Biology subjects

Dai, Z.

Publications and source records attributed to Dai, Z..

At least 19 recordsLinked to original sources

bioRxiv2026

RAPPL-Seq Enables Rapid, High-Sensitivity Ribosome Profiling of Scarce Samples

Ribosome profiling is a powerful method for transcriptome-wide monitoring of translation activity in vivo, but its use is limited by lengthy protocols, reliance on specialized equipment and inefficient recovery of ribosome-protected fragments (RPFs). To overcome these challenges, we developed RAPPL-Seq, a magnetic bead-based affinity capture method that enables fast and efficient RPF isolation. RAPPL-Seq achieves high recovery efficiency, short processing time, and robust performance with limited input material. It is broadly applicable across multiple sample types, including cell lines, primary tissues, and human biospecimens. RAPPL-Seq can also be paired with translation inhibitors to characterize inhibitor- and tissue-specific mRNA translation. RAPPL-Seq efficiently captured translatomes of glioblastoma (GBM) and adjacent non-tumor brain tissues from patient biopsies. Together, these findings establish RAPPL-Seq as a straightforward, easily accessible, and highly sensitive approach that extends translatome studies to scarce experimental and clinical samples, opening new avenues for mechanistic insight and therapeutic discovery.

molecular biology↗

bioRxiv2026

Charting sex divergence in the human brain across the lifespan

Biological sex fundamentally shapes human brain organization, but sex-specific normative neuroanatomical trajectories across the lifespan remain largely uncharted. Here, we constructed independent, sex-specific lifespan brain charts using structural neuroimaging data from 59,915 healthy individuals (29,760 males and 30,155 females) ranging in age from 266 postconception days to 100 years. By examining 296 structural phenotypes across global, cortical, and subcortical measures, these models revealed widespread sex differences in maturational timing, with males reaching peak milestones later than females. These trajectories demonstrate that sex differences evolve dynamically, with phenotype-specific windows of emergence and maximal separation. Compared with conventional sex-pooled references, sex-specific models achieved superior predictive accuracy and reduced misestimation of individual deviations in healthy populations. Across five neuropsychiatric conditions, sex-specific models improved the detection of extreme deviations and revealed both shared and sex-dependent patterns of disorder-related neuroanatomical abnormalities. These sex-specific charts establish tailored normative references for assessing brain development, ageing, and disease.

neuroscience↗

bioRxiv2026

Forsythoside B attenuates neuropathic pain by suppressing USP7/HIF-1α-mediated microglial glycolytic reprogramming

Neuropathic pain involves spinal microglial activation and metabolic changes.Forsythoside B (FB) has anti-inflammatory effects, but its role in neuropathic pain and microglial glycolysis remains unclear. We investigated the effects and mechanisms of FB in mice with chronic constriction injury (CCI) and in LPS-stimulated BV2 microglia.FB reduced mechanical allodynia and thermal hyperalgesia in CCI mice. FB also reduced the spinal levels of HIF-1, HK2, PKM2, LDHA, and CD86. It decreased the proportion of IBA1+/CD86+ cells and the levels of IL-1{beta}, IL-6, and TNF-. In LPS20 stimulated BV2 microglia, FB reduced glycolysis-related proteins, proinflammatory markers, and cytokine release. FB also reduced glycolytic activity and partly restored basal mitochondrial respiration. FB did not change Hif1a mRNA levels. However, it Manuscript Click here to access/download;Manuscript;Manuscript.docx increased HIF-1 ubiquitination and promoted its proteasome-dependent degradation. HIF-1 overexpression partly reversed the effects of FB on glycolytic enzymes, CD86 expression, and proinflammatory cytokine production. Immunoprecipitation followed by mass spectrometry and UbiBrowser analysis identified USP7 as a candidate HIF27 1-associated deubiquitinase. Molecular docking and cellular thermal shift assays supported a possible interaction between FB and USP7. FB reduced the association between USP7 and HIF-1. USP7 knockdown produced effects similar to those of FB on HIF-1 ubiquitination and downstream glycolytic and inflammatory responses.Overall, FB alleviated neuropathic pain and reduced proinflammatory microglial responses. These effects may involve the promotion of HIF-1 degradation through modulation of the USP7-HIF-1 regulatory axis.

neuroscience↗

bioRxiv2026

Whole-genome sequencing data of a diverse grapevine germplasm collection maintained in Bordeaux, France

