Biology subjects

Zheng, X.

Publications and source records attributed to Zheng, X..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

miR-210 locus deletion disrupts cellular homeostasis; an integrated genetic study

MiR-210 is widely recognized as the quintessential hypoxia-responsive miRNA and thought to fine-tune various facets of cellular homeostasis. We hereby present an integrative appraisal of phenotypic and molecular repercussions of disrupting the corresponding locus in human and mouse cells using multiple genetic strategies. Briefly, MIR210 deletion led to decreased cellular fitness and suboptimal responses to several stress types. Transcriptomic comparisons using different profiling platforms, performed independently by members of this collaboration, revealed consistent deregulation of neighboring genes, in locus-disrupted cells. Interestingly, the anticipated enrichment in miR-210 targets failed to materialize in unbiased analyses. Our results point to the biological significance of unrecognized regulatory elements that overlap miRNA genes and should serve as note of caution for studies based for genetic disruption of such loci.

molecular biology↗

bioRxiv2024

Temporal High-Resolution Atlas of Human Blood Leukocyte Composition in Response to Respiratory Virus Inoculation

BackgroundRespiratory viral infections produce highly variable clinical outcomes, even after controlled exposure. Human viral challenge studies are well suited to study this variation because they capture immune profiles before inoculation and across defined post-challenge intervals. However, how circulating immune-cell populations change over time, and which responses are shared or virus-specific across respiratory viruses, remains incompletely defined. MethodsWe leveraged HR-VILAGE-3K3M, a curated human respiratory viral challenge transcriptomic resource, to analyze longitudinal whole-blood profiles from H1N1, H3N2, RSV, and HRV challenge studies. Using statistical deconvolution and xCell-based digital sorting, we estimated changes in major leukocyte populations and 28 immune-cell subtypes in symptomatic infected (Sx/Inf) and asymptomatic uninfected (Asx/Uninf) participants. Across viruses, symptomatic infection was marked by a broad shared pattern of innate immune activation together with reduced circulating lymphocyte enrichment. Activated dendritic cells, monocytes, and neutrophils increased following challenge, whereas strong pDC activation was observed primarily in influenza studies. Most T-cell and B-cell populations decreased after challenge. Plasma-cell enrichment increased progressively over time. Despite this shared architecture, response timing differed by virus: H3N2 showed the earliest changes, followed by H1N1, whereas RSV responses were delayed and HRV showed more distinct immune-cell trajectories. Migration-associated transcriptional programs were detected across both innate and adaptive immune-cell populations, supporting coordinated immune-cell trafficking during infection. Baseline immune composition also differed between outcome groups, suggesting that pre-existing immune-state differences may influence infection outcomes. ConclusionsThese findings define a cellular atlas of human respiratory viral challenge responses and show that respiratory viruses induce a broadly conserved immune-response program with distinct virus-specific kinetics. This framework may help clarify immune features associated with natural resistance, symptomatic infection, and vaccine-relevant antiviral immunity.

genomics↗

bioRxiv2024

Evaluating Cross-Platform Normalization Methods for Integrated Microarray and RNA-seq Data Analysis

Integrated analysis of gene expression data across studies is important for understanding complex traits, but combining microarray and RNA-seq data remains challenging because of substantial platform-related technical differences. In this study, we evaluated ten commonly used batch-effect correction methods for cross-platform integration and classified them into three groups representing a spectrum from least to most data processing: unsupervised sample-wise methods, unsupervised gene-wise methods, and supervised methods. Unlike the first two groups, supervised methods use outcome information to guide correction. Performance was assessed for distribution alignment, clustering, outcome prediction, and differential expression (DE) analysis using three paired real microarray-RNA-seq datasets and simulation studies. Supervised methods achieved strong distribution alignment and clustering by biological group, but they introduced information leakage and inflated Type I error, making them unsuitable for unbiased discovery. Among unsupervised methods, sample-wise approaches were often conservative under balanced settings. They showed inflated Type I error under imbalanced settings. In contrast, gene-wise methods generally maintained appropriate Type I error control and achieved higher power, with limma showing the strongest DE performance. Meta-analysis that combines p-values also controlled Type I error well and provided competitive power. For outcome prediction, both sample-wise QN and gene-wise limma performed well, with limma providing the strongest overall performance and QN offering the practical advantage that new samples can be normalized to an existing reference distribution without refitting. Overall, limma is recommended as the best general-purpose method for cross-platform integration.

