelination phenotype caused by ER-phagy disruption. In summary, our findings establish ER-phagy as a key regulator of sphingolipid metabolism and reveal a mechanistic link between ER homeostasis and myelin production by oligodendrocytes, providing insight into mechanisms underlying pathological hypermyelination.

neuroscience↗

bioRxiv2026

A direct RNA sequencing workflow for simultaneous profiling of tRNA abundance and modifications in mouse liver

Transfer RNA (tRNA) is highly modified and difficult to profile using reverse-transcription-based sequencing. Here, we established a direct RNA sequencing (tRNA-DRS) workflow to simultaneously characterize tRNA abundance and modification signals in mouse liver. The workflow included small-RNA enrichment, deacylation, splint-adapter ligation, barcoding, reverse transcription, and nanopore sequencing on PromethION with modification-aware basecalling. From 1,678,666 raw reads, 1,421,279 (84.67%) reads were retained after 20-200 nt length filtering, and 17,094 uniquely mapped reads (MAPQ [≥] 10) were obtained. These reads covered 244 tRNA genes and represented all 23 tRNA isotypes. tRNA abundance was strongly skewed, with Asp, Gly, Ser, and Lys accounting for 56.6% of uniquely mapped reads. Read-body coverage indicated that most uniquely mapped reads spanned substantial portions of tRNA molecules (mean 71.1%, median 75.9%; 83.3% reads covering [≥]50% of the reference). Modification analysis identified 41,013 candidate sites, of which 711 passed stringent filtering (modification fraction [≥]50%, coverage [≥]5), spanning eight modification types and dominated by pseudouridine and m5C. Filtered sites showed position-specific clustering and isotype-dependent patterns. Together, these results support tRNA-DRS as a practical single-assay framework for simultaneous tRNA expression and epitranscriptomic profiling in mammalian tissue.

molecular biology↗

bioRxiv2026

Explainable t-SNE for Single-Cell RNA-seq Data Analysis: A Cell-DrivenInformation Fusion Framework

Single-cell RNA sequencing fundamentally depends on defining cell-to-cell similarity to resolve distinct cell states. However, conventional dimensional-reduction frameworks such as t-SNE and UMAP inherently rely on Euclidean geometry, a construct ill-suited for high-dimensional, sparse count matrices, and produce cluster boundaries that lack biological interpretability. Here, we introduce cell-driven information fusion, an end-to-end framework that constructs cell affinity directly from raw counts by integrating three biological signals: gene detection patterns, expression magnitude of dominant transcripts, and global profile correlation. A sparsity-adaptive operator merges these signals into a unified affinity matrix, while an entry-usage diagnostic traces which biological component governs local cluster boundaries. The framework comprises two complementary implementations: c-TSNE for low-to-moderate sparsity (below 80 percent), which consistently outperforms Euclidean baselines across six benchmarks, and c-UMAP for high-sparsity regimes. Evaluated across 29 datasets and two protocols against 11 baseline methods, c-UMAP achieved the highest mean normalized and adjusted mutual information (NMI and AMI) in every setting, with all improvements remaining significant after Bonferroni correction. Because a single fixed weight vector was applied across all 29 datasets per protocol, these gains reflect intrinsic algorithmic robustness rather than dataset-specific hyperparameter tuning. Furthermore, c-UMAP scales seamlessly to 1.14 million cells, running up to 22-fold faster than the leading baseline. Crucially, by operating directly on raw counts without variance-based gene selection, our approach avoids the median 46.9 percent loss of top differentially expressed genes per cell class, preserving essential lineage markers such as IAPP and FOXP3. Together, these results demonstrate that atlas-scale efficiency, raw-data preservation, and mechanistic interpretability are fully compatible.

bioinformatics↗

bioRxiv2026

Cellular and molecular coding of habit-driven behavior in the dorsal raphe nucleus

Chronic stress has potent effects on reward-seeking behavior, reducing hedonic drive but also biasing individuals toward habitual responding at the expense of goal-directed action. While prior studies have implicated corticostriatal circuits in these shifts, the contribution of the dorsal raphe nucleus (DRN) - a central neuromodulatory hub that regulates motivational states - remains poorly understood. Here, we identify a key role for DRN neurons in mediating stress-induced transitions from goal-directed to habit-driven behavior. Using two-photon calcium imaging in awake behaving mice, we show that DRN neurons encode representations of both effort expenditures and reward acquisition that are integrated at the single-neuron level. Chronic stress selectively enhances reward-related responses in habit-driven individuals, and deficits in reward-related activity in DRN neurons predict future habit formation after chronic stress. Single-nucleus transcriptional profiling revealed that chronic stress drives habit-related gene expression changes in GABAergic DRN neurons, including upregulation of genes implicated in synapse function and inhibitory signaling, and identified potential pharmacological treatment targets. Optogenetic inhibition of DRN GABA neurons rescued stress effects on habit formation, driving stable shifts in operant responding that persisted for days. Together, these findings establish the DRN as a critical modulator of stress-induced behavioral inflexibility, and identify a new role for DRN GABAergic neurons in determining stress susceptibility and driving stable and persistent switches in operant responding during recovery from chronic stress.

