Biology subjects

Nguyen, T. C.

Publications and source records attributed to Nguyen, T. C..

7 recordsLinked to original sources

bioRxiv2026

Mapping the regulatory wiring of endothelial cell differentiation reveals a critical role for Hippo mechanosignaling

At each step of development, stem cells encounter a branching decision to differentiate into one type of cell or another. This decision is executed through the action of competing gene programs that specify different cellular identities. Consequently, creating a comprehensive map of the gene programs that drive each branching step of human cell differentiation remains a long-sought goal of developmental and stem cell biology. Here, we introduce a framework combining genome-wide CRISPR screens, single-cell readouts, and gene program inference to systematically discover and characterize regulators of cell differentiation. This framework includes a method for CRISPR perturbations paired with single-cell RNA-seq called circular capture Perturb-seq (CC-Perturb-seq), which improves gRNA detection from split-pool combinatorial indexing protocols and enables perturbing many candidate regulators to map their effects on gene programs. We applied this framework to map how human pluripotent stem cells differentiate into arterial endothelial cells (ECs), and identified 174 regulators that promote or inhibit EC differentiation. By tracking gene programs across three stages of differentiation, we resolved when and how regulators divert cells toward alternative fates. This map revealed an unexpected requirement for the Hippo mechanosignaling pathway in EC specification. During lateral mesoderm differentiation, Hippo mechanosignaling was required to activate ETV2, the master transcriptional regulator of endothelial identity. Inhibiting Hippo blocked ETV2 even in the presence of VEGF and diverted progenitors to a mesenchymal fate in vitro. Likewise, Hippo signaling was required for maximal etv2 expression in developing zebrafish embryos. Conversely, pharmacologically activating the Hippo pathway increased the purity of both arterial and venous EC differentiation in vitro. Our framework thus identifies novel regulators of endothelial cell differentiation, improves stem-cell differentiation protocols via manipulation of mechanosignaling, and provides a generalizable platform for mapping the regulatory wiring of human development.

genomics↗

bioRxiv2026

Shifts in Genetic Diversity of Porcine Reproductive and Respiratory Syndrome Virus 2 in Vietnam Before and After African Swine Fever: Increased Diversity and Novel Sub-lineages

Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) remains one of the most important transboundary pathogens affecting swine production in Vietnam; however, it remains poorly understood how long-term evolutionary dynamics were impacted by the African swine fever (ASF) epidemic, a period of time where swine population demographics and movement were heavily perturbed. We investigated the molecular epidemiology, evolutionary history, and phylogeographic dynamics of PRRSV-2 circulating in Vietnam between 2007 and 2024 by integrating 366 Vietnamese ORF5 sequences with a globally curated lineage reference. Maximum-likelihood phylogenetic, Bayesian phylodynamic, and discrete phylogeographic analyses revealed that the Vietnamese PRRSV-2 population underwent substantial reshaping after the ASF epidemic, shifting from a predominantly endemic sub-lineage L8E population to a genetically diverse viral community comprising multiple established and newly emerging sub-lineages. Despite these epidemiological changes, the endemic sub-lineage L8E population maintained a relatively stable evolutionary rate across the pre- and post-ASF periods, suggesting that ASF reshaped viral population structure rather than intrinsic evolutionary dynamics. Two previously unclassified viral clusters circulating in Vietnam and Thailand fulfilled all criteria for formal designation and were recognized as the novel sub-lineages L1M and L10B by the International PRRSV-2 Nomenclature Consortium. Phylogeographic reconstruction further demonstrated contrasting transmission patterns among major sub-lineages, including long-term endemic persistence of L8E, repeated unidirectional introductions of sub-lineages L1M and L10B from Thailand, and bidirectional transpacific dissemination of sub-lineage L1A linking Southeast Asia and North America. Collectively, these findings demonstrate that the ASF epidemic coincided with a fundamental reshaping of the PRRSV-2 epidemiological landscape in Vietnam while revealing Southeast Asia as an active center of ongoing viral diversification. This study provides an updated evolutionary framework for PRRSV-2 surveillance and highlights the importance of continuous genomic monitoring and regional collaboration for the early detection and control of emerging transboundary variants.

genetics↗

bioRxiv2026

Heritable single-cell gene expression states shape functional variability in innate immune responses

