Biology subjects

Zhang, T.

Publications and source records attributed to Zhang, T..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Echoes as Signal, Not Noise: Reverberation Sharpens Sensitivity to Temporal Structure

Sensitivity to temporal structure is fundamental to hearing, yet how natural reverberation shapes this sensitivity is unclear. Here we identify echo-facilitated temporal sensitivity (EFTS), a principle whereby the auditory system exploits echoes to selectively enhance responses to rapid temporal changes. Using transitional click trains with subtle inter-click-interval (ICI) shifts, we first show that increasing echo strength systematically enlarges the sound-level step at ICI transitions in both recorded and simulated stimuli, sharpening the physical boundary between segments of distinct temporal structure. In humans, psychophysical detection of ICI changes improves monotonically with echo level in both simulated and real free-field environments, while a late EEG change response scales with echo strength as onset responses remain comparatively stable. In awake rats, electrocorticography over auditory cortex reveals parallel echo-dependent enhancement of transition-evoked activity. Single units exhibit echo-level-dependent amplification of change-related firing and improved neurometric discriminability. Laminar local field potential and current source density analyses further show that echo-dependent divergence emerges first in granular and infragranular layers before propagating to supragranular cortex, consistent with thalamocortical drive followed by intracortical amplification. Together, these findings establish EFTS as a cross-species mechanism that reframes echoes as structured signals the brain uses to sharpen temporal integration in everyday listening.

neuroscience↗

bioRxiv2025

ER-to-Golgi transport machinery promotes the excessive cargo-triggered unfolded protein response

Disruptions to ER homeostasis trigger the unfolded protein response (UPR) to restore proteostatic balance. While defects in the secretory machinery are known to induce ER stress, it remains unclear whether specific trafficking components directly modulate UPR signaling. Here, we demonstrate that neuronal overexpression of the gap junction protein UNC-9 activates the IRE1-XBP1 arm of the UPR in C. elegans. Genetic deletion of ERGIC2 or ERGIC3--genes encoding COPII-associated proteins required for UNC-9 transport--suppresses this UPR activation, revealing an unexpected role for these factors beyond cargo trafficking. Mechanistically, ERGIC2 and ERGIC3 interact with the ER chaperone BiP, facilitating its release from IRE1 to enable UPR and alleviate cargo aggregation. Our findings redefine the UPR as a process dynamically regulated by early secretory components and provide novel insights into how cells integrate trafficking demand with stress adaptation, with implications for ER stress-associated diseases such as neurodegeneration.

cell biology↗

bioRxiv2025

A map of the cortical functional network mediating naturalistic navigation

Navigation through the real world requires close coordination of perception, planning, and motor actions. Prior neuroimaging studies that used controlled stimuli and tasks have suggested that navigation-related information is represented broadly across the human cerebral cortex. While three regions in the anterior visual cortex have been well-studied1, the extent and functional properties of regions in the parietal and prefrontal cortices are not as well-characterized 2. To map and characterize the full cortical network that underpins active navigation in the real world, we used functional magnetic resonance imaging to record brain activity from participants performing a naturalistic navigation task. Banded ridge regression was used to fit high-dimensional encoding models for 28,134 features to this data. Results show that naturalistic navigation is supported by a network of 11 functionally distinct cortical regions: five prefrontal and three parietal regions, along with three regions in the visual cortex that had been identified and characterized in previous studies. Analysis of encoding model weights shows that these 11 regions transform perceptual inputs through decision-making processes to produce action outputs, and are organized along distributed cortical functional gradients. These results provide a unified description of the functional properties and organization of the cortical network that mediates naturalistic navigation. We anticipate that these maps will provide rich targets to inform more targeted future studies of human navigation.

neuroscience↗

bioRxiv2025

Genomic Structural Variation Underlies Cell-Type-Specific Betacyanin Variegation in Chenopodium quinoa

