Biology subjects

Zheng, D.

Publications and source records attributed to Zheng, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Development and Application of a Filamentous Phage-Based Rapid Detection Tool for Ralstonia pseudosolanacearum

Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is a devastating plant disease with a broad host range. Early detection is critical for disease management, yet conventional methods lack speed and specificity. This study developed a rapid detection system using engineered filamentous phages (RSCq) expressing bioluminescence genes (luxAB, nanoluc, and luxSit-i). Among the constructs, RSCqluxAB demonstrated optimal performance, detecting R. pseudosolanacearum at 1.58x103 CFU/mL within 12 hours, with minimal background noise. The phage retained stability for six months at 4{degrees}C, proving suitable for field applications. These findings highlight its potential for early pathogen monitoring, quarantine enforcement, and precision agriculture, though further validation in soil/plant samples is needed.

microbiology↗

bioRxiv2025

Exogenous Photoreceptor-Specific N-Glycosylated PROM1 Rescues Retinal Degeneration in Patient and Mouse Models

PROM1 is widely expressed across various tissues. However, its pathogenic mutations are exclusively associated with inherited retinal dystrophy (IRD). The mechanisms underlying this retina-specific vulnerability remain poorly understood, and no effective treatment currently exists for PROM1-IRD. Here, we utilized urine cells, hiPSCs, hiPSC-RPE cells, retinal organoids (ROs) and Prom1-/- mice to address these challenges. During photoreceptor development in ROs, PROM1 co-localized with ciliary marker ARL13B and outer segment (OS) marker PRPH2. It exhibited photoreceptor-specific mRNA splicing isoforms and unique N-glycosylation. In IRD patient-specific models with the PROM1 c.619G>T (p.E207X) homozygous mutation, we observed nonsense-mediated mRNA decay and altered splicing, leading to complete loss of PROM1 protein and OS-like structure disruption, faithfully recapitulating PROM1-IRD pathology. To rescue these defects, we engineered a photoreceptor-specific AAV7m8-CRXp-hPROM1, which successfully restored PROM1 expression and OS-like structures in patient-derived ROs. Therapeutic efficacy was further validated in Prom1-/- mice, where subretinal delivery of AAV8-CRXp-hPROM1 led to photoreceptor-specific expression of human PROM1, significantly preserving OS morphology and improving visual function. These findings not only provide the first solid preclinical evidence supporting gene therapy for PROM1-IRD, but also reveal photoreceptor-specific vulnerability to PROM1 mutations, offering a novel conceptual framework for investigating and treating related IRDs.

neuroscience↗

bioRxiv2025

Procrastination partly reflects an evolutionary byproduct of non-planning impulsivity

Procrastination has immediately visible repercussions on health and survival resilience, yet shows stably heritable and remains increasingly pervasive across human societies. Despite a paradox, this behavior is theoretically explained to represent a byproduct of evolutionary advantages underlying impulsivity, yet not deciphered well by scientific evidences. After adjusting psychometric endogeneity, we demonstrate the unique predictive roles of non-planning impulsivity (NPI) during late adolescence and early adulthood uniquely predicts procrastination in later adulthood in a twin cohort (N = 154). This association was further replicated in two independent cohorts (N = 327, N = 1,543). Using AE models, in conjunction of single-paper meta-analytic synthesis (N = 3,656 twin pairs), we observed significant shared genetic contributions underlying this NPI-procrastination association (rg = 0.51, 95% CI: 0.18 - 0.84). Beyond to the phenotypic heritability, employing a Genome-Wide-Association Study (GWAS), six NPI-procrastination overlapping SNPs are identified, functionally accounting for neural dysregulation. Thus, leveraging neurodevelopmental normative modelling (N = 37,407), online meta-analytic estimations (k = 198, loci = 5,855) and seed-based d mapping estimates (N = 893), cortical deviations in the left dorsolateral prefrontal cortex (DLPFC) - the brain region showing highest probabilistic overlap mapping NPI to procrastination, partly explains their shared genetic variants, but are substantially independent in genetic contribution. Mendelian Randomization analysis finally indicates causal roles of NPI and procrastination both, to DLPFC deviations. Our findings empirically clarified this theory that procrastination partly derives from NPI as an evolutionary byproduct indeed, but is still unique in neurogenetic entities. Brief summaryProcrastination is a puzzling human behavior that compromises survival-relevant outcomes yet remains both widespread and heritable. Although theorized as a byproduct of impulsivitys evolutionary advantages, empirical support for this account has been limited. Here, we provide converging evidence across psychometric, genetic, and neuroimaging modalities to show that non-planning impulsivity during late adolescence and early adulthood uniquely predicts later procrastination, and that the two traits share significant genetic overlap. We further identify specific genetic variants and morphological deviations in the DLPFC that link, but also partially dissociate, their biological pathways. These findings clarify the evolutionary and neurogenetic architecture of procrastination and underscore its partial derivation from impulsivity alongside distinct developmental origins.

