Biology subjects

Ding, C.

Publications and source records attributed to Ding, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Oncolytic Newcastle disease virus promotes tumor cell apoptosis through SUMO-1-dependent PRKN-mediated degradation of c-Myc

The oncogenic transcription factor c-Myc is aberrantly upregulated in many cancers and plays a central role in tumor cell proliferation and survival. However, direct pharmacological targeting of c-Myc remains challenging because of its intrinsically disordered structure. Newcastle disease virus (NDV) is an oncolytic virus with selective antitumor activity, but the molecular mechanisms by which NDV disrupts oncogenic signaling remain incompletely understood. Here, we show that NDV induces apoptosis in multiple tumor cell lines and suppresses tumor growth in an A549 xenograft model. NDV infection markedly reduced c-Myc protein levels in tumor cells in a time- and dose-dependent manner, and c-Myc knockdown further enhanced NDV-induced intrinsic apoptosis. Mechanistically, NDV promoted ubiquitin-proteasome-dependent degradation of c-Myc through ubiquitination at Lys142. Screening of candidate E3 ubiquitin ligases identified PRKN as a key mediator of NDV-induced c-Myc degradation. NDV infection induced SUMO-1-dependent nuclear translocation of PRKN, allowing PRKN to interact with nuclear c-Myc and promote its degradation. Disruption of this pathway by SUMO-1 or PRKN knockdown impaired PRKN nuclear accumulation, restored c-Myc stability, and attenuated NDV-induced apoptosis. Functionally, expression of the degradation-resistant c-Myc K142R mutant or restoration of c-Myc in c-Myc-knockdown cells protected tumor cells from NDV-induced apoptosis. Together, these findings identify a SUMO-1-PRKN-c-Myc signaling axis that mediates NDV-induced tumor cell apoptosis and reveal c-Myc destabilization as an important mechanism underlying the oncolytic activity of NDV.

cell biology↗

bioRxiv2026

Land use and climate warming interact to reshape global avian biodiversity through ecological filtering and homogenisation

Land-use and climate change are dominant drivers of terrestrial biodiversity change, yet are usually analysed separately although they co-occur and may interact. We integrated global bird assemblage records from PREDICTS with temperature anomalies and species' ecological characteristics to test how land use modifies biodiversity responses to climate warming across three dimensions: local abundance and richness, compositional dissimilarity among assemblages, and species occurrence across ecological groups. Land use modified warming associations for both abundance and richness. Relative to primary vegetation, warming associations were more positive in low-intensity agriculture for both responses, but more negative for richness in high-intensity agriculture and urban land. Predicted richness remained below the reference, defined as primary vegetation at temperature anomaly 0, across all modified land uses, with the largest declines in high-intensity agriculture (-17.9%) and urban land (-21.8%). Within land-use classes, greater warming exposure was generally associated with higher compositional similarity, consistent with warming associated biotic homogenisation. Occurrence models revealed ecological filtering: broad-niched generalists were favoured in warmer modified habitats, whereas range-restricted habitat specialists were filtered out under intensive land use and warming. Conservation assessments should therefore integrate land-use-warming interactions with changes in assemblage composition and ecological strategies, particularly in agricultural and urban landscapes where warming further disadvantaged range-restricted specialists.

ecology↗

bioRxiv2026

A comprehensive atlas of somatic mutation rates and mutational signatures in normal human cells

Over the course of a lifetime, somatic mutations accrue in normal human cells, causing variation in cell phenotype and engendering somatic evolution with outcomes ranging from the adaptive immune system to cancer. To inform understanding of somatic evolution in the human body we report the mutation rates and mutational signatures of 53 normal cell types. Most show evidence of linear mutation accumulation over time with single base substitution mutation rates ranging from ~3.5/year/diploid genome in spermatogonia and sperm, to ~20/year in postmitotic neurons, ~50/year in mitotically active colorectal epithelial cells, ~60/year in kidney proximal tubule cells and hepatocytes, 100s/year in sun-exposed skin epidermal cells and 10-50/year in the remainder. Certain cell types, including skin epidermis, cardiac myocytes, bladder urothelium, kidney proximal tubule cells, and hepatocytes, show substantial variability in mutation burdens around the linear age trend, indicating the influence of additional factors which differ between individuals and modulate mutation accumulation, including exogenous mutagen exposures. At least 18 single-base substitution and nine small insertion and deletion mutational signatures are present, some in all cell types, some in a subset and others in a single cell type. Known exogenous mutagen exposures and endogenous mutational processes account for some mutational signatures, but the origins and mechanisms underlying many are uncertain. This comprehensive survey of mutagenesis provides a foundation for understanding somatic evolution of human cell populations in health and disease.

