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Zheng, Y.

Publications and source records attributed to Zheng, Y..

At least 145 records · Page 8Linked to original sources

Gene-Corrected Basal Cells Restore CFTR In Vitro; Transplants Regenerate Epithelium in a Preclinical Sinus Model

BackgroundCystic fibrosis (CF) is caused by mutations in the CFTR gene, leading to epithelial dysfunction and progressive lung disease. Although CFTR modulators have transformed care, [~]10% of people with CF remain without effective therapy. Durable, mutation-agnostic approaches are urgently needed. MethodWe used a lentiviral (LV) vector to deliver wild-type CFTR to airway basal cells derived from 13 paediatric CF participants with a range of genotypes. Transduced cells were assessed for transgene expression, epithelial differentiation, and CFTR function using air-liquid interface (ALI) cultures. Separately, to evaluate regenerative capacity in vivo, LVGFP-transduced rabbit airway basal cells were transplanted into the denuded nasal septum of healthy New Zealand white rabbits using a biocompatible scaffold. ResultsTransduced basal cells retained multilineage differentiation capacity, forming well-organized, pseudostratified epithelium with intact barrier function and ciliary activity. CFTR channel activity was restored to levels comparable to or exceeding those achieved with elexacaftor/tezacaftor/ivacaftor (ETI), including in individuals with nonsense mutations. Combined CFTR transduction plus ETI treatment showed additive benefit. In vivo, transplanted rabbit basal cells engrafted and differentiated to regenerate a mucociliary epithelium, with improved nasal potential difference and mucociliary clearance compared to scaffold-only controls. ConclusionOur study demonstrates that LV-mediated CFTR gene addition restores CFTR function in vitro across genotypes and supports epithelial regeneration in a clinically relevant animal airway model. This two-part platform offers a scalable path toward cell therapies for all people with CF and may have broader applications in upper airway epithelial repair.

cell biology↗

PromptBio: A Multi-Agent AI Platform for Bioinformatics Data Analysis

PromptBio is a modular AI platform for scalable, reproducible, and user-adaptable bioinformatics analysis, powered by generative AI and natural language interaction. It supports three complementary modes of analysis designed to meet diverse research needs. PromptGenie is a multi-agent system that enables stepwise, human-in-the-loop workflows using prevalidated domain-standard tools. Within PromptGenie, specialized agents--including DataAgent, OmicsAgent, AnalysisAgent, and QAgent--collaborate to manage tasks such as data ingestion, pipeline execution, statistical analysis, and interactive summarization. DiscoverFlow provides integrated, automated workflows for large-scale multi-omics analysis, offering end-to-end execution and streamlined orchestration. ToolsGenie complements these modes by dynamically generating executable bioinformatics code for custom, user-defined analyses, enabling flexibility beyond standardized workflows. PromptGenie and DiscoverFlow leverage a suite of domain-specific tools, including Omics Tools for standardized omics pipelines, Analysis Tools for downstream statistical interpretation, and MLGenie for machine learning and multi-omics modeling. We present the design, capabilities, and validation of these components, highlight their integration into automated and customizable workflows, and discuss extensibility, monitoring, and compliance. PromptBio aims to democratize high-throughput bioinformatics through a large language model-powered, natural language understanding, workflow generation and agent orchestration.

bioinformatics↗

A chimeric Ad5-Envp-VLP vaccine platform confers broad-spectrum immunity against emerging and re-emerging pathogens

Integrating complementary vaccine modalities is essential for combating emerging infectious threats. Here, we developed Ad5-Envp-VLP, a chimeric adenoviral platform synergizing adenoviral delivery efficiency with virus-like particle (VLP) structural mimicry. This system stably produces self-assembling VLPs in suspension HEK293 cultures, exhibiting enhanced immunogenicity over soluble antigens. Following intramuscular immunization, the platform induces early B cell expansion and sustains germinal center reactions, driven by the upregulation of B cell cycle-related genes (Cdc6, Cdc45, Cdc20, Cdc25C, Aurka, Aurkb, and Ccnb1/2) and robust T follicular helper (Tfh) cell differentiation, generating durable neutralizing antibodies against both influenza virus and rabies virus. These effects are conserved across mouse, canine, and feline models. Crucially, integrated flow cytometry and scRNA-seq demonstrate that intranasal delivery recruits and functionally reprograms lung innate immune cells (notably alveolar macrophages and dendritic cells), driving mucosal sIgA secretion and CTL responses. A single nasal dose confers lasting protection against homologous and heterologous influenza A strains. The platform also elicits cross-neutralizing antibodies against SARS-CoV-2 variants. Together, Ad5-Envp-VLP thus establishes a modular vaccine platform for antigenically plastic pathogens by combining in vivo self-assembly with dual pulmonary-muscular delivery. One Sentence SummaryNovel mucosal and systemic vaccine delivers self-assembling particles, triggering strong lung immunity and broad virus protection across species.

