Biology subjects

Lu, H.

Publications and source records attributed to Lu, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Affinity Maturation Enables Dual Targeting of Cancer-Associated MUC1-Tn/STn and Drives Potent Tumor Control

A major challenge in solid tumor immunotherapy is identifying tumor-restricted antigens while overcoming intratumoral antigen heterogeneity. The truncated O-glycans Tn (GalNAc-O-Ser/Thr) and STn (Neu5Ac2-6GalNAc-O-Ser/Thr) are aberrantly displayed on the transmembrane glycoprotein MUC1 across a broad spectrum of epithelial malignancies, making MUC1-Tn/STn an attractive shared tumor-associated antigen class. However, heterogeneous intratumoral Tn/STn expression renders single-glycoform-specific antibodies vulnerable to antigen-driven escape. To address this challenge, we used structure-guided directed evolution and yeast surface display to affinity-mature the anti-MUC1-Tn antibody 5E5, generating variants with high-affinity dual recognition of MUC1-Tn and MUC1-STn. Co-crystal structures revealed that heavy-chain CDR loops cooperatively engage the GalNAc moiety primarily through hydrogen-bonding networks, in which HCDR3 residue 98 fine-tunes glycoform preference: Tyr98 favors MUC1-Tn recognition, whereas His98 enhances MUC1-STn engagement, while both support high-affinity recognition of both glycoforms. When reformatted as bispecific T-cell engagers, the affinity-matured variants mediated potent and durable cytolytic activity against cancer cells with heterogeneous glycan profiles, suppressed mixed Tn/STn tumors in vivo where the parental antibody failed, and showed enhanced activity in patient-derived tumor-like clusters. Together, these findings establish functional glycoform coverage as a design principle for antibody engineering, whereby a single paratope is optimized to recognize a defined spectrum of tumor-associated glycoforms while preserving antigen specificity, providing a strategy to overcome glycan heterogeneity in solid tumor immunotherapy.

cancer biology↗

bioRxiv2026

Benchmarking the Performance of a Commercial Electrostatic Linear Ion Trap (ELIT) Charge Detection Mass Spectrometer For Higher-Order Antibody Aggregate Analysis

Higher-order antibody aggregates remain challenging to characterize using conventional mass spectrometry because of their low abundance, broad mass distributions, and extensive heterogeneity. Here, the practical performance of a commercial electrostatic linear ion trap charge detection mass spectrometer (XevoTM CDMS) was evaluated for therapeutic antibody analysis. The platform provided reproducible mass and charge measurements, with repeatability and intermediate-precision RSDs below 1%, and maintained consistent mass determination across the concentration and solution conditions examined. Controlled mixtures of antibody-derived species showed a linear molar-ratio-dependent ion response, supporting semi-quantitative estimation of relative species abundance under defined conditions. For heat-stressed trastuzumab, CDMS measurements were qualitatively consistent with SEC-MALS, mass photometry, and conventional native MS, while enabling direct mass determination of individual ions within highly heterogeneous high-molecular-weight (HMW) populations that exhibited extensive charge-state overlap and could not be reliably deconvoluted by conventional native MS. High-duty-cycle acquisition increased sampling of low-abundance, high-m/z ions and improved access to higher-order aggregate signals. Joint single ion mass-charge analysis further differentiated statistical ion families within the broad HMW fraction and related major mass differences to independently obtained compositional information. These results support commercial XevoTM CDMS as a practical multidimensional platform for antibody aggregate characterization.

biochemistry↗

bioRxiv2026

Pan-cancer remodeling of reactive oxygen species homeostasis: distinct roles of the ROS-generation and antioxidant arms in immune context and outcome