genomics↗

bioRxiv2026

Plasma titration provides a physical ruler for cross-platform proteomics

Plasma proteomics is expanding across platforms and cohorts, and integrating these data for AI demands comparability at the protein level, not merely concordant associations1,2. Affinity and MS platforms use distinct probes (antibodies, aptamers, or peptides) and signal readouts, yielding contradictory cross-platform results3,4. Without a known quantitative truth, we cannot distinguish biology from measurement distortion, leaving no gold standard for integration. Here we introduce Plasmix--a plasma reference suite with predefined male:female ratios (M, 1:0; Y, 3:1; P, 1:1; X, 1:3; F, 0:1)--and show that preserving this quantitative titration gradient, not just technical repeatability, predicts cross-platform concordance and identifies protein measurements suitable for integration. Profiling Plasmix across five platforms (Olink, SomaScan, NULISA, AAgAtlas, and MS-DIA) and 12 protocols across 17 batches, we found discordance is dominated by signal generation, not sample identity, and platforms distort signals in a protein-specific manner. Crucially, proteins retaining the titration response showed stronger agreement in an independent cohort; anchoring to the Plasmix midpoint (P) via sample-to-reference ratios reduced distortions, extending harmonizable coverage by 10-20%. Plasmix thus provides a physical ruler to benchmark accuracy, identifying genuinely integrable measurements before pooling datasets or training AI models--a critical bottleneck for plasma proteomics.

molecular biology↗

bioRxiv2026

Rational antigen engineering and mucosal delivery design for next-generation RSV vaccines

Respiratory syncytial virus (RSV) prefusion F (preF) vaccines have transformed adult prophylaxis, yet unmet needs in antigen stability, pediatric safety, and mucosal protection persist. Here, we develop an integrated structure-guided RSV vaccine design platform that couples allosteric stabilization, epitope-focused immunogen engineering, and route-specific mRNA delivery for systemic and mucosal immune activations. By mapping prefusion F "breathing" motions and applying a ThermoNet-and Rosetta-guided screening funnel, we identified R296, a stabilized prefusion F immunogen that reinforces the 1-5 hinge and interprotomer interfaces while preserving key neutralizing epitopes. Cryo-EM confirmed that R296 retains a native-like prefusion architecture. And mRNA-LNP vaccination elicited potent, durable, and broadly protective neutralizing responses in mice, rats, and cotton rats, with clearance of detectable infectious virus and no evidence of Th2-skewed enhanced respiratory disease. To address pediatric safety, we designed a stalkless nanoparticle immunogen, Head38-50AB-3, which enriches high-potency apical epitopes while excluding stalk regions associated with low-potency or non-protective responses, conferring protection without VAERD-like pathology. Finally, we engineered an intranasal-delivered LNP that enables intranasal R296 mRNA delivery, inducing systemic neutralization together with robust nasal and bronchoalveolar secretory IgA (sIgA). R296 has now advanced to Phase 1 clinical trials. These results establish a modular framework for next-generation RSV vaccines.

microbiology↗

bioRxiv2026

Tumor-derived stearic acid induces macrophage Egr2 signaling to suppress anti-tumor immunity in breast cancer