genetics↗

bioRxiv2024

Cell extract-based in vitro DNA replication enables sustainable cell-free gene expression

Cell extract-based cell-free gene expression (CFE) systems break cellular boundaries and create emerging platforms for synthetic biology applications. However, these systems lack intrinsic DNA replication capability, thereby limiting sustained transcription and translation in a cell-free environment. Here, we introduce a LoopReX system based on E. coli CFE by integration of the DNA replication machinery, enabling iterative in vitro DNA replication and sustainable cell-free gene expression. We establish LoopReX by integrating phi29 DNA polymerase into the crude lysate-based E. coli CFE system, allowing for coupled DNA replication and protein expression. We elucidate the synergetic mechanisms between T7 RNA polymerase and phi29 DNA polymerase in facilitating in vitro DNA replication. Additionally, we optimize LoopReX reaction conditions by machine learning strategies. Finally, we demonstrate that the enhanced LoopReX system achieves highly efficient DNA replication and protein production in an iterative, scalable, and sustainable manner. We anticipate that LoopReX will significantly advance the application of CFE in synthetic biology.

synthetic biology↗

bioRxiv2024

STIX: Long-reads based Accurate Structural Variation Annotation at Population Scale

The prioritization of Structural Variants (SV), which is needed to rank and identify potential pathogenic alleles, is still in its infancy. This is exemplified over gnomAD only being able to annotate 33.5% of GIAB SVs. To overcome this, we present the first long-read based annotation resource for both GRCh38 and CHM13-T2T reference using STIX. In contrast to previous methods, STIX indexes SV-informative long-reads themselves, can thus be easily extended and accurately annotate all SV types including insertions. STIX successfully annotated 95.9% of GIAB Tier1 SVs. STIX further improved cancer based SV prioritization by highlighting 3,563 SV from COSMIC being common in the population. We further showcase that mosaic SV can be independently gained and may be widely spread throughout the population. This highlights the need for accurate SV population frequency annotation to further facilitate the adoption of SV via long-read sequencing in medical research and clinical applications.

bioinformatics↗

bioRxiv2024

A curated collection of transcriptome datasets to study the transcriptional response in blood and nasal samples following viral respiratory inoculation and vaccination

Our understanding of the human immune systems response to viral respiratory tract infections (VRTIs) and vaccines, including the molecular mechanisms and correlates of protection, remains incomplete. Extensive transcriptomic data from inoculation and vaccination studies have been deposited in publicly available databases. However, these studies are often separate and difficult to locate. We provide a curated compendium of public gene expression data repositories for researchers to reanalyze transcriptomes from human whole blood, peripheral blood mononuclear cells (PBMCs), and nasal swab samples. This enables the study of transcriptional responses to viral inoculation or vaccination. This collection includes 18 datasets from inoculation studies and 37 datasets from vaccination studies, sourced from the NCBI Gene Expression Omnibus (GEO), ImmPort Shared Data, and ArrayExpress.

genomics↗

bioRxiv2024

Decoding Specificity of Cyanobacterial MysDs in Mycosporine-Like Amino Acid Biosynthesis through Heterologous Expression in Saccharomyces cerevisiae

Mycosporine-like amino acids (MAAs) are potent natural UV-protectants, but their industrial production is hindered by efficiency and sustainability issues of large-scale extraction of their native hosts. Heterologous expression of MAA biosynthesis pathway genes in chassis organisms provides a promising alternative route, though the substrate promiscuity of the ATP-grasp ligase MysD complicates the biosynthesis of specific MAAs. In this study, we developed a Saccharomyces cerevisiae strain with enhanced capacity of producing mycosporine-glycine (MG), through genomic expression of biosynthesis pathway genes and knockout of competing pathway genes. This strain serves as an efficient MysD expression platform, which converts MG into shinorine and porphyra-334. Through structural modelling, site-directed mutagenesis and mutant characterization, we identified two residues on the omega-loop of MysD involved in determining product specificity. We further characterized the product specificity of 20 MysDs from diverse cyanobacterial lineages and confirmed the residue pattern-product specificity correlation. Our findings provide guidance for screening, selecting, and designing novel MysDs for industrial-scale MAA production through heterologous expression.