Reactive oxygen species (ROS) are double-edged in cancer: tumor cells sustain high ROS generation while up-regulating antioxidant defense, so that the net balance between the two arms, rather than absolute ROS abundance, is the biologically meaningful quantity. Whether that balance defines a conserved tumor state across cancer types has been unclear. Here an experimentally measured ROS phenotype, obtained from a three-channel gold-nanocluster array, was generalized to public transcriptomes through a 107-gene ROS program scored in a large cell-line panel and in pan-cancer tumor and adjacent-normal tissue. The optical readout was reproducible and fully discriminative between cell lines, establishing the fingerprint as a quantitative starting point. In tumors, the generation and antioxidant arms were coordinately up-regulated relative to normal tissue, yet the two arms dissociated in their biology. The composite balance score tracked reduced immune infiltration consistently across cohorts, but arm-level decomposition showed that it was carried by low generation-arm activity in immune-cold tumors and followed arithmetically from how the balance score is defined; the association does not implicate antioxidant defense in immune infiltration. The clinical association pointed the other way: adverse outcome was attributable to the antioxidant arm, whereas generation was null. In cohort-held-out validation, tumors were separated from adjacent normal tissue, with redox programs outperforming generic phenotypic programs, indicating that the same program transfers across tumor types. Tumor remodeling of ROS homeostasis is therefore widespread, but its two arms carry distinct meanings: the balance score, driven by its generation term, reports immune context, whereas the antioxidant arm reports clinical risk.

cancer biology↗

bioRxiv2026

Single-cell multiomic QTL mapping reveals state-dependent genetic regulation and associated gene during cellular senescence

How cellular senescence reshapes inherited regulatory effects across chromatin and transcription, and eventually contribute to non-coding risk loci of complex diseases, remains elusive. We generated single-cell multiome ATAC-RNA profiles from proliferating and replicatively senescent primary HUVECs derived from 100 genotyped donors. Alongside state-resolved eQTL and caQTL mapping, we implemented covariance-aware multivariate QTL mapping to identify chromatin accessibility-expression QTLs (caeQTLs), modeling accessibility and expression as a joint phenotype. Joint analysis recovered moderate, asymmetric and modality-distributed associations missed by single-modality scans, revealed senescence-associated regulatory programs, and prioritized candidate causal variants and effector genes at cardiovascular loci. Fine-mapping, chromatin-state annotation and heritability enrichment, together with independent SNP-to-gene algorithms, provided convergent orthogonal support. Mechanistic dissection revealed that rs2019090 modulates PDGFD expression and endothelial phenotypes through senescence-amplified, allele-specific, HMGA1-associated enhancer-promoter regulation. This study establishes senescence-resolved joint multiomic QTL mapping as a framework for narrowing the missing regulation gap in complex disease genetics.

genetics↗

bioRxiv2026

IL-27 induces a cytotoxic state in CD4+ T cells distinct from the Th1 lineage

CD4+ cytotoxic T lymphocytes (CD4-CTLs) are understudied immune mediators with ambiguous origins. Despite expressing RUNX3, granzyme B (GZMB), and perforin (PRF1), CD4-CTLs are frequently classified as Th1 extensions due to shared interferon-{gamma} (IFN{gamma}) and T-BET expression. Here, we identify interleukin-27 (IL-27) as a independent inducer of a distinct CD4-CTL program. Proteomics reveals that while IL-27-polarized CD4+ T cells share protein signatures with conventional Th1s and CD8+ T cells, they possess a unique molecular landscape with re-wired cytokine signaling networks and a potent cytotoxic protein profile. Mechanistically, this program requires STAT1 and T-BET but operates independently of the autocrine IFN{gamma} feedback that sustains Th1 cells. During acute murine cytomegalovirus infection, IL-27 receptor signaling contributes to CD4-CTL differentiation in vivo, as its loss leads to reduced GZMB expression and skews CD4+ T cells toward IFN{gamma}+ and FOXP3+ subsets. Together, these findings establish IL-27 as a potent and previously unappreciated inducer of CD4-CTLs.

immunology↗

bioRxiv2026

Exploratory profiling of defense system signatures in Klebsiella pneumoniae clonal populations

