Biology subjects

Yu, S.

Publications and source records attributed to Yu, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Saturated mutagenesis screen of M-MLV reverse transcriptase identifies variants enhancing prime editing efficiency

Prime editing enables the precise modification of genomes, thereby holding great potential for the treatment of genetic diseases. Despite substantial advancements in prime editing technology and the initiation of the first clinical trial for treating chronic granulomatous disease, further enhancement of editing efficiency across edit types is still urgently needed. Here, we developed a compact prime editor, PE2{Delta}R, by deleting the RNase H domain of the MMLV reverse transcriptase (MMLV-RT). We then conducted a saturated mutagenesis screen targeting two DNA interacting regions within the PE2{Delta}R-RT Fingers domain. By integrating three highly effective mutations (I61R, V101R, S67W) into PEmax lacking RNase H domain (termed PEmax{Delta}RM3), we achieved up to a 90% increase in editing efficiency across editing types compared to PEmax. Structural modelling using AlphaFold 3 suggests that these mutations enhance primer-template stabilization and guide the RNA/DNA hybrid into a catalytically favourable trajectory, providing a mechanistic explanation for the enhanced activity. Taken together, our study demonstrates proof-of-concept for the application of unbiased mutagenesis screen to identify novel mutations that enhance prime editor performance. Furthermore, we discovered that RT variants (I61R, V101R, S67W) synergize with PEmax and epegRNA to improve prime editing efficiency across edit types, with the strongest improvement observed in introducing small deletions.

molecular biology↗

bioRxiv2026

Scalable Production of a De Novo SARS-CoV-2 Antiviral miniprotein in Escherichia coli

The rapid emergence of SARS-CoV-2 variants that evade neutralizing antibodies underscores the need for next-generation antiviral biologics that combine molecular precision with scalable, cost-effective manufacturing. Computationally designed miniproteins targeting the receptor-binding domain (RBD) of the spike protein offer a compelling alternative to monoclonal antibodies due to their small size, high thermal stability, and compatibility with microbial expression systems. Here we report the end-to-end development and cGMP production of IPD-52520, a de novo antiviral miniprotein, using an optimized E. coli platform. Two miniprotein candidates, a homotrimeric construct (Trimer is referred to as IPD-52520, 17 kDa) and a tandem fusion (Daisy is referred to as IPD-52521, 25 kDa), were evaluated in parallel through systematic optimization of strain selection, media composition, fed-batch fermentation, inclusion-body solubilization, refolding, and chromatographic purification. The Trimer was downselected as the lead molecule based on superior preclinical efficacy, favorable pharmacokinetic properties, and higher volumetric manufacturing yields. The optimized process delivers approximately 2 g/L of purified protein at greater than 90% purity. Scale-up from 5 L to 50 L under cGMP conditions demonstrated excellent batch-to-batch reproducibility across six independent batches, supporting nonclinical and Phase 1 clinical supply. Comprehensive biophysical characterization confirmed a well-folded, predominantly alpha-helical trimer (Tm = 73.4 {degrees}C; polydispersity = 1.005) with an intact primary structure and strong target-binding affinity (KD < 1 pM). Real-time stability studies indicate that the drug substance is stable at 2-8 {degrees}C for at least 12 months, with ongoing stability studies. These results demonstrate the feasibility of translating computationally designed antiviral miniproteins into manufacturable biologics and provide a platform applicable to rapid-response therapeutics against current and future pandemic threats.

