Biology subjects

Zhai, W.

Publications and source records attributed to Zhai, W..

16 recordsLinked to original sources

bioRxiv2026

Single-crypt evolutionary trajectories of human sporadic and hereditary colorectal precancers

Our understanding of the earliest genomic processes and evolutionary trajectories that distinguish sporadic from hereditary human cancers remains limited, impeding early diagnosis and risk stratification. Here, we performed whole-genome sequencing of 319 single crypts dissected from normal colorectal mucosa, premalignant polyps and malignant colorectal cancers (CRCs) from five sporadic patients and three familial adenomatous polyposis (FAP) patients. We found 66% of premalignant crypts from sporadic polyps did not harbor APC mutations, but frequently accumulated non-canonical but positively selected driver mutations including KMT2C, CACNA1A and FBLN2. In contrast, most premalignant crypts (71%) in FAP indeed acquired one or more somatic APC mutations or 5q loss of heterogeneity (LOH). Sporadic polyps were dominated by clock-like mutational processes at single-crypt level. In contrast, FAP crypts evolved more diverse genomics processes, including reactive oxygen species-associated damages, APOBEC-associated mutagenesis and pks+ Escherichia coli-associated mutagenesis. Premalignant crypts in FAP also exhibited a 2-fold higher burden of LINE-1 retrotranspositions than sporadic ones, despite arising at a substantially younger age. Phylogenetic timing estimations showed that the first somatic APC mutation in FAP often occurs prenatally. Phylogeographic analysis further revealed spatial lineage segregation in early polyclonal polyps, followed by Big-Bang lineage intermixing in later monoclonal ones. Together, these data demonstrate that early colorectal tumorigenesis does not obey a universal APC-first model, where sporadic and hereditary precancers follow distinct evolutionary trajectories. Our study also highlights that polyclonal-to-monoclonal transition in premalignant stages represents the Big-Bang growth of colorectal tumors, offering crucial insight into early diagnosis and risk stratification.

cancer biology↗

bioRxiv2025

Cross-ancestry information transfer framework improves protein abundance prediction and protein-trait association identification

Genetics-informed proteome-wide association studies (PWAS) provide an effective way to map the complex molecular landscape of biological mechanisms for complex diseases. PWAS relies on an ancestry-matched reference panel to model protein expression using genetic variants as features and determine the proteins impact on phenotype. However, reference panels from underrepresented populations remain relatively limited. In this study, we developed an analytic framework that borrows information from potentially multiple ancestries to boost the protein abundance prediction accuracy in an underrepresented population. We illustrate the frameworks utility and reproducibility through application to PWAS in East Asians: BioBank Japan (BBJ), Korean Genome and Epidemiology Study (KoGES), and Taiwan Biobank (TWB). An ensemble of information-sharing approaches was integrated to build the Multi-Ancestry-based Best-performing Model (MABM). MABM substantially improved the prediction performance with higher performance observed in both cross-validation and an external validation dataset (Tongji-Huaxi-Shuangliu Birth Cohort). Leveraging the BBJ, we identified three times as many significant PWAS associations with MABM as with the baseline Lasso model. Notably, 47.5% of the MABM specific associations were reproduced in independent East Asian datasets with concordant effect sizes. Furthermore, MABM enhanced gene/protein prioritization for downstream functional validation by (1) confirming a greater number of well-established gene/protein-trait associations and (2) identifying previously uncharacterized trait-associated genes. The benefits of MABM were further validated in additional ancestries and demonstrated in brain tissue-based PWAS, underscoring its broad applicability. Our findings close critical gaps in multi-omics research, develop a new reference resource of genetic models of protein abundance, and facilitate trait-relevant protein discovery in underrepresented populations.

genomics↗

bioRxiv2025

The China Brain Multi-omics Atlas Project (CBMAP)