neuroscience↗

bioRxiv2025

SOX2 is a dispensable modulator of NUT carcinoma oncogenesis in mouse

NUT carcinoma (NC) is a highly aggressive malignancy driven by BRD4::NUTM1 and other NUTM1 fusion oncogenes. BRD4::NUTM1 aberrantly activates transcription factors (TFs) linked to basal progenitor identity, producing poorly differentiated squamous phenotypes. Among these TFs, SOX2 has been proposed as a critical oncogenic driver, but its functional requirement in NC has not been tested in vivo. Using a genetically engineered mouse model that faithfully recapitulates human NC, we performed lineage-specific conditional deletion of Sox2 in both squamous and non-squamous tissues. We found that Sox2 is dispensable for NC initiation and progression, with tumors retaining characteristic histology and expression of key drivers including BRD4::NUTM1, MYC, and TP63. Transcriptomic profiling revealed only modest changes in Sox2-deficient tumors, mainly affecting metabolic and biosynthetic pathways, without disrupting core oncogenic programs. These findings challenge the assumption that SOX2 is universally required in NC and suggest that SOX2-targeted therapies may have limited utility, refining the framework for therapeutic prioritization. Summary blurbThis study shows that SOX2 is not required for NUT carcinoma initiation or maintenance in vivo, challenging its assumed oncogenic role and refining therapeutic target prioritization.

cancer biology↗

bioRxiv2025

Tissue-specific consequences of tag fusions on protein expression in transgenic mice

Genetic fusion of protein tags is widely used to study protein functions in vivo. It is well known that tag fusion can cause unwanted changes in protein stability, but whether this is an inherent property of the tagged protein, or can be influenced by the cell and tissue environment, is unclear. Using a series of genome edited mouse models, we show that tag-dependent changes in protein expression can vary across different primary cell and tissue contexts. In one case (Ncaph2), a C-terminal auxin-inducible degron fusion strongly increased protein stability in some tissues but decreased it in others. Destabilisation resulted from tissue-specific leakage of the auxin-inducible degron, which depended on TIR1 expression, and occurred selectively in the small intestine where basal concentrations of auxin / indole-3-acetic acid can reach levels that are sufficient to trigger protein degradation in cultured cells. Stabilisation occurred in post-mitotic cells via an endogenous degradation signal situated at the Ncaph2 C-terminus, which normally undergoes activation upon cell cycle exit, but is inactivated by C-terminal tag fusion. Our results highlight the underappreciated importance of cell and tissue environment in determining the consequences of tag fusions on protein expression, which may be particularly important in animal models that contain diverse cell types.

molecular biology↗

bioRxiv2025

Mapping neurogenetic characteristics of psychopathological procrastination using normative modeling in a prospective twin cohort