neuroscience↗

bioRxiv2026

A PPARγ-like signalling axis integrates lipid homeostasis and mitochondrial quality control to preserve neuronal integrity

Peroxisome proliferator-activated receptor gamma (PPAR{gamma}) is a central regulator of lipid metabolism and a critical mediator of neuroprotection, yet the mechanisms linking these functions remain unclear. Here, we identify the Caenorhabditis elegans nuclear receptor SEX-1 as a functional PPAR{gamma}-like regulator and define a pathway that coordinates lipid metabolism with mitochondrial homeostasis to preserve neuronal function. Integrating comparative genomics, multi-omics profiling, meta-analysis, and experimental validation, we show that SEX-1 orchestrates membrane sphingolipid metabolism, lipid droplet (LD) dynamics, and mitochondrial quality control through interconnected lipogenic and autophagic programs. Loss of sex-1 disrupts this metabolic network, resulting in aberrant LD accumulation, mitochondrial dysfunction, and widespread alterations in sphingolipid metabolism. These defects compromise the structural integrity and thermosensory function of amphid neurons during early adulthood, while the capacity of SEX-1 to restrict neuronal lipid droplet accumulation declines with age. Notably, genetic modulation of sphingolipid metabolic pathways rescues neuronal defects, establishing a causal link between lipid metabolic homeostasis and neuronal maintenance. Together, our findings identify a PPAR{gamma}-like signalling axis that integrates sphingolipid metabolism, organelle quality control, and neuronal homeostasis, providing a mechanistic framework for understanding how metabolic regulation promotes neuroprotection.

cell biology↗

bioRxiv2026

A Saturated Aminotriester Lipid Enhances Amonafide Activity in Human Colorectal Cancer Cells

The delivery of small-molecule therapeutics across cellular membranes remains a fundamental challenge in drug development, particularly for compounds whose physicochemical properties limit intracellular bioavailability. Inspired by the low toxicity, biodegradability, and synthetic accessibility of triethanolamine-derived lipids, we investigated a series of C18 aminotriester lipids as excipients for the codelivery of anticancer therapeutics. Four structurally related triester lipids bearing saturated, cis-monounsaturated, trans-monounsaturated, and di-unsaturated C18 tails were synthesized through straightforward esterification reactions with triethanolamine. These lipids were evaluated for their ability to enhance the antiproliferative activity of several anticancer agents, including paclitaxel, doxorubicin, amonafide, homoharringtonine, camptothecin, and SN-38. Across multiple drug classes, the aminotriester lipids exhibited minimal intrinsic cytotoxicity and generally produced limited enhancement of drug potency. However, the fully saturated tris-stearate aminotriester lipid selectively enhanced the antiproliferative activity of amonafide in HCT-116 colorectal cancer cells, particularly at lower concentrations. In contrast, unsaturated lipid analogues displayed negligible enhancement effects, and the activity of the tris-stearate lipid was substantially attenuated in A549 lung adenocarcinoma cells, weakly observed in HT-29 colorectal cancer cells, and absent in CT26 murine colorectal cancer cells. Lactate dehydrogenase release assays indicated that these effects were not associated with membrane lysis or nonspecific cytotoxicity. Further, fluorescence microscopy time course experiments suggest improved membrane trafficking of amonafide when codelivered stoichiometrically with fully saturated C18 aminotriester lipids. Collectively, these findings demonstrate that saturated triethanolamine-based aminotriester lipids may function as selective and biocompatible codelivery excipients for certain small-molecule therapeutics. The observed dependence on both lipid saturation state and cellular context suggests that membrane organization and lipid packing may play important roles in mediating these effects. These results establish a foundation for further mechanistic investigations into aminotriester lipid-assisted small-molecule delivery systems.

cancer biology↗

bioRxiv2026

Parental Genome Assemblies of Suyunuo1 Reveal Structural Variation Underlying Edible Waxy Maize Evolution, Superior Hybrid Performance and Yield - Flavor Balance