The China Brain Multi-omics Atlas Project (CBMAP) aims to generate a comprehensive molecular reference map of over 1,000 human brains (Phase I), spanning a broad age range and multiple regions in China, to address the underrepresentation of East Asian populations in brain research. By integrating genome, epigenome, transcriptome, proteome (including multiple post-translational modifications), and metabolome data, CBMAP is set to provide a rich and invaluable resource for investigating the molecular underpinnings of aging-related brain phenotypes and neuropsychiatric disorders. Leveraging high-throughput omics data and advanced technologies, such as spatial transcriptomics, proteomics, and single-nucleus 3D chromatin structure analysis, this atlas will serve as a crucial resource for the brain science community, illuminating disease mechanisms and enhancing the utility of data from genome-wide association studies (GWAS). CBMAP is also poised to accelerate drug discovery and precision medicine for brain disorders.

neuroscience↗

bioRxiv2025

Next-Generation Mapping of the ACINUS-Mediated Alternative Splicing Machinery and Its Regulation by O-glycosylation in Arabidopsis

Alternative splicing (AS) is a key mechanism of gene regulation, but the full repertoire of proteins involved and the regulatory mechanisms governing this process remain poorly understood. Using TurboID-based proximity labeling coupled with mass spectrometry (PL-MS), we comprehensively mapped the Arabidopsis AS machinery, focusing on the evolutionarily conserved splicing factor ACINUS, its paralog PININ, and the stable interactor SR45. We identified 298 high-confidence components, including both established and novel interactors, providing strong evidence that alternative splicing is coupled to transcription and that multiple RNA processing steps occur simultaneously in plants. Bioinformatic analysis reveals high redundancy, conserved mechanisms, and unique plant-specific features. Selected known and novel interactors were validated by AS readouts and phenotypic analysis, which also revealed a coordinated influence on splicing. Furthermore, a systematic evaluation of O-glycosylation double mutants revealed that SECRET AGENT (O-GlcNAc transferase) and SPINDLY (O-fucose transferase) modulate AS through both ACINUS-dependent and -independent pathways. Our results reveal the conserved as well as plant-specific AS regulatory network and highlight the global role of sugar modification in RNA processing.

plant biology↗

bioRxiv2024

Single-cell and spatial atlas of steatotic liver-related hepatocellular carcinoma

Steatotic liver disease-related hepatocellular carcinoma (SLD-HCC) poses significant challenges in liver cancer management. Our current study investigates the tumor microenvironment (TME) of SLD-HCC using single-cell transcriptomic, proteomic and spatial transcriptomic analyses. We identified altered immune-related and lipid metabolism pathways, particularly in regulatory T cells (Tregs) and cancer-associated fibroblasts (CAFs) within the SLD-HCC microenvironment, suggesting distinct cellular adaptations to a high-fat TME and general immunosuppression. Cytometry by time-of-flight revealed a cold and immunosuppressive TME depleted with CD8+ T cells and enriched with Tregs, while spatial transcriptomics uncovered a unique spatial architecture with Treg/CAF clusters specifically located at the tumor margins in SLD-HCC. Crucially, we identified Treg-CAF interactions as a key mediator associated with lack of response to immunotherapy in SLD-HCC. Our findings highlight the intricate immune dynamics of SLD-HCC, indicating potential therapeutic targets to counteract immune evasion and restore anti-tumor immunity in SLD-HCC. HighlightsO_LIThe TME of SLD-HCC exhibits altered immune and lipid pathways C_LIO_LIImmunosuppressive SLD-HCC TME is depleted with CD8+ T cells and enriched with Tregs C_LIO_LISLD-HCC has a unique spatial architecture with Treg-CAF clusters at tumor margins C_LIO_LITreg-CAF interaction via TNFSF14-TNFRSF14 axis mediates immunotherapy resistance C_LI

immunology↗

bioRxiv2023

Intermittent fasting promotes ILC3s secreting IL-22 contributing to the beigeing of white adipose tissue