BackgroundMacrophages in breast cancer are highly heterogeneous and targeting both tissue-resident and bone marrow-derived macrophages represents a high-potential strategy in breast cancer immunotherapy. MethodsMyeloid-specific Egr2 knockout (KO) mice were used to determine roles of macrophage Egr2 signaling in tumor progression and anti-tumor immune responses. RNA-seq analysis and Flow cytometry were used to examine regulation of Egr2 in tumor-associated macrophages (TAMs) and fatty acid-stimulated macrophages. Tumor cell and macrophage admixture study was used to evaluate effects of fatty acid educated macrophages on anti-tumor responses. ResultsHere we showed that early growth response 2 (Egr2) was highly expressed in mammary tissue macrophages and recruited macrophages upon tumor progression. Depletion of Egr2 in myeloid cells significantly decreased the immunosuppressive function of polarized M2-like macrophages and TAMs. Tumor progression was delayed in myeloid cell Egr2 knockout mice, which was associated with enhanced function of effector CD8+ T cells and NK cells. Mechanistically, we showed that retinol and nicotinamide metabolism in TAMs were impaired after Egr2 depletion. Further, tumor cell-derived stearic acid (SA) was identified as an important fatty acid inducing Egr2 expression. SA stimulation induced macrophage-mediated immunosuppression in an Egr2 dependent manner. Addition of oleic acid (OA) uniquely repressed SA-induced Egr2 expression and immunosuppressive activity in macrophages. ConclusionsOur study thus uncovers a novel SA-Egr2 pathway driving macrophage immunosuppression and novel molecular mechanism of OA mediated anti-tumor effect. WHAT IS ALREADY KNOWN ON THIS TOPICLipid-associated macrophages (LAMs) accumulate lipids and promote immune suppression, tumor growth and metastasis in breast cancers. Fatty acids play a dual, complex role in tumor immunity, acting as both pro-tumorigenic and anti-tumorigenic effects. However, molecular mechanisms underlying fatty acid modulated macrophages and their roles in tumor remain not fully elucidated. WHAT THIS STUDY ADDSWe demonstrate that Egr2 is essential for the immunosuppressive function of IL-4 polarized M2-like macrophages and TAMs. Tumor cell-derived stearic acid (SA) was identified as an important fatty acid inducing Egr2 expression and immunosuppression in macrophages. Adding oleic acid (OA) uniquely repressed SA-induced Egr2 expression and immunosuppression. HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYSA-Egr2 axis is a novel pathway driving macrophage immunosuppression. OA treatment enhances macrophage anti-tumor immunity via inhibiting Egr2 signaling and immunosuppression. The data supports the notion that diets enriched in OA may have potential for prevention and suppression of breast cancer.

immunology↗

bioRxiv2026

Coronavirus papain-like protease antagonizes innate immunity by cleaving Importin α1 to disrupt nuclear transport

The Importin family, as key mediators of nucleocytoplasmic transport, represents a common target for viral immune evasion. However, whether coronaviruses directly manipulate Importin to disrupt nuclear trafficking and suppress antiviral immunity has remained unclear. In this study, we identify a previously unrecognized mechanism by which coronaviruses from all four genera subvert host innate immunity through the proteolytic inactivation of Importin 1, a key mediator of nuclear import of cargo proteins. We demonstrate that the membrane-associated papain-like protease (PLpro-TM) directly cleaves Importin 1 at specific glycine residues, G129 for PEDV and IBV PLpro, and G119 for MHV and PDCoV PLpro, thereby disrupting its nuclear import function. This cleavage impairs the nuclear translocation of multiple transcription factors (IRF3, STAT1, STAT2, and p65) and suppresses the expression of downstream antiviral genes, including IFN-{beta} and IFN-stimulated genes (ISGs). Importantly, cleavage-resistant mutants of Importin 1 (G129A or G119A) restore nuclear import capability and rescue IFN-{beta} signaling. Consequently, they exert a more potent inhibitory effect on viral replication than the wild-type Importin 1, fulfilling an antiviral role. Our work establishes PLpro-TM-mediated cleavage of Importin 1 as a conserved immune evasion strategy across coronaviruses and highlights this interaction as a potential target for broad-spectrum antiviral intervention. Author summaryThe nuclear transport of transcription factors is a critical checkpoint for the initiation of innate antiviral immunity. Here, we identify the PLpro-TM protein as a pan-coronavirus antagonist of nucleocytoplasmic trafficking and innate immune response. We demonstrate that PLpro-TM from four distinct coronavirus genera directly cleaves Importin 1 at specific glycine residues, thereby disabling its ability to mediate the nuclear import of key transcription factors and subsequent transcription of anti-viral genes. This work reveals a previously unrecognized, evolutionarily conserved immune evasion strategy shared across , {beta}, {gamma}, and {delta} coronaviruses. By uncovering the proteolytic inactivation of Importin 1 targeting by PLpro-TM, our findings not only resolve a long-standing question about how coronaviruses disrupt nuclear trafficking, but also establish PLpro-TM and Importin 1 as promising targets for the development of broad-spectrum antiviral therapeutics against current and emerging coronaviruses.

