Biology subjects

Phan, L.

Publications and source records attributed to Phan, L..

9 recordsLinked to original sources

bioRxiv2026

Early-life mucosal T cells direct intestinal stem cell fate via a coordinated developmental program

Although early-life immunity was once considered immature, the human fetal immune system is dynamic and compartmentalized by the second trimester. By 21 weeks of gestation, T lymphocytes become a major immune population in the fetal small intestine (SI), yet their functional roles within this tissue remain largely undefined. To explore their unique contributions to intestinal development, we established an ex vivo co-culture system in which mucosal T cells isolated from fetal, neonatal, or adult SI donors were cultured with tissue-derived 3D SI organoids derived from various ages. Homeostatic early-life (fetal and neonatal) SI T cells uniquely promoted organoid generation, a metric of stem cell renewal, by upregulating cell cycle-associated gene programs. These early-life T cells also directed intestinal stem cell differentiation toward the secretory lineage in both growth and differentiation phase, highlighting that T cells poise stem cells to adopt secretory fates. T cells from infants with necrotizing enterocolitis (NEC) - an inflammatory intestinal disease affecting predominantly preterm infants - failed to activate these same programs, suggesting a pathologic role for T cells in NEC. T cells from the adult SI similarly failed to support organoid growth or differentiation, revealing developmentally specialized, nonimmune functions for early-life T cells in the intestine. Similarly, T cells derived from cord blood did not enhance organoid generation, indicating that this function is not necessarily a generalized feature of early-life T cells but rather is restricted to mucosal T cells. Organoids derived from adults or NEC, however, could re-enter regenerative states when co-cultured with fetal T cells, indicating that fetal T cells can restore stem cell self-renewal across developmentally and disease-imposed states. We further identified that T cell-derived soluble factors alone were insufficient to modulate intestinal stem cell fate, implying the need for physical interactions. Concordant with this finding, we report that T cells heavily localize to the stem cell niche during prenatal development, where they express factors involved in Notch, Wnt, and growth factor signaling to support fetal stem cell function. Collectively, these findings reveal a coordinated developmental program in which fetal SI T cells balance stem cell self-renewal and differentiation, identifying a developmental immune-epithelial axis that can be harnessed to restore intestinal regeneration.

immunology↗

bioRxiv2025

Detection of serotonin and serotonin related gene reveals unique roles in human intestinal epithelial development

Although 95% of serotonin in the human body is produced in the gastrointestinal tract, most prior research work has focused on the brain. Despite its abundance in the gut, serotonins role in early intestinal development remains poorly understood. Here we show that serotonin is detected in both the small intestine and large intestine as early as 14-15 weeks gestational age. Using single-cell transcriptomics with histological validation, we generated a spatiotemporal atlas of serotonin and serotonin-related genes in the human gut from first trimester to late adulthood. The serotonin synthesis gene, TPH1, was exclusively expressed in enteroendocrine cells at all time points analyzed, with the highest expression in the second trimester. The serotonin reuptake gene, SLC6A4, was largely restricted to mature absorptive enterocytes and increased post-natally. Serotonin receptors also displayed distinct cellular and developmental expression patterns. HTR1E was confined to the first trimester during highly proliferative stage. HTR4 was enriched for in crypt regions, suggesting a role in proliferation for serotonin. Finally, HTR3E was associated with tuft cells throughout development. Together, these findings reveal the dynamic, cell-type-specific regulation of serotonin in the developing human gut, suggesting its importance in early intestinal development, and provide a framework to study its roles in intestinal development and diseases.

developmental biology↗

bioRxiv2025

Parkinson's Paradox: Alpha-synuclein's Selective Strike on SNc Dopamine Neurons over VTA

