Biology subjects

Phan, B.

Publications and source records attributed to Phan, B..

4 recordsLinked to original sources

bioRxiv2026

An integrated multi-omic atlas of the choroid plexus highlights conserved molecular programs of epithelial function

The choroid plexus (ChP) is a specialized epithelial tissue responsible for production of cerebrospinal fluid (CSF), maintenance of the blood-CSF barrier and regulation of CSF-borne signaling factors. However, despite the ChP's central role in CSF homeostasis, conserved molecular programs of ChP epithelial function across species and conditions remain incompletely defined. In this study, we integrated eight mouse and human single-cell/nucleus RNA-seq datasets to build a multi-species ChP atlas capturing major epithelial, stromal, vascular, and immune populations. Cross-dataset differential expression identified a conserved epithelial gene program encompassing ion transport, barrier function, ciliogenesis, and secretory signaling, while prioritizing understudied genes including CLIC6 and VAT1L. Co-expression network analysis resolved conserved epithelial meta-programs, and transcription factor regulatory inference identified OTX2, MSX1, and GLIS3 among conserved regulators of epithelial gene expression. We also generated a novel Visium HD spatial transcriptomic atlas of mouse fourth-ventricle ChP to orthogonally validate epithelial modules. Lastly, cross-tissue analyses revealed substantial transcriptional overlap between ChP and retinal pigment epithelium, including shared epithelial genes and OTX2-associated regulatory relationships. Together, these findings define conserved molecular programs of ChP epithelial specialization, nominate candidate regulators for functional investigation, and provide an integrated cross-species and spatial resource for studying ChP physiology.

neuroscience↗

bioRxiv2025

Characterization of astrocyte density in the Pitt-Hopkins Syndrome mouse model of ASD

Transcription factor 4 (TCF4) is a proneural basic helix-loop-helix transcription factor that plays a critical role in brain development and is associated with a variety of psychiatric disorders including autism spectrum disorder (ASD), major depressive disorder, and schizophrenia. Autosomal dominant mutations in TCF4 result in a profound neurodevelopmental disorder called Pitt-Hopkins Syndrome (PTHS). Germline TCF4 loss-of-function (LOF) studies using human and mouse models have identified dysregulation in neural cell proliferation, genesis, and specification which lead to disruption in neuronal, astroglial and oligodendroglial lineages. In this study, we focused on the role of TCF4 in the genesis of the astrocyte lineage, specifically in the context of modeling PTHS. We show that germline heterozygous mutations in Tcf4 had no effect on the expression of astrocyte marker genes in primary astrocyte cultures and whole brain lysates. Immunohistochemical (IHC) analysis of pan- and subclass-specific astrocyte markers showed Tcf4 mutation had no effect on the proportions of astrocytes in the dorsal cortex and corpus callosum. Lastly, we tracked ventrally-derived astrocytes using an Nkx2.1 reporter mouse and observed that germline Tcf4 LOF did not result in misallocation of ventrally-derived astrocytes into the dorsal cortex, a phenotype previously observed when both Tcf4 alleles were conditionally deleted in the Nkx2.1 lineage. These data indicate that germline heterozygous TCF4 LOF, which models PTHS, does not appear to affect the astrocyte lineage at the cell population level.

neuroscience↗

bioRxiv2022

Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease

Alzheimers disease (AD) involves aggregation of amyloid {beta} and tau, neuron loss, cognitive decline, and neuroinflammatory responses. Both resident microglia and peripheral immune cells have been associated with the immune component of AD. However, the relative contribution of resident and peripheral immune cell types to AD predisposition has not been thoroughly explored due to their similarity in gene expression and function. To study the effects of AD associated variants on cis-regulatory elements, we train convolutional neural network (CNN) regression models that link genome sequence to cell type-specific levels of open chromatin, a proxy for regulatory element activity. We then use in silico mutagenesis of regulatory sequences to predict the relative impact of candidate variants across these cell types. We develop and apply criteria for evaluating our models and refine our models using massively parallel reporter assay (MPRA) data. Our models identify many AD-associated variants with a greater predicted impact in peripheral cells relative to microglia or neurons but few with greater predicted impact in microglia and neurons. Our results suggest that peripheral immune cells themselves may mediate a component of AD predisposition and support their use as models to study the effects of AD associated variants. We make our library of CNN models and predictions available as a resource for the community to study immune and neurological disorders.

genomics↗

bioRxiv2020

Transcriptional alterations in opioid use disorder reveal an interplay between neuroinflammation and synaptic remodeling

BackgroundPrevalence rates of opioid use disorder (OUD) have increased dramatically, accompanied by a surge of overdose deaths. While opioid dependence has been extensively studied in preclinical models, an understanding of the biological alterations that occur in the brains of people who chronically use opioids and who are diagnosed with OUD remains limited. To address this limitation, RNA-sequencing (RNA-seq) was conducted on the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc), regions heavily implicated in OUD, from postmortem brains in subjects with OUD. MethodsWe performed RNA-seq on the DLPFC and NAc from unaffected comparison subjects (n=20) and subjects diagnosed with OUD (n=20). Our transcriptomic analyses identified differentially expressed (DE) transcripts and investigated the transcriptional coherence between brain regions using rank-rank hypergeometric ordering (RRHO). Weighted gene co-expression analyses (WGCNA) also identified OUD-specific modules and gene networks. Integrative analyses between DE transcripts and GWAS datasets using linkage disequilibrium score (LDSC) assessed the genetic liability psychiatric-related phenotypes. ResultsRRHO analyses revealed extensive overlap in transcripts between DLPFC and NAc in OUD, primarily relating to synaptic remodeling and neuroinflammation. Identified transcripts were enriched for factors that control pro-inflammatory cytokine-mediated, chondroitin sulfate, and extracellular matrix signaling. Cell-type deconvolution implicated a role for microglia as a critical driver for opioid-induced neuroplasticity. Using LDSC, we discovered genetic liabilities for risky behavior, attention deficit hyperactivity disorder, and depression. ConclusionsOverall, our findings reveal new connections between the brains immune system and opioid dependence in the human brain.

neuroscience↗