Bacterial defense systems against bacteriophages are critical for bacterial genome stability and fitness, yet their distribution and epidemiological relevance in Klebsiella pneumoniae remain unexplored. We aimed to characterize defense system signatures across major K. pneumoniae clonal lineages and evaluate their utility as genomic signatures for tracking clonal dissemination. Here, we analyzed 6,346 genomes to characterize population structure, defense system signatures, and their coevolution with resistance determinants and plasmid backbones. PopPUNK clustering resolved 146 lineages that stratified into major clonal lineages (G-ST-KL combinations) with distinct resistance and virulence profiles. DefenseFinder and PADLOC identified 320 distinct defense systems, revealing that each clonal lineage harbors a unique defensotype characterized by systematic module replacement rather than stochastic gene loss. Co-occurrence networks further showed that these systems are organized into lineage-specific functional modules, with contrasting architectures even among lineages sharing the same sequence type. Integration of defense, resistance, and plasmid data uncovered strong lineage-specific associations, whereby broad-host-range plasmid backbones acquired distinct defense-resistance payloads in different clonal backgrounds. Geographic and host-niche analyses demonstrated that defense system distribution reflects clonal lineage expansion rather than independent geographic selection, and analysis of 689 Chinese genomes confirmed vertical inheritance of lineage-specific signatures along transmission chains. Collectively, defense systems in K. pneumoniae are organized into lineage-specific defensotypes shaped by synergistic modules and clonal evolutionary dynamics. Defense system profiling provides an additional layer of epidemiological resolution beyond conventional typing and offers practical utility for genomic surveillance, particularly in resource-limited settings where PCR-based detection of conserved systems could serve as a rapid proxy for identifying high-risk K. pneumoniae clones.

bioinformatics↗

bioRxiv2026

Functional and evolutionary insights into the emerging tet(X4)-carrying non-O1/O139 Vibrio cholerae from retail pork

The tigecycline resistance gene tet(X4) is prevalent in Enterobacteriaceae, particularly in Escherichia coli. To our knowledge, no study has reported the dissemination dynamics of tet(X4) in Vibrio spp. Herein, we isolated and characterized a first tet(X4)-positive non-O1/O139 Vibrio cholerae isolate from retail pork. Genomic sequencing identified a novel tet(X4) variant in the V. cholerae chromosome, harboring a G568A nucleotide substitution that resulted in an Ala190Thr (A190T) amino acid substitution in Tet(X4). While this Tet(X4)-A190T variant conferred lower phenotypic resistance to tetracyclines (including tigecycline) than the wild-type Tet(X4), its overall catalytic efficiency against these antibiotics was paradoxically enhanced despite a reduced substrate affinity. Genomic comparisons revealed that two copies of ISCR2 flanked the variant gene, and the structure was ISCR2-hp-hp-abh-tet(X4)G568A -ISCR2, which is highly homologous to the reported E. coli plasmids carrying tet(X4). In addition, it confirmed the presence of an ISCR2-mediated circular intermediate, proving this modules capacity for horizontal transfer of the tet(X4)G568A variant. Furthermore, the ISCR2-tet(X4) genetic structure carrying the G568A substitution was integrated within a chimeric SXT/R391-like integrative and conjugative element (ICE), which is also serving as a vehicle for genetic dissemination. As per our knowledge, this is the first report on the emergence of SXT/R391-like ICE carrying tet(X4) in Vibrio strains. Our finding demonstrates that the clinically relevant tigecycline resistance gene tet(X4), previously confined mainly to Enterobacterales from humans and livestock, is now actively spreading into environmental Vibrio populations. This cross-species transfer highlights a previously underappreciated ecological and public health concern in aquatic ecosystems.

microbiology↗

bioRxiv2026

12-plex DiLeu enables robust quantification of the feeding neuropeptidome

Understanding the feeding-induced neuropeptidome cascade requires analytical strategies capable of quantifying low-abundance, highly modified peptides across multiple tissues and time points. Herein, we apply 12-plex N,N-dimethyl leucine (DiLeu) isobaric labeling to perform the first multiplexed, tissue-wide, temporal quantitation of the Cancer borealis feeding neuropeptidome. This approach enabled sensitive measurement of neuropeptides across five tissues over six timepoints, revealing distinct regulatory patterns. The pericardial organ (PO) showed rapid early upregulation followed by suppression aligned with foregut emptying, whereas the thoracic ganglion (TG) displayed inverse and strongly condition-dependent responses, indicating previously unrecognized neuromodulatory roles. Single-residue variants and post-translational modifications, including pyro-Glu formation and amidation, produced markedly different temporal profiles, underscoring the functional specificity of closely related isoforms. We further identify differential regulation of proctolin and its amidated form, suggesting modified variants may contribute uniquely to feeding physiology. Collectively, these results establish multiplexed DiLeu labeling as a powerful platform for quantitative neuropeptidomics and reveal new dimensions of peptide-mediated feeding regulation.

