Biology subjects

Lee, H.

Publications and source records attributed to Lee, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Microcystis-triggered shifts in the symbiotic microbiome of Myriophyllum spicatum rapidly suppress Microcystis aeruginosa

While the suppression of toxic cyanobacteria by aquatic plants has long been recognized, few studies have clearly differentiated between the allelopathic effects of the plant itself and the inhibitory influence of its associated microbiome. This study aimed to clarify the primary inhibitory agent by pre-culturing Myriophyllum spicatum (Eurasian watermilfoil) under three conditions: (1) BG11 medium, (2) live Microcystis aeruginosa KW culture, and (3) a Microcystis-symbiotic microbiome (excluding Microcystis cells). After a 7-day pre-culture, Myriophyllum shoots were transferred to fresh Microcystis culture. The Myriophyllum pre-cultured in Microcystis culture exhibited rapid inhibition against Microcystis (84% within day 1), whereas the Myriophyllum pre-cultured in BG11 medium showed delayed responses (89% by day 7). In contrast, inhibition remained below 50% in the Myriophyllum pre-cultured with the Microcystis-symbiotic microbiome. Notably, plant-derived soluble compounds exhibited weak inhibitory effects, whereas the microbiome showed stronger inhibitory activity, indicating that the plant-associated microbiome plays a more dominant role than the plant itself. Exposure to Microcystis triggered significant shifts in plant-symbiotic microbial community composition, leading to rapid enhancement of inhibitory activity in the Myriophyllum microbiome. Microbial community analysis identified 28 bacterial taxa closely associated with the inhibitory response, including strains involved in organic matter degradation, adhesion, biofilm formation, and predatory behavior. Meta-transcriptomic analysis further confirmed increased expression of genes related to bacterial adhesion, biofilm formation, and carbohydrate metabolism following Microcystis exposure, highlighting functional adaptations linked to cyanobacterial suppression. These findings underline the role of microbiome-mediated cyanobactericidal mechanisms, providing new insights into a nature-based solution for mitigating Microcystis-dominated harmful algal blooms.

ecology↗

bioRxiv2026

AI-driven framework modeling perturbation in brain organoids reveals candidate genes for autism

Autism gene discovery is constrained by the rarity and heterogeneity of damaging variants, requiring large cohorts to identify susceptibility genes. Neural organoids and single-cell foundation models enable perturbation modeling in neurodevelopmental contexts. Here, we show that perturbation-informed foundation modeling of neural organoids can provide functional context for prioritizing candidate genes with genomic and clinical support. We constructed a 3.6-million-cell organoid atlas and trained models to predict genome-wide perturbation responses. Benchmarking 17 models identified a telencephalic neuron-specific model best preserving autism-relevant perturbation structure. Genome-wide profiling revealed two clusters associated with mid-fetal synaptic neuronal processes and early radial glia ubiquitin signaling. These clusters were supported by damaging-variant enrichment and clinical phenotypes across 89,916 family-based samples. Logistic-regression prioritization identified 343 candidates, including 167 in the key clusters, with convergence across TADA signals and recurrent evidence for NBEA and KLHDC10. This framework integrates predicted perturbation effects with genomic evidence to support autism candidate prioritization.

bioinformatics↗

bioRxiv2026

The KRAS G12C Inhibitor Divarasib Stabilizes RBM39 and Antagonizes Aryl-Sulfonamide Degraders

KRAS G12C inhibitors have demonstrated meaningful clinical benefit in KRAS G12C-mutant non-small cell lung cancer (NSCLC), yet responses remain heterogeneous and treatment-associated toxicities persist for reasons that are incompletely understood. Cysteine profiling indicates that these covalent inhibitors are highly selective for mutant KRAS; however, such approaches cannot detect noncovalent engagement of additional non-RAS proteins. Here, we used a protein-folding stability profiling technique, stability of proteins from rates of oxidation (SPROX), to identify protein targets of the clinical KRAS G12C inhibitor, divarasib (GDC-6036), in KRAS-mutant NSCLC lysates. SPROX revealed a focused set of candidate interactors, including the essential splicing factor RBM39, which was reproducibly stabilized at both divarasib concentrations tested. We subsequently confirmed that divarasib directly and noncovalently binds to RBM39 protein. In NSCLC cells, divarasib increased RBM39 protein abundance and antagonized RBM39 degradation induced by the aryl-sulfonamide molecular glue indisulam through a post-transcriptional mechanism. Divarasib and RBM39 degraders reciprocally antagonized each other's cytotoxicity, and RBM39 knockdown modestly reduced divarasib-induced cell death. Mechanistically, divarasib-mediated RBM39 stabilization regulated both INSR expression and alternative splicing, altered downstream insulin receptor signaling, and contributed to divarasib-associated cytotoxicity. Consistent with these findings, RBM39 and INSR expression were positively correlated across multiple human cancer types. Collectively, these findings identify RBM39 as a previously unrecognized noncovalent target of divarasib and uncover an RBM39-INSR signaling axis that modulates cellular responses to both divarasib and RBM39 degraders.