Procrastination, affecting over 70% global population, is pervasively incurring negative outcomes in human society. This has long been studied as a bad daily habit, but it loses in delineating neurogenetic substrates underlying its psychopathological phenotyping. Using a prospective twin adolescent cohort, we demonstrate moderate heritability of this subclinical condition - PPS. Neuroimaging normative modeling analysis, further reveals that neurodevelopmental deviations in nucleus accumbens during adolescence, are predictive of PPS in adulthood, while such deviations-PPS mappings were highly genetically shared. Beyond to regional anomalies, PPS-specific whole-brain deviation patterns, notably in the default mode network, are neurobiologically enriched with changes in cortical manifolds (gradients) and neurotransmitter systems. Integrating these neuroimaging markers with transcriptomic atlas, we capture significant PPS-specific neurogenetic signatures associated with molecular transport system, neuroimmune responses, and neuroinflammation, particularly in serotonergic and dopaminergic pathways. These findings shed light on the multisystem neurogenetic architecture underlying PPS, providing evidence to theoretically conceptualize this psychopathological phenotype as a subclinical "brain disorder". TeaserPsychopathological procrastination is not a bad daily habit solely, but a "brain disorder" associated with multiscale neurodevelopment.

neuroscience↗

bioRxiv2025

Copper acquisition in Bacillus subtilis involves Cu(II) exchange between YcnI and YcnJ

The transition metal copper is biologically essential across all three domains of life. Several copper-dependent proteins and enzymes produced by the Gram-positive bacterium Bacillus subtilis have been characterized. However, many questions remain about how copper is recognized and trafficked to metalate cuproproteins. The ycnKJI operon in B. subtilis encodes a suite of proteins implicated in copper uptake and regulation, including the copper-binding protein YcnI and the putative copper importer YcnJ. Here, we demonstrate that one of the extracellular domains within YcnJ (YcnJCopC) binds Cu(II) in 1:1 stoichiometry with high affinity using a histidine brace motif. Biochemical results reveal that YcnJCopC and YcnI can exchange Cu(II). Genetic studies reveal that loss of either YcnI or YcnJ, or mutation of the key residues required for Cu(II)-binding, leads to a growth defect under conditions of copper limitation. Together, these data suggest that the Cu(II)-binding sites in both YcnI and YcnJ contribute to efficient import under Cu limited conditions. Our results support a model in which YcnI may sequester Cu(II) from YcnJ, serving a regulatory role to limit the amount of copper that enters the cytoplasm and allowing Cu(II) to be stored for later import in the outer face of the membrane. This transfer of Cu(II) between extracellular domains of membrane-bound proteins represents a potential new paradigm in bacterial copper usage.

biochemistry↗

bioRxiv2025

Hematopoietic Single Cell Atlas Reveals a Diverse Repertoire of Lymphoid Cells in Larval Zebrafish

Embryonic development is a critical time window for the establishment of the hematopoietic and immune systems. During embryogenesis, hematopoietic stem and progenitor cells (HSPCs) that possess divergent differentiation preferences arise and sustain lifelong hematopoiesis. How the pace and differentiation repertoire of native hematopoiesis is set in development and how it evolves as the organism grows is incompletely elucidated. Here, we use temporal lineage tracing of the emerging hematopoietic system during zebrafish development coupled with single cell RNA sequencing to define the origins of larval and adult hematopoietic cells. In both larvae and adult tissues, HSPCs arising earlier during embryogenesis show a predilection for lymphoid lineage production while those arising later are skewed towards erythroid. Moreover, early arising HSPCs are the main contributors to adult tissue resident lymphocytes. Mechanistically, early and late arising HSPCs show divergent transcriptional signatures and differential sensitivities to the levels of the transcription factor Runx1. Additionally, we identified that young larvae possess a more heterogeneous set of lymphoid cells than previously recognized including diverse T-lymphocytes and Innate Lymphoid-like Cells (ILCs). We demonstrated that these newly described larval ILC-like cells reside in lymphoid and mucosal organs and are responsive to viral mimic immune stimulation, indicating their relevance in early vertebrate life. The work provides new fundamental knowledge on how the heterogeneous HSPC pool establishes early immune hierarchies during embryogenesis and its persistence in adulthood.