microbiology↗

bioRxiv2026

The kinetochore proteins Ndc80 and Dsn1 are required for survival of postmitotic neurons

Dsn1 and Ndc80 are essential proteins of the kinetochore complex and required for chromosome segregation in dividing cells and for regulating development and microtubule dynamics in postmitotic neurons. With conditional deletion of floxed alleles, we here show that Dsn1 and Ndc80 are also required for the viability of postmitotic neurons, both in cultures of hippocampal and cortical neurons and in vivo in the retina. Loss of these proteins triggers apoptosis, as indicated by caspase cleavage and an increase in nuclear DNA breakage. The pro-survival function of the kinetochore components is distinct from that which was previously demonstrated for regulation of neuronal synaptogenesis. The microtubule-binding domain of Ndc80 is required for the synaptogenic functions but Ndc80 lacking this domain can nonetheless rescue the viability of neurons from which Ndc80 has been deleted. Similarly, whereas the synaptogenic function involves regulation of microtubules in axons and dendrites, a nucleus-localized Dsn1 is sufficient to rescue the viability of neurons from which Dsn1 has been deleted. Thus, postmitotic neurons retain a nuclear requirement for components of the kinetochore in order to prevent apoptosis.

neuroscience↗

bioRxiv2026

“Mapping of Gonadal Development in Cryptorchidism: UTF-1 and Germ Cell Dysgenesis”

Study questionHow does cryptorchidism affect germ cell development and UTF-1-mediated pluripotency potential at the time of orchiopexy? Summary answerCryptorchidism was associated with the following germ cell abnormalities: germ cell clustering with many cords/tubules lacking germ cells and reduced UTF-1 expression, suggesting limited germ cell differentiation into spermatogonia What is known alreadyCryptorchidism, affecting 1.6-9% of male newborns, is known to increase the risk of infertility and testicular cancer due to abnormal germ cell development. Germ cells and pluripotent stem cell gene, UTF-1, play critical roles in spermatogonia differentiation, self-renewal, and spermatogenesis. No prior study has evaluated the testicular development by immunohistochemically mapping of these cell populations, Study design, size, durationA cross-sectional study of 31 postnatal cryptorchid testis and 5 age-matched scrotal testicular biopsies obtained from UCSFs pathology department performed between 1993-2023. Participants/materials, setting, methodsSpecimens were grouped by age at surgery (6-18 months, 19 months-7 years, 8-12 years, and [≥]13 years) and testis location (palpable vs. non-palpable). Scrotal prepubertal testis biopsies were sourced through the Pedi-LIFE program, a fertility preservation research biobank, with at least one control per age group. Immunohistochemistry was performed to stain specimens for germ cell (DDX4, OCT4, TSPY), pluripotent cell marker (UTF-1), as well as other key testis cell markers (A-actin, AR, P450, Sox-9), with staining graded based on control expression levels. The number of germ cells per seminiferous tubule was quantified and compared across anatomical locations using appropriate statistical analyses. Main results and the role of chanceThis study included 36 specimens, comprising 31 cryptorchid testes (86%) and 5 scrotal control testes (16%). The cryptorchid group exhibited testicular dysgenesis and reduced germ cell expression, correlated with increased age and testis location. Qualitative assessment revealed reduced germ cell expression across all ages in cryptorchid testes. The number of germ cells per tubule was markedly reduced in cryptorchid compared with scrotal testes after 19 months of age for DDX4, TSPY, and UTF-1. Germ cell clusters were identified in 15 out of 31 cryptorchid specimens (48%) stained for DDX4 and TSPY. UTF-1 expression was lower in cryptorchid testes across all age groups. No significant differences were noted in other testicular cell markers. Large scale dataNA Limitations, reasons for cautionFirst, the power and generalizability of the study are limited by the availability of specimens within each age group, particularly for scrotal testes, as biopsies of these tissues are not routinely performed. Second, a cross-sectional study design limits a longitudinal comparison to evaluate changes in marker expression, delayed maturation, or irreversible germ cell loss. Third, immunohistochemistry data is semi-quantitative, and protein detection is affected by antibody sensitivity and tissue preservation and influenced by antibody sensitivity. Lastly, scrotal testis used as controls were obtained from cryopreserved tissue from patients with other unrelated pathology, which may influence histological profiles. Wider implications of the findingsCollectively, our findings support a model in which cryptorchidism involves both germ cell depletion and disrupted SSC lineage formation, with UTF-1 downregulation and germ cell clustering as early signatures of testicular dysgenesis. These features may help identify high-risk patients for worsening gonadal dysgenesis and infertility and can provide a rationale for earlier orchiopexy or SSC-preserving strategies. Study funding/competing interest(s)The authors declare no conflicts of interest and received no funding for this study. Data Availability StatementThe data underlying this article cannot be shared publicly due to ethical and legal restrictions related to the use of human tissue specimens, which may compromise donor privacy and confidentiality. Data are available from the corresponding author upon reasonable request and subject to institutional and ethical approvals.

