Biology subjects

Jiang, M.

Publications and source records attributed to Jiang, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Testis-Specific MAGEA3/6 Regulate Glycolysis to Promote Metabolic Flexibility and Reveal Therapeutic Vulnerabilities in Pancreatic Cancer Cells

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive tumor characterized by metabolic plasticity that enables cancer cells to survive nutrient deprivation and therapeutic stress. Melanoma-associated antigens A3 and A6 (MAGEA3/6), members of the cancer-testis antigen family with a previously identified protective role in spermatogenesis during nutritional stress, have been implicated in cancer progression and metabolic regulation. However, their contribution to metabolic adaptation in pancreatic cancer remains poorly understood. Here, we investigated the molecular mechanisms underlying MAGEA3/6-mediated resistance to glycolytic inhibition using complementary gain- and loss-of-function models, pharmacological inhibition of metabolic pathways, cellular metabolic assays, and integrated transcriptomic, proteomic, metabolomic, and lipidomic analyses. MAGEA3/6 expression enhanced resistance to 2-deoxy-D-glucose (2-DG), with MAGEA6-expressing MIA PaCa-2 cells exhibiting a greater than 2.5-fold increase in the half-maximal inhibitory concentration (IC50). Conversely, MAGEA3/6 depletion reduced clonogenic growth and migration and increased sensitivity to 2-DG. Resistance persisted despite pharmacological inhibition of mTORC1, the pentose phosphate pathway, or glutaminase, suggesting metabolic adaptations beyond these pathways. Unexpectedly, MAGEA6 expression was associated with increased rather than decreased AMPK1 protein abundance, contrasting with previously reported MAGEA3/6-mediated AMPK degradation and suggesting context-dependent regulation of this master regulator of cellular metabolism. MAGEA6 also reduced hexokinase HK1 and HK2 abundance while increasing several downstream glycolytic enzymes, revealing discordant regulation of glycolysis. Seahorse analyses and integrated multi-omics profiling identified extensive remodeling of mitochondrial metabolism, glutamine-aspartate metabolism, phospholipid composition, lipid storage, and redox homeostasis. Interestingly, despite enhanced resistance to glycolytic inhibition, MAGEA6-expressing cells exhibited increased sensitivity to hydrogen peroxide-induced oxidative stress, revealing a potential metabolic vulnerability. Given that MAGEA3/6 are physiologically expressed primarily in the male germline during early spermatogenesis, a process highly sensitive to metabolic and oxidative stress, these findings also raise important questions about their physiological roles in protecting developing germ cells and maintaining metabolic and redox homeostasis. Together, our findings recognize MAGEA3/6 as regulators of metabolic plasticity in PDAC and highlight how understanding their molecular functions in both spermatogenesis and cancer may uncover previously unrecognized metabolic vulnerabilities and potential therapeutic opportunities.

cancer biology↗

bioRxiv2026

Scalable Enzyme Reaction Retrieval Enables Metagenomic Biocatalyst Discovery

Enzyme catalyzed reactions drive metabolism and enable diverse applications in biotechnology and sustainable synthesis, but assigning catalytic functions to uncharacterized enzymes and finding enzymes for target reactions remain major challenges. Despite recent advances in machine learning, translating enzyme function prediction into systematic discovery across the vast space of uncharacterized proteins and biochemical reactions remains challenging. Here we present EzHit, a lightweight framework for bidirectional enzyme reaction retrieval. Across enzyme annotation, orphan-reaction retrieval and family-specific fine-tuning benchmarks, EzHit achieved strong top-ranked performance and outperformed representative enzyme reaction matching baselines. We further show that Mahalanobis distance based geometric confidence provides more useful reliability estimates than probability-derived uncertainty metrics or evidential learning, enabling confidence-aware prioritization of high scoring candidates. Owing to its efficiency, EzHit was applied to a nearly trillion-scale OMG_Prot50 with RHEA screen, yielding 8.20 billion retained enzyme reaction associations across 30.27 million predicted enzyme sequences. Experimental validation further confirmed the activity of EzHit prioritized metagenomic enzyme candidates for a sparsely annotated reaction. Together, these results establish EzHit as a scalable framework for enzyme annotation, reaction-guided mining and biocatalyst discovery