The allotetraploid crop quinoa (Chenopodium quinoa) accumulates red/violet betacyanins, which function as vital stress-mitigating antioxidants. We investigated the genetic basis of red/green variegation observed in the aerial organs of the P0429 accession. We demonstrated that this color mosaic is primarily localized to the epidermal bladder cells (EBCs), with red EBCs accumulating [~]50-fold higher betacyanin levels than colorless EBCs. Cell-type-specific RNA-sequencing of EBCs identified the cytochrome P450 gene Cqu0091301 (CYP76AD) as the dominant and rate-limiting factor, exhibiting strong upregulation in red EBCs. This high pigmentation requires a specific structural variation in the P0429 accession: a [~]4-kb genomic insertion that restores the full functionality of Cqu0091301, which is otherwise truncated and non-functional in common reference genomes. Genomic analysis reveals that Cqu0091301 is part of a CYP76AD-DODA gene cluster. Notably, expression analysis revealed functional divergence between the quinoa subgenomes, with B-subgenome CYP76AD genes highly dominant in EBCs, while A-subgenome homologs were preferentially expressed in other tissues. Our results establish a clear link between structural genomic variation and cell-type-specific betalain biosynthesis, providing molecular insight into pigment regulation and subgenome specialization in allotetraploid quinoa.

plant biology↗

bioRxiv2025

An in situ generated CAR-M with IFNg and negative dominance Sirpa isoform augments hepatocellular carcinoma immunotherapy

Background and AimsChimeric antigen receptor (CAR) T cells have shown strong efficacy in hematological cancers but limited success in solid tumors. Macrophages, with their natural ability to infiltrate tumors, modulate immunity, and phagocytose cancer cells, offer a promising alternative when engineered with CARs. While studies have demonstrated the feasibility and anti-tumor activity of CAR macrophages (CAR-M), enhancing their persistence and phagocytic capacity remains a key challenge. Methods and ResultsBuilding on first-generation CD3{zeta}-based CAR-M, we developed a novel CAR targeting human GPC3, incorporating IFN-{gamma} and the extracellular domain of SIRP (SIRPECD) to improve CAR-M persistence and block the CD47-SIRP immune checkpoint. Following delivery via lipid nanoparticle-encapsulated mRNA (LNP-mRNA), the self-secreted IFN-{gamma} sustained M1 polarization through phospho-STAT1 activation. Meanwhile, the ectopically expressed SIRPECD competitively bound to CD47 on tumor cells, thereby blocking the endogenous SIRP-SHP2 interaction in a dominant-negative manner. This design enhanced pro-inflammatory activity and anti-tumor efficacy compared to CD3{zeta}-only CAR-M. Single-cell RNA sequencing and cellular analysis showed that in situ programmed CAR-M reprogrammed the tumor microenvironment toward inflammation in a murine HCC model. Moreover, CAR-M derived from human peripheral blood mononuclear cells (PBMCs) effectively phagocytosed human HCC organoids while sparing healthy tissues, indicating clinical potential. ConclusionsCollectively, our work presents a novel CAR design that enhances phagocytic function and sustains anti-tumor activity, offering a promising strategy for human solid tumor immunotherapy.

cancer biology↗

bioRxiv2025

The Notch/snRNA negative feedback regulation and its implications in Alzheimer's disease

Alzheimers disease (AD) is a multifactorial disorder whose hallmark lesions have been recognized for more than a century, yet its molecular pathobiology remains fragmentary. During our AD research, we discovered a direct mechanistic axis that links the Notch signalling pathway -- a crucial regulator of cell differentiation and proliferation--with the small nuclear RNAs (snRNAs) that drive pre-mRNA splicing. For the first time, our discovery unifies two previously siloed paradigms -- cell signal transduction and RNA splicing, expanding the fundamental knowledge of gene expression and its regulation. The first contribution of the present study is the discovery and validation of the Notch/snRNA negative feedback regulation. More implications include: (1) it reframes splicing-related diseases as dynamic consequences of pathway dysregulation rather than static snRNA-gene mutations; (2) it explains why global splicing abnormalities appear in AD, aging, and cancer even when snRNA genes themselves are not mutated; and (3) it provides an immediate, druggable "splicing rheostat" for any Notch-hyperactive disorder, such as AD.

cell biology↗

bioRxiv2025

Functional characterization of the 9q34.13 locus identifies RAPGEF1 as modulating risk for melanoma and nevi via RAS activation