developmental biology↗

bioRxiv2025

Machine learning-assisted enzyme engineering through ultra-high throughput sorting and large-scale sequence-function data generation

Machine learning (ML) shows great promise in protein engineering but has yet to be integrated with ultra-high throughput sorting (ultra-HTS) and NGS for large-scale sequence-function data generation to harness its capability to explore wider search space and more complex mutation events. Here, we introduce PUSDA, a framework that rapidly sorts mutant libraries into multiple performance groups with good accuracy and generates large-scale sequence-function data to power ML-driven protein design. As a demonstration, PUSDA generated over five million sequence-function data of an enzyme, with data processing revealing over 1.3 million unique enzyme mutants being sorted in a single day. With a trained ML model that achieved 93.52% accuracy, we further analysed combinatorial mutation events and applied a ratio-based selection approach to design novel enzyme sequences. Validation experiment demonstrated a 16.67-fold improvement in efficiency of identifying high-performance enzymes using PUSDA compared to using ultra-HTS alone. The designed novel enzyme achieved 8.23-fold increase in productivity compared to wild type. PUSDA lays a foundation to integrate ultra-HTS, NGS, and ML for future predictive enzyme engineering, offering a data-driven tool for accelerating breakthroughs in biotechnology.

synthetic biology↗

bioRxiv2025

Longitudinal analysis of retinal cell state transitions in RB1-deficient retinal organoids reveals the nascent cone precursors are the earliest cell-origin of human retinoblastoma

All cancers develop from malignant transformation of normal cells, while it is challenging to identify these "cells-of-origin" since it is impossible to witness the dynamic changes in human cancers. Retinoblastoma (Rb), an intraocular malignant cancer, is a typical model for study the molecular and cellular mechanisms of cancers. Although the maturing cone precursors (CPs) are proposed as the cellular origin of human Rb, it is unknow whether other retinal cells are also sensitive to RB1 inactivation. Here we developed RB1-deficient human retinal organoids (ROs) models from RB1-/- or RB1+/- human induced pluripotent stem cells (hiPSCs). RB1-/- hiPSCs developed into Rb tumors which recapitulated the features of human native Rb and had the ability to form consecutive orthotopic xenografts in mice. Importantly, RB1 loss induced the overproliferation of ATOH7+ neurogenic retinal progenitor cells (nRPCs), which disrupted the retinal development by generating proliferative, nascent retinal cells including retinal ganglion cells and CPs. scRNA-seq analysis verified the ATOH7+/RXR{gamma}+ nascent CPs survived and finally drove Rb development. In contrast, monoallelic RB1 inactivation with low pRB expression did not induce nascent CPs proliferation, but only induced nRPCs overproliferation which caused retinocytoma-like phenotype. Finally, a potential therapeutic agent for Rb was identified from multi-omics data. Our findings firstly indicate that nRPCs are the most sensitive cells to RB1 loss inducing nascent retinal cells abnormal proliferation, and ATOH7+ nascent CPs are the earliest cellular origin of human Rb, facilitating drug development for Rb.

cell biology↗

bioRxiv2024

Dynamic p21-dependency during quiescence arrest unveiled by a rapid p21 depletion system