Developmental Biology↗

bioRxiv2026

An ASXL3-thyroid hormone axis in parvalbumin interneurons controls autism-like behaviors

Pathogenic variants in ASXL3 underlie autism spectrum disorder (ASD), but how they perturb neural circuits and whether defects are reversible remain unclear. Here we show that Asxl3 haploinsufficiency in mice reduces cortical thickness and upper-layer projection neurons while increasing parvalbumin (PV) interneuron density and producing ASD-like behavioral abnormalities. Mechanistically, Asxl3 loss derepresses the thyroid hormone (TH)-inactivating enzyme DIO3 via altered histone H2A monoubiquitination, depleting brain TH. Conditional deletion of the TH receptor Thra in inhibitory neuron progenitors phenocopies the PV interneuron expansion, linking impaired TH signaling to PV circuit remodeling. Neonatal, but not adolescent, TH supplementation restores PV interneuron numbers and rescues behavior in Asxl3+/- mice, defining a critical early window for intervention. An intein-based AAV system that reconstitutes full-length ASXL3 normalizes cortical architecture and behavior in Asxl3+/- mice and drives efficient ASXL3 expression in non-human primate brain, establishing an ASXL3-TH-PV interneuron axis as a targetable pathway in ASD.

neuroscience↗

bioRxiv2026

iCNG99: a validated genome-scale metabolic model of Cryptococcus neoformans strain H99

Cryptococcus neoformans is a ubiquitous environmental fungus that can also cause life-threatening infections in immunocompromised individuals. As a competent pathogen, Cryptococcus needs to reprogram its metabolism to adapt to the drastic differences between environmental niches and host niches. A well-curated genome-scale metabolic model (GEM) is a powerful tool to facilitate the investigation of the metabolic resilience of an organism. Here we reconstructed and validated iCNG99, a GEM for C. neoformans reference strain H99, and evaluated its predictive performance across 43 growth conditions and gene essentiality benchmarks. The model achieved high confidence essential gene prediction (precision = 0.77) and recapitulated pathways targeted by clinically available antifungals. Integration with transcriptomic and metabolomic data enabled iCNG99 to capture condition-specific metabolic adaptations and to identify candidate vulnerabilities in drug tolerance, revealing metabolic adaptations associated with survival within host conditions and drug susceptibility. Together, iCNG99 provides a systems-level computational platform for investigating C. neoformans metabolism and for prioritizing antifungal vulnerabilities.

systems biology↗

bioRxiv2026

Systemic mutagen exposures reported by normal kidney cell genomes

Lifestyle, environmental and other exposures to exogenous mutagens generate somatic mutations in normal human cells in vivo and increase cancer risk. However, the global repertoire of exogenous mutagen exposures is uncertain. The mutational signatures of mutagens in normal tissues offer opportunities to detect such exposures and survey them at population level. Using single-molecule duplex sequencing of normal kidney (n=319) and blood (n=272) samples from 10 countries, we show that normal kidney cell genomes report an extensive repertoire of somatic mutational signatures. Microdissection of kidney structures revealed that proximal tubules exhibit higher mutation rates than other components of the nephron and most normal cell types despite low cell division rates. This is explained by marked enrichment of mutational signatures due to known exogenous carcinogenic mutagens including the plant-derived aristolochic acids, as well as several signatures of unknown causes including an unknown agent prevalent in Japan (SBS12), and signatures of uncertain origins (SBS40b and SBS40c). The results suggest the existence of multiple, common, systemically circulating mutagens affecting human populations and indicate that the genomes of kidney proximal tubule cells report such exposures with high sensitivity.