neuroscience↗

bioRxiv2026

Single Channel Strongly-Coupled Geometry Surface Coil for Small Mammal Whole Brain fMRI

1Abstract/SummarySingle-channel surface coils remain central to rodent MRI, but conventional circular loop designs face an inherent trade-off between surface and depth sensitivity, limiting whole-brain coverage for applications such as resting-state BOLD fMRI. This work introduces a single-channel strongly-coupled geometry surface coil. It consists of a stop-sign shaped loop inductively overcoupled to a nested, three-turn elongated racetrack spiral designed to improve depth sensitivity and thru-plane coverage while remaining robust to variable sample loading. Benchtop characterization across three phantoms of differing size showed the parallel resonant mode and loaded quality factor changed negligibly with loading. In phantom imaging at 9.4 T, the SCG coil achieved in-plane SNR and temporal SNR comparable to, and at shallow depths exceeding, a commercial Bruker 2x2 receive-only rat brain array, while showing substantially more consistent tSNR across loading conditions. The SCG coil also demonstrated superior thru-plane tSNR over a 20 mm slice range at 3.5 mm depth, approximating the anterior-posterior extent of the rat brain. In vivo resting-state BOLD fMRI in eight rats, acquired with a double asymmetric spin-echo EPI sequence, yielded a default mode network consistent with prior reports and revealed a previously undescribed subcortical network spanning superior/inferior colliculi and cerebellar regions. These results establish the single-channel SCG as a promising foundation for next-generation rodent receive coil arrays, combining loading-independent tuning with extended sensitive coverage suitable for whole-brain functional imaging.

biophysics↗

bioRxiv2026

Characterizing Functional Clusters of V4 Neurons in Digital Twins

Neurons in primate visual cortical area V4 display tuning for multiple visual features, including color, shape, texture, and depth. Whether and how these neurons are organized into functional architectures remains largely unknown. Using two-photon calcium imaging in anesthetized macaques, we recorded responses of hundreds of V4 neurons to natural images and used these data to train deep convolutional neural network models (digital twins), obtaining synthetic images (SI) that maximized neuronal responses. Based on their SIs, these neurons clustered into classes that spatially matched the orientation, color, and curvature maps from intrinsic signal imaging. Furthermore, lesion study in digital twins revealed different integration rules for different neuron classes. Thus, digital twins of V4 neurons can be applied as a promising tool to characterize neurons fundamental features, which underlie the functional clustering in this area. HighlightsO_LINeurons in V4 are examined with two-photon calcium imaging and DCNN modeling (digital twins) C_LIO_LISynthetic images derived from neurons digital twins reveal distinct neuron groups C_LIO_LIThese groups match functional types defined by intrinsic signal optical imaging C_LIO_LILesion study in digital twins demonstrates neural mechanisms underlying feature tuning C_LI

neuroscience↗

bioRxiv2026

Pathogen context reshapes antimicrobial peptide generation

Antimicrobial peptides are a promising source of new anti-infective agents, but their discovery is limited by a practical bottleneck: selecting a small set of candidates to synthesize and test for a specific pathogen. Existing peptide generators can expand antimicrobial-like sequence space, but most leave pathogen specificity to predictors or filters after generation. Here, we use AMPHORA, a pathogen-conditioned sequence-structure generator, to build antimicrobial peptide libraries shaped by target context. AMPHORA couples a short-peptide representation model to latent-flow generation conditioned on target class, genome-derived features and strain-description text. In matched, partial and shuffled controls, pathogen context redirected generated peptide pools beyond broad activity labels, with the strongest effects when genome and text conditions were combined. Counterfactual generation from the same initial noise showed that strain descriptions primarily changed amino-acid choices, whereas genome-derived features contributed more strongly to predicted structural properties. Across species, AMPHORA produced target-dependent enrichment, and matched bacterial context shifted APEX-predicted potency-score distributions compared with class-only generation. The generated peptides remained diverse, novel and peptide-like by sequence and predicted-structure analyses. Collectively, our results establish pathogen context as an active design signal for antimicrobial peptide generation and provide a target-aware route to pre-synthesis library design.