pharmacology and toxicology↗

bioRxiv2026

Structural proteomics reveals a coagulation-complement accessibility signature of macrovascular invasion in hepatocellular carcinoma

Macrovascular invasion (MVI) and extrahepatic spread (EHS) define the most aggressive, treatment-refractory hepatocellular carcinoma (HCC), yet blood-based markers that report the underlying protein-network biology are lacking. Conventional proteomics measures protein abundance but not the conformational and protein-protein-interaction (PPI) states that govern function. We applied covalent proteome painting (CPP)--a dimethylation-based accessibility assay that reads out binding-site openness--to matched tumor and serum, reasoning that intravascular tumor dissemination remodels plasma protein complexes in a manner detectable as changes in accessibility. Eight treatment-native HCC patients were profiled by CPP using matched FFPE tumor and top-14- depleted serum on a Q Exactive Orbitrap HF. The 85 tumor-serum common proteins defined an 81-protein targeted panel, validated by multiple-reaction-monitoring (MRM) mass spectrometry with heavy stable-isotope-standard peptides (296 peptides; 3,717 light/heavy transition pairs) in 22 FFPE tumors and 22 matched sera. Accessibility was the light/heavy ratio (high, open; low, closed). We assessed differential accessibility, serum-tissue translatability, pathway enrichment, and biomarker/survival performance. Aggressive disease showed broadly decreased protein accessibility. MVI-associated changes were directionally concordant between tumor and serum (Spearman {rho}=0.21; 59% concordant), driven by coagulation and complement proteins (FGG, CTSD, LBP, C4BPA); the EHS axis did not translate. Decreased-accessibility proteins were enriched for complement-coagulation cascades and IGF/IGFBP transport. A six-protein serum accessibility signature discriminated MVI (leave-one-out cross-validated AUC 0.80; best single markers ceruloplasmin 0.83 and haemoglobin- 0.77), and MVI status trended with shorter overall survival (log-rank p=0.06). Accessibility-based serum proteomics captures MVI-associated protein-complex remodeling that abundance assays miss, nominating a coagulation/complement-anchored serum signature for vascular-invasive HCC that warrants prospective validation.

systems biology↗

bioRxiv2026

High-throughput Virtual Screen of Endocrine-disrupting Chemicals Identifies Disruptors of EGFR Signaling

Chemical exposures during pregnancy are linked to an increased risk of pregnancy complications that contribute significantly to maternal and infant morbidity and mortality and can lead to long term health consequences for both the mother and the offspring. The placenta, a central regulator of pregnancy health, is a direct target of environmental toxicants. Epidermal growth factor receptor (EGFR), highly expressed in the placenta, regulates proliferation, migration, invasion, fusion, and cellular bioenergetics. To identify compounds of environmental concern with potential for EGFR-disrupting activity, we optimized a high-throughput virtual screening protocol for the identification of EGFR inhibitors and achieved enrichment factors of EF1% = 10.09, EF5% = 3.86, and EF10% = 3.0 in a benchmarking dataset. We applied this protocol to screen the Collaborative Estrogen Receptor Activity Prediction Project database, finding that top-scoring compounds were enriched for aromatic and fused-ring chemical classes, including dyes. Kinase activity assays revealed that two out of thirteen selected compounds, Vat Red 32 and Reactive Red 136, inhibited EGFR kinase activity with micromolar IC50 values. Additionally, pose refinement with molecular dynamics simulations characterized the binding interactions of Reactive Red 136 within the EGFR kinase domain, and functional assays in HTR-8/SVneo placental trophoblast cells showed that Reactive Red 136, but not Vat Red 32, partially attenuated EGF-mediated cell migration despite both compounds inhibiting EGFR kinase activity. Together, this study has generated an enriched dataset of candidate environmental EGFR modulators, with experimental validation confirming enrichment for EGFR-disrupting activity among the selected compounds. These results provide a valuable resource for toxicological studies.