Grapevine (Vitis vinifera) is one of the worlds most economically important fruit crops and a model species for perennial fruit tree genetics and genomics. The extensive genetic diversity found in cultivated and wild Vitis species provides a valuable resource for studies of domestication, adaptation, trait evolution, and breeding. This article presents a standardized whole-genome variant dataset comprising 547 grapevine accessions maintained in the INRAE Bordeaux grapevine germplasm collection, including 397 domesticated V. vinifera cultivars and 150 wild Vitis accessions. Whole-genome sequencing data were generated at a target sequencing depth of approximately 20x, and sequence variants were identified using a standardized Genome Analysis Toolkit (GATK) workflow against the reference genome PN40024v4 (40X). Variant discovery was carried out simultaneously across the complete sample set to ensure consistent genotype calling. All accessions were sequenced using the same technology and processed using the same reference genome, sequence alignment, variant-calling, and filtering workflow to produce a standardized variant dataset comprising ca. 9.1M SNPs and 0.77M INDELs. The resulting VCF files provide a harmonized genomic resource that can be readily reused for studies of grapevine genetics, germplasm characterization, population genomics, comparative genomics, genome-wide association studies, and the development and benchmarking of bioinformatic methods. SPECIFICATIONS TABLE O_TBL View this table: org.highwire.dtl.DTLVardef@14f2b12org.highwire.dtl.DTLVardef@94b5acorg.highwire.dtl.DTLVardef@1232f80org.highwire.dtl.DTLVardef@1038e85org.highwire.dtl.DTLVardef@81ec71_HPS_FORMAT_FIGEXP M_TBL C_TBL VALUE OF THE DATAO_LIThis dataset provides whole-genome raw sequencing for 118 wild Vitis accessions originating from North America and Asia and a sequencing-derived variant data for these accessions and 429 Vitis vinifera cultivars and wild accessions from the INRAE Bordeaux germplasm collection, previously published by Dong et al. 2023[1]. The dataset captures genetic variation across a total of 547 grapevine accessions, including domesticated and wild grapevine germplasm using a common variant-calling pipeline, facilitating direct comparisons among accessions. C_LIO_LIThe inclusion of wild Vitis species together with cultivated grapevine accessions provides a resource for studies of grapevine diversity, domestication, phylogenetic relationships, and comparative genomics. The dataset enables the investigation of genetic variation across multiple Vitis species using a standardized set of genomic variants. C_LIO_LIThe variant call format (VCF) file can be reused for population genetics, phylogenetic analyses, genetic diversity assessments, introgression analyses, and the identification of genomic regions of interest. The dataset is compatible with widely used bioinformatics software and can be integrated with other publicly available grapevine genomic resources. C_LIO_LIThis dataset constitutes a genomic resource for grapevine breeding and conservation research. Researchers can use these data to identify genetic diversity in wild relatives, compare allelic variation between cultivated and wild germplasm, investigate candidate loci associated with traits of interest, and support the management and characterization of grapevine germplasm collections. C_LI

genomics↗

bioRxiv2026

Epitope-Focused Immunogens Confer Broad Protection against Coronaviruses

Variable regions in coronavirus spike dominate antibody responses elicited by infection or conventional vaccination and limit induction of broad neutralization. In contrast, conserved S2 elements, including the stem helix (SH) and fusion peptide proximal region (FPPR), are promising but subdominant targets of protective immunity. Here, we employed computational design to generate de novo epitope-focused immunogens that precisely present the SH and FPPR epitopes. Formulated as combinatorial immunogens, this vaccine elicited consistent serum responses with broad reactivity across known human coronaviruses and induced epitope-specific antibodies with broad neutralizing activity. As a heterologous boost, epitope-focused immunogens protected mice against challenge with phylogenetically distinct coronaviruses, including bat SARS-related RsSHC014-CoV and MERS-CoV, establishing a generalizable strategy for precision immune focusing and advancing universal coronavirus vaccine development.