synthetic biology↗

bioRxiv2024

OsWHY1/OsTRXz/OsMORFs complex is essential for RNA modification and early chloroplast development in rice

WHIRLY (WHY) proteins are single-stranded DNA/RNA-binding proteins that play multifaceted roles in various plant species. The regulatory mechanisms of WHY proteins in rice remains blank. Here we demonstrate that OsWHY1 in rice is required for early chloroplast development. CRISPR/Cas9-generated oswhy1 knockout lines displayed albino seedling phenotypes, abnormal chloroplast structure and comprised redox balance in leaves. OsWHY1 interacts with multiple plastid proteins, including the thioredoxin OsTRXz and two multiple organellar RNA editing factors (OsMORF8 and OsMORF9) in chloroplasts. Accordingly, several plastid genes dependent on plastid-encoded RNA polymerase (PEP) in the oswhy1 mutants were significantly depressed at both transcript and protein levels. The editing of rps14 transcripts and splicing of rpl2, along with their protein expression, were defective in the oswhy1 mutants. OsWHY1 exhibited RNA-binding activity, specifically binding to rps14 and rpl2 precursor RNAs, which underscores its role as a post-transcriptional regulator essential for normal protein synthesis in chloroplasts. Loss-of- function mutants of either OsWHY1 or OsMORF9 and OsTRXz displayed albino phenotypes, disrupted H2O2 homeostasis, and defective RNA processing in rps14 and rpl2, suggesting the OsWHY1-OsTRXz-OsMORFs regulatory module is vital for maintaining chloroplast stability and integrity through its RNA-binding activity and its role in recruiting OsTRXz and OsMORFs to ensure proper RNA modification. One sentence summaryOsWHY1 is integral to chloroplast development in rice through its RNA-binding activity and its role in recruiting OsTRXz and OsMORFs to ensure proper RNA modification.

plant biology↗

bioRxiv2024

Deep Visual Proteomics reveals DNA replication stress as a hallmark of Signet Ring Cell Carcinoma

Signet Ring Cell Carcinoma (SRCC) is a rare and highly malignant form of adenocarcinoma with increasing incidence and poor prognosis due to late diagnosis and limited treatment options. We employed Deep Visual Proteomics (DVP), which combines AI directed cell segmentation and classification with laser microdissection and ultra-high sensitivity mass spectrometry, for cell-type specific proteomic analysis of SRCC across the bladder, prostate, liver, and lymph nodes of a single patient. DVP identified significant alterations in DNA damage response (DDR) proteins, particularly within the ATR and mismatch repair (MMR) pathways, indicating replication stress as a crucial factor in SRCC mutagenicity. Additionally, we observed substantial enrichment of immune-related proteins, reflecting high levels of cytotoxic T lymphocyte infiltration and elevated PD-1 expression. These findings suggest that pembrolizumab immunotherapy may be more effective than conventional chemotherapy for this patient. Our results provide novel insights into the proteomic landscape of SRCC, identifying potential targets and open up for personalized therapeutic strategies in managing SRCC.

cancer biology↗

bioRxiv2024

Involvement of OsS40-14 in ROS and plastid organization related regulatory networks of dark-induced senescence in rice