Genome-wide association studies identified a melanoma- and nevus count-associated locus on chromosome band 9q34.13. Fine-mapping and melanocyte expression data collectively suggest two potential causal genes with opposite association with risk: higher levels of Rap guanine nucleotide exchange factor 1 (RAPGEF1) and lower levels of uridine-cytidine kinase 1 (UCK1). Colocalization analyses and conditional TWAS suggest multiple causal cis-regulatory sequence variants in partial linkage disequilibrium (LD) to each other. Melanocyte capture-HiC and CRISPR-inhibition demonstrated regulatory interactions between fine-mapped variants and the RAPGEF1 and UCK1 promoters. Focusing on RAPGEF1, we demonstrate RAPGEF1 expression promotes melanocyte growth and drives malignant transformation of human immortalized melanocytes. Following treatment with human EGF, RAPGEF1 overexpression activated both RAP1 and RAS. Further, we show RAPGEF1 expression is significantly enriched in melanomas lacking strongly activating RAS-MAPK mutations, suggesting that RAPGEF1 may promote oncogenic RAS-MAPK signaling in melanomas. Furthermore, in these tumors, we provide preliminary evidence to support the prognostic relevance of RAPGEF1 expression in patients lacking RAS or BRAF mutations. Together with other recent studies, these data suggest that germline variation influencing RAS activation may play a key role in nevus development and melanoma risk.

genetics↗

bioRxiv2025

Rapamycin Differentially Impacts Germline Stem Cell Quiescence Across Diverse Genetic Backgrounds of Drosophila Melanogaster

In response to ionizing radiation, stem cells enter a state of temporary quiescence, safeguarding the stem cell pool for tissue regeneration. Quiescence requires the inhibition of mTORC1, a kinase complex that promotes growth and suppresses autophagy, and cell cycle re-entry requires the reactivation of mTORC1. The pharmacological inhibition of mTORC1 in quiescent stem cells by rapamycin prevents cell cycle re-entry and subsequent tissue regeneration. It is well established that pharmacological responses can vary across genetic backgrounds, however, the extent to which genetic variation can impact the quiescence response to rapamycin is unclear. Here, we tested the sensitivity of stem cell quiescence to rapamycin in different genetic backgrounds within the Drosophila Genetic Reference Panel. These analyses revealed substantial variation across different genetic backgrounds, indicating that genetic variation can modulate drug-induced effects on stem cell dynamics. Our analyses suggest that mitophagy, rather than DNA damage response, is associated with the persistence of quiescence and delayed tissue regeneration by rapamycin. This work underscores the critical role of genetic background in determining drug efficacy, highlighting important implications for the therapeutic application of rapamycin.

developmental biology↗

bioRxiv2025

Overcoming EGFR resistance by monovalent and bident inhibitors targeting Cys775

Covalent targeting of EGFR cysteine 797 by osimertinib is one of the most successful breakthroughs in targeted therapy, fundamentally transforming the treatment landscape for non-small cell lung cancer (NSCLC) patients. However, resistance driven by mutation of C797 remains a major clinical challenge. Developing novel covalent strategies beyond C797 targeting presents a compelling opportunity for next-generation EGFR inhibitors. We first demonstrated that cysteine 775, located deep within the ATP-binding pocket, is accessible by a rationally designed covalent molecule ZNL-3, which as the first-in-class covalent cysteine 775 inhibitor exhibited strong efficacy in osimertinib-resistant mouse models. To further enhance resilience to resistance-causing mutations, we developed a dual-warhead, bident compound--YNW-1--which covalently targets both cysteine 775 and 797 simultaneously. YNW-1 is the first intramolecular lock to exhibit balanced reactive efficiency on both cysteines, rendering single-site mutations ineffective to confer resistance. The discovery of ZNL-3 and YNW-1 represents significant advancements in EGFR-targeted drug development, and further optimization toward clinical translation is a worthwhile strategy. SIGNIFICANCE: This study establishes the therapeutic potential of an EGFR covalent inhibitor through unprecedented targeting of cysteine 775 and provides the first demonstration that dual cysteine engagement offers superior efficacy over conventional covalent inhibitors by delaying resistance.

cancer biology↗

bioRxiv2025

Flexible Skull-Conformal Phased Array for Aberration-Corrected Transcranial Focused Ultrasound Therapy