bioengineering↗

bioRxiv2026

CD133+ progenitor cells promote pulmonary hypertension through CXCR4 signaling

BackgroundPulmonary hypertension (PH) is characterized by pulmonary vascular remodeling and smooth muscle cell accumulation, but the progenitor-like cells that contribute to this process remain incompletely defined. MethodsWe combined analyses of human pulmonary arterial hypertension lungs and experimental PH models with bulk and single-cell RNA sequencing, lineage tracing, inducible ablation of CD133+ cells, and conditional deletion of Cxcr4 in CD133+ cells. ResultsCD133 expression was markedly increased in human and experimental PH lungs. Transcriptomic analyses identified inflammatory, metabolic, chemokine-associated, and smooth muscle cell-like programs in CD133+ cells from PH lungs. Lineage tracing showed that CD133+ cells contributed to endothelial and smooth muscle cell compartments during experimental PH. Genetic ablation of CD133+ cells attenuated hypoxia-induced PH and pulmonary vascular remodeling, whereas Cxcr4 deletion in CD133+ cells reduced PH severity. ConclusionsCD133+ progenitor cells are functional contributors to pulmonary vascular remodeling, and CXCR4 signaling mediates their pathogenic activity. Targeting pathogenic CD133+ cell states or CXCL12/CXCR4 signaling may provide a strategy to limit vascular remodeling in PH.

pathology↗

bioRxiv2026

Characterizing Functional Clusters of V4 Neurons in Digital Twins

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

neuroscience↗

bioRxiv2026

E2F1 Drives Endothelial Arterial Programming in Pulmonary Arterial Hypertension

BackgroundPulmonary arterial hypertension (PAH) is driven by maladaptive endothelial remodeling, but the transcriptional regulators that couple proliferative stress to arterialized endothelial states remain incompletely defined. E2F transcription factor 1 (E2F1) is classically viewed as a cell-cycle regulator; whether E2F1 functions as a disease-driving node that promotes endothelial arterial programming in PAH remains unknown. MethodsWe integrated human PAH lung transcriptomic analyses, deconvolution-based endothelial-state scoring, and complementary mouse and rat PH models with bulk RNA-seq, single-cell RNA-seq, pseudotime analysis, and CellChat inference. E2F1 function was tested using adenoviral E2F1 overexpression, pharmacological pan-E2F inhibition with HLM006474, and genetic E2f1 loss on a tamoxifen-inducible endothelial Egln1-deletion background. ResultsIn PAH lungs, E2F1 was increased and arterial endothelial cell (AEC) fraction and expanded arterial program scores were elevated. Similarly, Egln1Tie2Cre lungs showed increased E2F1, induction of arterial remodeling genes, and activation of an E2F target program. Genetic loss of E2f1 reduced right ventricle systolic pressure, right ventricle hypertrophy, vascular remodeling, and distal muscularization in Egln1-driven PH mice model. Bulk RNA-seq showed suppression of E2F, mitotic, epithelial mesenchymal transition, and extracellular matrix-remodeling programs. Single-cell RNA-seq showed reduced AEC accumulation, normalized CAP1/CAP2 distribution, and reduced progression along the CAP1-AEC trajectory. CellChat analysis identified loss of an arterial communication hub, including reduced ECM, VEGF, and Notch signaling when E2F1 is loss. Conversely, E2F1 overexpression in human lung microvascular ECs increased proliferation, activated E2F/cell-cycle and Notch/arterial programs. Pharmacological inhibition of E2F via HLM006474 suppressed endothelial proliferation and attenuated Egln1-driven and MCT-induced PH, including reversal of established MCT-PH. ConclusionsE2F1 acts as a disease-relevant transcriptional factor linking endothelial cell-cycle activation to arterial programming, matrix and angiogenic communication programs, and pulmonary vascular remodeling. Genetic or pharmacological E2F inhibition mitigates experimental PH, supporting E2F1 as a therapeutic target in PAH. Clinical Perspective What is new?1. This study identifies E2F1 as a previously unrecognized driver of PAH rather than only a downstream marker of cell-cycle activation. 2. Genetic loss of E2f1 rescues hemodynamic and structural features of Egln1-driven PAH, and pharmacological E2F inhibition attenuates both Egln1-driven and monocrotaline-induced PH. 3. Mechanistically, E2F1 links endothelial proliferation to Notch-associated arterial programming, AEC accumulation, and CAP1-to-iAEC-to-AEC trajectory progression. What are the clinical implications?1. E2F1 defines a tractable transcriptional node that integrates proliferative stress with arterial endothelial reprogramming, a core pathological feature of PAH vascular remodeling. 2. Pan-E2F small-molecule inhibitors, several of which are in development for oncology, may be repurposable for PAH if E2F1-dependent endothelial arterial-programming signatures identify responsive disease states. 3. Plasma- or tissue-based readouts of E2F1 activity may identify PAH patients most likely to benefit from E2F-directed therapy.