Dark-induced senescence triggers significant metabolic changes that recycle resources and ensure plant survival. In this study, we identified a transcription factor OsS40-14 in rice, which can form homo-oligomers. The oss40-14 knockout mutants exhibited stay-green phenotype of primary leaf and flag leaf during dark-induced condition, with substantial retention of chlorophylls and photosynthetic capacity as well as remarkably reduced reactive oxygen species (ROS), while OsS40-14 overexpressing transgenic lines (oeOsS40-14) showed an accelerated senescence phenotype under dark-induced leaf senescence conditions. Transcriptome analysis revealed that when the detached leaves of oss40-14 and WT were treated in darkness condition for 72 hours, 1585 DEGs (|Log2FC| [≥]1, P value<0.05) were reprogrammed in oss40-14 relative to WT. CUT&Tag-seq analysis in protoplast transient expression of OsS40-14 system showed that OsS40-14 was 40.95% enriched in the transcription start site (TSS) of the genome. Sequence clustering analysis showed that OsS40-14 protein was mainly enriched and bound to TACCCACAAGACAC conserved elements. The seed region "ACCCA" of OsS40 proteins was identified by single nucleotide mutagenesis EMSA. The integrative analysis of transcriptome and CUT&Tag-seq datasets showed 153 OsS40-14-targeted DEGs, they mainly enriched in plastid organization and photosynthesis process at dark-induced condition in oss40-14 relative to WT. Among them, eleven candidate targets of OsS40-14 such as Glucose 6-phosphate/phosphate translocator, Na+/H+ antiporter, Catalase, Chitinase 2, Phosphate transporter 19, OsWAK32, and OsRLCK319 were directly targeted and upregulated confirmed by ChIP-PCR and RT-qPCR. It demonstrates a novel model of OsS40-14 mediating macromolecule metabolism and nutrient recycling controls the plastid organization during dark-induced leaf senescence. Significant statementInvolvement of OsS40-14 in macromolecule catabolism, nutrient recycling, and ROS homeostasis revealed a plastid organization defection of dark-induced senescence in rice

plant biology↗

bioRxiv2024

Cholecystokinin modulates age-dependent Thalamocortical Neuroplasticity

The thalamocortical pathways exhibit neuroplasticity not only during the critical period but also in adulthood. In this study, we investigated how cholecystokinin (CCK) modulates age-dependent thalamocortical plasticity. Our findings demonstrated that CCK is expressed in thalamocortical neurons and that high-frequency stimulation (HFS) of the thalamocortical pathway triggers the release of CCK in auditory cortex (ACx), as detected by a CCK sensor. HFS of the medial geniculate body (MGB) induced thalamocortical long-term potentiation (LTP) in wild-type young adult mice. However, knockdown of Cck expression in MGB neurons or blockade of the CCK-B receptor (CCKBR) in the ACx abolished HFS-induced LTP. Interestingly, this LTP could not be elicited in juvenile (3-week-old) or aged mice (over 18-month-old) due to distinct mechanisms: the absence of CCKBR in juveniles and the inability to release CCK in aged mice. Notably, exogenous administration of CCK into the ACx rescued LTP in aged mice and significantly improved frequency discrimination. These findings highlight the potential of CCK as a therapeutic intervention for ameliorating neuroplasticity deficits associated with thalamocortical connectivity.

neuroscience↗

bioRxiv2024

Efficient generation of CAR NK cells from human umbilical cord blood CD34+ stem and progenitors for democratizing affordable immunotherapy

Chimeric antigen receptor (CAR) natural killer cells (CAR NK) cells, leveraging safety and not requiring HLA match in adoptive infusion, have emerged as promising alternative cells to CAR-T cells for immunotherapies. High and multiple doses of CAR NK cell infusions are essential to maintain therapeutic efficacy in clinical trials. This requires efficient methods for generating large-scale CAR NK cells and significantly reducing CAR engineering costs. In this study, we develop a three-step strategy to generate highly high yields of induced NK (iNK) and CAR iNK cells from human umbilical cord blood CD34+ hematopoietic stem and progenitor cells (CD34+ HSPCs). Starting from a single umbilical cord blood CD34+ HSPC, our reliable method efficiently produces 14-83 million mature iNK cells or 7-32 million CAR iNK cells with high expression levels of CD16 and zero T cell contaminations. Introducing CAR expression elements at the HSPC level reduces the quantities of CAR pseudoviruses to 1 / 140.000 - 1 / 600,000 compared to engineering CARs in mature NK cells. The iNK and CAR iNK cells, including fresh cells and thawed cells from cryopreserved conditions, demonstrate remarkable tumoricidal activities against various human cancer cells and significantly prolong the survival of human tumor-bearing animals. The high yields of CAR NK cells and negligible costs of CAR engineering of our method support the broad applications of CAR NK cells for treating cancer patients.