bioengineering↗

bioRxiv2026

Experiment-free learning of exoskeleton assistance is not an unsolved problem

We present three quantitative methods: 1) estimation of exoskeleton mechanical power and energy ratio from published data, 2) a systematic review of the exoskeleton literature on reported energy ratios, and 3) timing correction analysis of the replication experiment, to address concerns raised by Collins et al. (2026) about Luo et al. (2024). Together, these analyses support the reported metabolic reductions and the validity of exoskeleton control via learning in simulation. The critique rests on an unsupported premise: that exoskeleton energy ratios above 4 are physiologically implausible. This premise of Collins et al. (2026) is not supported by the cited evidence, and the error originates in their own cited source. Sawicki and Ferris (2009), the paper they invoke as authority for the limit of 4, state explicitly that "reported values of the muscular efficiency range from 0.10 to 0.34, with many sources assuming an average of [~]0.25." The value of 4 corresponds to this average, it is not a physiological ceiling. Treating an average as a physiological upper limit is a fundamental error. The published exoskeleton literature further contradicts the claim, including work by the authors of the critique themselves (Collins et al., 2015: 4.3; Young et al., 2017: 5.0) and independent work (Malcolm et al., 2013: 4.8; Seo et al., 2017: 6.7). In contrast, our walking energy ratio is 2.4, calculated directly from Fig. 4 of our paper. Our device delivers higher peak torque (14.1 Nm vs. 10.9 Nm, Lim et al., 2019) and achieves a slightly larger metabolic reduction (24.3% vs. 21%). Independent groups have since demonstrated meaningful metabolic reductions using learning-in-simulation frameworks, including Barati et al. (2026, 15.2% mean and 22.5% maximum) and Zhou et al. (2025, [~]20% during running). The claim of Collins et al. (2026) that this problem "remains unsolved" is directly contradicted by these independent results. The experiment in the critique is not a valid replication of our method. Our controller is a neural network with [~]10,000 parameters learned through deep reinforcement learning in musculoskeletal simulation; the critique instead applies a pre-programmed fixed torque curve with no learnable parameters. Beyond this, the replication contains three methodological errors: 1) a heel-strike timing assumption producing offsets up to 30% of the gait cycle; 2) an averaged torque profile that discards subject-specific control; and 3) a device [~]50% heavier than ours (4.8 kg vs. 3.2 kg) without measuring the metabolic penalty of the added weight. The critique also misreports Samsung data, with reported values approximately double those in the original publication, errors that directly underpin their physiological limit argument.

bioengineering↗

bioRxiv2026

Conserved Cell Type Signatures Across the Brainstem and Spinal Cord in the Mouse Central Nervous System

Understanding how cell types are organized across the central nervous system (CNS) is key to uncovering neural function. Here, we integrate single-nucleus Multiome (RNA+ATAC) sequencing, spatial transcriptomics, and computational analyses to map conserved cell type signatures in the adult mouse brainstem and spinal cord. We identify a shared core of neuronal and non-neuronal cell types, alongside region-specific specializations reflecting distinct functions. Spatial data reveal conserved cellular niches across the brainstem-spinal cord boundary, indicating a continuous organizational logic. Cross-region comparisons uncover recurrent gene expression modules and signaling programs that may support shared circuit features. Chromatin accessibility profiling highlights cell-type-specific regulatory programs and implicates Hox transcription factors in positional identity. Notably, cell-type and positional identities are largely orthogonal, with varying regional influence across neuronal classes: motor neurons show strong positional coupling, whereas glutamatergic and GABAergic interneurons show minimal entrainment. This work provides a reference for the shared molecular architecture of these CNS regions.

neuroscience↗

bioRxiv2026

Heme orchestrates a tissue stress response to proteolytic damage

Whereas cellular stress responses are well defined, tissue-level stress remains poorly understood. Proteases are among the most widespread enzymes, and excessive proteolytic activity drives diseases such as arthritis and chronic obstructive pulmonary disease, yet unifying features of this stress are unclear. Here, using the lung and diverse proteases, we identify a conserved injury signature of proteolytic stress marked by vascular disruption, red blood cell extravasation, and heme release that triggers oxidative stress. We show that alveolar macrophages act as primary sensors of this stress response, activating NRF2-dependent heme detoxification program and fibroblasts produce protease inhibitors to limit damage. Repeated exposure to proteolytic stress induces tissue adaptation and protects against subsequent injury and infection. These findings define a unifying framework for tissue-level proteolytic stress sensing and adaptation.

immunology↗

bioRxiv2026

Semantic map learning and externalization in an embodied neural agent: A comparison to human behavioral and neural data