bioinformatics↗

bioRxiv2026

EEG biomarkers of reinforcement learning and motivation: A multi-task battery

Serotonin and dopamine make dissociable contributions to reinforcement learning (RL) sub-components, yet we lack neural biomarkers capable of detecting their differential effects. Here, we report the development of a five-task EEG battery designed to probe these dissociable RL mechanisms. Using a model-free analytical approach in healthy volunteers, we identify distinct neural markers across probabilistic instrumental learning, motivational vigour, Pavlovian-instrumental transfer, reversal learning, and a working memory-RL task. A centroparietal P300 tracked incremental learning across three paradigms and showed cross-task convergent validity. Readiness potentials and beta suppression indexed value-based motor preparation, while frontal theta captured Pavlovian-instrumental conflict. The largely independent pattern across markers supports the batterys capacity to detect selective pharmacological effects on distinct neural systems.

neuroscience↗

bioRxiv2026

CellOS: Learning a World Model of Cellular State through Joint Embedding Prediction

Foundation models learned from single-cell transcriptomes are central to the prospect of AI virtual cell that can represent, query and predict cellular state. However, most current single-cell foundation models learn from a single view of gene expression and are optimized primarily through reconstruction or next-token prediction. As a result, they capture expression abundance but cannot explicitly reconcile complementary views of cellular state. Here we present CellOS, a multi-view foundation model that learns cellular representations from paired expression and perception views. CellOS integrates complementary views through a scalable three-stage training strategy that combines causal cell-sentence language modelling, function-preserving dense-to-mixture-of-experts expansion and latent-space alignment via an LLM-JEPA objective. Using this framework, we trained a 12-billion-parameter model on 390.5 million single-cell transcriptomes. Across diverse benchmarks spanning cell-state annotation, batch integration and perturbation-response prediction, CellOS consistently outperformed state-of-the-art single-cell foundation models. Together, these results suggest that predictive alignment between complementary cellular views provides a scalable path toward representation-centric cellular world models and transferable AI virtual cells.

bioinformatics↗

bioRxiv2026

A GPX4 phosphorylation switch by FGFR1 guards against ferroptosis

Ferroptosis is driven by lipid peroxidation, yet the mechanisms by which cells rapidly adjust their sensitivity to ferroptosis in response to extracellular cues remain elusive. We identify a direct phosphorylation switch controlling the activity of glutathione peroxidase 4 (GPX4), the core ferroptosis regulator. The receptor tyrosine kinase FGFR1 directly binds and phosphorylates GPX4 at Tyr180/Tyr196 in a kinase-dependent manner, requiring its Tyr730 as a docking site. This phosphorylation enhances GPX4s catalytic activity and suppresses ferroptosis. In cardiac ischemia/reperfusion injury, the FGFR1-GPX4 axis is suppressed, and a selective FGFR1 agonist (FGF-1{Delta}NT) reactivates it to protect against ferroptosis-mediated damage. Critically, a phosphorylation-deficient GPX4 knock-in mouse exhibits hypersensitivity to injury and non-responsive to this agonist, proving that GPX4 phosphorylation is essential. Our findings reveal a rapid mechanism for regulating ferroptosis via GPX4 tyrosine phosphorylation, directly linking receptor tyrosine kinase signaling to ferroptosis, and offering new strategies for treating ischemic-and other ferroptosis-associated diseases.

Cell Biology↗

bioRxiv2026

A Transformer-based Multi-omics Model for Translation Efficiency in S. cerevisiae

Precise regulation of protein synthesis is fundamental to cellular homeostasis and remains a primary target for synthetic biology applications. However, the non-linear relationship between mRNA abundance and protein levels presents complexities that poses challenges for predictive engineering. Here, we present TRIM, a Transformer-based RNA Inference Model that leverages full-length mRNA sequences and multi-omics data to predict translation efficiency. By employing a Parallel Expert Mixer, TRIM achieves robust prediction accuracy (R2 [≥] 0.8,Pearson r [≥] 0.9). Trained on multimodal data from massive Saccharomyces cerevisiae isolates, TRIM demonstrates outstanding biological interpretability, helping to decipher complex translational patterns such as synergistic effects between bases, sequence-dependent codon preference in different stages, and distinct attention on key secondary structures. These results indicate that the integration of multi-omics data with holistic sequence modeling can effectively decode the cis-regulatory grammar of translation as well as providing a scalable and interpretable generative framework for future synthetic biology engineering. Availability and ImplementationThe source code and data used to produce the results and analyses presented in the manuscript are available from Github (https://github.com/ZeusLiu666/TRIM).