immunology↗

The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs

The Spatial Atlas of Human Anatomy (SAHA) represents the first multimodal, subcellular- resolution reference of healthy adult human tissues across multiple organ systems. Integrating spatial transcriptomics, proteomics, and histological features across over 15 million cells from more than 100 donors, SAHA maps conserved and organ-specific cellular niches in gastrointestinal and immune tissues. High-resolution profiling using CosMx SMI, 10x Xenium, RNAscope, GeoMx DSP, and single-nucleus RNA-seq reveals spatially organized cell states, rare adaptive immune populations, and tissue-specific cell-cell interactions and ligand-receptor pairs. Comparative analyses with colorectal cancer and inflammatory bowel disease demonstrate the power of SAHA to detect disease-associated spatial disruptions, including crypt dedifferentiation, perineural invasion, and therapy-resistant immune remodeling. All data are openly accessible through a FAIR-compliant interactive portal to support exploration, benchmarking, and machine learning model training. Through SAHA, we provide a foundational framework for spatial diagnostics and next-generation precision medicine grounded in a comprehensive human tissue atlas, enabling the development of context-aware models that simulate tissue behavior, decode complex pathologies, and accelerate therapeutic innovation at unprecedented scale.

systems biology↗

LazySlide: accessible and interoperable whole slide image analysis

Histopathological data are foundational in both biological research and clinical diagnostics but remain siloed from modern multimodal and single-cell frameworks. We introduce LazySlide, an open-source Python package built on the scverse ecosystem for efficient whole-slide image (WSI) analysis and multimodal integration. By leveraging vision-language foundation models and adhering to scverse data standards, LazySlide bridges histopathology with omics workflows. It supports tissue and cell segmentation, feature extraction, cross-modal querying, and zero-shot classification, with minimal setup. Its modular design empowers both novice and expert users, lowering the barrier to advanced histopathology analysis and accelerating AI-driven discovery in tissue biology and pathology.

bioinformatics↗

Single-cell Characterization of DNA Hydroxymethylation of the Mouse Brain During Aging

DNA methylation dynamics, including 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC), critically regulate brain function, yet conventional methods cannot distinguish these modifications, obscuring their distinct roles in gene regulation and aging. We present Joint- Cabernet, a bisulfite-free single-cell platform enabling simultaneous profiling of 5hmC, 5mC, and transcriptomes. Applying Joint-Cabernet to 84,071 nuclei from adult and aged mouse brains, we resolved cell-type-specific DNA hydroxymethylation landscapes, revealing elevated 5hmCG and 5hmCH levels in transcriptionally active genes across neuronal subtypes and spatial gradients in cortical layers. During aging, 5hmCG accumulates globally but is selectively enriched at open chromatin loci, aligning with the upregulation of cell-type-specific genes in distinct brain cell types. This single-cell DNA methylation brain cell atlas provides a framework for studying methylation- driven mechanisms in brain aging and neurodegenerative diseases.

genetics↗

Tensor-Based Integration of Time-Series Measurements Reveals Relationships Between Underlying Disease, Early Injury, and CD4+ Polarization in Liver Transplantation

