Biology subjects

Pei, G.

Publications and source records attributed to Pei, G..

16 recordsLinked to original sources

bioRxiv2026

A human gut-BBB-brain microphysiological model for studying neurodegenerative diseases

The gut-brain axis has emerged as a crucial factor in neurodegeneration, with growing evidence linking gut dysbiosis and metabolic dysfunction to Alzheimers disease (AD) progression. Unfortunately, the lack of human-relevant in vitro models limits our ability to effectively explore the mechanism of this axis. To address this gap, we have developed a human induced pluripotent stem cell (iPSC)-derived gut-blood-brain barrier (BBB)-brain microphysiological system that enables systematic investigation of gut-brain interaction in the context of AD under controlled conditions. Our findings reveal that the interaction between gut and brain organoids can promote the maturation of brain organoids, making them more similar to their physiological characteristics in vivo. Additionally, co-culture gut and brain organoids better recapitulates the pathological features of AD. We also discovered that gut organoids of AD can trigger neurodegenerative disease manifestations in healthy brain organoids. In summary, our microphysiological system provides a novel and versatile in vitro platform for studying the interaction between the gut and brain in neurodegenerative diseases.

neuroscience↗

bioRxiv2026

Cell Type Architecture and Positional Gene Gradients in an Adult Animal at Subcellular Resolution

The spatial organization of cell types and gene expression underlies tissue architecture and organismal physiology. However, resolving complete cellular and molecular landscapes within a three-dimensional context remains challenging, particularly in organisms with high cellular heterogeneity and complex geometry. Here, we developed a semi-supervised workflow to reconstruct high-resolution three-dimensional spatial transcriptomic models of the planarian Schmidtea mediterranea at single-cell resolution. Planarians are basal bilaterians capable of regenerating body structures after injury. Our reconstruction maps the distribution of cell types and spatially patterned gene expression across the intact organism and identifies 119 candidate positional control genes (PCGs). These genes are expressed across muscle, neural, and epidermal populations. Functional perturbation of selected candidates, including pitx3, ptpn11, pi4ka, upf3b, and cul1, revealed roles in regeneration following injury. In addition, we identify intestinal cells as prominent components of the microenvironment surrounding adult tgs1 pluripotent stem cells (neoblasts). Together, these results demonstrate the utility of three-dimensional spatial transcriptomic reconstruction for mapping cellular architecture and positional gene regulation in complex adult organisms.

developmental biology↗

bioRxiv2026

4D Single-Cell Spatial Transcriptomics Reveals Dynamic Morphogenetic Gradients and Regenerative Domains in Planarians

Regeneration relies on precise spatiotemporal gene expression and cellular responses to establish tissue identity and body patterning. Using high-resolution Stereo-seq (715 nm) on 353 sections from 16 whole animals at 8 regeneration timepoints, we constructed a 4D spatiotemporal transcriptomic map of planarian regeneration. Our analysis captured 36 refined cell types from 3,508,004 segmented cells, enabling genome-wide transcriptional imputation of gene expression dynamics across body axes at cellular, tissue, and organismal scales. We identified dynamic positional gradients and distinct spatially distributed cell types during regeneration, including an injury-induced Anterior Regenerative Zone (ARZ). The ARZ exhibited enriched positional signals in epidermal, muscle, and neural cells and was regulated by Mediator 8, which is crucial for polarity remodeling and blastema formation. This study provides a comprehensive spatial molecular and cellular map of regenerative processes, highlighting injury-induced spatial domains and key regulatory factors in planarian regeneration. We also provide an interactive web portal, offering a valuable resource for exploring and analyzing regeneration mechanisms in a spatiotemporal context.

developmental biology↗

bioRxiv2025

A spatial atlas of chemoradiation therapy in pancreatic cancer identifies cellular and microenvironmental determinants of persister populations

The molecular pathways involved in the response to radiation therapy in pancreatic ductal adenocarcinoma (PDAC) remain poorly understood. We aimed to elucidate the adaptive mechanisms and cellular interactions within PDAC to radiation therapy (RT). We constructed a transcriptomic landscape of the cellular subtypes and spatially resolved neighborhoods from 50 patient samples, including 16 longitudinally matched single cell RNA sequencing and 34 spatial transcriptomics specimens. To resolve shortcomings of cell-type mixtures in spatial data, we developed a novel statistical method called SpaCCI (spatially aware analysis of cell-cell interactions) to profile cell-cell interactions and ligand-receptor enrichment. This revealed CXCL12/TGF{beta}-driven persister cell niches where activated fibroblasts reprogram tumor- associated macrophages and spatially exclude stress-response CD8 T cells after RT. Persister cancer cells displayed transcriptional evidence of recalcitrance to metal-induced cell death pathways of ferroptosis and cuproptosis which were recapitulated in preclinical models. Our study reveals the selective pressures experienced by PDAC following RT that may help provide insight for future multimodal therapeutic strategies.