Edible waxy maize is a unique domesticated cereal valued for its superior sensory and nutritional properties, yet high quality gap free genomes remain lacking, hindering the exploration of structural variations (SVs) and domestication related divergence. Here, we assembled two chromosome level, gap free genomes of the elite waxy maize inbred lines Tongxi 5 and Hengbai 522, the parents of the widely cultivated hybrid Suyunuo 1. Comparative genomic analysis revealed substantial genome size variation, prominent megabase scale SVs, and extensive knob repeat expansion in Tongxi 5. We identified widespread gene presence absence variation and hyperdivergent regions enriched in transposable elements, which largely underpin genomic differentiation between waxy and field maize. Population genomic analyses further demonstrated asymmetric introgression from field maize into the two parents, whereas the conserved waxy haplotype supports a shared ancestral origin. Integrative GWAS based on SNPs, InDels and SVs revealed that SVs substantially contribute to phenotypic diversity and mediate the co-regulation of yield traits and flavor-related metabolites. Our results uncover key genomic events underlying post-domestication divergence and highlight the essential roles of SVs in heterosis and flavor-yield balance, providing valuable genomic resources for waxy maize improvement.

plant biology↗

bioRxiv2026

A tumor-cell MHC-II program is associated with checkpoint-blockade outcomes across stages of bladder cancer

Purpose: A minority of patients with bladder cancer derive lasting benefit from immunotherapy, and current biomarkers capture only part of the biology. We evaluated whether tumor-cell MHC class II defines an immune state associated with outcome across disease stages and after PD-1/PD-L1 blockade. Experimental Design: We localized differential MHC-II activity to malignant epithelial cells by single-nucleus and single-cell RNA sequencing and confirmed HLA-DR expression by immunohistochemistry in 122 specimens. Chromatin profiling and IFN-{gamma} stimulation of cell lines and primary tumors supported derivation of an 11-gene tumor-cell program. Associations were tested in 434 patients with non-muscle-invasive disease, 82 receiving neoadjuvant pembrolizumab, and 288 receiving atezolizumab for metastatic disease. Results: Tumor-cell MHC-II was present in approximately one third of bladder cancers, and malignant cells accounted for the differential signal between MHC-II-high and MHC-II-low tumors. The program was inducible by IFN-{gamma} through JAK/STAT signaling. Within luminal non-muscle-invasive disease, MHC-II-low status was associated with progression (HR 3.31, 95% CI 1.37 to 7.99). In PURE-01, the 11-gene program was associated with pathological complete response (52% versus 24%, p = 0.018) and recurrence-free survival (p = 0.0054), retaining an independent association in models including tumor mutational burden and PD-L1. In bladder-primary metastatic disease, program-high status was associated with overall survival in unadjusted analysis (HR 0.62, 95% CI 0.44 to 0.89); the association did not extend to upper tract tumors (interaction p = 0.0018). Conclusions: Tumor-cell MHC-II defines an inducible state associated with outcomes across bladder cancer stages and after checkpoint blockade, supporting prospective evaluation by RNA and immunohistochemistry.

cancer biology↗

bioRxiv2026

Regulation of protein kinase pathways in primary neuron model of anti-NMDA receptor encephalitis.

The most common form of autoimmune encephalitis is associated with antibodies that target N-methyl-D-aspartic acid receptors (NMDARs). NMDARs play a pivotal role in neurotransmission and synaptic plasticity. Mounting evidence has shown that antibody targeting of the NMDAR GluN1 subunit, as in anti-NMDAR encephalitis, leads to NMDAR cross-linking and receptor internalization. However, the underlying signaling pathways affected by antibodies targeting NMDARs remain to be explored. We previously demonstrated that a human GluN1 monoclonal antibody 5F5 (GluN1 mAb 5F5) rapidly localizes to and regulates synaptic NMDAR function at native synapses of primary hippocampal neurons. Here, we sought to explore signaling targets of GluN1 mAb 5F5 in primary cortical neurons of either sex using subcellular fractionation, Western blotting, and label-free quantitative phosphoproteomics by mass spectrometry. We find that human GluN1 mAb 5F5 does not change NMDAR abundance or surface levels of GluN1 on primary cortical neurons at 2 hr. Despite this, we observe that GluN1 mAb 5F5 alters the phosphoproteome in synaptoneurosomes and regulates numerous synapse-related biological processes and protein kinase activities. Bioinformatic analyses suggest that these phosphoproteomic changes are positively correlated with NMDAR activation and negatively correlated with NMDAR inhibition. Together, these data suggest that GluN1 mAb 5F5 alters intracellular kinase signaling pathways in primary cortical neurons, likely by activating the NMDAR. These studies may help to identify novel therapeutic strategies for anti-NMDAR encephalitis and other antibody-mediated encephalitides targeting cell surface antigens.