bioinformatics↗

bioRxiv2026

Functional recovery of vitrified and nanowarmed human-scale pig kidneys

Organ transplantation is critically constrained by the short preservation window for donor organs, limiting allocation and contributing to organ discard and waitlist mortality. Cryogenic organ banking could extend preservation from hours to months or years, but ice formation, thermal stress and cryoprotectant toxicity become increasingly difficult to control as organ size increases. Vitrification and nanowarming have enabled long-term preservation and transplantation of rodent kidneys but have not been demonstrated at the scale of clinically relevant organs. Here we show that vitrification and electromagnetic nanowarming enable long-term cryogenic storage and functional recovery of human-scale porcine kidneys. Kidneys 100-fold larger than previously nanowarmed kidneys were successfully recovered after storage at -150 {degrees}C for up to one year. A new cryoprotectant formulation and multithermic perfusion strategy enabled ice-free vitrification at cooling rates achievable in large kidneys, while controlled cooling with annealing and staged volumetric nanowarming limited thermal stress and enabled rapid rewarming without cracking. Rewarmed kidneys demonstrated vascular, metabolic and excretory function during normothermic perfusion, with limited histological injury, and reperfused homogeneously and produced urine immediately after transplantation. Functional recovery approached static cold storage outcomes across several measures and was similar to that of kidneys exposed to cryoprotectant alone, suggesting minimal additional functional injury from vitrification, cryogenic storage and nanowarming. These findings overcome major scale and storage-duration barriers to organ cryopreservation and establish a path toward organ banking on timescales far beyond those of conventional preservation.

bioengineering↗

bioRxiv2026

SMYD3 protein degraders in HPV-negative head and neck squamous cell carcinoma.

Despite the advent of immunotherapy in the treatment of human-papilloma-virus (HPV)-negative head and neck squamous cell carcinoma, the overall prognosis still remains dismal. Novel therapeutic approaches are thus urgently needed. We recently reported that SET and MYND containing 3 (SMYD3), a protein methyltransferase that is known to activate the transcription of its target genes through H3K4me3, is overexpressed in ~60% of HPV-negative HNSCC tumors, it drives proliferation and invasion, and induces resistance to immunotherapy in HPV-negative HNSCC. These phenotypes are mediated partially through transcriptional regulation of cell cycle, EMT and immune-related target genes by SMYD3. Despite its enzymatic inhibitory potency in HPV-negative HNSC cell lines, the commercially available SMYD3 inhibitors EPZ031686 and BAY-6035 demonstrated no in vitro phenotypic efficacy in these cell lines, supporting that SMYD3 exerts its oncogenic functions predominantly through catalytically-independent mechanisms. Thus, to effectively target SMYD3, we designed a series of SMYD3 proteolysis targeting chimeras (PROTACs). Treatment of HPV-negative HNSCC cell lines with SMYD3 PROTACs at nanomolar concentrations degraded SMYD3 effectively and induced a drastic decrease in the proliferative and invasive potential of HPV-negative HNSCC cells. One of the designed compounds, IAP-08, showed a promising DC50 at ~177nM with Dmax of ~90%, and effectively induced the formation of ternary complexes with SMYD3 and the XIAP E3 ligase. Furthermore, IAP-08 showed a favorable pharmacokinetic profile in vivo, underscoring the feasibility for further clinical development of this compound. Mass spectrometry analysis of IAP-08 supported its high specificity towards SMYD3. SMYD3 depletion by IAP-08 in HNSCC cells revealed transcriptional regulation of cell cycle, EMT- and type I IFN response genes, in contrast to SMYD3 inhibition which had only a weak transcriptional effect. In summary, we show that inhibition of the enzymatic activity of SMYD3 is not sufficient to repress its oncogenic activity and provide evidence that depletion through PROTACs effectively targets the oncogenic functions of SMYD3 in HPV-negative HNSCC.