Transcranial focused ultrasound (tFUS) is a promising non-invasive tool for precise deep-brain interventions, including neuromodulation, blood-brain barrier opening, and drug delivery. However, conventional rigid tFUS arrays suffer from poor skull conformity, compromising patient comfort and targeting precision, while skull-induced aberrations degrade focal accuracy and efficiency. To address these challenges, we present the first flexible, skull-conformal aberration-corrected phased array (F-SCAPA), a transformative solution integrating mechanical adaptability with advanced acoustic correction. The 0.5-MHz array--comprising 8x8 elements--features an optimized fabrication process that enhances material efficiency, ensures flexibility and stretchability, and maintains uniform electrical performance. Coupled with CT-based skull modeling and time-reversal aberration correction, F-SCAPA dynamically conforms to cranial anatomy while compensating for phase distortions. Transcranial validation in a human skull demonstrates precise focusing at 36 mm depth, achieving an axial full width at half maximum (FWHM) of 8.9 mm. This breakthrough overcomes existing limitations by combining mechanical adaptability with high-resolution transcranial focusing, establishing F-SCAPA as a robust, patient-compatible platform for next-generation non-invasive brain therapies.

bioengineering↗

bioRxiv2025

Thermal boundaries and underlying systems biology mechanisms in two waterbloom cyanobacteria

Climate change and recent heatwaves have elevated temperature to the level of nutrients in driving CHABs. In this new dimension of CHABs ecology, it is important to understand the thermal boundaries of each blooming species. One well-known example is the temporal and thermal partitioning between filamentous, nitrogen-fixing taxa such as Dolichospermum spp. and Pseudanabaena spp., which dominate in spring, and colonial/coccoid Microcystis aeruginosa, which predominates in summer and autumn. Here we show that Dolichospermum sp. and M. aeruginosa display converse temperature-growth relations, Dolichospermum sp. grows better at low temperatures (13-15{degrees}C) and M. aeruginosa grows better at high temperatures (29-31{degrees}C), with similar growth rates between 18 and 25{degrees}C. This thermal separation is sustained by systems-level changes, in terms of the macromolecule contents--proteins, ATP, carbohydrates, and lipids--and transcriptome and metabolic fluxes to critical unsaturated fatty acids, which were experimentally verified by supplementing these FAs. The gene regulatory and systems biology mechanisms are explored. Through homologous and evolutionary analyses, a conserved Hik34-Rre1-RpoD cascade underlying differential temperature-responsive gene regulation. Enzyme-constrained metabolic models reproduced genus-specific lipid shifts and uncovered contrasting flux reorganizations under thermal stress. Together, these results establish the metabolic and regulatory foundations that shape the distinct thermal niches of bloom-forming cyanobacteria, providing mechanistic insight into how climate warming may restructure their seasonal dominance.

systems biology↗

bioRxiv2025

Hepatocyte FGFR2 Mediates the Antifibrotic Effects of FGF10 in Advanced Liver Fibrosis.

Fibroblast growth factor 10 (FGF10) supports epithelial repair, but its role in liver fibrogenesis remains uncertain. Here we found that hepatic FGF10 and its receptor FGFR2 decline with progression to advanced fibrosis in patient biopsies and in carbon tetrachloride (CCl4)- and diet-induced mouse models. Restoring hepatic FGF10 with recombinant human FGF10 or adeno-associated virus mediated liver-targeted expression attenuated and partially reversed established advanced bridging fibrosis, reduced inflammation, and decreased hepatocyte apoptosis, and these benefits required hepatocyte FGFR2 because hepatocyte-specific Fgfr2 deletion abolished protection. In primary hepatocytes, FGF10 activated FGFR2-FRS2, increased inhibitory GSK3{beta}(Ser9) phosphorylation, and suppressed NF-{kappa}B activation, reducing TGF-{beta}1 and other cytokines and thereby limiting paracrine hepatic stellate cells activation. The molecular and histologic benefits extended to metabolically primed steatohepatitis, supporting translatability beyond toxicant injury. Mechanistic signaling readouts confirm FGFR2 engagement, while the main text centers on the hepatocyte FGF10-FGFR2 axis as an intrinsic brake on fibrogenesis. Together, these data identify a hepatocyte-centric FGF10-FGFR2 axis as a negative regulator and potential regressor of fibrogenesis, highlighting it as a tractable therapeutic target in advanced liver fibrosis.