cancer biology↗

bioRxiv2024

Exploring virus-host interactions through combined proteomic approaches identifies BANF1 as a new essential factor for African Swine Fever Virus.

African swine fever virus (ASFV) causes a highly lethal disease in pigs and represents a significant threat to the global pork industry due to the lack of effective vaccines or treatments. Despite intensive research, many ASFV proteins remain uncharacterized. This study aimed to elucidate the functions of two ASFV proteins, MGF360-21R and A151R, through comprehensive analysis of their interactions with host proteins. Using affinity purification-mass spectrometry and yeast two-hybrid screening approaches, we identified the host protein barrier- to-autointegration factor 1 (BANF1) as a key interactor of both viral proteins. Biochemical and colocalization assays confirmed these interactions and demonstrated that MGF360-21R and A151R expression leads to cytoplasmic relocalization of BANF1. Functionally, BANF1 silencing significantly reduced ASFV replication, indicating its proviral role. Given BANF1s established function in regulating the cGAS/STING-dependent type I interferon (IFN-I) response, we postulated that A151R and MGF360-21R could inhibit this pathway. Using different strategies, we showed that both A151R and MGF360-21R did indeed inhibit IFN-I induction. Generation of ASFV deficient of A151R or MGF360-21R showed that both mutant viruses enhanced the host IFN response in primary porcine macrophages compared to wild-type virus. However, their capacity to inhibit this pathway could occur through mechanisms independent of BANF1. Proteomic analysis of BANF1 interactors during ASFV infection highlighted potentially roles in chromatin remodeling, nuclear transport, and innate immune response pathways. Altogether, our data provide new insights into ASFV-host interactions, identifying BANF1 as an important new host factor required for replication and uncovering novel functions for A151R and MGF360-21R. Author SummaryAfrican swine fever virus (ASFV) is a highly contagious and deadly disease affecting pigs worldwide, for which there are currently no effective vaccines or treatments. Despite extensive research, many ASFV proteins remain poorly understood. Our study investigated two ASFV proteins, MGF360-21R and A151R, to better understand their functions and interactions with host proteins. Using proteomic approaches, we found both these viral proteins interact with a host protein called barrier-to-autointegration factor 1 (BANF1). Importantly, BANF1 silencing significantly reduced ASFV replication, indicating its important role in the viral life cycle. We also showed that MGF360-21R and A151R help the virus evade the immune system by blocking the production of interferons, which are key defensive molecules against viral infections. However, this immune evasion does not seem to depend on their interaction with BANF1. Additionally, our analysis of BANF1s interactions during ASFV infection revealed potential roles in chromatin remodeling, nuclear transport, and the innate immune response. These findings provide new insights into how ASFV interacts with its host and highlight BANF1 as a critical factor in viral replication and immune evasion. Our work contributes to a better understanding of ASFV and could pave the way for developing more effective strategies to fight this virus.

microbiology↗

bioRxiv2024

Sequence Composition Dictates Condensate Miscibility

Numerous biomolecular condensates coexist within cells, yet the mechanisms governing their mixing and demixing remain elusive. To investigate how the amino acid composition of intrinsically disordered regions (IDRs) affects condensate coexistence, we paired and tested 28 IDRs in 378 different combinations. Our results reveal that IDRs enriched in serine or aromatic amino acids tend to form miscible condensates. Conversely, IDRs with high charge levels form immiscible condensates, even when the serine levels are artificially boosted. Additionally, phosphorylation acts as a switch, modulating condensate miscibility. We also observed that the miscibility between transcription factor condensates and Pol II condensates profoundly influences transcription. We engineered transcription factors by increasing serine content, enhancing both their miscibility with Pol II and their transcriptional activity. However, introducing high levels of charge had the opposite effect. These findings shed light on the fundamental mechanisms controlling condensate miscibility and offer insights for designing specific functional condensates.