cancer biology↗

bioRxiv2026

Compartmentalized Nanozyme Transduction Enables Regenerative Molecular Amplification for Multiplexed miRNA-Based Prostate Cancer Stratification

Circulating microRNAs (miRNAs) have emerged as promising liquid biopsy markers; however, their clinical translation is restricted by low abundance, biological heterogeneity, and the complexity of multiplex profiling. Herein, we develop a targeted cycling-mediated duplex-specific nuclease (DSN)-nanozyme signal amplification platform (TC-DSN-Nano) that establishes a compartmentalized catalytic transduction strategy for multiplexed miRNA analysis. By encapsulating gold nanozymes within liposomal nanoreactors, this platform spatially separates molecular recognition from catalytic signal generation, preserving nanozyme activity during sensor construction. Upon target miRNA recognition, DSN-mediated recycling induces regenerative release of nanozyme-loaded liposomes from magnetic substrates, converting individual miRNA molecules into amplified catalytic outputs without conventional nucleic acid amplification. The platform enables programmable profiling of six prostate cancer (PCa) associated miRNAs in serum samples. Furthermore, machine learning-assisted integration of multiplexed miRNA signatures enables accurate discrimination among healthy donors, nonmetastatic PCa patients, and metastatic PCa patients, achieving an overall classification accuracy of 90.5%. This work establishes a general compartmentalized nanozyme transduction framework that integrates molecular recycling, catalytic amplification, and computational analysis for liquid biopsy-based cancer stratification.

bioengineering↗

bioRxiv2026

Distinct Spatial Immune Architectures in Tumor and Tumor-Adjacent Tissues of Early-Stage Non-Small Cell Lung Cancer

Background: Lung cancer remains the leading cause of cancer-related deaths in the United States with over 124,000 estimated deaths for 2026. Previous studies have found that tumor-adjacent lung tissues may provide additional insight into the immune microenvironment of early-stage NSCLC. Methods: Multiplex immunofluorescence (mIF) imaging was performed on 192 tissues from 101 early-stage non-small cell lung cancer patients including 91 matched tumor-adjacent pairs, using three mIF panels. Spatial analyses were performed to identify distinctions between tissues and identify associations with clinical and genomic features. Results: Tumor tissue showed significantly higher densities of T cells, macrophages, B cells, and memory/regulatory populations than adjacent tissue (p<0.001). Tumors exhibited greater spatial heterogeneity, with higher prevalence of spatial patterning (47.7% vs. 31.2%) and more consistently localized organization, whereas adjacent tissue showed stronger individual-cell clustering. Pairwise colocalization (Ripley's L-cross) revealed selective spatial segregation in tumors (including B-cells from memory/regulatory cells and among cytotoxic T-cell subsets) and reduced immune proximity to malignant cells relative to the strong immune-epithelial association in adjacent tissue. Spatial features were linked to genomic features or patient outcomes: tumor neoantigen burden exhibited a positive association with CD3+ T cells in the tumor, while colocalization between CD45RO+CD57+GZMB+ cells and CD57+GZMB+ cells was negatively associated with overall survival outside the tumor. Conclusion: Tumor and adjacent tissues harbor distinct spatial immune architectures, with spatial features displaying associations with genomic features or patient outcomes. These findings highlight immune microenvironment reorganization and the importance of incorporating spatial context from both compartments into risk assessment in NSCLC.

immunology↗

bioRxiv2026

Early-Stage Cultures of Acidithiobacillus ferrooxidans Enable Efficient Bioleaching of Li-ion Battery Cathode Material