All mammals can build internal cognitive maps from sensory input, supporting spatial learning and planning. While rodent studies have shown the mammalian navigation system solves the SLAM (Simultaneous Localization and Mapping) problem, its role in human spatial memory and overt recall are less understood. To investigate this, we adapted a spiking semantic SLAM algorithm for a "Treasure Hunt" task, where human participants navigate a 3D beach in virtual reality and later point to remembered object locations. Our agent integrates networks for bipedal locomotion, vision, memory, and arm control to enable first-person learning of place-object associations, and externalizing that knowledge by pointing and expressing confidence. Comparing model observables to human data, we replicate key behavioral and neural effects: monotonic scaling of accuracy with confidence, and recall-dependence on local field potential power observed in the left hippocampus. This work offers a mechanistic framework linking embodied navigation, memory, and communication in human spatial cognition.

animal behavior and cognition↗

bioRxiv2026

Prediction of Transcription Factor DNA Binding Affinity with High-Throughput Kd Measurements and Deep Learning

Transcription factors (TFs) regulate gene expression through specific interactions with genomic DNA. While TF binding motifs from public databases describe sequence preferences, quantifying genome-wide affinity (Kd) is highly desirable for a more accurate thermodynamic description. Here, we report ivtFOODIE (in vitro FOOtprinting with DeamInasE), an assay that leverages deaminase-mediated cytosine-to-uracil conversion to measure Kd values for a given TF across accessible genomic regions from human cells. By pre-training on TF binding sites from JASPAR and fine-tuning with our ivtFOODIE data from 46 TFs representing 13 different DNA-binding domains (DBDs), we developed Seq2Kd, a deep learning model capable of predicting a TFs absolute binding affinity on DNA sequences. Seq2Kd enables de novo motif discovery of [~]500 previously uncharacterized human TFs and reveals the effects of genetic variation both in TF-coding regions and DNA-binding sites on gene expression and disease susceptibility. By correlating predicted affinity changes with the sign and magnitude of expression quantitative trait locus (eQTL) effects, we stratified TFs into activator-like and repressor-like groups. Compared to clinically benign variants, pathogenic single-nucleotide variants (SNVs) within regulatory and protein-coding regions show significantly larger predicted shifts in Kd. We provide an interactive web portal, the ENcyclopedia of Transcription-factor Interactions with Regulatory Elements (ENTIRE), which integrates the Seq2Kd model with the ivtFOODIE dataset. This resource offers thermodynamic prediction for TF-DNA interactions for functional genomics and human disease.

biophysics↗

bioRxiv2026

Systematic profiling of WD40 proteins reveals Wcp1, a cyclophilin linking CO2/heat tolerance to acidic pH adaptation in Cryptococcus neoformans

WD40 domains are major protein-protein interaction (PPI) scaffolds, yet their contributions to fungal pathogenicity remain poorly defined. We systematically analysed 94 canonical WD40 proteins in Cryptococcus neoformans. Conditional knockdown and sporulation identified 36 essential WD40 proteins, while in vitro and in vivo profiling of 103 signature-tagged deletion strains spanning 52 genes uncovered 31 pathogenicity-related WD40 proteins, including epigenetic and post-transcriptional regulators. We identified Wcp1, a dual-domain protein whose WD40-repeat and cyclophilin domains are required for growth at 37{degrees}C under 5% CO2. Its WD40 scaffold and PPIase domain supported CO2/heat tolerance and virulence. Notably, Wcp1 couples these functions to acidic pH adaptation: wcp1{Delta} failed to grow under elevated temperature and CO2 at acidic pH, exhibited enhanced intracellular acidification, reduced macrophage survival and attenuated virulence in Drosophila and mice. Integrated transcriptomic and proteomic analyses place Wcp1 at the centre of intracellular pH homeostasis, coordinating proton transport, metabolic adaptation and stress-buffering networks.

