Biology subjects

Tran, P. V.

Publications and source records attributed to Tran, P. V..

12 recordsLinked to original sources

bioRxiv2026

Hierarchical Transcriptomic and Epigenetic Recovery and Remodeling in the Developing Hippocampus Following Early-life Environmental Insults: An Iron Deficiency Rat Model

BackgroundsEarly-life environmental insults cause persistent neurodevelopmental abnormalities accompanied by transcriptional and epigenetic dysregulation despite removal of the original insult or postnatal intervention. However, transcriptomic and epigenomic responses to developmental insults and subsequent treatment during active neurodevelopment remain insufficiently characterized. Developmental iron deficiency (ID) provides a unique model for investigating this question because iron is an essential cofactor for TET DNA dioxygenases and developmental ID causes persistent behavioral and molecular alterations despite iron repletion. ResultsWe integrated the hippocampal transcriptome, DNA methylome (5mC), and hydroxymethylome (5hmC) in male rats at postnatal day 15 following developmental ID and postnatal iron treatment, using Oxford Nanopore sequencing for native DNA modification profiling. Developmental ID induced substantial transcriptional and epigenetic alterations associated with synaptic function, neurodevelopment, and neuroinflammation. Postnatal iron treatment induced a hierarchical response across molecular layers: while transcriptomic alterations largely normalized, 5mC showed only partial recovery, and 5hmC showed extensive de novo modifications. Recovered, persistent, and newly emerged epigenetic marks were associated with increasingly specialized biological functions, from broad neurodevelopmental processes to specific pathways. Furthermore, while 5mC enrichment was associated with transcriptionally suppressed pathways, 5hmC enrichment showed weaker coupling with concurrent transcriptomic activity, suggesting epigenetic poising rather than immediate transcriptional output. MergeOmics integration identified key driver genes showing post-treatment epigenetic regulation despite transcriptional recovery. ConclusionsMolecular recovery following developmental ID extends beyond transcriptomic normalization, involving persistent and extensive epigenetic remodeling. This study provides a framework for understanding molecular responses following early-life environmental insults and highlights the importance of delineating persistent regulatory reprogramming.

genomics↗

bioRxiv2025

Targeting Ogt in ADPKD mitigates metabolic reprogramming and renal cystogenesis, extending survival

Aberrant cell metabolism drives autosomal dominant polycystic kidney disease (ADPKD). O-GlcNAcylation, a metabolically regulated post-translational modification, is elevated in ADPKD kidneys. Using rapidly and slowly progressive ADPKD mouse models, we demonstrate that deleting O-GlcNAc transferase (Ogt) reduces renal cystogenesis and extends survival in a rapidly progressive model from postnatal day 21 to over a year. Pharmacological OGT inhibition similarly reduced cyst formation of patient-derived renal epithelial cells in vitro. In Pkd1 conditional knockout kidneys, Ogt deletion maintained phosphorylated AMPK and mitochondrial respiratory chain complex levels, preserving cellular energy sensing and production. Further, metabolomic analysis revealed normalization of glycolysis and of the hexosamine and hyaluronic acid biosynthesis pathways. In contrast, dysregulation of these pathways in Pkd1 conditional knockout kidneys culminated in increased tricarboxylic acid cycle entry, increased O-GlcNAc, and increased hyaluronic acid in the extracellular matrix, respectively. These findings identify Ogt as a central metabolic regulator and therapeutic target, linking metabolism to intracellular and extracellular mechanisms of cyst formation.