In response to the growing need to recycle E-waste, specifically that of lithium-ion batteries (LIBs), the development of sustainable recycling methodologies will be vital. As one of the most sustainable and low-cost options, biohydrometallurgy (BioHM) uses biological organisms to facilitate the recovery of critical metals from spent LIBs. Despite the advantages of BioHM, its slow kinetics, due to the reliance on the metabolic activity of microorganisms, limit its large-scale application for the closed-loop recycling of LIBs. In this work, we investigate the correlation between the incubation time of Acidithiobacillus ferrooxidans (Atf) and its leaching efficiency of four common elements in LIBs: Li, Ni, Mn, and Co. We assess how specific incubation times along the biological growth curve affect the leaching efficiency of Li[Ni0.6Mn0.2Co0.2]O2 (NMC622), a model electrode material. Our results show that pH alone is not an accurate descriptor of the leaching efficiency of Atf cultures used at different growth stages. The addition of NMC622 during the bacterial lag phase reaches similar or even improved extraction compared to cultures used after reaching the exponential or stationary phases. A simple model of leaching dynamics shows predictions consistent with our experimental observations under the condition that the inhibition of bacterial growth by NMC is not severe. Our findings indicate that early-stage cultures can alleviate the kinetic bottleneck and improve the throughput of recovering critical materials from spent batteries.

microbiology↗

bioRxiv2026

Cross-Species Efficacy of Combinatorial Gene Therapy for Osteoarthritis and Correction of Neuro-Inflammatory Pain Mechanisms

Osteoarthritis is a leading cause of chronic pain and disability, which lacks disease-modifying treatment. Given the complex multi-tissue and multifactorial drivers behind disease progression, effective treatments will require simultaneously targeting several mechanisms underlying joint degeneration and pain. Here, we developed and evaluated a combinatorial gene therapy, consisting of a high-capacity adenoviral vector carrying two therapeutic genes to target distinct pathological mechanisms: inflammation (IL-1Ra) and chondrocyte health (PRG4). Intra-articular delivery of this treatment improved functional, structural, and pain outcomes in murine and equine osteoarthritis models. In addition, treatment normalized inflammatory environments in joint tissues, as well as in the dorsal root ganglia (DRG) known to harbor joint-innervating sensory neurons. Moreover, gene therapy reversed OA-induced molecular signatures of neural hyperexcitability, suggesting amelioration of peripheral sensitization. Collectively, these findings support combinatorial gene therapy as a promising treatment for osteoarthritis, while identifying neuroinflammatory signatures for correction of disease progression and pain. One Sentence SummaryA single intra-articular injection of a combinatorial gene therapy slows OA progression and reduces pain in small and large animal models.

systems biology↗

bioRxiv2026

Ribosome-tethered in situ sequencing for single-cell translatome analysis

Translational regulation plays a critical role in shaping cellular states and functions, yet approaches for spatially resolved translatome profiling at single-cell resolution remain limited. Here, we develop Ribosome-tethered In Situ Sequencing (Ribo-ISS), an imaging-based spatial translatomics technology that enables high-throughput mapping of ribosome-associated mRNAs in intact tissues. Ribo-ISS integrates ribosome-dependent molecular anchoring with multiplexed in situ sequencing, allowing specific detection of translation-associated transcripts without genetic manipulation or exogenous ribosome labeling. We demonstrate that Ribo-ISS achieves high specificity and enables single-cell spatial translatome profiling in mouse brain, accurately recapitulating major cell types and their anatomical organization. Applied to a sleep deprivation model, Ribo-ISS simultaneously resolved transcriptional and translational changes, revealing extensive transcription-translation uncoupling and distinct cell-type-specific translational responses. Ribo-ISS provides a scalable framework for investigating spatially organized translational programs and expands the capability of spatial omics toward understanding gene regulation beyond transcription. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/740970v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@40da8dorg.highwire.dtl.DTLVardef@1cc76b4org.highwire.dtl.DTLVardef@8535c8org.highwire.dtl.DTLVardef@18e009d_HPS_FORMAT_FIGEXP M_FIG C_FIG Ribo-ISS integrates ribosome-dependent molecular anchoring with multiplexed in situ sequencing, enabling specific detection of ribosome-bound transcripts in intact tissues without genetic manipulation or exogenous labeling. As an imaging-based spatial translatomics technology, it resolves translatome profiling at single-cell resolution. This scalable approach reveals spatial translational programs, extending spatial omics beyond transcription.