neuroscience↗

bioRxiv2026

Hygrochastic Seedpods: Engineering Microclimates for Forest Restoration

Forest restoration at scale depends on sowing seeds directly onto the land, yet seedling establishment is often poor and inconsistent. Seed enhancement technologies, such as priming, coating, and pelleting, improve germination under water, temperature, and salinity stress by supplying polymers, nutrients, or microorganisms at the seed surface. Being mainly conformal films, they act continuously once wetted and cannot gate when a seed is exposed to the soil. They also enclose no air volume, so the microenvironment they create is inseparable from the surrounding soil and has been inferred from plant performance rather than measured directly. Whether an engineered carrier can instead set both the state and the duration of the post-dispersal microenvironment, and how such an effect can be directly quantified, remains unexplored. Here we show that hygrochastic seedpods hold seeds in a timed, directly measurable microclimate and accelerate seedling emergence. The pods are programmable, responsive conical shells enclosing an air cavity around the seed. Two design solutions were investigated in parallel: wooden seedpods that crack open upon hydration, and poly(vinyl alcohol)/boric acid seedpods that gradually disintegrate after sustained wetting. In both, wax coatings act as a programmable diffusion-limited timer that sets activation from hours to days. The pod cavity permits direct sensing and monitoring, which no coating geometries allow. As directly measured during the initial phase after deployment, seedpod interiors ran 2 - 3 C warmer and drier than the surrounding soil, and these differences persisted after opening. Across indoor and field trials in several tree species, pods accelerated early seedling emergence without penalizing subsequent growth. These results identify artificial hygrochastic seedpods as a transient ecological mediator that regulates both the timing of seed exposure and the microclimate around the seed, offering a strategy for improving forest restoration under variable environmental conditions.

bioengineering↗

bioRxiv2026

Latent generative search unlocks de novo design of untapped biomolecular interactions at scale

De novo protein design has advanced rapidly, yet designing binders to polar, solvent-exposed epitopes and small, flexible ligands remains challenging. Such hydrated surfaces and flexible molecules, including carbohydrates, provide few of the hydrophobic contacts favoured by current methods and have largely resisted de novo binders. To address this challenge, here we introduce latent generative search for binder design, a novel framework that uses reward-guided search at inference time to steer the Proteina-Complexa generative model. The model codesigns sequence and structure - generating them together in a continuous latent space - and thereby removes the inverse-folding step on which current methods rely. In a screen of more than one million designs by multiplexed phage display, latent generative search produced more validated binders than every other method tested, its codesigned sequences surpassing post hoc redesign. It delivered high-affinity binders across therapeutic receptors, a viral attachment protein and intracellular signalling targets. Our approach also accessed previously untapped biology, generating the first de novo proteins that bind a free carbohydrate, including one that discriminates between blood-group antigens - a polar, flexible target class beyond the reach of current design methods.

bioengineering↗

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

A conserved transcriptional axis links cortical organization, developmental timing and autism-associated perturbations

Much of our mechanistic understanding of cortical development and neurodevelopmental disorders comes from studies in mice, yet translating these insights to humans rests on a fundamental assumption: that the cortex is organized according to conserved principles across species. Here, by independently decomposing human and mouse cortical transcriptomes, we test this assumption and identify a shared organizational axis extending from limbic anterior ventral (AV) to primary sensory posterior dorsal (PD) cortex. This axis aligns with conserved variation in cell-type composition, thalamocortical connectivity, myelination and excitation-inhibition balance. Its spatial topology emerges by mid-gestation and is progressively refined while remaining stable in orientation across subsequent development. What varies systematically along the axis is developmental timing: AV-enriched genes preferentially retained earlier cortical-construction features and progressively decline after birth, whereas PD-enriched genes preferentially reflected later maturation processes and progressively increased, with developmental rates graded along the axis. Across genetically distinct autism mouse models, developmental dysregulation converged on this axis, following a shared pattern that generally intensified toward the PD pole. The same axis also organized genotype-specific patterns of cortical volume alteration, while human autism risk genes showed corresponding enrichment along this transcriptional coordinate. Overall, we identify a conserved transcriptional axis that links cortical architecture to developmental timing and organizes the heterogeneous cortical effects of autism-associated mutations.

neuroscience↗