pharmacology and toxicology↗

bioRxiv2026

Sex-dependent chronic neurological dysfunction following isoflurane anesthesia and surgery is associated with circulating extracellular vesicle-mediated neuroinflammatory signaling

PurposeIt is well established that volatile anesthetics and surgery induce acute and subacute changes in the cellular and molecular landscape of the brain and peripheral circulation and can impair neurological function. However, the chronic neurological sequelae of isoflurane (Iso) anesthesia combined with surgical operation (OP), as well as the underlying mechanisms of postoperative neurological dysfunction, remain poorly understood. MethodsYoung adult male (M) and female (F) C57BL/6 mice underwent 4 h of 2% Iso plus laparotomy or sham treatment. At 12 weeks, olfactory and cognitive function were assessed by odor memory, buried food, Y-maze, and active avoidance tests. Olfactory bulbs (OB) and hippocampi (HI) were collected for RNAseq, while plasma extracellular vesicles (EVs) were isolated, characterized by NanoFCM, and profiled by Olink proteomics. Lastly, EVs were injected into the HI of naive male mice, and cytokine/chemokine responses were measured 24 h later. ResultsBoth sexes showed olfactory impairment after chronic Iso/OP, with greater deficits in females. Iso/OP mice, especially females, exhibited impaired odor recognition in the OM test and longer latencies to locate buried food. Female mice also showed greater hippocampal-dependent spatial working memory deficits in the Y-maze, with more arm returns and fewer alternations than Sham/F mice, whereas Iso/OP/M mice performed similarly to controls. Likewise, female, but not male, Iso/OP mice displayed impaired associative learning in the active avoidance test, evidenced by fewer avoided trials and more escape responses. These long-term behavioral abnormalities were accompanied by sex-divergent transcriptomic remodeling in the OB and HI, including altered synaptic, neurodevelopmental, extracellular matrix, stress-response, and chemotaxis-related pathways. Iso/OP reduced plasma EV particle numbers in both sexes and shifted EV size distributions, with prominent reductions in the 40-100 nm EV fraction. Proteomics revealed distinct sex-and condition-specific EV profiles, with several EV-associated proteins showing opposing sex-dependent expression patterns. Hippocampal injection of Iso/OP-derived EVs induced donor sex-dependent cytokine remodeling, confirming inflammatory bioactivity. ConclusionsFour-hour isoflurane (Iso) exposure combined with laparotomy in young adult mice induces chronic, sex-dependent neurological deficits with distinct transcriptomic remodeling across brain subregions. Persistent alterations in circulating EV abundance and inflammatory cargo may drive chronic neuroinflammation and long-term brain dysfunction.

neuroscience↗

bioRxiv2026

Isoflurane and surgery aggravate APOE4-dependent lipid dysregulation and neural dysfunction, leading to neurological impairment in male mice

PurposePerioperative exposure to the volatile anesthetic isoflurane (ISO) has been associated with cognitive and olfactory deficits and may increase the risk of Alzheimers disease (AD). Apolipoprotein E4 (APOE4), the strongest genetic risk factor for AD, contributes to disease pathogenesis through disrupted lipid homeostasis. However, whether and how isoflurane interacts with APOE genotype to influence neurological vulnerability remains unclear. MethodsYoung adult, presymptomatic humanized APOE4 and APOE3 knock-in mice underwent laparotomy under 2 h of isoflurane anesthesia. Microglia and astrocytes were isolated from the olfactory bulb (OB) and hippocampus (HI) by magnetic-activated cell sorting. Lipid composition, transcriptional responses, and functional outcomes were assessed using lipidomic, bulk RNA-seq, and longitudinal behavioral testing. In vivo and ex vivo electrophysiological recordings evaluated neuronal excitability and synaptic transmission in both regions. ResultsBy day 7 post-anesthesia, cell type-specific lipidomic profiling of both OB and HI revealed more pronounced lipid perturbations in microglia and astrocytes from APOE4/ISO mice than from APOE3 mice, characterized by elevated free fatty acids, increased lipid peroxidation, triglyceride depletion, and reduced hippocampal hexosylceramides and cardiolipins. Electrophysiological recordings showed greater olfactory circuit dysfunction in APOE4/ISO mice, accompanied by persistent odor memory deficits, transient olfactory sensitivity loss, early motor coordination impairments, and delayed cognitive deficits. RNA sequencing of the OB identified downregulated lipid metabolism and atherosclerosis-related pathways. ConclusionThese findings establish a mechanistic link between APOE4-dependent glial lipid dysregulation, olfactory circuit dysfunction, and delayed cognitive impairment following isoflurane anesthesia and surgery, highlighting lipid homeostasis as a potential therapeutic target.