molecular biology↗

bioRxiv2026

Cryoaerosolization Enables Scalable Vitrification-Based Cell Cryopreservation

Cell therapies hold transformative potential for treating cancer, neurologic disorders, organ failure, diabetes, and other conditions, but their widespread clinical deployment is constrained by the lack of scalable cryopreservation methods that maintain high post-thaw viability. Current standard practice using slow freezing can lead to cell death and impaired cell function. Vitrification offers an alternative by cooling samples rapidly enough to bypass ice formation entirely, better preserving cell structure and function. The high cooling and warming rates required for vitrification have previously been achieved by quenching microliter-scale samples directly into convective cooling and warming baths. Here, we present a cryopreservation platform that overcomes the throughput limitations of existing systems by combining a vibrating orifice aerosol generator with an impinging conical nozzle to generate and confine micrometer-scale droplets mid-flight in liquid nitrogen. This approach mitigates cooling losses due to the inverse Leidenfrost effect, increasing cooling and warming rates by nearly an order of magnitude compared to conventional droplet vitrification, while improving throughput by two orders of magnitude. To test the efficacy of this system, we cryoaerosolized and rewarmed human induced pluripotent stem cells, porcine red blood cells, and human dermal fibroblasts using only 190-25 wt% (2.5-3.7 M) permeating cryoprotective agent, achieving >90% post-thaw viability for HDFs and hiPSCs and 94% recovery for RBCs, with retained colony-forming capacity additionally demonstrated in hiPSCs. This work demonstrates the first scalable vitrification-based cryopreservation method capable of achieving both high cooling ({approx} 200, 000 K min-1) and warming rates ({approx} 1, 000, 000 K min-1) while maintaining the high-throughput processing required ([≥]100 mL h-1) for next-generation cell therapies. Significance StatementCell therapies require robust long-term storage methods to enable widespread clinical deployment. Current approaches utilizing refrigeration or small-scale vitrification cannot meet the scalability and viability requirements for next-generation therapeutics. In this work we demonstrate a cryoaerosolization process that achieves both ultra-rapid cooling rates (>200,000 {degrees}C min-1) and high throughput (>100 mL h-1) by generating micrometer-scale droplets and spraying in a liquid nitrogen impingement stream. Using only as little as 19 wt% cryoprotectant, we achieved >90% cell viability and maintained function, comparable to low-throughput methods, but at two orders of magnitude higher processing rates. We also introduce a just-in-time CPA loading approach that reduces toxicity exposure. This technique enables scalable vitrification-based cryopreservation of large-volume cell products.

bioengineering↗

bioRxiv2026

RBM6-mediated alternative splicing facilitates the adaptation of Eurasian avian-like H1N1 swine influenza virus

The Eurasian avian{square}like (EA) H1N1 swine influenza virus (SIV), derived from avian influenza viruses (AIV), poses a serious threat to public health due to its capacity for cross{square}species transmission and pandemic emergence. The molecular determinants underlying its replication advantage over AIV remain poorly defined. Here, we identify RNA{square}binding motif protein 6 (RBM6) as a novel host factor that differentially regulates the replication of EA H1N1 SIV and AIV. Mechanistically, RBM6 binds to the critical M901 site of the viral M segment, thereby modulating RNA splicing. Substitution of M901C with M901T markedly reduced RBM6 binding, impaired M segment splicing, and attenuated viral replication both in vitro and in vivo. Conservation analysis revealed that M901T is common in avian strains, whereas M901C is predominantly maintained in swine strains, underscoring M901C as a determinant of swine adaptation. Complementation experiments further demonstrated that swine RBM6, but not avian RBM6, restored EA H1N1 SIV replication. Taken together, our findings uncover a previously unrecognized role of RBM6 in shaping influenza virus replication and highlight the RBM6-M901C axis may serve as potential targets for controlling influenza virus adaptation and interspecies transmission.