Mechanism underlying the metabolic benefit of intermittent fasting remains largely unknown. Here, we reported that intermittent fasting promoted IL-22 production by type 3 innate lymphoid cells (ILC3s) and subsequent beigeing of subcutaneous white adipose tissue. Adoptive transfer of intestinal ILC3s increased beigeing of white adipose tissue in diet-induced-obese mice. Exogenous IL-22 significantly increased the beigeing of subcutaneous white adipose tissue. Deficiency of IL-22 receptor attenuated the beigeing induced by intermittent fasting. Single-cell sequencing of sorted intestinal immune cells revealed that intermittent fasting increased aryl hydrocarbon receptor signaling in ILC3s. Analysis of cell-cell ligand receptor interactions indicated that intermittent fasting may stimulate the interaction of ILC3s with dendritic cells (DCs) and macrophages. These results establish the role of intestinal ILC3s in beigeing of white adipose tissue, suggesting that ILC3/IL-22/IL-22R axis contributes to the metabolic benefit of intermittent fasting.

physiology↗

bioRxiv2023

A Cost-Effective CRISPR/Cas9-Based Method for Sequencing the Functional Antibody Kappa Chain cDNA from Hybridomas Expressing Aberrant Kappa Chain mRNAs

One prerequisite for generating recombinant antibodies for therapeutic and non-therapeutic purposes from hybridoma clones is the reliable, efficient, and cost-effective sequencing of the hybridoma clone that produces the desired antibody. However, many hybridoma fusion partners produce aberrant endogenous mRNA transcripts most of which resemble kappa chains. These aberrant kappa chain mRNAs can interfere with or even prevent the determination of the functional murine antibody kappa chain cDNA sequences during the PCR amplification step. In this paper, we report the development of a rapid and cost-effective CRISPR/Cas9 based method to eliminate the aberrant endogenous sequence. We have demonstrated the effectiveness of this method by significantly reducing the number of an endogenous aberrant kappa chain transcript known as the aberrant SP2/0 kappa chain. This transcript is produced by the commonly used fusion partner known as SP2/0 which is a myeloma-derived cell line. Here, we first cloned and sequenced two hybridoma clones using this method (clones A1E7 and A9E11). Our results showed a 24 to 25 percent reduction of the aberrant chain sequences (method 1) from the sequencing results. We then optimized this method (method 2) and used it to clone and sequence a third hybridoma clone (clone 262). This optimized method allowed us to achieve an 88% reduction of the aberrant kappa chain sequences.

molecular biology↗

bioRxiv2023

Gene expression plasticity followed by genetic change during colonization a high-elevation environment

Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called "plasticity first". Herein we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestral stage), experimentally implemented hypoxia acclimation (plastic stage) and colonized highland (colonized stage). Using a group of co-expressed genes from the cardiac and flight muscle, respectively, we demonstrate that gene expression plasticity to hypoxia tolerance is more often reversed than reinforced at the colonized stage. By correlating gene expression change with muscle phenotypes, we show that colonized tree sparrows reduce maladaptive plasticity that largely associates with decrease hypoxia tolerance. Conversely, adaptive plasticity that is congruent with increase hypoxia tolerance is often reinforced in the colonized tree sparrows. Genes displaying large levels of reinforcement or reversion plasticity (i.e., 200% of original level) show greater genetic divergence between ancestral and colonized populations. Overall, our work demonstrates that gene expression plasticity at the initial stage of high-elevation colonization can be reversed or reinforced through selection-driven adaptive modification.

evolutionary biology↗

bioRxiv2022

Phen2Disease: A Phenotype-driven Semantic Similarity-based Integrated Model for Disease and Gene Prioritization

By utilizing the Human Phenotype Ontology (HPO), recent approaches to prioritizing disease-causing genes for patients become popular. However, these approaches do not comprehensively use information about phenotypes of diseases and patients. We present a new method called Phen2Disease that calculates similarity scores between two phenotype sets of patients and diseases by which to prioritize diseases and genes. Specifically, we calculate three scores of information content-based similarities using the phenotypes, and their combination as the respective benchmarks, and integrate them as a final score. Comprehensive experiments were conducted on six real data cohorts with 2051 cases and two simulated data cohorts with 1000 cases. Compared with the three state-of-the-art methods, if we only use phenotype information and HPO knowledge base, Phen2Disease outperformed all of them, particularly in cohorts with the less average numbers of HPO terms. We have found that patients with higher information content scores had more specific information so their predictions would be more accurate. In addition, Phen2Disease has high interpretability with ranked diseases and patient HPO terms provided.