cell biology↗

bioRxiv2024

Genetic diversity and evolution of rice centromeres

AbstractUnderstanding the mechanisms driving centromere evolution is crucial for deciphering eukaryotic evolution and speciation processes. Despite their widely recognized characteristics of conserved function in cell division, the centromeres have showed high diversity in composition and structure between species. The mechanism underlying this paradox remain poorly understood. Here, we assembled 67 high-quality rice genomes from Oryza AA group, encompassing both Asian and African rice species, and conducted an extensive analysis of over 800 nearly complete centromeres. Through de novo annotation of satellite sequences and employing a progressive compression strategy, we quantified the local homogenization and multi-layer nested structures of rice centromeres and found that genetic innovations in rice centromeres primarily arise from internal structural variations and retrotransposon insertions, along with a certain number of non-canonical satellite repeats (sati). Despite these rapid structural alterations, the single-base substitution rate in rice centromeres appears relatively lower compared to the chromosome arms. Contrary to the KARMA model for Arabidopsis centromere evolution, our model (RICE) suggests that centrophilic LTRs contribute to the decline of progenitor centromeres composed of satellite repeats, and facilitate the formation of evolutionary neo-centromeres, which are enriched with extended CENH3 binding regions beyond the native satellite arrays in plant genomes. In summary, this study provides novel insights into genomic divergence and reproductive barriers among rice species and subspecies, and advances our understanding of plant centromere evolution.

genetics↗

bioRxiv2024

VPS28 regulates triglyceride synthesis and is mediated by the ubiquitination pathway in a bovine mammary epithelial cell line and mouse model

VPS28 (vacuolar protein sorting 28) is a subunit of the endosomal sorting complexes required for transport (ESCRTs), and is involved in ubiquitination. Ubiquitination is a crucial system for protein degradation in eukaryotes. Considering the recent findings on the role of ubiquitination in regulating lipid metabolism, we hypothesized that VPS28 might affect the expression of genes involved in milk fat synthesis. To test this hypothesis, we modulated VPS28 expression in the bovine mammary epithelial cell (MAC-T) line and measured the effects on triglyceride (TG) synthesis using lentivirus-mediated techniques. The results indicated that VPS28 knockdown significantly upregulated the fatty acid transporter CD36 (CD36 molecule) and the adipose differentiation-related protein (ADFP), leading to increased TG and fatty acid production, alongside elevated expression of ubiquitin (UB) protein and reduced proteasome activity. In contrast, VPS28 overexpression increased CD36 levels without significantly affecting ADFP and TG levels, showing a trend toward reduced lipid droplets and increased UB expression and proteasome activity. Furthermore, the inhibition of the ubiquitin-proteasome system and endosomal-lysosomal pathway using epoxomicin and chloroquine, respectively, resulted in a further elevation of CD36, ADFP, and TG levels, thereby enhancing cell viability. These in vitro findings were validated in vivo by a mouse model, where VPS28 knockdown enhanced CD36, ADFP, UB expression, TG content, and lipid droplets in mammary glands, without pathological changes in mammary tissue or blood TG alterations. These results confirm the pivotal role of VPS28 in regulating TG synthesis via the ubiquitination pathway, offering novel insights into the molecular mechanisms of milk fat production in a bovine in vitro cell model.

genetics↗

bioRxiv2024

Reticulate leaf venation in Pilea peperomioides is a Voronoi diagram

Reticulate leaf venation, characterized by the presence of loops, is a distinguishing feature of many flowering plants. However, our understanding of both the geometry and the morphogenesis of reticulate vein patterns is far from complete. We show that in the Chinese money plant (Pilea peperomioides), major veins form an approximate Voronoi diagram surrounding secretory pores known as hydathodes. We also propose a mechanistic model based on polar transport of the plant hormone auxin to produce Voronoi patterns. In contrast with classical models where veins directly connect auxin sources to sinks, our model generates veins that bisect the space between adjacent auxin sources, collectively forming loops. The paradigm change offered by this model may open the door to study reticulate vein formation in other species.