microbiology↗

bioRxiv2026

Conditional Deletion of All Neurexins Defines Diversity of Essential Synaptic Organizer Functions for Neurexins

Presynaptic neurexins are key regulators of synapse properties that arguably represent the best-studied synaptic adhesion molecules. Despite thousands of papers, however, no direct comparison of overall neurexin functions in different types of synapses is available. A decade ago, we provided such an analysis but we recently retracted this paper because four images contained microduplications that, although without discernible impact on the paper's conclusions, could not be corrected. As a result, the scientific community lost access to primary data that established the fundamental principle that neurexins perform profoundly different functions in different types of synapses. In the present study, we have therefore reanalyzed the original raw data and expanded their conclusions with new experiments to document, in a single study, the basic contributions of neurexins to different synapses. We used triple conditional knockout mice targeting all neurexins except for Neurexin-1r and applied neuron-specific manipulations combined with slice electrophysiology, two-photon Ca2+-imaging, and immunohistochemistry. With this approach, we focused on excitatory climbing-fiber synapses in the cerebellum and on inhibitory synapses formed by parvalbumin- or somatostatin-positive neurons in the cerebellum, hippocampus, and medial prefrontal cortex. Our results show that pan-neurexin deletions produce dramatically different phenotypes in synapses, ranging from modest to massive impairments in synapse assembly (climbing-fiber and parvalbumin-positive synapses) to severe but selective decreases in action potential-induced presynaptic Ca2+-transients (somatostatin-positive synapses). Thus, neurexins perform powerful but distinct context-dependent roles in different synapses that shape the brain's circuits.

neuroscience↗

bioRxiv2026

Specific F1 ATP synthase inhibition delivers transient mitochondrial stress for selective targeting of acute myeloid leukemia

Targeting oxidative phosphorylation (OXPHOS) represents an attractive therapeutic strategy in acute myeloid leukemia, which exhibits exceptional dependence on mitochondrial respiration compared to normal hematopoietic cells. However, clinical attempts to exploit this vulnerability have been limited by on-target toxicity to healthy tissue. Here, we comprehensively compare the cellular consequences of inhibiting distinct nodes of the electron transport chain in AML. We demonstrate that selective inhibition of the F1 subunit of ATP synthase with EB2023 (ammocidin A) delivers an energetic stress to AML cells without the profound redox stress that characterizes complex I inhibition, preventing NAD/NADH imbalance and allowing continued TCA cycling. Further, the duration of OXPHOS inhibition is transient in nature in vivo, a finding revealed through pharmacokinetic and serial pharmacodynamic monitoring of AMPK phosphorylation accompanied by OPA1-mediated mitochondrial structural remodeling that primes AML cells for BCL2 inhibitor synergy. EB2023 in combination with venetoclax demonstrates potent anti-AML activity across cell lines and patient-derived xenograft models at doses that spare normal hematopoietic progenitors and avoid the neuropathy and sustained detrimental systemic metabolic rewiring in healthy tissues associated with prior efforts to target OXPHOS. These findings establish F1-selective ATP synthase inhibition as a clinically actionable therapeutic strategy in AML and establish the duration of OXPHOS inhibition as a critical and previously underappreciated determinant of therapeutic index.

cancer biology↗

bioRxiv2026

Lactylation of Influenza Virus Polymerase Acidic Protein Promotes Viral Replication and Pathogenicity

Influenza virus poses a potential risk of triggering the next global pandemic. In-depth investigation into the mechanisms underlying influenza virus replication and pathogenicity will provide robust support for controlling influenza virus infection. Although post-translational modifications are known to regulate viral infection, the role of lactylation in influenza virus replication remains elusive. In this study, influenza virus ribonucleoprotein complex subunits are found to be lactylated. Specifically, ATAT1 promotes viral polymerase acidic protein (PA) lactylation and enhances viral replication. In contrast, SIRT1 mediates de-lactylation of PA and exerts an inhibitory effect on viral replication. Further investigations reveal lactylation of PA at residues K605 and K609 is essential for viral replication and pathogenicity. Mechanistically, PA K605/609 residues are localized at the interaction interface of the ANP32-mediated polymerase asymmetric dimer; mutation at these residues inhibits polymerase asymmetric dimerization, thereby impairing RNA production during viral genome replication. Collectively, this study uncovers a novel mechanism by which influenza virus hijacks host enzymes to mediate PA lactylation, and expands the molecular regulatory network of influenza virus infection.