genetics↗

bioRxiv2022

Cell division history encodes directional information of fate transitions

Single-cell RNA-sequencing (scRNA-seq) enables systematic mapping of cellular differentiation trajectories. However, inferring the cell-fate transitions under diseases or perturbations is still challenging due to the high cellular plasticity. Here, we demonstrate that monotonically expressed genes (MEGs) along cell divisions record the directions of state transitions regardless of the cellular processes. We developed a computational framework (PhyloVelo) to identify MEGs and reconstruct a novel transcriptomic velocity field by leveraging both scRNA-seq and phylogenetic information. PhyloVelo accurately recovered linear, bifurcated and convergent differentiations in simulations and C. elegans. It outperformed current approaches for delineating cellular trajectories in embryo development and tumor evolution through analysis of five CRISPR/Cas9-based lineage tracing datasets. Together, our study unveils an internal cellular clock and provides a powerful method for cellfate analysis in diverse biological contexts.

genomics↗

bioRxiv2022

Probabilistic embedding and clustering with alignment for spatial transcriptomics data integration with PRECAST

Spatially resolved transcriptomics involves a set of emerging technologies that enable the transcriptomic profiling of tissues with the physical location of expressions. Although a variety of methods have been developed for data integration, most of them are for single-cell RNA-seq datasets without consideration of spatial information. Thus, methods that can integrate spatial transcriptomics data from multiple tissue slides, possibly from multiple individuals, are needed. Here, we present PRECAST, a data integration method for multiple spatial transcriptomics datasets with complex batch effects and/or biological effects between slides. PRECAST unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, while requiring only partially shared cell/domain clusters across datasets. Using both simulated and four real datasets, we show improved cell/domain detection with outstanding visualization, and the estimated aligned embeddings and cell/domain labels facilitate many downstream analyses. We demonstrate that PRECAST is computationally scalable and applicable to spatial transcriptomics datasets from different platforms.

genomics↗

bioRxiv2021

Dysfunction of novel energy sensor NFE2L1 leads to uncontrollable AMPK signal and glucose metabolism reprogramming

NFE2L1 (also called Nrf1) acts a core regulator of redox signaling and metabolism homeostasis, and thus its dysfunction results in multiple systemic metabolic diseases. However, the molecular mechanism(s) by which NFE2L1 regulates glycose and lipid metabolism is still elusive. Here, we found that the loss of NFE2L1 in human HepG2 cells led to a lethal phenotype upon glucose deprivation. The uptake of glucose was also affected by NFE2L1 deficiency. Further experiments unveiled that although the glycosylation of NFE2L1 was monitored through the glycolysis pathway, it enabled to sense the energy state and directly interacted with AMPK. These indicate that NFE2L1 can serve as a dual sensor and regulator of glucose homeostasis. In-depth sights into transcriptome, metabolome and seahorse data further unraveled that glucose metabolism was reprogrammed by disruption of NFE2L1, so as to aggravate the Warburg effect in NFE2L1-silenced hepatoma cells, along with the mitochondrial damage observed under the electron microscope. Collectively, these demonstrate that disfunction of NFE2L1 triggers the uncontrollable signaling by AMPK towards glucose metabolism reprogramming in the liver cancer development.

molecular biology↗

bioRxiv2021

Small RNA profiling in Mycobacterium insights into stress adapt ability

Mycobacteria would encounter a number of environment changes during infection, and respond to it using different mechanisms. sRNA is a posttranscriptionally regulatory system for the function of genes and has been investigated in many other bacteria. Here, we used Mycobacterium tuberculosis and Mycobacterium bovis BCG infection models and sequenced the whole bacterial RNAs before and after host cells infection. Comparison of differential expressed sRNAs, by using GO and KEGG, and target predication, was carried out. Six pathogenically relevant stresses, drug resistance test, growth rate and morphology were used for screening and identify sRNAs. From these data, we identified a subset of sRNAs that are differentially expressed in multiple infection groups and stress conditions. We found that many of them were associated with lipid metabolism. Among them, ncBCG427, was significantly down-regulated when BCG entered into macrophages, and was associated with increase of biofilm formation and changed in drug susceptibility. Then, reduction of virulence possibility depends on regulating lipid metabolism.