For patients with end-stage liver failure, liver transplantation (LT) remains the standard-of-care, though five-year allograft survival rates remain below 80%. Liver ischemia reperfusion injuries (LIRI) arise during transplant and contribute to allograft dysfunction. While many drivers of LIRI have been well-characterized, the relationships between LIRI and later immunological signatures remain poorly understood, possibly because of limited integrated studies examining immunological signatures across the LT process. Furthermore, the role of underlying disease in LT remains poorly understood as it is unknown if later immunological signatures are universal or etiology dependent. To better examine etiology- and LIRI-driven immunological mechanisms across the LT lifetime, we collected cytokine and liver function test (LFT) measurements from LT donors and recipients at multiple pre- and post-operative timepoints. By developing a tensor-based factorization method to integrate these longitudinal measurements, we reduced the datasets to four immunological signatures that manifested across cytokines, LFTs, and time. Correlative analyses revealed associations between these integrated immunological signatures with etiology and LIRI. Later integration of allograft survival into this factorization method reduced these four signatures to two that were predictive of five-year allograft survival. Examination of these signatures prognostic of allograft survival found that CD4+ hyperpolarization towards Th1 or Th2 subtypes impaired growth factor expression and led to increased allograft loss risk. Clinical correlates revealed that donor and recipient age alongside etiology and donor liver health modulate this balance of CD4+ polarization in LT. Collectively, these results link immunological mechanisms to etiology and LIRI offering immediately actionable clinical insights alongside etiology- and donor-specific therapeutic targets for improving LT outcomes.

immunology↗

Alternatively activated monocyte-derived myeloid cells promote extracellular pathogen persistence within pulmonary fungal granulomas.

Inhaled fungal pathogens often generate granuloma-contained latent infections that can reactivate to cause invasive disease. However, the mechanisms underlying the inability to generate sterilizing immunity against latent infection remains poorly understood. Here, we leveraged spatial transcriptomics and flow cytometry to characterize the immune dynamics and cellular architecture of cryptococcal granulomas. Using fate mapping and murine genetic tools, we demonstrate that alternative activation of monocyte-derived myeloid cells by CD4+ T helper 2 cells antagonizes pulmonary fungal clearance during latent infection. In contrast to the prevailing view in the field, we find that alternatively activated myeloid cells are not an intrinsic replication niche for the fungus and more broadly, Cryptococcus predominantly resides in the extracellular environment. We propose a T helper 2 cell-myeloid circuit establishes a local immunosuppressive environment to drive extracellular fungal persistence, which could be leveraged as a new target for host-directed therapy to treat latent fungal infections.

immunology↗

TypeSINE: Genome-Wide Detection of SINE Retrotransposon Polymorphisms Reveals Functional Variants Linked to Body Size Variation in Pigs

The genotyping of Short Interspersed Element (SINE) retrotransposon insertion polymorphisms (RIPs) from large-scale sequencing data remains technically challenging. To overcome this limitation, we developed TypeSINE to genotype SINE-RIPs from short-read sequencing data. Analyzing 362 porcine genomes, we identified 749,835 SINE-RIPs (>85% accuracy), including 65,917 common variants (5-95% frequency). These showed uniform genomic distribution ([~]22/Mb), with 40% in introns. Population analyses based on SINE-RIPs revealed independent domestication of Asian and European pigs from local wild populations, followed by introgression. GWAS detected body size-associated regions using SINE-RIPs. We created pigRIPdb (82,227 curated SINE-RIPs) with browsing and visualization tools. The methods cross-species applicability is supported by conserved SINE evolutionary patterns, enabling polymorphism discovery of SINEs in livestock and humans. TypeSINE represents an efficient, scalable solution for genome-wide SINE-RIP analysis, advancing population genomics research. TeaserAn integrated SINE-RIP genotyping platform with companion database enables large-scale analysis of SINE evolution and population genetics in swine

bioinformatics↗

Sequential Amino Acid Mutagenesis-Driven De Novo Evolution of Adenine Deaminases Enables Efficient In Vivo Base Editing in Primate