Stress- or developmentally-induced signals can trigger G0/G1 cell cycle arrest through the upregulation of p21, a key inhibitor that halts proliferation. While p21 is widely recognized as essential for establishing this arrest, its degradation is generally assumed to be a prerequisite for the exit from arrest and cell cycle re-entry. Using a rapid p21 degradation system that allows for both endogenous p21 tracking and controlled depletion, we uncovered an extended role for p21 during the exit from G0/G1 arrest. Our results showed that removal of the arrest inducing signals did not lead to an immediate decline of p21 during the exit process; instead, p21 levels continued to maintain for a period before its gradual down-regulation. Importantly, premature depletion of p21 during this process weakened the capacity of cell cycle re-entry, particularly in cells with high levels of pre-existent p21. We found that during the release from arrest, cells with high levels of pre-existent p21 but a premature p21 depletion exhibited reduced capacity to restore KRAS/ERK activity, and supplementing KRAS/ERK activity rescued the failure of cell cycle re-entry in these cells. These findings reveal a previously unappreciated function for p21 during the exit from G0/G1 arrest, aside and distinct from its role in initiating the arrest. This new paradigm extends across multiple cell lines and stress-induced arrest contexts, offering a new framework for understanding p21 function in response to anticancer therapies and in development.

cell biology↗

bioRxiv2024

Comparative RT-qPCR and qPCR reveals early infection, low-titer infection, and relative cell activity of the HLB bacterium, Candidatus Liberibacter asiaticus

Candidatus Liberibacter asiaticus (Las) is one of the causal agents of citrus huanglongbing (HLB) epidemics worldwide. Due to its fastidious nature, intracellular and systemic infection, detecting Las at early and/or low-titer infection, as well as differentiating between live or dead cells in the host psyllids and citrus plants is critical for effective HLB management. To achieve both sensitive Las detection and differentiation, we employed one-step reverse transcription-quantitative PCR (RT-qPCR) using total nucleic acids as template. This method allows use of both Las 16S rRNA and rDNA as template in the same reaction and increases detection sensitivity by up to 1000-fold in comparison with quantitative PCR (qPCR). The increased sensitivity significantly reduces false negative detection and detects the otherwise undetectable low-titer Las infections. Furthermore, the greater the abundance of 16S rRNA present in the samples, the bigger the Ct gap obtained between RT-qPCR and qPCR results. The numerical Ct gap can be used to deduce relative Las cellular activity and indirectly infer whether cells are alive or dead. In addition, this comparative detection method also can be used to select inoculum and monitor relative cell activity during in vitro Las culture and evaluate the effectiveness of antimicrobial treatments against Las bacteria.

molecular biology↗

bioRxiv2024

CELL-Diff: Unified diffusion modeling for protein sequences and microscopy images

Fluorescence microscopy is ubiquitously used in cell biology research to characterize the cellular role of a protein. To help elucidate the relationship between the amino acid sequence of a protein and its cellular function, we introduce CELL-Diff, a unified diffusion model facilitating bidirectional transformations between protein sequences and their corresponding microscopy images. Utilizing reference cell morphology images and a protein sequence, CELL-Diff efficiently generates corresponding protein images. Conversely, given a protein image, the model out-puts protein sequences. CELL-Diff integrates continuous and diffusion models within a unified framework and is implemented using a transformer-based network. We train CELL-Diff on the Human Protein Atlas (HPA) dataset and finetune it on the OpenCell dataset. Experimental results demonstrate that CELL-Diff outperforms existing methods in generating high-fidelity protein images, making it a practical tool for investigating subcellular protein localization and interactions.

bioinformatics↗

bioRxiv2024

H2AK119ub dynamics controls hair follicle stem cell quiescence

The transition of stem cells from a quiescent state to an active state is a finely tuned process that requires the dismantling of the quiescence program and the establishment of a cell cycle-promoting transcriptional landscape. Whether epigenetic processes control stem cell states to promote the regeneration of adult tissues remains elusive. In this study, we show that a repressive histone modification, H2AK119ub, is dynamic between quiescent and active hair follicle stem cells (HFSCs) in the adult murine skin. Ablation of H2AK119ub in HFSCs leads to impaired quiescence leading to premature activation and an eventual exhaustion of HFSC pool. Transcriptional and chromatin studies revealed that H2AK119ub directly represses a proliferation promoting transcriptional program in the HFSCs to preserve quiescence. Lastly, we identify that the inhibitory FGF signaling produced by the hair follicle niche keratinocytes maintains H2AK119ub in quiescent HFSCs. Together, these findings reveal that a repressive histone mark, H2AK119ub, is under the dynamic regulation of inhibitory niche signaling to prevent the untimely establishment of an activated state to preserve SC function and longevity.