Molecular Biology↗

bioRxiv2026

Structural basis of substrate recognition and allosteric inhibition in human B0AT2

The SLC6 family is a major target for neuropsychiatric therapeutics. Human B0AT2 (SLC6A15) regulates amino acid homeostasis and glutamatergic transmission and is linked to major depressive disorder, yet its transport and inhibition mechanisms remain unclear. Here we report cryo-EM structures of B0AT2 in apo state and in complex with substrates (proline, leucine, methionine) and inhibitors (loratadine, tiagabine), capturing outward-open, early substrate-bound intermediate, outward-occluded, and inward-open conformations along the transport cycle. These structures reveal an early substrate-sensing mechanism at the substrate-binding pocket (S1), where a substrate-dependent rotameric switch of Phe308 remodels pocket geometry to tune substrate accommodation and selectivity. Loratadine stabilizes an outward-occluded state via allosteric inhibition at the extracellular S2 pocket, whereas tiagabine stabilizes the inward-open state through cooperative multi-site inhibition involving S1 and two previously unrecognized intracellular cavities (S3 and S4). Together with functional assays, these data define the molecular basis of B0AT2 substrate selectivity and state-dependent inhibition. Notably, the two intracellular cavities are conserved across SLC6 transporters, reflecting a shared intracellular vestibular architecture and enabling rational design of conformation-selective modulators for neuropsychiatric disorders.

biophysics↗

bioRxiv2026

A horizontally transferred fungal deubiquitinase facilitates insecticides resistance in whitefly

Horizontal gene transfer (HGT) has enabled insects to acquire novel genetic material that can fuel adaptation to environmental change. However, the role of HGT in the evolution of insecticide resistance remains poorly characterised. Here, we identify BtUCH19, a fungal gene that has integrated into the genome of the global pest Bemisia tabaci and functions as a deubiquitinating enzyme (DUB). We show that compared to endogenous DUB, BtUCH19 specifically removes K63-linked ubiquitin chains from a cytochrome P450, CYP4C64, thereby stabilizing this key detoxification enzyme in vivo. Sustained CYP4C64 abundance enhances metabolic detoxification of two commonly used insecticides thiamethoxam (TMX) and clothianidin (CLO) to their low-toxicity products TMX-Urea and CLO-Urea. Consequently, BtUCH19 drives insecticide resistance through a novel "HGT-PTM-Metab" axis. Our work reveals the instrumental role of a HGT in orchestrating ubiquitin-proteasome system (UPS)-mediated protein level regulation of a key detoxification pathway. These findings offer new insights into the intricate mechanisms underlying co-evolutionary biology, and provide a new molecular target for Integrated Pest Management (IPM).

zoology↗

bioRxiv2026

From Spectra to Digital Phenotypes: Wearable Multispectral Sensing for Precision Light and Green Space Exposure

Light is a modifiable determinant of health, yet real-world exposure assessment is often reduced to illuminance alone, lacks environmental context, or relies on privacy-sensitive sensing. We present SpectraVita, a low-cost, compact multispectral wearable that continuously samples 11 ultraviolet-to-near-infrared bands and, through a privacy-preserving pipeline without cameras or location tracking, produces interpretable digital phenotypes of lighting environment (natural vs. artificial and source type) and vegetation context alongside standard visual and non-visual light metrics. In extensive in-the-wild recordings spanning diverse scenes, times of day, weather conditions, and light sources, we observe distinctive spectral signatures that enable supervised models to achieve a macro-averaged F1 score of 0.988{+/-}0.004 for light-source classification and green-space detection in boundary-free environments. A sensor-derived normalized difference vegetation index (NDVI) emerges as an explainable, physically grounded marker linking natural light exposure and greenness. Robustness is supported by scenario-shift testing, image-segmentation validation, and mixed-environment experiments that demonstrate sensitivity to partial and transient exposures, as well as by longitudinal stationary monitoring and deployment in a cohort of thousands of participants capturing seasonal and behavioral variability. SpectraVita enables individualized, privacy-preserving, longitudinal monitoring of light and greenness exposure at scale, addressing a key measurement gap for precision and population health studies of daily photic environments.

bioengineering↗