In synucleinopathies, including Parkinsons disease (PD), dopamine neurons in the substantia nigra pars compacta (SNc) exhibit greater vulnerability to degeneration than those in the ventral tegmental area (VTA). While -synuclein (Syn) pathology is implicated in nigral dopamine neuron loss, the mechanisms by which Syn affects neuronal activity and midbrain dopamine network connectivity prior to cell death remain unclear. This study tested the hypothesis that elevated Syn expression induces pathophysiological changes in firing activity and disrupts network connectivity dynamics of dopamine neurons before neuronal loss. We employed two mouse models of synucleinopathy: preformed Syn fibril (PFF) injection and AAV-mediated expression of human Syn (hSyn) under the control of the tyrosine hydroxylase (TH) promoter, both targeting the VTA and SNc. Four weeks post-injection, brain sections underwent histological, electrophysiological, and network analyses. Immunohistochemistry for TH, hSyn, and phospho-Ser129 Syn assessed Syn expression and dopaminergic neuron alterations. Neuronal viability was evaluated using two complementary approaches: quantification of TH+ or FOX3+ and TUNEL labeling. Importantly, these analyses revealed no significant changes in neuronal counts or TUNEL+ cells at this time point, confirming that subsequent functional assessments captured pre-neurodegenerative, Syn-induced alterations rather than late-stage neurodegeneration. Electrophysiological recordings revealed a differential effect of hSyn expression. SNc dopamine neurons exhibited significantly increased baseline firing rates, whereas VTA dopamine neurons remained unchanged. These findings indicate a region-specific vulnerability to Syn-induced hyperactivity of dopamine neurons. Further analysis revealed impaired homeostatic firing rate regulation in SNc, but not VTA, dopamine neurons, demonstrated by a reduced capacity to recover baseline firing following hyperpolarization. Collectively, our results demonstrate that, prior to neurodegeneration, elevated Syn expression differentially disrupts both basal firing activity and network stability of SNc dopamine neurons, while sparing VTA dopamine neurons. By identifying neurophysiological changes preceding dopaminergic neuron loss, these findings provide critical insights into the pathophysiological mechanisms predisposing SNc neurons to degeneration in Parkinsons disease. Significance StatementA central question in Parkinsons disease research is why dopamine neurons in the substantia nigra pars compacta (SNc) are more vulnerable than those in the ventral tegmental area (VTA). This study reveals that alpha-synuclein (Syn) pathology differentially impacts dopamine neuronal activity and network connectivity, causing changes in the SNc before neuronal loss occurs, but not in the VTA. These findings provide a mechanism to explain the differential resilience of these neighboring dopamine neuron populations and provide insights into Parkinsons disease progression. The methodologies developed in this study establish a foundation for investigating network topology in deep brain structures and its role in neurodegenerative disorders.

neuroscience↗

bioRxiv2025

Lamin B loss in nuclear blebs is rupture dependent while increased DNA damage is rupture independent

The nucleus houses genetic information and functions separate from the rest of the cell. Loss of nuclear shape results in nuclear ruptures. Nuclear blebs are deformations identified by decreased DNA density, while lamin B levels vary drastically. To determine if decreased lamin B levels are due to nuclear rupture, we used immunofluorescence to measure levels of lamin B and emerin, a nuclear envelope protein that enriches to sites of nuclear rupture. We observed that cell types that exhibit decreased levels of lamin B also show an enrichment of emerin in nuclear blebs. Oppositely, in other cell types, nuclear blebs display maintained levels of lamin B1 and showed no emerin enrichment. To determine how nuclear rupture affects DNA damage, we time lapse imaged nuclear rupture dynamics then fixed the same cells to conduct immunofluorescence of {gamma}H2AX and emerin. We find that DNA damage levels are higher in blebbed nuclei independent of nuclear rupture. Thus, we confirm that lamin B1 loss in nuclear blebs is due to nuclear rupture and blebbed nuclei have increased DNA damage that is independent of rupture. Summary statement (180-200 characters): We measured lamin B and DNA damage in blebbed nuclei to determine the effect of nuclear rupture. We find that nuclear rupture causes loss of lamin B in nuclear blebs but that increased DNA damage in blebbed nuclei is independent of rupture.

cell biology↗

bioRxiv2024

Cell-material interactions in 3D bioprinted plant cells

3D bioprinting is an additive manufacturing technology with promise towards facilitating tissue engineering and single-cell investigations of cellular development and microenvironment responses. 3D bioprinting is still a new technology in the field of plant biology so its optimization with plant cells is still widely needed. Here, we present a study in which 3D bioprinting parameters, such as needle gauge, extrusion pressure, and scaffold type, were all tested in 3D bioprinted Tobacco BY-2 cells to evaluate how cell viability is responsive to each parameter. As a result, this study revealed an optimal range of extrusion pressures and needle gauges that resulted in an optimum cell viability. Furthermore, this study applied the identified optimal 3D bioprinting parameters to a different cell line, Arabidopsis root protoplasts, and stress condition, phosphate starvation, to confirm that the identified parameters were optimal in a different species, cell type, and cellular microenvironment. This suggested that phosphate-starved bioprinted Arabidopsis cells were less viable by 7 days, which was consistent with whole root phosphate starvation responses. As a result, the 3D bioprinter optimization yielded optimal cell viabilities in both BY-2 and Arabidopsis cells and facilitated an applied investigation into phosphate starvation stress.

cell biology↗

bioRxiv2022

Enriching Biomedical Knowledge for Low-resource Language Through Translation

Biomedical data and benchmarks are highly valuable yet very limited in low-resource languages other than English such as Vietnamese. In this paper, we make use of a state-of-theart translation model in English-Vietnamese to translate and produce both pretrained as well as supervised data in the biomedical domains. Thanks to such large-scale translation, we introduce ViPubmedT5, a pretrained Encoder-Decoder Transformer model trained on 20 million translated abstracts from the high-quality public PubMed corpus. ViPubMedT5 demonstrates state-of-the-art results on two different biomedical benchmarks in summarization and acronym disambiguation. Further, we release ViMedNLI a new NLP task in Vietnamese translated from MedNLI using the recently public En-vi translation model and carefully refined by human experts, with evaluations of existing methods against ViPubmedT5.