Base editing allows for the precise modification of genetic information, providing new avenues for treating diseases1. The adenine base editor ABE8e is currently the most efficient and widely used tool for adenine base editing. ABE8e was developed through multiple rounds of directed evolution of Escherichia coli tRNA adenine deaminase, including phage-assisted continuous evolution (PACE)2,3. While PACE is highly effective, it is a complex system that poses challenges for implementation4. Despite its high efficiency, ABE8e is associated with limitations such as relatively higher bystander editing effects and elevated off-target activity5, which need to be addressed to further enhance its precision and safety. Here, we developed a novel method for the de novo discovery of evolved ABE components, particularly adenine deaminases. This process involves identifying candidate proteins through AI-based structural prediction and clustering, followed by the enhancement of deaminase editing activity through screening libraries created by sequential amino acid saturation mutagenesis. This evolutionary strategy simplifies the approach by employing saturation mutagenesis libraries tailored to specific segments, thereby enabling exploration of an expanded sequence space and increasing the likelihood of discovering adenine deaminases with superior capabilities. The newly developed hpABE5.20 here demonstrates a more refined editing window, reduced DNA off-target effects that are both sgRNA-dependent and -independent, and minimized RNA off-target activity, while maintaining robust editing efficiency relative to ABE8e. Furthermore, hpABE5.20 has been successfully applied for precise and effective therapeutic adenine base editing in cellular disease models, humanized mice, and non-human primates.

bioengineering↗

The bivalent epigenetic regulator ULTRAPETALA1 promotes the Arabidopsis floral transition via recruitment of Polycomb histone methyltransferases for H3K27me3 deposition at the FLC locus

Floral induction is a major transition during the plant life cycle that contributes to reproductive fitness in annual and perennial plants. Flowering occurs in response to multiple environmental and endogenous cues. In Arabidopsis thaliana, many of these cues converge on the regulation of the FLOWERING LOCUS C (FLC) gene, which encodes a MADS domain transcription factor that functions as the main floral repressor. Here we demonstrate that the bivalent epigenetic regulator ULTRAPETALA1 (ULT1) is both necessary and sufficient to promote flowering. We identify ULT1 as a novel component of the autonomous pathway (AP) and show that it accelerates flowering by directly repressing FLC transcription. We demonstrate that ULT1 physically associates with the SWINGER (SWN) and CURLY LEAF (CLF) histone methyltransferase components of Polycomb Repressive Complex 2 (PRC2) to regulate FLC transcription by altering the accumulation of H3K27me3 marks. Our data indicate that ULT1 promotes the floral transition by interacting with SWN and CLF to recruit PRC2 to the FLC locus to deposit repressive histone methylation and reduce transcription of this key floral repressor.

plant biology↗

Macrophage Migration Inhibitory Factor Suppresses Natural Killer Cell Response and Promotes Hypoimmunogenic Stem Cell Engraftment Following Spinal Cord Injury

Human induced pluripotent stem cells (iPSCs) offer immense potential as a source for cell therapy in spinal cord injury (SCI) and other diseases. The development of hypoimmunogenic, universal cells that could be transplanted to any recipient without requiring a matching donor, could significantly enhance their therapeutic potential and accelerate clinical translation. To create off-the-shelf hypoimmunogenic cells, we used CRISPR-Cas9 to delete B2M (HLA class I) and CIITA (master regulator of HLA class II). Double-knockout (DKO) iPSC-derived neural progenitor cells (NPCs) evaded T cell-mediated immune rejection in vitro and after grafting into the injured spinal cord of athymic rats and humanized mice. However, loss of HLA class I heightened susceptibility to host natural killer (NK) cell attack, limiting graft survival. To counter this negative effect, we engineered DKO NPCs to overexpress macrophage migration inhibitory factor (MIF), an NK cell checkpoint ligand. MIF expression markedly reduced NK cell-mediated cytotoxicity and improved long-term engraftment and integration of NPCs in the animal models for spinal cord injury. These findings demonstrate that MIF overexpression, combined with concurrent B2M and CIITA deletion, generates hiPSC neural derivatives that escape both T- and NK-cell surveillance. This strategy provides a scalable route to universal donor cells for regenerative therapies in SCI and potentially other disorders.

cell biology↗

ArchLips: A comprehensive in silico database for high-throughput identification of archaeal lipids

Archaeal membrane lipids are markedly distinct from those in bacteria and eukaryotes, serving as unique biomarkers for unraveling their ecological and biogeochemical roles. Recent advancements in lipidomics have facilitated detailed cellular-level characterizations of lipid compounds. However, the lack of a comprehensive and dedicated database has severely limited large-scale, high-throughput investigations of archaeal lipids. We present ArchLips, a comprehensive database containing 218,868 in silico molecular structures and tandem mass spectra of 199,248 corresponding archaeal lipids. ArchLips enables the rapid and accurate identification of characterized archaeal lipid compounds from both pure cultures and environmental samples, serving as a transformative tool for enhancing our understanding of archaeal diversity and their ecological and evolutionary significance within global ecosystems.