cell biology↗

bioRxiv2025

Genetic interaction of Specc1l and Thm1 reveals cytoskeletal - ciliary crosstalk

Cilium formation and actin cytoskeleton dynamics are interconnected, with evidence showing that elevated filamentous actin (F-actin) negatively regulates primary cilia length. Loss of the cytoskeletal protein SPECC1L, which itself does not localize to cilia, leads to increased F-actin and shortened cilia. Depolymerizing F-actin in Specc1l mutant cells restored cilia lengths, substantiating this inverse relationship. In cells harboring a Specc1l allele lacking only the coiled-coil domain 2, intracellular regions with both elevated and reduced F-actin were observed together with cilia shortening. Notably, F-actin was decreased at the ciliary base, suggesting that a different F-actin subpopulation contributes to the inverse relationship. We also identified a genetic interaction between Specc1l and Thm1, which encodes an intraflagellar transport-A (IFT-A) protein. Double or compound heterozygotes for Specc1l and Thm1 exhibited a higher penetrance of cleft palate compared to Specc1l heterozygotes alone. Together, these findings reveal a role for SPECC1L in cytoskeletal regulation of ciliogenesis affecting palate development.

cell biology↗

bioRxiv2025

Brain-derived exosome biomarkers of neuroinflammation and neuronal functional iron deficiency in newborns of overweight-obese mothers

BackgroundNon-infectious neuroinflammation (NINI) in early life and neonatal neural iron deficiency (nID) have been proposed to contribute to neurodevelopmental dysfunction and disorders, including autism, through toxic effects on neural cells and impaired molecular signaling. Early detection of NINI and nID may enable interventions to restore neurodevelopmental homeostasis and reduce long-term impact. However, such diagnoses are impossible due to ethical reason to access to the central nervous system (e.g., lumbar puncture) when there is no suspicion of brain infection (e.g., meningitis). MethodsWe refined a methodology to isolate and quantify inflammatory and iron-regulatory proteins in high-quality brain-derived extracellular vesicles (BDEVs) from human umbilical cord blood. A preclinical model was used to validate that BDEV contents reflect the brain microenvironment. We then applied this approach to evaluate biomarkers of NINI and nID in BDEVs isolated from cord plasma of newborns of mothers with obesity, a non-infectious pro-inflammatory gestational condition and a risk factor for nID. FindingsPlasma BDEV analytes correlated more strongly with brain analytes and showed stronger associations among functionally related molecules compared with whole plasma analytes. Maternal obesity induced an anti-inflammatory response in the brain compartment, a pro-inflammatory response in the periphery, and functional nID. InterpretationBDEVs may provide a more sensitive representation of the brain microenvironment than blood-based measures (e.g., plasma), enabling non-invasive, early detection of infants with NINI and neonatal nID. FundingSupported by NIH, the Masonic Institute for Developing Brain, Hennepin Healthcare Research Institute, UnityPoint Health Meriter Foundation, and American Academy of Pediatrics Resident Research Grant. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSPrevious studies hypothesized that gestational inflammatory environments (e.g., maternal obesity) increase risk of neonatal neural iron deficiency (nID), neuroinflammation, and neurodevelopmental disorders. However, assessing non-infectious neuroinflammation (NINI) in infants from these high-risk groups is not feasible or clinically justifiable using invasive methods (e.g., cerebrospinal fluid collection), and analytes from whole blood or plasma may not accurately reflect brain physiological status. Added value of this studyWe refined a protocol to isolate brain-derived extracellular vesicles (BDEVs) from a small amount of plasma sample (100 {micro}L) and characterized their contents to approximate brain physiology. We demonstrated that BDEVs more accurately reflect brain status compared with whole plasma. In newborns of mothers with obesity during pregnancy, we found evidence of a low-grade peripheral inflammation accompanied by a protective anti-inflammatory response in the brain. Maternal obesity was also found to induce neonatal nID. Implications of all the available evidenceBDEVs can serve as an accurate, non-invasive tool to assess brain condition. In clinical settings, this approach may be used for early diagnosis, monitoring disease progression, and evaluating treatment effects. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/648967v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@108caa9org.highwire.dtl.DTLVardef@311ecdorg.highwire.dtl.DTLVardef@dd4086org.highwire.dtl.DTLVardef@1b747ea_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2024