microbiology↗

bioRxiv2026

A Decade of Deep Learning-based Biomedical Image Segmentation

Biomedical image segmentation is a fundamental problem in computational biomedicine that aims to precisely delineate anatomical and biological structures, tissue types, or pathological regions in biomedical images. Accurate segmentation is essential for interpretation, decision-making, and quantitative analysis across a wide range of biological and medical applications. Over the past decade, the field has undergone a profound paradigm shift, evolving from task-specific specialist models to universal foundation models. This review provides an in-depth analysis of the evolution, tracing how the limitations of local discriminative learning drove the transition toward transformer-based global modeling, and large-scale generative pre-training. To help navigate the diverse landscape of interaction paradigms, we introduce the first systematic taxonomy of promptable biomedical image segmentation, categorizing existing methods into six distinct types, enabling users to intuitively select appropriate prompting strategies based on visual demonstrations and quickly pinpoint relevant literature (Prompt Type Visualization). Beyond model architectures, we discuss parallel advancements in dataset development, evaluation protocols, and application-specific adaptations across radiology, pathology, and biology. Integrating these powerful foundation models with rigorous domain-specific adaptation has great potential to improve patient outcomes and healthcare efficiency. Finally, we highlight key challenges in trustworthiness and clinical integration that must be overcome to realize the potential of the next generation of biological and medical generalists.

bioengineering↗

bioRxiv2026

A pooled screening approach reveals bacterial chemoreceptors for short-chain carboxylic acids

Bacterial chemotaxis is a key process in host colonization and virulence, mediated by large repertoires of chemoreceptors. Despite their physiological and ecological importance, mapping these chemoreceptors to their cognate metabolic ligands remains a major challenge due to the vast number of potential interactions. To address this, we developed a pooled screening assay that enriches functional chemoreceptors from a gene library. Using this approach, we identified a previously uncharacterized group of chemoreceptors in Pseudomonas species with Cache_3-Cache_2 domains that sense short-chain C3 carboxylic acids. Sequence and computational structural analyses revealed that these chemoreceptors exhibit domain features similar to a recently reported C1 formate chemoreceptor despite substantial sequence divergence. Functional assays of representative chemoreceptors confirmed robust chemotactic responses to C3 carboxylic acids, with limited responses to formate. Integrating structural and molecular dynamics analyses suggests that increased binding pocket size and altered flexibility, relative to the formate chemoreceptor, facilitate recognition of larger C3 carboxylic acid ligands. Together, our approach provides a simple and scalable framework for mapping ligand-chemoreceptor interactions and enables systematic characterization across diverse metabolites.

microbiology↗

bioRxiv2026

Low-intensity vibration (LIV) cellular mechanotherapy reprograms tumor transcriptomes to suppress cancer-promoting inflammation

LIV is a non-pharmacological intervention for multiple pathologies, most notably pain, yet its potential in oncology remains unexplored due to poorly understood mechanotransduction pathways. Its therapeutic efficacy depends on precise dosing parameters - frequency, amplitude, and duration; suboptimal application, whether excessive or insufficient, risks exacerbating symptoms or rendering treatment ineffective. In a breast cancer-immune cell co-culture model, a 15-min regimen of 90-Hz, 0.43-g LIV attenuates protumorigenic crosstalk by suppressing proinflammatory cytokines and reprogramming malignant cells into a transient metastasis-incompetent "benignant" state that retains oncogenic markers but loses invasive capacity. Our results reveal LIV as a non-drug inhibitor of IFN{gamma} and CXCL12{beta} - silencing IFN{gamma} impairs inflammatory bursts, while silencing CXCL12{beta} starves the CXCR4/CXCR7 axis, depriving tumor cells of motility cues. LIV enforces a genome-wide transcriptional brake, upregulating tumor-suppressive miRNAs (hsa-miR-141, hsa-miR-122) while downregulating protumorigenic miRNAs (hsa-miR-105-5p, hsa-miR-181a-5p). This work repositions LIV as a non-drug modality for coordinately targeting multiple cancer hallmarks. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/716739v1_ufig1.gif" ALT="Figure 1"> View larger version (80K): org.highwire.dtl.DTLVardef@1100863org.highwire.dtl.DTLVardef@196bcf4org.highwire.dtl.DTLVardef@14f3903org.highwire.dtl.DTLVardef@2802fd_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_ST_ABSDosing PrecisionC_ST_ABSLIV mechanotherapy has an optimal therapeutic window. Too little is ineffective, while too much can exacerbate symptoms. This mirrors the pharmacokinetic language of classical pharmacology. The "Benignant" ConceptA 15-min regimen of 90-Hz, 0.43-g LIV attenuates protumorigenic crosstalk by suppressing proinflammatory cytokines and reprogramming malignant cells into a transient, metastasis-incompetent benignant state defined by mechanical constraint rather than pharmacological intervention. Dual Cytokine SilencingLIV acts as a non-pharmaco-logical inhibitor of IFN{gamma} and CXCL12{beta}. IFN{gamma} is a double-edged sword in cancer (pro-immunity vs. exhaustion), and CXCL12{beta} is the specific isoform implicated in metastasis. Targeting both simultaneously addresses immune crosstalk and chemotaxis. In briefMeena et al. demonstrate that the efficacy of LIV hinges on optimal dosing parameters. When applied correctly, it functions as a non-drug modality to target multiple oncogenic and inflammatory pathways. At the molecular level, LIV drives global transcriptional repression via miRNA regulation, increasing tumor-suppressive miRNAs (hsa-miR-141, hsa-miR-122) and decreasing protumorigenic miRNAs (hsa-miR-105-5p, hsa-miR-181a-5p).