neuroscience↗

bioRxiv2026

Synaptic engram underlies memory

Memory encoding cells, or engram cells, are sparsely distributed across the brain. Recent findings have shown that memory formation coincides with the strengthening of interregional synaptic connectivity between engram ensembles. However, whether this learning-induced synaptic reorganization causally supports memory, independently or in concert with heterosynaptic and intrinsic plasticity, remains elusive. Here we developed optically implemented spike-timing-dependent plasticity (oSTDP), which induces synaptic depression selectively at target synapses by controlling the relative timing of pre- and postsynaptic activity. In vivo application of oSTDP to the synapses between entorhinal cortex (EC) and dentate gyrus (DG) engram cells caused a significant synaptic depression and the resultant memory impairment. Our results demonstrate that plasticity of functional connectivity between memory-encoding ensembles causally underlies memory.

neuroscience↗

bioRxiv2026

A targeted plasma-proteomic axis separates autoimmune thyroid disease from growth-hormone deficiency

Targeted mass spectrometry (multiple-reaction monitoring, MRM) enables reproducible, multiplexed quantification of plasma proteins, but whether a fixed targeted panel can resolve endocrine disorders with overlapping systemic features is unknown. We analyzed a 256-protein targeted panel (1,894 peptides; 3,790 transitions) quantified in 57 participants spanning autoimmune thyroid disease (Hashimotos thyroiditis, n=7; Graves disease, n=5) and growth-hormone deficiency (GHD; partial, n=26; complete, n=19). Protein abundances were obtained by transition summation, log2 transformation, and per-sample median normalization. We applied unsupervised analysis (PCA, PERMANOVA), differential expression (limma), an ordered severity-trend test, and leave-one-out cross-validated classification with feature selection performed strictly inside each fold. All 256 proteins were quantified in every sample (median inter-sample r=0.875). PC1 (36% variance) separated autoimmune thyroid disease from GHD (p=0.016), whereas the global four-group structure was not significant (PERMANOVA p=0.17). No protein reached FDR<0.05, but the autoimmune-versus-GHD contrast was strongly enriched for low p-values (26 proteins at p<0.05; binomial p=5.4x10-4). The signal was biologically coherent: immunoglobulin/B-cell-receptor proteins, including CD79A, were lower, whereas proteasome subunits (PSMC5, PSMC3) and the NF-{kappa}B subunit RELA were higher in autoimmune disease. A cross-validated classifier separated the two classes (AUC 0.72; permutation p=0.05; eight proteins selected in all folds), whereas GHD severity was not predictable (AUC 0.31). A fixed 256-protein targeted panel reproducibly captures an immunoglobulin/B-cell-receptor and proteasome/NF-{kappa}B axis that distinguishes autoimmune thyroid disease from GHD but cannot resolve within-class severity.

systems biology↗

bioRxiv2026

Sex and race shape serum protein biomarkers and bias diagnostic reference intervals

Clinical protein biomarkers--whether measured by FDA-cleared in-vitro diagnostic (IVD) assays or deployed as laboratory-developed tests (LDTs)--are routinely interpreted against fixed, population-agnostic reference intervals. Whether the baseline serum concentrations of these proteins differ systematically by sex and by self-reported race in healthy individuals has not been tested across a broad clinical panel on a single standardized platform. Using scheduled multiple reaction monitoring - mass spectrometry (MRM-MS) with stable-isotope-labelled internal standards, we quantified 87 proteins (39 FDA-cleared analytes; 48 LDT/research markers) in 60 healthy, age-matched donors balanced across three races (White, Hispanic, Black) and both sexes. Sex was a pervasive axis of variation: donors separated by sex in unsupervised multivariate space (PERMANOVA p = 0.020) but not by race (p = 0.14). Three FDA-target proteins differed by sex at FDR q < 0.05--sex hormone-binding globulin, haemoglobin- and albumin--with directions preserved within every race. Race differences were real but protein-specific, exemplified by ancestry-associated CD14. Critically, applying a single pooled 95% reference interval mis-flagged as many as [~]25% of a demographic subgroup as abnormal, versus the 5% expected. Demographic context should therefore be incorporated into reference intervals and decision thresholds for protein-based diagnostics.