Activation of innate immunity at the single-cell level is inherently heterogeneous, yet the mechanisms underlying this variability remain incompletely understood. Here, we integrate transcriptomics, high-content imaging and mathematical modelling to quantify transcriptional heritability within the evolutionarily conserved Toll-like receptor (TLR) system. RNA-seq-based fluctuation tests identified a subset of TLR4-dependent genes, including cytokines and immune effectors, that retain transcriptional heritability for more than 25 cell divisions in clonal macrophage populations. High-content microscopy confirmed gene-specific propagation of heritable states and revealed that environmental context shapes their persistence and expression. CD36, a scavenger receptor involved in bacterial recognition and lipid uptake, exhibited a stable, cell density-reinforced heritable state, whereas the inflammatory programme exemplified by IL1{beta} was transient, with heritability decaying upon clonal expansion. The interplay between heritable transcriptional states and population context generated emergent spatial organisation in high-density populations, with CD36-high cells forming discrete pockets and IL1{beta}-high cells enriched in surrounding regions. Functionally, CD36 expression determined clonal susceptibility to Listeria monocytogenes infection, linking transcriptional heritability to heterogeneous infection outcomes. Together, these findings identify transcriptional heritability as a key determinant of innate immune heterogeneity and demonstrate how heritable cellular states interact with population context to generate complex immune behaviours. Key point summaryO_LIMemorySeq and scRNA-seq identify long-term heritable gene expression states within TLR4-induced macrophage populations. C_LIO_LIHigh-content imaging across thousands of clonal populations reveals gene-specific dynamics of heritable states at the protein level. C_LIO_LIIl1{beta} and Cd36 define mutually exclusive heritable states that are differently regulated by population context and drive spatial organisation in cellular monolayers. C_LIO_LIHeritable CD36 protein expression shapes heterogeneous outcomes during Listeria monocytogenes infection. C_LI

immunology↗

bioRxiv2025

Perinatal Shifts in Fecal-Derived Metabolites and Associations with Postpartum Depression

IntroductionResearch on maternal depression is largely limited to static, blood-derived biomarkers in the postpartum period and mechanistic targets derived from populations outside the physiological contexts of pregnancy and postpartum, resulting in critical gaps in understanding context-specific mechanisms underlying this debilitating condition. ObjectivesTo examine temporal shifts in the maternal gut metabolome and associations between pregnancy-specific shifts and postpartum depression (PPD). MethodsWe applied untargeted metabolomics (UPLC-MS/MS) to fecal samples collected from participants (N= 25) enrolled in the Maternal and Infant NutriTion (MINT) study. Random forest analysis was used to identify key pathways and metabolites contributing to temporal shifts. Fold change analysis and paired t-tests were used to quantify the magnitude and significance of metabolite changes. Associations between pregnancy-specific changes and PPD (Edinburgh Postnatal Depression Scale at 6 weeks) were identified using Pearsons correlation. ResultsLipid, amino acid, and xenobiotic metabolism emerged as core pathways driving temporal changes in the maternal gut metabolome. The most pronounced shifts occurred from 35 weeks gestation to postpartum, with 55 metabolites significantly altered compared to 24 from 24-to 35 weeks gestation and 26 from 24 weeks gestation to postpartum. Of the 29 metabolites associated with PPD; 68.9% were metabolic intermediates, primarily involved in lipid and amino acid metabolism (58.6%). ConclusionsThis study provides some of the first evidence of temporal shifts in the maternal gut metabolome and associations with PPD, highlighting the importance of lipid and amino acid metabolism and laying the groundwork for future multi-omics research.

systems biology↗

bioRxiv2025

Dissecting regulatory syntax in human development with scalable multiomics and deep learning

Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expression. Mapping accessible chromatin offers critical insights into transcriptional control, but available datasets for human development are restricted to bulk tissue, single organs, or single modalities. Here, we present the Human Development Multiomic Atlas (HDMA), a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types and over 1 million candidate cis-regulatory elements, many of which exhibit organ-specific in vivo enhancer activity. Deep learning models trained to predict accessibility from local DNA sequence unravel a comprehensive lexicon of motifs which influence accessibility, including composite motifs exhibiting distinct syntactic constraints predicted to mediate TF cooperativity. We identify "hard" syntactic rules requiring precise motif spacing and orientation, "soft" rules allowing flexible motif arrangements, and ubiquitous motifs that inhibit accessibility. Model-based interpretation of genetic variants reveals that disruption of motifs with positive and negative effects is associated with concordant effects on gene expression. Our work delineates how motif syntax governs cell type-specific chromatin accessibility and provides a foundational resource for decoding cis-regulatory logic and interpreting genetic variation during human development.

genomics↗

bioRxiv2023

An encyclopedia of enhancer-gene regulatory interactions in the human genome

Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease1-6. Here we create and evaluate a resource of >13 million enhancer-gene regulatory interactions across 352 cell types and tissues, by integrating predictive models, measurements of chromatin state and 3D contacts, and large-scale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,411 element-gene pairs measured in CRISPR perturbation experiments, >30,000 fine-mapped eQTLs, and 569 fine-mapped GWAS variants linked to a likely causal gene. Using this framework, we develop a new predictive model, ENCODE-rE2G, that achieves state-of-the-art performance across multiple prediction tasks, demonstrating a strategy involving iterative perturbations and supervised machine learning to build increasingly accurate predictive models of enhancer regulation. Using the ENCODE-rE2G model, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, which reveals global properties of enhancer networks, identifies differences in the functions of genes that have more or less complex regulatory landscapes, and improves analyses to link noncoding variants to target genes and cell types for common, complex diseases. By interpreting the model, we find evidence that, beyond enhancer activity and 3D enhancer-promoter contacts, additional features guide enhancer-promoter communication including promoter class and enhancer-enhancer synergy. Altogether, these genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models, and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.

genomics↗

bioRxiv2021

Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells

The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.

genomics↗