cancer biology↗

bioRxiv2026

Raybloc: A Marine Bioactive Silica-Microsponge Formulation Confers Superior Protection against Blue Light and Infrared-A Induced Skin Damage in Murine Model

Long-term exposure to high-energy visible (HEV) blue light and infrared-A (IR-A) radiation accelerates oxidative stress, inflammation, and transepidermal water loss (TEWL), leading to photoaging and damage to the skin barrier. In this study, we developed Raybloc(R), a marine bioactive silica microsponge formulation, and evaluated its protective effects against combined high-energy visible (HEV; 410-480 nm) and infrared-A (IR-A; 700-1400 nm) exposure in a preclinical model. We divided 36 nude BALB/c-nu/nu mice into six groups: one that didnt get any treatment, one that got Raybloc(R) (no radiation), one that got Raybloc(R) 5%, one that got Raybloc(R) 8%, one that got HA 0.5%, and one that got HA 0.8%. Animals underwent topical treatment for 14 days under regulated exposure to HEV (410-480 nm, 100 J/cm2/day) and IR-A (700-1400 nm, 30 mW/cm2). We examined transepidermal water loss (TEWL), skin hydration, oxidative stress, inflammatory cytokines (IL-1{beta}, IL-6, TNF-, IL-10), and histological indicators of collagen preservation through biophysical, biochemical, and histopathological techniques. In the Raybloc(R) 8% group, TEWL dropped by 48.3 {+/-} 4.6% (p < 0.001), and skin hydration went up by 62.7 {+/-} 5.1%. The levels of ROS and MMP-1 expression decreased by 63.4% and 57.2%, respectively, while collagen I increased by 2.1 times compared to HA 0.8%. There was a big drop in the pro-inflammatory cytokines IL-1{beta}, IL-6, and TNF- (-54%, -49%, and -46%), and a big rise in IL-10 (+38%). Histological analysis demonstrated well-preserved epidermal integrity and dense collagen bundles in Raybloc(R)-treated mice, whereas irradiated controls exhibited dermal disorganization and inflammatory infiltration. Raybloc(R) showed better photoprotective, antioxidant, and moisturizing effects than HA-based products. It also helped reduce oxidative and inflammatory skin damage caused by blue light and IR-A. These results support Raybloc(R) as a next-generation multifunctional dermocosmetic that can help stop photoaging caused by digital and solar radiation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/713389v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@54e046org.highwire.dtl.DTLVardef@502f87org.highwire.dtl.DTLVardef@6088daorg.highwire.dtl.DTLVardef@1b8c241_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