molecular biology↗

bioRxiv2026

A targeted mass-spectrometry plasma proteome for simultaneous multi-disease screening

Population health screening is fragmented across dozens of single-condition assays. We asked whether one targeted mass-spectrometry measurement of the plasma proteome could screen simultaneously for many common diseases. Using multiple-reaction-monitoring LC-MS/MS, we quantified 126 proteins (509 peptides) directly in crude plasma from 490 individuals spanning 16 diseases (eight cancers, three inflammatory or renal conditions, and five metabolic and lifestyle disorders) plus age- and sex-matched controls, each protein referenced to a stable-isotope-labelled internal standard. Proteome variation was organised primarily by disease rather than demographics. Cross-validated classifiers detected each disease against matched controls with a mean AUROC of 0.979, a 17-way model identified the specific disease at roughly ten times chance, and a 20-protein subset reproduced full-panel performance. We show that these within-cohort estimates are optimistic upper bounds because each disease was acquired as a separate case-control batch without independent validation. We quantify this, establishing analytical feasibility and defining the validation required for translation.

molecular biology↗

bioRxiv2026

Age-dependent Structural Reorganization of the Human Plasma Proteome

Aging is characterized by progressive physiological decline, yet the molecular mechanisms underlying these changes remain incompletely understood. Although extensive work has examined age-related alterations in protein abundance, the age-dependent structural reorganization of proteins and their interaction networks remains largely unexplored. Here, we quantitatively characterize the structural dynamics of plasma proteins across healthy adult aging and identify age-dependent accessibility patterns that may serve as candidate structural biomarkers. We employed Covalent Protein Painting (CPP) coupled with multiple reaction monitoring (MRM)-based LC-MS/MS to analyze plasma from 24 healthy individuals spanning four age groups (20s to 50s, n = 6 per group). Lysine surface accessibility changes were analyzed using cosine similarity trajectory matching and limma-based linear modeling. The intersection of the two approaches defined five reproducible age-dependent trajectories encompassing 27 proteins and 57 peptides. Integrating STRING/Cytoscape network analysis with AlphaFold3 multimer complex prediction localized several CPP-detected peptides to within [~]5 [A] of predicted protein-protein interaction interfaces (KNG1, C3; REN, ALB; and ALB, FGB), suggesting that age-associated accessibility changes are organized at interaction interfaces rather than occurring as isolated local events. Our findings indicate that the human plasma proteome undergoes coordinated, network-level changes in structural accessibility during adult aging, providing a framework for structure-based biomarker discovery. Because CPP signal reflects both conformational accessibility and protein abundance, and because the cohort is modest and cross-sectional, the trajectories reported here are framed as hypothesis-generating and are interpreted with these constraints made explicit throughout.

molecular biology↗

bioRxiv2026

ProteinSketch translates spatial intuition into protein design with bimanual interaction in VR

Generative AI-based protein design can create diverse structures for desired functions but offers human designers limited control over three-dimensional architectures. We developed ProteinSketch, a bimanual virtual reality platform in which immersive backbone sketches and volumetric envelopes are directly created and translated into constraints for diffusion-based protein generation. RFdiffusion-based real-time refinement enabled interactive exploration and construction of user-specified protein topologies. Volumetric conditioning of sketched envelopes enabled high-fidelity control of anisometric geometries, confirmed by cryo-electron microscopy. These user-defined volumetric constraints enabled functional-binder design and extension of pre-existing minibinders to surfaces otherwise difficult to access within complex molecular environments using conventional design approaches. This collaborative human-AI framework integrates human spatial reasoning with generative AI for spatially directed, shape-controlled design of protein structure and function. One-sentence summaryImmersive ProteinSketch embeds human spatial reasoning in AI-guided design of protein topology, shape, and function.

bioengineering↗

bioRxiv2026

Drinking Motives Synchronize Behavioral and Neural Craving Responses to Alcohol-drinking Videos