biochemistry↗

Age-related declines in niche self-renewal factors controls testis aging and spermatogonial stem cell competition through Hairless, Imp, and Chinmo

Aging is associated with progressive tissue decline and shifts in stem cell clonality. The role of niche signals in driving these processes remains poorly understood. Using the Drosophila testis, we identify a regulatory axis in which age-related decline of niche signals (BMPs) lead to upregulation of the co-repressor Hairless, which downregulates the RNA-binding protein Imp in aged germline stem cells (GSCs). Reduced Imp causes loss of Chinmo, a key factor in GSC aging and competition. Reduced Chinmo causes ectopic Perlecan secretion which accumulates in the testis lumen and causes GSC loss. Aging of the testis is reversed by increasing BMPs in the niche, or by overexpressing Imp or depleting Hairless in GSCs. Furthermore, GSC clones with reduced Imp or increased Hairless are more competitive, expelling wild-type neighbors and monopolizing the niche. Thus, BMPs regulate testicular niche aging through the Hairless-Imp-Chinmo axis and "winning" GSCs usurp these aging mechanisms. HighlightsO_LIAged niche cells produce less BMPs, resulting in more Hairless (H) in aged GSCs C_LIO_LIElevated H represses Imp, resulting in less Chinmo and in ectopic ECM secretion C_LIO_LIAging is prevented by higher BMP in niche cells, or by higher Imp or lower H in GSCs C_LIO_LIGSCs with low Imp or high H exploit these aging mechanisms to colonize the GSC pool C_LI

genetics↗

Ancient DNA Reveals Hominoid Evolution: Intermediate DNA Sequences and Advances in Molecular Paleontology

AbstractFossils and ancient crude pottery vessels function as physical "DNA containers," preserving oriDNA (original, in situ DNA) and accumulating eDNA (environmental DNA) over time. Ancient DNA (aDNA) serves as molecular fossils, chronicling evolutionaryhistory. Using "nano-affinitybead technology", we extracted and sequenced DNAfrom Lycoptera fossils in the Jehol region and a "round-bellied jar (Jar)" from the Erlitou period in Guangwu Town, yielding 236,545 primate sequences from the fossils and 86,908 from the pottery. We observed that the AFF value of DNA sequences negatively corre lates with species divergence time1, offering a quantitative measure of DNA preservation and host divergence. Some fragments distinct from modern genomic sequences, termed "intermediate DNAsequences" (IDS), have been identified. Many IDS exhibit an upper age limit, preserving characteristics of the last common ancestor (LCA) of the Hominidae and offering molecular insights into "Darwins puzzle". Among IDS, the SRRA subtype (Sequence Reversal and Rearrangement), identified in mRNA-coding exonic sequences, arises from the incorporation of a complementary antisense strand upstream of the sense strand, either adjacent to it or separated bya sequence interval. This introduces a novel post-transcriptional regulatory mechanism at the mRNA level, driven by SRRA, which presets hairpin structures and Indels in the UTR or CDS of exonic sequences, modulating gene variation. We propose: "SRRAs played a critical trial-and-error role in early Hominidae evolution, facilitating adaptive genomic changes, with some SRRA sequences later excised from exons", positioning SRRAas an evolutionary "genetic switch". Additionally, seven species -specific fragments (SSFs) of non-human primates (NHPs) linked to Asian Homo erectus were identified in the fossils, and pottery DNA reveale d sequences from tropical species (e.g., zebrass, oil palms), providing evidence of climate-driven local extinction and supporting paleo-ecological and paleo-environmental reconstruction. This method of analyzing aDNA from non-skeletal materials opens new avenues in paleontology, archaeology, and geology, guiding the tracing of ancient migration patterns and fossil searches. DNAfragments preserved within "DNA containers " exhibit an "old-few, new-many" turnover pattern, with many aDNA fragments displaying non-deamination. This evidence challenges prevailing perspectives, the authenticity criteria for aDNA, and the capabilities and scope of the traditional research method, necessitating a thorough reevaluation of the relevant knowledge framework. Furthermore, this study opens new opportunities for frontier research.