molecular biology↗

bioRxiv2024

Astrocyte-specific secretome profiling reveals its correlation with neurological disorders

Secreted proteins mediate intercellular communication throughout the lives of multicellular organisms. However, due to the lack of new technology for secreted protein capturing, the progress of "secretomics lags behind. Here, we report a two-step secretome enrichment method (tsSEM) combining unnatural amino acid labeling and click chemistry-based biorthogonal reaction, which enables in vitro secretome profiling in the presence of serum. Using this novel method, we systematically investigated the secretome of human iPSCs-derived astrocytes (iAst) in different disease models and identified a panel of astrocyte-secreted proteins that are responsible for its non-cell autonomous toxicity under disease conditions. Furthermore, we validated two astrocytes-derived novel neurotrophic proteins, FAM3C and KITLG, which we identified from disease models, and found that they could boost neurite outgrowth, protect neurons, and promote neural progenitor proliferation. Our study highlights the utility of secretome profiling of iAst and demonstrates its applications in disease study and target identification and validation in drug development.

neuroscience↗

bioRxiv2024

Interpretable scRNA-seq Analysis with Intelligent Gene Selection

AO_SCPLOWBSTRACTC_SCPLOWSingle-cell RNA sequencing (scRNA-seq) data analysis faces multiple challenges, including high dimensionality, significant noise, and data loss. To effectively address these issues, we introduce AIGS, a robust and transparent single-cell analysis framework. AIGS utilizes an intelligent gene selection method that systematically identifies the most informative genes for clustering based on the normalized mutual information between pre-learned pseudo-labels and quantified genes. Additionally, AIGS incorporates a scale-invariant distance metric to assess cell-to-cell similarity, enhancing connections between homogenous cells and ensuring more accurate and robust results. Through comprehensive comparisons with state-of-the-art techniques, AIGS demonstrates superior performance in both clustering accuracy and multi-resolution visualization quality. Our in-depth analysis of clustering and visualization results further reveals that AIGS can uncover complex, stage-specific gene expression patterns during the same developmental cell stage.

bioinformatics↗

bioRxiv2024

Reconstructing bat antiviral immunity using epithelial organoids

Bats are remarkably resilient to viruses with pandemic potential. To resolve largely unknown molecular mechanisms governing their exceptional antiviral immunity, we established an organoid platform to model the entire respiratory airway and intestinal epithelium of the important viral reservoir species Rousettus aegyptiacus (Egyptian fruit bat). These bat organoids exhibit an unexpected diversity of cell types and support replication of highly pathogenic zoonotic viruses including Marburg virus (MARV) and MERS-Coronavirus. Following virus infection, bat organoids unleash a strong interferon response, uniquely regulated through virus-dependent and virus-independent mechanisms. By contrast, MARV infected human organoids fail to induce an antiviral gene response and express pro-inflammatory cytokines after interferon stimulation, revealing important molecular differences between bats and humans with implications for lethal Marburg virus infections in primates. These data provide the most comprehensive organoid platform in bats to decode species-specific differences and uncover fundamental principles of bat disease resilience to emerging viruses with pandemic potential.

immunology↗

bioRxiv2023

Competitive fitness and homologous recombination of SARS-CoV-2 variants of concern

SARS-CoV-2 variants continue to emerge and cocirculate in humans and wild animals. The factors driving the emergence and replacement of novel variants and recombinants remain incompletely understood. Herein, we comprehensively characterized the competitive fitness of SARS-CoV-2 wild type (WT) and three variants of concern (VOCs), Alpha, Beta and Delta, by coinfection and serial passaging assays in different susceptible cells. Deep sequencing analyses revealed cell-specific competitive fitness: the Beta variant showed enhanced replication fitness during serial passage in Caco-2 cells, whereas the WT and Alpha variant showed elevated fitness in Vero E6 cells. Interestingly, a high level of neutralizing antibody sped up competition and completely reshaped the fitness advantages of different variants. More importantly, single clone purification identified a significant proportion of homologous recombinants that emerged during the passage history, and immune pressure reduced the frequency of recombination. Interestingly, a recombination hot region located between nucleotide sites 22995 and 28866 of the viral genomes could be identified in most of the detected recombinants. Our study not only profiled the variable competitive fitness of SARS-CoV-2 under different conditions, but also provided direct experimental evidence of homologous recombination between SARS-CoV-2 viruses, as well as a model for investigating SARS-CoV-2 recombination. ImportanceSARS-CoV-2 variants or subvariants keep emerging and the epidemic strains keeps changing in humans and animals. The continued replacement of the epidemic strains was attributed to higher competitive fitness evolved by the newly appeared ones than the older ones, but which factors affect the final outcomes are still not entirely clear. In this study, we performed in vitro coinfection and serial passage with three VOCs and WT under different conditions. Our results showed that the competition outcomes of these viral strains varied in different cell lines or under different immune pressure, confirming the probable effects of these two factors for the competitive fitness of different SARS-CoV-2 viral strains. Meanwhile, strikingly, we found that coinfection and serial passage with different SARS-CoV-2 viral strains can mimic the recombination process of SARS-CoV-2 occurred in coinfection individual, indicating it is a novel model to investigate the SARS-CoV-2 recombination mechanism.