Alcohol drinking motives vary among individuals and shape experiences and beliefs about alcohol, influencing the processing of alcohol-related cues. In real-life settings, these cues are contextually rich, amplifying the role of such individualized drinking motives on cue processing. However, previous literature has primarily relied on images of alcohol, which lack contexts and differ significantly from real-life. Here, aiming to investigate real-life craving, we examined the role of alcohol drinking motives in craving in response to naturalistic alcohol-drinking videos. We asked fifty-three problematic alcohol users to speak about their reasons for drinking alcohol to capture unique alcohol drinking motives of each individual. Participants also underwent functional MRI while watching fifteen alcohol-drinking videos, and reported their subjective level of craving and self-relatedness for each video. Behavioral data analysis revealed that individuals with greater alcohol use severity tended to report greater cue-induced craving, but only when they reported that a video was related to themselves. Inter-subject representational similarity analysis showed that participants with similar alcohol drinking motives, reflected in shared drinking reasons and similar self-relatedness to the videos, exhibited synchronized craving-related neural responses during video-watching. Notably, these shared neural processes mediated the link between similar drinking motives and similar self-reported craving levels across participants. Together, our findings highlight the crucial role of alcohol drinking motives in shaping cue-induced alcohol craving, and provide deeper insights into craving in real-world contexts.

neuroscience↗

bioRxiv2026

A family of RRM-1 RNA binding proteins enables cold adaptation and environmental resilience in Bacteroides

Bacteria use post-transcriptional regulatory mechanisms to rapidly adjust gene expression during environmental change. In the gut-associated genus Bacteroides, these mechanisms remain poorly defined as these organisms lack canonical RNA chaperones like Hfq and CsrA that coordinate post-transcriptional stress responses in many well-studied model bacteria. Most Bacteroides possess conserved RNA recognition motif-1 (RRM-1) domain-containing RNA-binding proteins (more common in eukaryotes than bacteria) that have been proposed to act as global RNA chaperones. Here, we show that these RNA binding proteins (RBPs) are central to cold stress adaptation. Simultaneous deletion of all rbp genes produces a cold-sensitive growth defect across multiple Bacteroides species, while single deletions do not, revealing conserved functional redundancy. RBP transcripts and proteins accumulate rapidly after temperature downshift, and loss of RBPs extensively reprograms the transcriptome. Cold sensitivity of Bacteroides rbp mutants is not caused by defects in ribosome assembly or rRNA maturation. Instead, we find that in Bacteroides thetaiotaomicron, RBPs act together with BT1884, the sole canonical cold shock protein possessed by this organism. The combined loss of RBPs and BT1884 produces a synthetic severe cold sensitivity phenotype, defining two functionally redundant cold stress systems belonging to unrelated protein families. Strains lacking RBPs show reduced survival under simultaneous cold and oxygen stress, the conditions Bacteroides cells are expected to encounter during host-to-host transmission. Together, these findings establish RRM-1 RBPs as non-canonical cold shock proteins that enable cold adaptation and environmental survival in Bacteroides and suggest how these organisms withstand the stresses of transmission between hosts. IMPORTANCEBacteroides species are among the most abundant and stable members of the human gut microbiome, and they are also among the most readily transmitted between people. Reaching a new host requires surviving conditions outside the gut, including cold and oxygen exposure, yet how these bacteria withstand such stress is not well understood. Most bacteria manage stress using a well-defined set of RNA-binding proteins, but Bacteroides lack these canonical factors. We show that Bacteroides instead rely on a different family of RNA-binding proteins, more typical of eukaryotes than bacteria, to survive cold stress, and that these proteins promote survival under the conditions encountered during transmission. This work identifies a molecular system that allows an abundant and ecologically successful gut bacterium to endure the environmental challenges of moving between hosts.

microbiology↗

bioRxiv2026

RulePep: Interpretable ESM-Guided Neural-Symbolic Peptide Classification

Peptides are increasingly explored as therapeutic candidates, delivery vectors, and functional biomolecules, but experimental screening of peptide activity and safety remains costly because the sequence space is vast and small sequence changes can alter functionality. Computational peptide classification can therefore help prioritize candidates. However, many protein-language-model-based classifiers achieve strong performance using opaque prediction heads, making it difficult to determine which learned evidence supports or opposes a prediction. We present RulePep, an ESM-2-guided neural-symbolic classifier for peptide-function prediction. RulePep maps frozen ESM-2 sequence representation to learned latent predicates, polarity-constrained differentiable rules, and an additive symbolic logit whose components can be inspected at the case level. We evaluate RulePep on three biologically distinct peptide classification tasks: blood-brain barrier penetration, hemolytic potency, and anticancer activity. On the BBPpredict, HemoPI3, and AntiCP 2.0 alternate benchmark datasets, RulePep achieved AUROC/MCC values of 0.8869/0.6850, 0.9155/0.6820, and 0.9765/0.8633, respectively. Ablation experiments supported the contributions of multi-layer representation pooling, rule polarity, mined-rule initialization, symbolic capacity, and rule-derived aggregation. RulePep combines competitive predictive performance with additive logit reconstruction, rule-level evidence reporting, and predicate-suppression auditing, providing a transparent sequence-based framework for peptide candidate prioritization.