plant biology↗

bioRxiv2024

An applicable and efficient retrograde monosynaptic circuit mapping tool for larval zebrafish

The larval zebrafish is a vertebrate model for in vivo monitoring and manipulation of whole-brain neuronal activity. Tracing its neural circuits remains challenging. Here, we report an applicable methodology tailored for larval zebrafish to achieve efficient retrograde trans-monosynaptic tracing from genetically defined neurons via EnvA-pseudotyped glycoprotein-deleted rabies viruses. By combinatorially optimizing multiple factors involved, we identified the CVS strain trans-complemented with advanced expression of N2cG at 36 {degrees}C as the optimal combination. It yielded a tracing efficiency of up to 20 inputs per starter cell. Its low cytotoxicity enabled the viable labeling and calcium imaging of infected neurons 10 days post-infection, spanning larval ages commonly used for functional examination. Cre-dependent labeling was further developed to enable cell-type-specific input tracing and circuit reconstruction. We mapped cerebellar circuits and uncovered the ipsilateral preference and subtype specificity of granule cell-to-Purkinje cell connections. Our method offers an efficient way for tracing neural circuits in larval zebrafish.

neuroscience↗

bioRxiv2024

Deep Visual Proteomics Unveils Precision Medicine Insights in Composite Small Lymphocytic and Classical Hodgkin Lymphoma

Coexistence of two cancer types in the same organ presents challenges for clinical decision-making, calling for personalized treatment strategies. Deep Visual Proteomics (DVP) combines AI driven single cell type analysis with laser microdissection and ultrasensitive mass spectrometry. In a composite case of classical Hodgkin lymphoma (cHL) and small lymphocytic lymphoma (SLL) in a single patient, we investigated the potential of DVP to inform precision oncology. We quantified the proteomic landscapes in the cHL and SLL to a depth of thousands of proteins. Our analysis revealed distinct proteome profiles in cHL and SLL populations, highlighting their clonal unrelatedness. Our data suggested standardized chemotherapy and interleukin-4 inhibition as potential strategies to manage chemo-resistance - instead of bone marrow transplantation. DVP highlighted minichromosome maintenance protein and proteasome inhibitors for cHL and H3K27 methylation and receptor tyrosine kinase inhibitors for SLL as subtype-specific treatments. Thus cell-type specific insights of DVP can guide personalized oncological treatments.

cancer biology↗

bioRxiv2024

Interactively Integrating Reach and Grasp Information in Macaque Premotor Cortex

Successful reach-to-grasp movements necessitate the integration of both object location and grip type information. However, how these two types of information are encoded in a single brain region and to what extend they interact with each other, remain largely unknown. We designed a novel experimental paradigm that sequentially prompted reach and grasp cues to monkeys and recorded neural activity in the dorsal premotor cortex (PMd) to investigate how the encoding structures change and interact during arm reaching and hand grasping movements. This paradigm required monkeys to retain the first prompted cue when the second one arrived, and integrate both to accomplish a final goal movement. PMd neurons represented both reach and grasp to similar extend, yet the encodings were not independent. Upon the arrival of second cue, PMd continued to encode the first cue, albeit with a significantly altered structure, as evidenced by more than half of the neurons displaying incongruent modulation. At a population level, the encoding structure formed a distinct subspace that differed from, but was not entirely orthogonal to, the original one. Employing canonical correlation analysis, we identified a subspace that consistently preserved the encoding of the initial cue, potentially serving as a mechanism for downstream brain regions to extract coherent information. Furthermore, this shared subspace comprised a diverse population of neurons, including both congruent and incongruent units. these findings support the argument that reach and grasp information are interactively integrated within PMd, with a shared subspace likely underpinning a consistent encoding framework.

neuroscience↗