microbiology↗

bioRxiv2022

Single-cell multi-omics decodes regulatory programs during development of mouse secondary palate

The abnormal perturbation in gene regulation during palatogenesis may lead to cleft palate, a major congenital birth defect in humans and mice. However, a comprehensive multi-omic map of the developing secondary palate at single-cell resolution is lacking. In this study, we performed single-cell multiome sequencing and profiled chromatin accessibility and gene expression simultaneously within the same cells (n = 36,154) isolated from mouse secondary palate across embryonic days (E) 12.5, E13.5, E14.0, and E14.5. Application of optimal transport reconstructed five trajectories, representing continuous differentiation of multipotent cells into different subpopulations in later stages. By linking open chromatin signals to gene expression changes, we discovered a list of lineage-determining transcription factors, such as Shox2 for the anterior and Dlx1/2 for the posterior palatal mesenchymal trajectories. In conclusion, this study charted epigenetic and transcriptional dynamics during palatogenesis, which provides a valuable resource for the community and facilitate future research in cleft palate. HighlightsO_LIThe first report on building a single-cell multi-omics atlas with joint chromatin accessibility and gene expression measurements from the same cells during the development of mouse secondary palate. C_LIO_LIApplication of optimal transport calculated fate probabilities to different terminal states and recovered continuous landscapes during mouse secondary palate development. C_LIO_LIBy linking cis-regulatory DNA elements to target genes, we characterized a series of transcription factors governing the differentiation of cranial neural crest-derived multipotent cells to the anterior and posterior palatal mesenchymal trajectories, respectively. C_LIO_LITranscription factors Shox2 and Dlx1/2 exhibited top regulatory roles for the anterior and posterior palatal mesenchymal trajectories, respectively, showing significant enrichment in both motif accessibility and gene expression. C_LI

developmental biology↗

bioRxiv2022

A single-cell atlas of the human brain in Alzheimer's disease and its implications for personalized drug repositioning

Alzheimers disease (AD) is a neurodegenerative disease with complex pathophysiology, and AD-dysregulated pathways are inconsistent across different brain regions and patients. Although single-cell RNA sequencing (scRNA-seq) has been performed in different regions of postmortem AD brains, the common and distinct molecular features among different regions remains largely unclear. This hinders the discovery of repurposable and personalized drugs for AD. We combined four scRNA-seq datasets and systematically investigated the common and distinct cellular responses, cell subpopulations, and transcription factors involved in AD. Moreover, we explored the transcriptional heterogeneity of different AD subtypes at the single-cell level. Finally, we conducted individual-based drug repurposing analysis to explore repurposable and personalized drugs. Six major brain cell types were detected after scRNA-seq batch-effect removal and noise cells filtering. Integration with genome-wide association studies (GWAS) summary statistics demonstrated that AD-susceptible genes were mainly enriched with differentially expressed genes (DEGs) in glial cells rather than neuronal cells. While most of DEGs were regulated in opposite directions among different cell types, cell-cell communication analysis revealed several common cellular interaction events involved in neurogenesis, as well as increased cell-cell adhesion. Our comprehensive drug repositioning analysis identified new candidates for AD treatment, including trichostatin, which was predicted to be broadly applicable to different identified AD subtypes, and vorinostat, which was specific for one subtype of AD. In summary, we delineated a cell-specific atlas of the AD transcriptome. Our work illustrated strong cellular heterogeneity in AD for defining AD subtypes. The cell-specific features are important for understanding AD etiology, progression, and drug discovery.

bioinformatics↗

bioRxiv2021

deCS: A tool for systematic cell type annotations of single-cell RNA sequencing data among human tissues

Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex and dynamic cellular mechanisms. However, cell-type annotation remains a main challenge as it largely relies on a priori knowledge and manual curation, which is cumbersome and less accurate. The increasing number of scRNA-seq data sets, as well as numerous published genetic studies, motivated us to build a comprehensive human cell type reference atlas. Here, we present deCS (decoding Cell type-Specificity), an automatic cell type annotation method augmented by a comprehensive collection of human cell type expression profiles and marker genes. We used deCS to annotate scRNA-seq data from various tissue types and systematically evaluated the annotation accuracy under different conditions, including reference panels, sequencing depth and feature selection strategies. Our results demonstrated that expanding the references is critical for improving annotation accuracy. Compared to many existing state-of-the-art annotation tools, deCS significantly reduced computation time and increased accuracy. deCS can be integrated into the standard scRNA-seq analytical pipeline to enhance cell type annotation. Finally, we demonstrated the broad utility of deCS to identify trait-cell type associations in 51 human complex traits, providing deeper insights into the cellular mechanisms of disease pathogenesis. All documents, including source code, user manual, demo data, and tutorials, are freely available at https://github.com/bsml320/deCS.

bioinformatics↗

bioRxiv2020

Extensive High-Order Complexes within SARS-CoV-2 Proteome Revealed by Compartmentalization-Aided Interaction Screening

Bearing the largest single-stranded RNA genome in nature, SARS-CoV-2 utilizes sophisticated replication/transcription complexes (RTCs), mainly composed of a network of nonstructural proteins and nucleocapsid protein, to establish efficient infection. Here, we developed an innovative interaction screening strategy based on phase separation in cellulo, namely compartmentalization of protein-protein interactions in cells (CoPIC). Utilizing CoPIC screening, we mapped the interaction network among RTC-related viral proteins. We identified a total of 47 binary interactions among 14 proteins governing replication, discontinuous transcription, and translation of coronaviruses. Further exploration via CoPIC led to the discovery of extensive ternary complexes composed of these components, which infer potential higher-order complexes. Taken together, our results present an efficient, and robust interaction screening strategy, and indicate the existence of a complex interaction network among RTC-related factors, thus opening up new opportunities to understand SARS-CoV-2 biology and develop therapeutic interventions for COVID-19.

microbiology↗

bioRxiv2020

Berberine reverses multidrug resistance in Candida albicans by hijacking the drug efflux pump Mdr1p

Clinical use of antimicrobials faces great challenges from the emergence of multidrug resistant (MDR) pathogens. The overexpression of drug efflux pumps is one of the major contributors to MDR. It is considered as a promising approach to overcome MDR by reversing the function of drug efflux pumps. In the life-threatening fungal pathogen Candida albicans, the major facilitator superfamily (MFS) transporter Mdr1p can excrete many structurally unrelated antifungals, leading to multidrug resistance. Here we report a counterintuitive case of reversing multidrug resistance in C. albicans by using a natural product berberine to hijack the overexpressed Mdr1p for its own importation. Moreover, we illustrate that the imported berberine accumulates in mitochondria, and compromises the mitochondrial function by impairing mitochondrial membrane potential and mitochondrial Complex I. It results in the selective elimination of Mdr1p overexpressed C. albicans cells. Furthermore, we show that berberine treatment can prolong the mean survival time (MST) of mice with a blood-borne dissemination of Mdr1p overexpressed multidrug resistant candidiasis. This study provided a potential direction of novel anti-MDR drug discovery by screening for multidrug efflux pump converters.

microbiology↗

bioRxiv2018

Tissue-Specific Enrichment Analysis (TSEA) to decode tissue specificity

MotivationDiseases and traits are under dynamic tissue-specific regulation. However, heterogeneous tissues are often collected in biomedical studies, which reduce the power in the identification of disease-associated variants and gene expression profiles.\n\nResultsWe present TSEA, an R package to conduct Tissue-Specific Enrichment Analysis (TSEA) with two built-in reference panels. Statistical methods are developed and implemented for detecting tissue-specific genes and for enrichment test of different forms of query data. Our applications using multi-trait genome-wide association data and cancer expression data showed that TSEA could effectively identify the most relevant tissues for each query trait or sample, providing insights for future studies.\n\nAvailabilityhttps://github.com/bsml320/TSEA\n\nContactpeilin.jia@uth.tmc.edu or zhongming.zhao@uth.tmc.edu

bioinformatics↗