zoology↗

bioRxiv2021

Obtaining Spatially Resolved Tumor Purity Maps Using Deep Multiple Instance Learning In A Pan-cancer Study

Tumor purity is the proportion of cancer cells in the tumor tissue. An accurate tumor purity estimation is crucial for accurate pathologic evaluation and for sample selection to minimize normal cell contamination in high throughput genomic analysis. We developed a novel deep multiple instance learning model predicting tumor purity from H&E stained digital histopathology slides. Our model successfully predicted tumor purity from slides of fresh-frozen sections in eight different TCGA cohorts and formalin-fixed paraffin-embedded sections in a local Singapore cohort. The predictions were highly consistent with genomic tumor purity values, which were inferred from genomic data and accepted as the golden standard. Besides, we obtained spatially resolved tumor purity maps and showed that tumor purity varies spatially within a sample. Our analyses on tumor purity maps also suggested that pathologists might have chosen high tumor content regions inside the slides during tumor purity estimation in the TCGA cohorts, which resulted in higher values than genomic tumor purity values. In short, our model can be utilized for high throughput sample selection for genomic analysis, which will help reduce pathologists workload and decrease inter-observer variability. Moreover, spatial tumor purity maps can help better understand the tumor microenvironment as a key determinant in tumor formation and therapeutic response.

cancer biology↗

bioRxiv2018

Genome sequencing analysis identifies high-risk Epstein-Barr virus subtypes for nasopharyngeal carcinoma

Epstein-Barr virus (EBV) infection is ubiquitous worldwide and associated with multiple cancers including nasopharyngeal carcinoma (NPC). The role of EBV viral genomic variation in NPC development and its striking endemicity in southern China has been poorly explored. Through large-scale genome sequencing and association study of EBV isolates from China, we identified two non-synonymous EBV variants within BALF2 strongly associated with NPC risk (conditional P value 1.75x10-6 for SNP162476_C and 3.23x10-13 for SNP163364_T), whose cumulative effects contributed to 83% of the overall risk in southern China. Phylogenetic analysis of the risk variants revealed a unique origin in southern China followed by clonal expansion. EBV BALF2 haplotype carrying the risk variants were shown to reduce viral lytic DNA replication, as a result potentially promoting viral latency. Our discovery has not only provided insight to the unique endemic pattern of NPC occurrence in southern China, but also paved the way for the identification of individuals at high risk of NPC and effective intervention program to reduce the disease burden in southern China.

genetics↗

bioRxiv2018

Preclinical Study: Sunitinib-suppressed MiR-452-5p Facilitates Renal Cancer Cell Invasion and Metastasis Through Modulating SMAD4/SMAD7/EMT Signals

Although microRNAs (miRNAs) have been revealed as crucial modulators in tumor metastasis and target therapy, our understanding of their roles in metastatic renal cell carcinoma (mRCC) and Sunitinib treatment is limited. Here, We focused on 2 published microarray data to select out our anchored miRNA which was downregulated after Sunitinib treatment while upregulated in metastasis RCC tissues. Then we discovered that treating with Sunitinib, the targeted receptor tyrosine kinase inhibitor (TKI), inhibited renal cell migration and invasion via attenuating the expression of miR-452-5p. The novel identified miR-452-5p was upregulated and associated with poor prognosis in RCC. Preclinical studies using multiple RCC cells and xenografts model illustrated that miR-452-5p could promote RCC cell migration and invasion in vitro and in vivo. Mechanistically, P65 could directly bind to the miR-452-5p promoter and thus transcriptionally induce miR-452-5p expression, which led to post-transcriptionally abrogate SMAD4 expression, thus inhibition of its downstream signals including SMAD7 and EMT (Epithelial-Mesenchymal Transition) associated genes. Our study presented a road map for targeting this newly identified miR-452-5p and its SMAD4/SMAD7/EMT signals pathway, which imparted a new potential therapeutic strategy for mRCC treatment.

cancer biology↗