bioinformatics↗

bioRxiv2026

L-5--glutamine PET of Breast Cancer: Kinetic Analysis in Mouse Models to Evaluate Glutamine Metabolism

BackgroundGlutamine addiction is a hallmark of aggressive tumors, yet glutaminase (GLS1) inhibitor CB-839 showed disappointing anti-tumor efficacy in clinical trials. L-5-[{superscript 1}{superscript 1}C]-glutamine ([{superscript 1}{superscript 1}C]glutamine) PET enables non-invasive assessment of glutamine metabolism in vivo, providing a tool to test mechanistic hypotheses, and identify tumors likely to respond to GLS1 inhibition: focusing on compartmentation of GLS1-derived glutamate, CB-839 impact on flux, and reciprocal glutamine synthesis. MethodsGlutaminolytic TNBC (HCC1806) and poorly glutaminolytic ER+ (MCF-7) xenograft mice with or without CB-839, underwent dynamic [11C]glutamine PET. HPLC quantified fractional radioactivity of [11C]glutamine, soluble metabolites ([11C]glutamate, [11C]CO2), and macromolecule-incorporated metabolites from blood and tumor. A four-tissue compartment model characterized GLS1 activity (kGLS) and flux, glutamine synthetase activity (kGS), and subcellular glutamate distribution by comparing single vs. dual glutamate pool models. Averaged tumor curves and HPLC-derived tumor metabolites were fit. Monte Carlo simulations assessed parameter estimation performance. ResultsThe single glutamate pool model showed high correlations between kGLS and other parameters, yielding inflated kGLS estimates. The dual glutamate pool model reduced correlations, improved kGLS recovery, and yielded subcellular glutamate distributions consistent with in vitro measurements. In TNBC, kGLS was 3-fold higher than ER+ tumors (non-overlapping 95% CI) with glutamate concentrated in the mitochondrial compartment. CB-839 reduced kGLS in TNBC and depleted mitochondrial glutamate (non-overlapping 95% CI), though glutaminolytic flux showed no distinguishable change. ER+ tumors showed higher kGS compared to TNBC. Conclusion[11C]glutamine PET kinetic analysis reveals distinct glutamine metabolic phenotypes in breast cancer subtypes. Preserved glutaminolytic flux and cytosolic glutamate in TNBC provide mechanistic hypotheses for clinical failure of GLS1 inhibitors, informing ongoing studies.

bioengineering↗

bioRxiv2026

Expression-linked promoter selection (ELiPS) engineers short, strong ubiquitous promoters for gene therapy applications

Adeno-associated virus (AAV)-based gene therapy has made steady progress towards efficient delivery to numerous target cell populations, yet the viruss 5 kb packaging limit remains a challenge for effective and in some cases cell-selective cargo expression. Here, we introduce Expression-Linked Promoter Selection (ELiPS), a high-throughput platform for generating and functionally screening >106 engineered, short promoter variants using an AAV expression platform. ELiPS relies on a Golden Gate cloning method to build random oligomers of selected transcription factor binding sites (TFBSs) upstream of a minimal promoter, GFP, and a unique 3 barcode. As a proof of concept, to engineer short ([~]250 bp), synthetic, ubiquitous promoters, we applied ELiPS to build two libraries composed of TFBSs for ubiquitously expressed transcription factors (TFs) and screened them via AAV-mediated transduction in vitro. This strategy identified promoters with expression surpassing human cytomegalovirus (CMV) and CAG in vitro, and one variant was capable of driving therapeutic expression of B-domain-deleted Factor VIII (BDDFVIII) in vivo at levels comparable to a liver-specific promoter benchmark. ELiPS thus establishes a scalable framework for promoter discovery, enabling the design of compact, ubiquitous or cell-selective expression cassettes that enable further precision and efficacy in AAV-based gene therapies.

bioengineering↗