pharmacology and toxicology↗

bioRxiv2025

Genetic Convergence Analysis of CRISPR Perturbations Deciphers Gene Functional Similarity

Pooled CRISPR screens with single-cell RNA sequencing readout (Perturb-seq) have emerged as a key technique to determine the functionality of a gene by directly perturbing the DNA of the gene. One of the most intriguing recent problems is quantifying the similarity between CRISPR perturbations, for example, whether they upregulate the same set of downstream genes. In this context, genetic convergence refers to the phenomenon where CRISPR disruptions of different genes lead to a similar downstream outcome. Existing methods are mostly heuristic. We present XConTest, a two-step, cross-validated procedure for assessing the genetic convergence problem. The test statistics calculated from that procedure are approximately standard normal when the two perturbations have an orthogonal influence on the cell expression profile. We apply XConTest to two studies: an investigation of the common impact of a suite of autism genes, and a large-scale study of genes associated with immune response to determine sets of genes with common functionality.

genomics↗

bioRxiv2025

Accurate interpretation of within-host dissemination using barcoded bacteria

Bacterial dissemination across tissues is a critically important process influencing infection outcomes. Monitoring within-host dissemination is challenging because conventional measures of bulk bacterial burden cannot distinguish between lineages that are shared between tissues and those that replicate locally. This limitation can be overcome using barcoded bacteria, where deep sequencing of the barcode locus and comparisons of barcodes between tissues define which lineages spread within the host. Numerous studies have used barcoded bacteria to generate high-resolution maps of dissemination. However, since multiple cells in the infectious inoculum can contain identical barcodes, inferences about dissemination can be confounded when distinct lineages from the inoculum with identical barcodes are observed in different tissues. Thus, even though the same barcodes can be observed in different tissues, dissemination between these tissues may not have occurred. Here, we aimed to develop an approach that would provide a solution to this confounding effect. We developed a simulation-based distance metric that quantifies the significance of observing shared barcodes between tissues. We validated this approach using simulated datasets spanning three orders of magnitude in barcode diversities and on three published experimental infection datasets. Our reanalysis reveals previously unappreciated patterns of Escherichia coli spread during liver abscess formation, clarifies the role of the Muc2 mucin in Listeria monocytogenes systemic spread, and quantifies how Klebsiella pneumoniae replication in the lungs drives systemic dissemination. As barcoding studies expand across diverse infection models, this approach provides an essential tool for accurate interpretation of within-host bacterial dissemination. ImportanceHow microbes move between tissues in the host is an important factor that controls the outcome and severity of infections. A powerful method to monitor within-host microbial dissemination is the use of barcoded bacteria and lineage tracing. Comparisons of barcodes between tissues enables inferences of microbial dissemination, and this method has been applied to diverse contexts of bacterial infections. Here we demonstrate that inferences of microbial dissemination are confounded, where observing identical barcodes in different tissues does not always signify that dissemination has occurred. To overcome this limitation, we define a metric to quantify the extent to which sharing of barcodes is meaningful and provide new insights into previous barcoding studies in E. coli, L. monocytogenes, and K. pneumoniae. As bacterial lineage tracing continues to be applied across diverse models, our method will help ensure accurate interpretations of microbial dissemination.

microbiology↗

bioRxiv2025

Non-Enzymatic Structural Modifications Reshape Peptide Presentation and Antigen Recognition

Cytotoxic T lymphocytes recognize infected and transformed cells through peptide antigens presented by MHC-I. Peptide sequence is assumed to dictate recognition, yet non-enzymatic post-translational modifications (PTMs) installed by reactive electrophiles can render a peptide chemically distinct from the form against which tolerance was established. Here we show that non-enzymatic PTMs arising from oxidative, inflammatory, metabolic, and carbonyl stress alter peptide-MHC-I stability and frequently disrupt recognition by a cognate TCR despite preserved MHC-I binding. Using a thioester probe, we demonstrate proof-of-concept capture of acylation-susceptible MHC-I ligands from the cellular immunopeptidome. Environmental chemicals, pharmaceuticals, and dietary isothiocyanates likewise modify antigenic peptides and impair T cell activation, and chemically distinct adducts at a single residue span the range from complete loss to full retention. Finally, methylglyoxal glycation impairs antigen-specific activation, and scavenging by creatine prevents it. Antigenic identity therefore reflects not only sequence but a peptides cumulative chemical history.