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

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

bioengineering↗

bioRxiv2026

A Single-Cell Temporal Atlas of Mouse Nasal Embryonic Development

The mammals breathe and perceive odors through anatomically and functionally distinct respiratory and olfactory regions of the nose; however, how the early embryo endows this system remains largely unknown. Here, we present a temporal high-resolution single-cell RNA sequencing (scRNA-seq) atlas of mouse nasal development, comprising 183,247 cells collected from 20 embryos spanning embryonic day 10.5 (E10.5) to E18.5. We identified 7 major cell clusters and 52 molecularly defined subtypes, including previously unrecognized rare populations and niche-derived signaling components involved in progenitor cell maintenance. Lineage reconstruction of epithelial and mesenchymal compartments revealed dynamic cell fate transitions and highlighted candidate regulators of lineage specification, including Foxa1 as a regulator of nasal respiratory ciliated epithelium differentiation. Integration with adult nasal epithelium datasets further delineated transcriptional dynamics of olfactory stem cells. This study provides a molecular roadmap of nasal development and offers a valuable resource for future research into nasal biology and regenerative strategies.

developmental biology↗

bioRxiv2026

An Advanced Humanized Systemic Lupus Erythematosus Model Enables Parallel Profiling of B Cell-Targeted Therapies

B cell-targeted therapies represent a transformative frontier for systemic lupus erythematosus (SLE) intervention, yet clinical recommendation of specific treatment is hampered by the challenge to perform head-to-head comparisons of efficacy-toxicity trade-offs and tissue-specific impacts in patients. To address this gap, an advanced Toll-like receptor 7 (TLR7) agonist-induced SLE model is developed in a NCG-M (NOD-Prkdcem26Cd52Il2rgem26Cd22Rosa26em1Cin(hCSF2&IL3&KITLG)/Gpt) human immune system (HIS) mice. This model enables parallel evaluation of multiple B cell-directed therapies within a controlled cohort study. It recapitulates core SLE pathologies--including immune effector cell augmentation, autoantibody production and glomerulonephritis--within 2 months, demonstrating greater severity and clinical fidelity than conventional pristane-induced systems. Validated through replication of clinical responses to rituximab and belimumab, the platform directly compares two emerging modalities: universal chimeric antigen receptor-T cells (UCAR-T) elicits delayed but profound B-cell reset correlating with superior reduction in renal pathology and autoantibodies, while T cell engagers (TCEs) mediate rapid yet partial B-cell depletion and transient efficacy. UCAR-T concurrently induces greater acute inflammatory responses, aligning with its distinct toxicity profile. By resolving therapy-specific effects on human immune dynamics and symptom control, this study empowers context-specific therapeutic selection for SLE, advancing tailored management strategies.

immunology↗

bioRxiv2026

Uncovering Conceptual Biases in DNA Stabilization: A Student-Led Investigation

Deoxyribonucleic acid (DNA) stands as one of the most foundational concepts in life sciences, essential for students to master. However, when surveyed about the forces that stabilize the double-stranded DNA structure, many students exhibited a conceptual bias-- favoring base pairing as the primary stabilizing force, while overlooking the equally critical role of base stacking interactions. To investigate the origins of this misconception, students conducted a comprehensive analysis of 35 widely used textbooks. Their findings revealed that one-third of these texts explicitly emphasized base pairing as the sole stabilizing force in their written content. Furthermore, two-thirds of the textbook contained illustrations that reinforced this bias, visually highlighting base pairing while neglecting base stacking. Recognizing this bias, students embarked on a literature review to gain a more accurate and nuanced understanding of DNA stabilization. Through this research, we identified three concept areas--DNA structure and function, environmental effects on DNA, and DNA-protein interactions--to illustrate how base pairing and base stacking work in concert to stabilize the antiparallel double helical structure of DNA. This interplay between base pairing and base stacking is crucial not only for the structural integrity of DNA, but also for its biological functionality. By addressing this conceptual bias, we aim to promote a more balanced and scientifically accurate representation of DNA stabilization in educational materials.

scientific communication and education↗

bioRxiv2026

GBA1 deficiency differentially affects endolysosomal trafficking in neurons versus astrocytes