genomics↗

bioRxiv2026

A uniquely leptin sensitive hypothalamic neuron population limits hyperphagia and weight gain in diet-induced obesity

Despite widespread loss of leptin responsiveness in obesity, endogenous leptin continues to restrain feeding, yet the neural substrates that remain sensitive and mediate this effect are unknown. Combining spatial transcriptomics with single-nucleus RNA sequencing in mice with diet-induced obesity (DIO), we show that while most hypothalamic leptin receptor (Lepr) neurons minimally respond to elevated leptin, a single population defined by glucagon-like peptide-1 receptor (Glp1r) co-expression retains robust leptin sensitivity. These Lepr/Glp1r neurons project onto and restrain orexigenic Agrp neurons. Lepr deletion from Lepr/Glp1r neurons blocks the anorectic effect of exogenous leptin, reinstates hyperphagic responses normally suppressed in DIO, amplifies the obesogenic response to palatable diet, and unexpectedly attenuates hypothalamic microglial activation- a hallmark of DIO previously attributed to diet rather than leptin signaling. Hence, preserved leptin action through a single neuronal population governs downstream circuit activity to limit hyperphagia and weight gain during obesity.

molecular biology↗

bioRxiv2026

Quantal PCR: A Calibrator-Free Method for Determining the Unit for Nucleic Acid Quantification

Quantitative polymerase chain reaction (qPCR) is limited in measuring absolute nucleic acid copy numbers due to the inherent variability of calibrators. Here, we introduce the Quantal PCR (quPCR), a novel method that eliminates the need for calibrators by defining an intrinsic quantal unit derived from the thermodynamic and kinetic properties of the replication system. This approach first determines amplification efficiency at high template concentrations, which is then used as the replication probability to construct quantification cycle (Cq) distribution profiles. These profiles are compared with those from limiting dilution PCR to derive the Cq value for the minimal quantal-replication unit ("quCq"), enabling calculation of the sample copy number. Validation using a dual-target DNA template showed near-identical copy numbers using two distinct target-specific replication systems. Thus, quPCR represents a new method for absolute nucleic acid quantification at the single-molecule level, offering a calibrator-free alternative for absolute quantification.

biochemistry↗

bioRxiv2026

Selective targeting of type II tRNAs underlies SLFN14-mediated translational repression and its dysregulation by thrombocytopenia-linked mutations

Schlafens (SLFNs) are interferon-inducible regulators of RNA metabolism and cell fate. SLFN14 is a ribosome-associated endoribonuclease whose pathogenic variants cause autosomal dominant inherited thrombocytopenia (IT), but the underlying disease mechanism has been unclear. We show that SLFN14 represses global protein synthesis through selective cleavage of type II tRNAs. IT-linked mutations alter RNA substrate specificity, enhancing degradation of type II tRNAs while reducing rRNA cleavage. This shift promotes ribosome stalling at codons decoded by type II tRNAs, triggering global translational arrest, stress signaling, and cell death. These findings define the molecular basis of SLFN14-associated thrombocytopenia and highlight selective tRNA targeting as a mechanism regulating translation and cell fate.

molecular biology↗

bioRxiv2025

AAV-mediated CSNK2B gene replacement rescues ASD-relevant phenotypes and establishes EEG biomarkers for translation in Csnk2b haploinsufficient mice