physiology↗

bioRxiv2026

Water as a thermal contrast agent for artificial-intelligence-enhanced in vivo mid-infrared thermography

In vivo infrared thermography is limited by the inherently poor spatial resolution at long wavelengths, low contrast, and the lack of biocompatible contrast agents. Here, we present 3-5 m mid-wave infrared (MWIR) thermography enhanced by an artificial intelligence (AI) network and cold phosphate-buffered saline (PBS) as a thermal contrast agent for noninvasive in vivo imaging with high contrast and resolution. MWIR imaging enabled high thermal sensitivity with microscale spatial resolution, strong relative thermal contrast, and facilitated visualization of the subcutaneous vasculature in the human arm, hand, ankle, the femoral artery and vein in rats, and the femoral vessels in mice, with image contrast further enhanced by AI networks. In a 4T1 tumor-bearing mouse model, AI-enhanced MWIR resolved early-stage tumors of [~]2.3 mm and metastases as small as [~]1.7 mm. Using cold PBS as a MWIR thermal contrast agent, we achieved precise tumor boundary visualization and real-time imaging-guided tumor resection. AI-enhanced MWIR offers a promising solution for early diagnosis and improved surgical precision.

bioengineering↗

bioRxiv2026

Near-Infrared II Scintillator for High-Resolution X-ray Imaging

Light scattering in scintillators is a pervasive problem and a key factor limiting X-ray imaging resolution. Here, we shift scintillator radioluminescence from the traditional visible range into the short-wave infrared (SWIR) or near-infrared II (NIR-II, 1000-3000 nm) window to mitigate light scattering and thereby enhance light penetration and X-ray imaging resolution. We present an NIR-II MgGa2O4:Ni2+ scintillator with peak emission at 1340 nm, achieving a threefold improvement in X-ray imaging resolution compared with visible scintillators owing to reduced light scattering. This heavy-metal-free NIR-II scintillator exhibits intense radioluminescence comparable to that of conventional visible-emitting CsI:Tl, achieving a detection limit of 56 nanograys per second, [~]100-fold lower than typical doses used in medical imaging. We show that this NIR-II scintillator enables high-resolution X-ray radiography of electronic circuit boards and biological tissues.

biophysics↗

bioRxiv2026

Focal astrocyte Kir4.1 loss drives seizures, spreading depolarizations and postictal impairments

Astrocytic dysfunction is increasingly recognised as an important contributor to epileptogenesis and seizure dynamics. Kir4.1 potassium channels expressed in astrocytes play a critical role in activity-dependent extracellular potassium buffering, and their loss may impair network stability and promote pathological hyperexcitability. In epilepsy, seizures can be accompanied by spreading depolarizations (SDs), propagating waves of neuronal and glial depolarization. While seizure-associated SDs have been proposed to terminate seizures and limit seizure spread, they have also been implicated in postictal dysfunction and sudden unexpected death in epilepsy (SUDEP), and their significance in chronic epilepsy remains unclear. Here, we tested whether focal loss of astrocytic Kir4.1 in the adult hippocampus is sufficient to disrupt potassium buffering, generate spontaneous seizures, and promote seizure-associated SDs. Using astrocyte-targeted viral vector Cre recombinase in adult Kir4.1-floxed mice, we induced focal hippocampal reduction of Kir4.1 expression. This impaired activity-dependent potassium buffering, producing enhanced stimulation-evoked extracellular potassium accumulation and larger DC shifts in hippocampal slices. Chronic wireless EEG recordings demonstrated that focal astrocytic Kir4.1 loss was sufficient to induce spontaneous recurrent seizures and interictal epileptiform activity. To investigate seizure-associated SDs, we combined optogenetic stimulation with graphene-based micro-transistor recordings capable of stable full-bandwidth DC electrophysiology in awake head-fixed mice. Focal hippocampal loss of astrocytic Kir4.1 markedly increased susceptibility to evoked seizures accompanied by SDs. We used chronic wireless DC-coupled video-telemetry recordings to continuously monitor seizure and SD dynamics in freely moving mice. SDs occurred frequently during generalized seizures and were first detected in cortical channels. Seizures accompanied by SDs exhibited greater spectral power, longer duration, and prolonged postictal depression compared with seizures alone. Behaviourally, seizures accompanied by SDs were linked to postictal impairment characterised by behavioural arrest and abnormal motor behaviours. These findings highlight the utility of graphene micro-transistor arrays and chronic DC-coupled telemetry for resolving infraslow (<0.1 Hz) epileptic dynamics that are largely inaccessible using conventional electrophysiological approaches. Ground-truth DC-coupled recordings enabled identification of AC-band electrographic signatures that segregated seizures with SDs from seizures alone, raising the possibility that SD-associated seizures may be retrospectively inferred from conventional AC-coupled epilepsy datasets. We demonstrate that focal astrocytic Kir4.1 loss in the adult brain impairs potassium buffering and is sufficient to drive spontaneous seizures, supporting astrocytic potassium dysregulation as a determinant of seizure and spreading depolarization susceptibility in epilepsy. Furthermore, seizure-associated SDs are strongly linked to increased postictal impairments, supporting the concept that SDs are major determinants of pathological postictal states.