microbiology↗

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

Phenotype-first covalent fragment screening identifies a synthetic lethal TYMS inhibitor in ATRX-deficient cells

Chemoproteomic mapping of covalent fragment libraries is expanding the ligandable human proteome with direct evidence of cellular target engagement. However, understanding the functional consequences of specific covalent modifications typically requires extensive downstream biological characterisation. Here we present a phenotype-first approach that integrates covalent fragment screening with chemoproteomics and genetic deconvolution in a disease-relevant context. Using isogenic ATRX wild-type and knockout eHAP iCAS9 cells, we screened a library of around 500 cysteine-reactive fragments for differential cell killing and identified a chloroacetamide fragment, PP12, that selectively impairs the viability of ATRX-deficient cells. By combining competitive click-chemoproteomics with genome-wide CRISPR synthetic lethal datasets, we identified thymidylate synthase (TYMS) as a phenotypically relevant target of PP12. Target validation was supported by crystallography, competition with the active-site inhibitor 5-fluorouracil, and impaired dTMP synthesis in cells. Mechanistically, TYMS inhibition induces replication stress that is selectively cytotoxic to ATRX-deficient cells and is dependent on FAM111A and SLFN11. This work establishes a generalisable workflow linking covalent fragment phenotypes to target deconvolution using chemoproteomics and mechanistic validation.

cell biology↗

bioRxiv2026

Quercetin Promotes Adipose Thermogenesis and Metabolic Health

The activation of thermogenesis in brown adipose tissue (BAT) represents a pivotal target for ameliorating disorders of glucose and lipid metabolism. This study sought to elucidate the regulatory effects of quercetin on thermogenesis and glucose-lipid metabolism within brown adipocytes, alongside its underlying molecular mechanisms. The findings demonstrated that quercetin markedly upregulated the expression of uncoupling protein 1 (UCP1), a critical thermogenic protein in brown adipocytes, thereby enhancing cellular thermogenic capacity and effectively mitigating glucose and lipid metabolism disorders. Subsequent mechanistic investigations confirmed that quercetin activated the COX2-PGE2-EP4-UCP1 signaling axis by augmenting the stability of cyclooxygenase 2 (COX2) protein, thus mediating its thermogenic-promoting and metabolism-improving effects. This study identifies quercetin as a potential therapeutic agent for the improvement of glucose and lipid metabolism disorders, uncovers a novel molecular mechanism through which quercetin regulates brown adipocyte thermogenesis, and provides a theoretical and experimental foundation for the application of quercetin in the prevention and treatment of obesity and related metabolic diseases.

molecular biology↗

bioRxiv2026

Interpretable Biological Sequence Clustering with iClust

Biological sequence clustering is a fundamental problem in bioinformatics, yet most existing methods mainly optimize clustering quality or efficiency while offering limited insight into why sequences are grouped together. This restricts their usefulness in downstream analysis, where representative sequences and clear cluster boundaries are often needed. To address this issue, we propose iClust, an interpretable clustering method that characterizes each cluster by a representative prototype and an adaptive radius. By adapting to local sequence structure rather than relying on a single global threshold, iClust produces clusters that are both meaningful and explainable. A final consolidation step further reduces tiny fragments and improves structural stability. Experiments on simulated and real biological sequence datasets show that iClust achieves competitive clustering performance while providing clearer cluster-level explanations than conventional threshold-based methods. In addition to its empirical impact as a practical clustering method for biological sequences, this article opens up new avenues for developing biological sequence clustering approaches from the viewpoint of interpretable machine learning.

bioinformatics↗