Mutations in the gene glucosidase, beta acid 1 (GBA1) are the strongest genetic risk factor for Parkinsons disease (PD) and are associated with faster disease progression. GBA1 is expressed in all cell types of the central nervous system, with some evidence supporting higher expression in glial cells than neurons. To elucidate possible specific functions in neurons versus glia, we differentiated human induced pluripotent stem cells (iPSCs) generated from an individual with PD heterozygous for the GBA1 pathogenic null variant IVS2+1 (GBA1IVS/+), homozygous GBA1 IVS2+1 isogenic to GBA1IVS/+ (GBA1IVS/IVS) and a healthy unaffected age-and sex-matched individual (GBA1+/+). GBA1 expression was reduced in GBA1IVS/+ and GBA1IVS/IVS neurons and astrocytes. Endolysosomal trafficking was significantly altered in GBA1-deficient neurons with enlarged early and recycling endosome and lysosome compartments in neurons but not in astrocytes. High molecular weight oligomerization of -synuclein and phosphorylated Ser129 -synuclein were present in GBA1IVS/+ and GBA1IVS/IVS neurons but not in GBA1+/+ neurons, or in GBA1-deficient or GBA1+/+ astrocytes. Transcriptomic analysis of GBA1-deficient neurons and astrocytes revealed cell-type specific profiles. GBA1 deficiency in neurons downregulated immune response and upregulated cholesterol synthesis pathways, while GBA1 deficiency in astrocytes downregulated genes associated with translation and upregulated genes involved in extracellular matrix biogenesis. Transcriptomic analysis also suggests that GBA1 deficiency induces neurotoxic reactivity in astrocytes. Together, these findings indicate that GBA1 deficiency has cell type-specific effects, with increased neuronal vulnerability to endolysosomal trafficking leading to -synucleinopathy while GBA1 deficiency in astrocytes leads to increased neurotoxic reactivity independent of endolysosomal trafficking and -synucleinopathy. HighlightsO_LIiPSC-derived neurons and astrocytes modeled GBA1 deficiency C_LIO_LIEndolysosomal trafficking defects occurred only in GBA1-deficient neurons C_LIO_LI-synuclein oligomers accumulated in GBA1-deficient neurons, not astrocytes C_LIO_LIAstrocyte GBA1 loss drove neurotoxic reactive gene signatures C_LIO_LIGBA1 deficiency causes cell-type specific pathology C_LI

neuroscience↗

bioRxiv2026

Computational design of orthogonal TCR α/β interfaces for dual-TCR therapeutics

T-cell receptors (TCRs) recognize peptides presented by MHC, enabling access to intracellular targets that are largely inaccessible to antibodies and difficult to target with small molecules. Despite this potential, their inherent cross-reactivity limits tumor specificity, while single-antigen targeting provides limited coverage of intratumoral heterogeneity. Dual-TCR therapeutics comprising two distinct TCRs could enhance tumor specificity via combinatorial recognition while broadening coverage across heterogeneous antigens. However, practical development of dual-TCR therapeutics has been limited by /{beta} subunit mispairing that prevents efficient production and creates undesired binding properties. Here, we develop orthogonal TCR /{beta} interfaces that prevent subunit mispairing. Using computational multistate design and second-site suppressor strategies implemented in Rosetta, we identified over 250 TCR variants for experimental screening to assess protein stability and pairing fidelity. The top-performing designs achieved approximately 95% correct pairing, as validated by mass spectrometry and X-ray crystallography. Focusing mutations on constant domains and conserved framework regions of variable domains enabled broad applicability across diverse TCRs while preserving antigen recognition. Using these orthogonal interfaces, we developed trispecific T-cell engagers (TriTEs) that target two cancer-testis antigens and CD3 on T cells, demonstrating enhanced potency under dual-antigen engagement (EC50 of 380 fM) while maintaining high activity when targeting cells displaying a single antigen (EC50s of 48 pM and 20 pM). This orthogonal TCR interface technology establishes a generalizable platform for engineering multi-specific immune therapeutics targeting diverse cancer antigens.

bioengineering↗