neuroscience↗

bioRxiv2026

Oxidized protein states define metastatic fitness in lung cancer

AbstractReactive oxygen species (ROS) are a pervasive feature of human cancers, yet the protein targets through which ROS-regulated cell states shape tumor biology remains poorly understood. Here, using cysteine chemical proteomics, we define signatures of protein states under distinct cellular ROS environments that capture protein oxidation and conformational changes. Quantifying these signatures in primary lung tumors and brain metastases revealed a surprising enrichment of oxidative states in metastasis. To determine how these states support fitness, we performed genome-wide CRISPR screens and identified the mitochondrial Complex I subunit NDUFA10 as a key oxidation-dependent vulnerability. Oxidation of NDUFA10*Cys253 supports Complex I function through a previously unrecognized nucleotide kinase activity that maintains mitochondrial DNA levels. Enforcing a reduced conformation in NDUFA10 disrupts brain metastatic colonization in vivo. These findings establish ROS regulated protein states as a functional layer of tumor fitness, providing a framework for identifying redox-dependent mechanisms that support cancer progression.

Cancer Biology↗

bioRxiv2026

Systematic comparisons between long-read and short-read based amplicon sequencing to characterize mixed microalgal communities.

The 18S rRNA gene has emerged as the primary molecular marker for amplicon-based characterization of microalgal communities, including in wastewater treatment systems, yet trade-offs between short- and long-read approaches remain poorly defined. We systematically compared V8-V9 short-read sequencing (Illumina MiSeq), full-length long-read sequencing with ss5ss3 primers (PacBio Sequel II), and computationally extracted V8-V9 regions from long-read data. Both in silico and in vitro analyses confirmed V8-V9 captured broader taxonomic coverage than ss5ss3, though partial reference sequences and taxonomic mis-annotations biased in silico assessments. Long-reads taxonomic advantage was database-dependent, constrained by SILVA databases genus-level curation but fully realized when paired with the species-level-curated and eukaryotes-focused PR{superscript 2} (Protist Ribosomal Reference) database. Long-read sequencing uniquely identified amplicon sequence variants (ASVs) assigned to key phosphorus assimilators (Scenedesmus obliquus, Desmodesmus sp., and Acutodesmus sp.) at species level during successful phosphorus removal in a full-scale microalgal cultivation system, while V8-V9 short-read sequencing revealed ASVs assigned to algal-predatory (Leptophryidae) and bacterivorous (Choanoflagellata and Rhogostoma-lineage) protists when performance declined, suggesting grazing pressure on the phosphorus-removing community. Although both approaches performed comparably for operational monitoring, these complementary strengths support short-read sequencing for routine community profiling and long-read sequencing for detailed functional investigations of Chlorophyta.

microbiology↗

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

Expectation triggers a change-like EEG response without acoustic change

Predictive processing theories posit that the auditory system continuously generates expectations and updates internal models when incoming evidence violates those expectations. Whether such updating can be expressed as a temporally precise, change-like neural response at a context-defined moment during continuous stimulation--without any physical change--has remained unclear. Using a transitional click-train paradigm in human EEG, we show that listeners reliably detect subtle midpoint transitions when click timing is fixed, whereas temporal uncertainty markedly weakens this sensory-driven detection. Strikingly, even in a physically unchanged stimulus, variable click timing elicits a robust response time-locked to the nominal midpoint. This endogenous change-like signal is stimulus-statistics dependent--absent in the fixed-timing no-change control--temporally confined to the early post-change window, and strongly state dependent, being amplified during active change detection relative to passive listening. Moreover, within identical no-change trials, the response tracks subjective change reports. Together, these findings show that temporal uncertainty and task engagement jointly gate predictive updating in continuous auditory streams, providing a compact assay to dissociate sensory-driven change responses from context- and state-dependent predictive signals.