De novo CSNK2B variants are strongly associated with autism spectrum disorder (ASD) and early-onset epilepsy, yet in vivo therapeutic evidence and translatable biomarkers remain limited. We generated Csnk2b haploinsufficient (Csnk2b+/-) mice that recapitulate core clinical features--ASD-like social and cognitive deficits, heightened anxiety, spontaneous seizures, cortical and hippocampal structural compromise, and reduced PV-interneuron density with impaired cortical inhibition. Neonatal brain-wide AAV-PHP.eB-mediated CSNK2B replacement (hsyn or CAG promoters, retro-orbital P3) restored cortical/hippocampal structure, normalized neuronal numbers, prolonged survival, and ameliorated seizures and ASD-like behaviors with comparable efficacy across promoters. Critically, treatment also corrected quantitative EEG signatures that are directly deployable in human trials: theta and gamma band power were normalized, theta/gamma (and beta/gamma) ratios recovered, and inter-areal coherence and gamma-band effective connectivity were restored, indicating re-established excitation/inhibition balance and large-scale network coordination. These EEG endpoints constitute a compact, noninvasive biomarker panel of target engagement and physiological efficacy that can be harmonized with clinical EEG to support dose finding, early decision-making, and longitudinal monitoring in CSNK2B gene-therapy trials. Together, our data provide preclinical proof-of-concept that early AAV-mediated CSNK2B replacement is therapeutically effective and nominate band-limited EEG metrics as translational readouts to accelerate first-in-human studies for CSNK2B-linked neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

A universal law of thermodynamics-kinetics coupling shapes enzyme allocation and glycolytic efficiency across species

Efficient use of limited cellular resources is fundamental to metabolism. Although flux optimization is widely recognized as a central objective of metabolic networks, how flux efficiency influences the allocation of the metabolic proteome remains unclear and lacks direct validation. Here, we derive a simple analytical relationship linking the equilibrium constant and the catalytic-abundance quotient of reactions within a pathway that defines the condition for maximal efficiency. We refer to this principle as the law of thermodynamics-kinetics coupling. By integrating reaction thermodynamics, enzyme kinetics, transcriptomic, and proteomic data, we show that glycolytic enzyme allocation consistently obeys this law across evolutionarily distant species. Moreover, the drive to optimize glycolytic efficiency is strengthened under oncogenic signaling and limited cellular budget for glycolytic enzymes. These findings establish a universal principle governing enzyme allocation in metabolic pathways and reveal key determinants of efficiency optimality in glycolysis. Significance statementCurrent models of metabolic optimality either rely on coarse-grained proteome allocation or constraint-based simulations, largely neglecting the fundamental constraints imposed by enzyme kinetics and thermodynamics on pathway efficiency. Here, we derive and validate a universal law of thermodynamics-kinetics coupling that robustly governs the allocation of glycolytic enzymes across species under optimal efficiency. This study has three major advances: it reveals universal economic principles of metabolism with simple, generalized mathematical form, uncovers determinants underlying the heterogeneity of metabolic efficiency optimization, and provides a practical blueprint for efficiency optimization of engineered pathways.

systems biology↗

bioRxiv2025

RABEP1 amplifies front signaling in neutrophil migration

Neutrophils are the first responders of our innate immune system, crucial for defense against various infections. The intricate regulation of neutrophil migration is essential for neutrophil function. However, a complete mechanistic understanding is missing. We performed a miRNA overexpression screen and identified miR-190 as a potent suppressor of neutrophil migration in zebrafish. Through a second round of small-scale screening using neutrophil-specific knockouts of putative miR-190 targets, we identified that rabep1 (Rabaptin-5, RAB GTPase binding effector protein 1) is essential for neutrophil motility and chemotaxis in zebrafish. Re-expressing full-length RABEP1 in the knockout, but not a truncated form lacking the Rab4/Rab5 binding domain, rescued cell motility. Knocking down RABEP1 in human dHL-60 cells consistently reduced cell motility. RABEP1-deficient dHL-60 cells accumulate excessive members inside the cells. The Rab5 GTP level is unaffected, but the RABEP1 knockdown cells displayed reduced PAK phosphorylation and overall reduced actin polymerization, but still appropriately polarized upon chemokine stimulation. Overexpression of dominant-negative Rab4 or Rab5 similarly inhibits neutrophil migration. Our data suggests that RABEP1 drives endosomal recycling, Rac activation, and leading-edge actin polymerization, providing significant insights into the role of the endocytic pathway in neutrophil motility.

cell biology↗