cell biology↗

bioRxiv2024

Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes

Characterizing shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and novel biological functions. However, it is unclear if such coordination extends to translation. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of translation efficiency covariation (TEC), identifying coordinated translation patterns across cell types. We nominate candidate mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and uncovers gene functions that are not evident from RNA or protein co-expression. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish TEC as a conserved organizing principle of mammalian transcriptomes.

bioinformatics↗

bioRxiv2024

Predicting the translation efficiency of messenger RNA in mammalian cells

The degree to which translational control is specified by mRNA sequence is poorly understood in mammalian cells. Here, we constructed and leveraged a compendium of 3,819 ribosomal profiling datasets, distilling them into a transcriptome-wide atlas of translation efficiency (TE) measurements encompassing >140 human and mouse cell types. We subsequently developed RiboNN, a multitask deep convolutional neural network, and classic machine learning models to predict TEs in hundreds of cell types from sequence-encoded mRNA features, achieving state-of-the-art performance (r=0.79 in human and r=0.78 in mouse for mean TE across cell types). While the majority of earlier models solely considered 5' UTR sequence1, RiboNN integrates contributions from the full-length mRNA sequence, learning that the 5' UTR, CDS, and 3' UTR respectively possess [~]67%, 31%, and 2% per-nucleotide information density in the specification of mammalian TEs. Interpretation of RiboNN revealed that the spatial positioning of low-level di- and tri-nucleotide features (i.e., including codons) largely explain model performance, capturing mechanistic principles such as how ribosomal processivity and tRNA abundance control translational output. RiboNN is predictive of the translational behavior of base-modified therapeutic RNA, and can explain evolutionary selection pressures in human 5' UTRs. Finally, it detects a common language governing mRNA regulatory control and highlights the interconnectedness of mRNA translation, stability, and localization in mammalian organisms.

bioinformatics↗

bioRxiv2024

Aging limits stemness and tumorigenesis in the lung by reprogramming iron homeostasis

Aging is associated with a decline in the number and fitness of adult stem cells1-4. Aging-associated loss of stemness is posited to suppress tumorigenesis5,6, but this hypothesis has not been tested in vivo. Here, using physiologically aged autochthonous genetically engineered mouse models and primary cells7,8, we demonstrate aging suppresses lung cancer initiation and progression by degrading stemness of the alveolar cell of origin. This phenotype is underpinned by aging-associated induction of the transcription factor NUPR1 and its downstream target lipocalin-2 in the cell of origin in mice and humans, leading to a functional iron insufficiency in the aged cells. Genetic inactivation of the NUPR1--lipocalin-2 axis or iron supplementation rescue stemness and promote tumorigenic potential of aged alveolar cells. Conversely, targeting the NUPR1-- lipocalin-2 axis is detrimental to young alveolar cells via induction of ferroptosis. We find that aging-associated DNA hypomethylation at specific enhancer sites associates with elevated NUPR1 expression, which is recapitulated in young alveolar cells by inhibition of DNA methylation. We uncover that aging drives a functional iron insufficiency, which leads to loss of stemness and tumorigenesis, but promotes resistance to ferroptosis. These findings have significant implications for the therapeutic modulation of cellular iron homeostasis in regenerative medicine and in cancer prevention. Furthermore, our findings are consistent with a model whereby most human cancers initiate in young individuals, revealing a critical window for such cancer prevention efforts.

cancer biology↗

bioRxiv2024

TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer

Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.

cancer biology↗