neuroscience↗

bioRxiv2026

Precision DNA Impurity Reduction Approaches for Ultra-Pure rAAV Manufacturing

Recombinant adeno-associated virus (rAAV) vectors are a leading platform for gene delivery in basic and clinical research, yet large-scale manufacturing remains constrained by residual nucleic-acid impurities that compromise safety. In this study, we profiled the DNA species packaged within rAAV capsids and identified plasmid backbone sequences and host cell genomic DNA (hcDNA) as predominant contaminants. To mitigate this critical quality attribute, we implemented upstream strategies designed to fragment or excise backbone DNA, including TelN/TelROL excision, I-SceI meganuclease digestion, CRISPR/Cas9 cleavage, and Cre/LoxP recombination. Quantitatively, TelN/TelROL and I-SceI reduced encapsidated plasmid backbone DNA to approximately 20-30% and 20-40% of baseline levels, respectively, while CRISPR/Cas9 lowered it to about 10-20%. Notably, the Cre/LoxP system eliminated detectable plasmid backbone DNA without compromising vector-genome titers, indicating preserved genomic integrity. Additionlly, supplementating cell culture with a caspase inhibitor significantly reduced hcDNA contamination in rAAV particles to 1-5% of the baseline level. Collectively, these interventions provide practical bioprocess frameworks that markedly enhance rAAV purity via targeted DNA minimization and prevention of hcDNA fragmentation, thereby strengthening the safety profile of rAAV therapeutics in alignment with current Good Manufacturing Practice (cGMP) expectations.

molecular biology↗

bioRxiv2026

Cost-saving, trading, and internalization of externality: three economic strategies underlying amino acid archetypes of human metabolic enzymes

Amino acid composition of proteome reflects principles of metabolic resource allocation. While amino acids with higher biosynthetic costs are used less frequently in unicellular organisms, whether this rule extends to complex multicellular life remains elusive. Here we show that amino acid composition of human metabolic enzymes does not follow a simple cost-minimizing mode but instead segregate into four distinct amino-acid composition modules each associated with specific metabolic functions, a phenomenon we term emergence of amino acid archetypes (AArchetypes). By comparing ten phylogenetically diverse species, we find that AArchetypes emerge only in multicellular organisms, indicating a fundamental shift in proteome-level economics. We further demonstrate that these AArchetypes correspond to three distinct economic strategies: cost-saving in young, fast-evolving enzymes; trading in conserved central carbon metabolic enzymes whose amino-acid compositions match that of dietary intake; and internalization of negative externalities in liquid-liquid phase separation (LLPS)-prone, intrinsically disordered proteins through elevated biosynthetic costs of LLPS-associated amino acids. Together, these results reveal that multicellular proteomes are governed not by a single cost-minimization principle, but by a multi-layered economic system that integrates production, exchange, and regulation.

systems biology↗

bioRxiv2026

Structural Rewiring of IL-7R Dimerization by an Oncogenic Transmembrane Mutation Can Be Reversed by Rational Design

Mutations within the transmembrane domains (TMDs) of single-pass transmembrane receptors often cause aberrant, ligand-independent receptor signaling associated with diverse malignancies, but their mechanism of action remain largely unknown. These TMD mutations are generally not targetable as they are buried in membrane. Here, we determined the mechanism of a gain-of-function (GOF) TMD mutation of interleukin-7 receptor (IL-7R) associated with T-cell acute lymphoblastic leukemia, and addressed the possibility of directly targeting the TMD mutation by using rationally designed transmembrane helices to restore order to uncontrolled signaling. We find that the GOF mutation of IL-7R severely shifts the TMD homodimerization interface, causing the receptor to homodimerize in a geometry that activates downstream signaling independent of ligand. Designed transmembrane helices that interfere with the new interface, delivered with mRNA technology, selectively block ligand-independent but not ligand-dependent signaling. Our study provides a conceptual framework for understanding and repairing disease-causing TMD mutations of single-pass cytokine receptors.

biophysics↗