paleontology↗

Systematic evaluation of blood contamination in nanoparticle-based plasma proteomics

Circulating blood proteomics enables minimally invasive biomarker discovery. Nanoparticle (NP)-based circulating plasma proteomics studies have reported varying number of proteins, ranging from ca 2000 to 7000 but its not clear whether higher protein number is more informative. Here, we first develop OmniProt - a silica-NP workflow for plasma proteomics which is optimized through systematic evaluation of NP types and protein corona formation parameters. Next, we present an Astral spectral library for 10,109 protein groups expressed in human plasma. Using Astral with a throughput of 60 sample-per-day, OmniProt identifies ca 3000 to 6000 protein groups from human plasma. Notably, we found that platelet/erythrocyte/coagulation-related contamination artificially elevates protein identifications and compromises quantification accuracy for circulating plasma proteins in NP-enriched samples. Through controlled contamination experiments, we identified and validated protein biomarkers for contaminations of platelet, erythrocyte, and coagulation, respectively, in NP-based plasma proteomics experiments. We further developed an open-access software Baize for accessing plasma proteomics contamination. Finally, we validated our OmniProt workflow and Baize software in a clinical cohort of 193 patients with CT-indistinct benign nodules or early lung cancers. On average, we identified ca 4400 protein groups for each plasma sample without significant contamination. Five samples were flagged out as contaminated. In conclusion, this study reveals that contamination of plasma samples significantly alters the protein identification and quantification in NP-based plasma proteomics experiments, and presents an open-access software Baize to evaluate plasma proteome contamination.

biochemistry↗

Targeting RhoA activity rejuvenates aged hematopoietic stem cells

Biomechanical alterations contribute to the decreased regenerative capacity of hematopoietic stem cells (HSCs) upon aging. RhoA is a key regulator of mechano-signaling but its role for mechanotransduction in stem cell aging has not been investigated yet. Here, we show that murine HSCs respond to increased nuclear envelope (NE) tension by inducing NE translocation of P-cPLA2, which cell intrinsically activates RhoA. Interestingly, aged HSCs experience physiologically higher intrinsic NE tension, associated with increased NE P-cPLA2 and RhoA activity. Reducing RhoA activity lowers NE tension in aged HSCs. Feature image analysis of HSC nuclei reveals that chromatin remodeling is associated to RhoA inhibition, which includes the restoration of youthful levels of the heterochromatin marker H3K9me2 and a decrease in chromatin accessibility and transcription at retrotransposons. Eventually, we demonstrate that RhoA inhibition upregulates Klf4 expression and transcriptional activity, improving aged HSCs regenerative capacity and lympho/myeloid skewing in vivo. Overall, our data support that an intrinsic mechano-signaling axis dependent on RhoA can be pharmacologically targeted to rejuvenate stem cell function upon aging.

cell biology↗

A Telomere-to-Telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet

Recent advances in sequencing technologies have enabled the complete assembly of human genomes from telomere to telomere (T2T), resolving previously inaccessible regions such as centromeres and segmental duplications. Here, we present an updated, higher-quality, haplotype-phased T2T assembly of the Chinese Quartet (T2T-CQ), a family cohort comprising monozygotic twins and their parents, generated using high-coverage ONT ultralong and PacBio HiFi sequencing. The T2T-CQ assembly serves as a crucial reference genome for integrating publicly available multi-omics data and advances the utility of the Quartet reference materials. The T2T-CQ assembly scores highly on multiple metrics of continuity and completeness, with Genome Continuity Inspector (GCI) scores of 77.76 (maternal) and 76.41 (paternal), quality values (QV) > 70, and Clipping Reveals Assembly Quality (CRAQ) scores > 99.6 for both haplotypes, enabling complete annotation of centromeric regions. Within these regions, we identified novel 13-mer higher-order repeat patterns on chromosome 17 which exhibited a monophyletic origin and emerged approximately 230 thousand years ago. Overall, this work establishes an essential genomic resource for the Han Chinese population and advances the development of a T2T pan-Chinese reference genome, which will significantly enable future investigations both into population-specific structural variants and the evolutionary dynamics of centromeres.

genomics↗