immunology↗

bioRxiv2025

High-throughput functional characterization of enhancers in totipotent-like cells

Zygotic genome activation (ZGA) marks the initial transcription event in embryogenesis, yet the cis-regulatory mechanism remains unclear. Here, utilizing massively parallel reporter assays, we functionally dissect enhancers across mouse genome in DUX-induced 2C-like cells (2CLCs). Integrated analysis with epigenomic and transcriptomic data from 2CLCs and 2-cell (2C) embryos, active enhancers in totipotent cells are depicted. Among them, a notable proportion of promoters exhibit enhancer activities, showing elevated active chromatin features and correlating with enhanced gene expression during ZGA. Furthermore, only half of the MT2_Mm exhibit enhancer activities in 2CLCs. In addition, 2CLC enhancers augment transcription in 2C embryos. Finally, deleting enhancer regions in both 2CLCs and 2C embryos highlighted their crucial role in facilitating transcription of ZGA genes. These findings advance our comprehension of the cis-regulatory mechanism governing ZGA process.

developmental biology↗

bioRxiv2025

Design and Development of DNA Damage Chemical Inducers of Proximity (DD-CIP) for Targeted Cancer Therapy

Many chemotherapies are effective against cancers that display high levels of genome instability by disrupting or overwhelming the DNA damage response to induce cell death. PARP inhibitors (PARPi) exploit this vulnerability by stalling DNA repair particularly in homologous recombination (HR)-deficient cancer cells. Although PARPi are now used to treat BRCA1/2-mutated cancers such as ovarian and breast cancers, they are still limited to a narrow range of clinical indications and are susceptible to acquired resistance. Here, we introduce "DNA Damage Chemical Inducers of Proximity" (DD-CIPs), bivalent molecules that rewire the mechanism of action of conventional PARPi. The DD-CIPs function through chemical induced proximity between PARP1/2 and the chromatin remodeling protein, BRD4. From a candidate library of DD-CIPs, we identified DD-CIP1 which induces the DNA damage response (DDR) and apoptosis to a range of cancer lines at two-digit nanomolar concentrations. Further optimization yielded DD-CIP2, which induces tumor cell death at nanomolar concentrations across diverse blood and solid cancer cells, including cancer types that are insensitive to PARPi. Using small-cell lung cancer (SCLC) as a model, we found that DD-CIP2 triggers DDR, cell cycle arrest, and apoptosis in vitro, leading to anti-tumor efficacy without substantial toxicity in preclinical SCLC xenograft models at well tolerated doses. Our findings demonstrate that DD-CIPs may provide an opportunity to address the limitations of traditional PARPi and establish chemical induced proximity as a strategy for modulating the DDR in cancer.

cancer biology↗

bioRxiv2025

Computational Discovery of Core Protein - Targeted Therapeutics Against Ginger Wilt Pathogen Ralstonia solanacearum

Bacterial wilt caused by Ralstonia solanacearum poses a severe threat to ginger production worldwide, as no consistently effective control measures exist. Here, we present a comprehensive strategy integrating pangenome analysis, functional enrichment, molecular docking, and state-of-the-art protein structure prediction to identify antibacterial agents targeting this phytopathogen. By prioritizing core, evolutionarily conserved proteins in R. solanacearum, we utilized AutoDock Vina and the recently developed AlphaFold3 to assess the binding affinity and validate protein-ligand interactions of key candidates from commercially available antibacterial pesticides. In vitro antibacterial assays confirmed strong inhibitory effects for several compounds, notably streptomycin sulfate, phellodendrine chloride, chlorogenic acid, and allicin. Our results highlight the power of combining large-scale computational screening with experimental validation for accelerating the discovery of novel antibacterial agents against highly divergent, recalcitrant plant pathogens. ImportanceThe indiscriminate use of broad-spectrum agrochemicals causes pollution and antimicrobial resistance. Our study proposes a targeted strategy against Ralstonia solanacearum by focusing on essential core proteins. This approach aims to develop specific agents that minimize harm to soil microbiota and reduce resistance selection. Our in silico framework aligns with green chemistry, offering a sustainable path for crop protection with a lower environmental footprint.

bioinformatics↗