bioinformatics↗

bioRxiv2021

Scalable Clustering with Supervised Linkage Methods

Data clustering plays a significant role in biomedical sciences, particularly in single-cell data analysis. Researchers use clustering algorithms to group individual cells into populations that can be evaluated across different levels of disease progression, drug response, and other clinical statuses. In many cases, multiple sets of clusters must be generated to assess varying levels of cluster specificity. For example, there are many subtypes of leukocytes (e.g. T cells), whose individual preponderance and phenotype must be assessed for statistical/functional significance. In this report, we introduce a novel hierarchical density clustering algorithm (HAL-x) that uses supervised linkage methods to build a cluster hierarchy on raw single-cell data. With this new approach, HAL-x can quickly predict multiple sets of labels for immense datasets, achieving a considerable improvement in computational efficiency on large datasets compared to existing methods. We also show that cell clusters generated by HAL-x yield near-perfect F1-scores when classifying different clinical statuses based on single-cell profiles. Our hierarchical density clustering algorithm achieves high accuracy in single cell classification in a scalable, tunable and rapid manner. We make HAL-x publicly available at: https://pypi.org/project/hal-x/

bioinformatics↗

bioRxiv2019

SPDI: Data Model for Variants and Applications at NCBI

MotivationNormalizing diverse representations of sequence variants is critical to the elucidation of the genetic basis of disease and biological function. NCBI has long wrestled with integrating data from multiple submitters to build databases such as dbSNP and ClinVar. Inconsistent representation of variants among variant callers, local databases, and tools results in discrepancies and duplications that complicate analysis. Current tools are not robust enough to manage variants in different formats and different reference sequence coordinates. ResultsThe SPDI (pronounced "speedy") data model defines variants as a sequence of 4 operations: start at the boundary before the first position in the sequence S, advance P positions, delete D positions, then insert the sequence in the string I, giving the data model its name, SPDI. The SPDI model can thus be applied to both nucleotide and protein variants, but the services discussed here are limited to nucleotide. Current services convert representations between HGVS, VCF, and SPDI and provide two forms of normalization. The first, based on the NCBI Variant Overprecision Correction Algorithm, returns a unique, normalized representation termed the "Contextual Allele" for any input. The SPDI name, with its four operations, defines exactly the reference subsequence potentially affected by the variant, even in low complexity regions such as homopolymer and dinucleotide sequence repeats. The second level of normalization depends on an alignment dataset (ADS). SPDI services perform remapping (AKA lift-over) of variants from the input reference sequence to return a list of all equivalent Contextual Alleles based on the transcript or genomic sequences that were aligned. One of these contextual alleles is selected to represent all, usually that based on the latest genomic assembly such as GRCh38 and is designated as the unique "Canonical Allele". ADS includes alignments between non-assembly RefSeq sequences (prefixed NM, NR, NG), as well inter- and intra-assembly-associated genomic sequences (NCs, NTs and NWs) and this allow for robust remapping and normalization of variants across sequences and assembly versions. Availability and implementationThe SPDI services are available for open access at: https://api.ncbi.nlm.nih.gov/variation/v0/ Contactholmesbr@ncbi.nlm.nih.gov

genomics↗

bioRxiv2018

iCn3D, a Web-based 3D Viewer for the Visualization of Biomolecular Structure and Sequence Annotation

SummaryiCn3D (l-see-in-3D) is a web-based 3D molecular structure viewer implemented in JavaScript. It invites users to explore sequence-structure relationships by displaying 3D structures, protein and nucleotide sequences, and biological annotations such as protein domains, Single Nucleotide Variations, functional sites, molecular contacts, as well as user defined features. Customized and user-annotated displays can be shared with colleagues or publishers via a simple URL, or embedded in web pages as live 3D displays. iCn3D is unique in its ability to simultaneously show 3D structure, 2D molecular networks and interactions, and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of molecules or residues, utilizing flexible user interfaces. These selections are synchronized dynamically in all displays. They can, for example, be shown as tracks in the 1D sequence/annotation browser with simultaneous 3D representations. They can be saved and reused throughout a single user session, or exported for subsequent sessions and further external analysis. iCn3D is rich in structural analysis and visualization features and has a built-in user interface that supports both command line- and menu-driven operation. Session commands can be saved, replayed and shared. iCn3D can display superimposed structures obtained from NCBFs VAST+ structural alignment resource, for comparative analysis of tertiary or quaternary structure. iCn3D can also display electron density maps for crystal structures and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1.\n\nAvailability and implementationiCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d.

bioinformatics↗