Differential gene expression and chromatin accessibility in the rat medial prefrontal cortex mediating individual variability in vulnerability to opioid use

We characterized gene transcriptional activity in the medial prefrontal cortex of rats associated with individual differences in vulnerability to three distinct phases of opioid use disorder (OUD). Resilient rats showed many more changes in canonical pathway activity than Vulnerable rats in models of both early and advanced OUD, involving passive opioid exposure and opioid self-administration (SA), respectively. The Resilient/Vulnerable phenotype was also associated across phases with functionally specific gene networks, including those mediating epigenetic, neuroimmune, and neuroplasticity function. In contrast, we identified two phase-specific effects. First, differential activity of a myelination-related gene network was associated with Resilience/Vulnerability measured after passive morphine exposure. Second, expression of the calmodulin-inhibitor Pcp4, a gene recently implicated in a rat opioid SA GWAS analysis, was associated with Resilience/Vulnerability measured after SA but not after passive morphine exposure. Thus, we have identified both general and phase-specific transcriptional signatures involved in OUD vulnerability across its trajectory. TeaserAdaptations in the brain transcriptome are associated with resilience and vulnerability to opioid use disorder.

neuroscience↗

bioRxiv2022

Sex-Specific Effects of Early-Life Iron Deficiency and Prenatal Choline Treatment on Adult Rat Hippocampal Transcriptome

BackgroundFetal-neonatal iron deficiency (ID) causes long-term neurocognitive and affective dysfunctions. Clinical and preclinical studies have shown that early-life ID produces sex-specific effects. However, little is known about the molecular mechanisms underlying these early-life ID-induced sex-specific effects on neural gene regulation. ObjectiveTo illustrate sex-specific transcriptome alteration in adult rat hippocampus induced by fetal-neonatal ID and prenatal choline treatment. MethodsPregnant rats were fed an iron-deficient (4 mg/kg Fe) or iron-sufficient (200 mg/kg Fe) diet from gestational day (G) 2 to postnatal day (P) 7 with or without choline supplementation (5 g/kg choline) from G11-18. Hippocampi were collected from P65 offspring of both sexes and analyzed for changes in gene expression. ResultsBoth early-life ID and choline treatment induced transcriptional changes in adult female and male rat hippocampus. Both sexes showed ID-induced alterations in gene networks leading to enhanced neuroinflammation. In females, ID-induced changes indicating enhanced activity of oxidative phosphorylation and fatty acid metabolism, which are contrary to the ID effect in males. Prenatal choline supplementation induced the most robust changes in gene expression, particularly in the iron-deficient animals where it partially rescued ID-induced dysregulations. Choline supplementation also altered hippocampal transcriptome in the iron-sufficient rats with indications for both beneficial and adverse effects. ConclusionsThis study provided unbiased global assessments of gene expression regulated by iron and choline status in a sex-specific manner, with greater effects in female than male rats. Our new findings highlight potential sex-specific gene networks regulated by iron and choline status for further investigation.

neuroscience↗

bioRxiv2022

ATAC and histone H3K9me3 landscapes revealed the altered epigenome by fetal-neonatal iron deficiency in the adult male rat hippocampus

Iron deficiency during the fetal-neonatal period results in long-term neurodevelopmental impairments associated with pervasive and widespread hippocampal gene dysregulation. Globally, fetal-neonatal iron deficiency produces both long-term activation and repression of hundreds of loci in the adult rat hippocampus. Prenatal choline (a methyl donor) supplementation can partially reverse these effects, suggesting an interaction between iron and choline in regulating the hippocampal transcriptome. To gain insights into the underlying epigenetic signatures, we integrate hippocampal transcriptomes and epigenetic marks of active (transposase accessible chromatin/ATAC) and repressed (H3K9me3 enrichment) genes in adult rats that had been exposed to fetal-neonatal iron deficiency with or without prenatal choline supplementation. Rats were made iron-deficient during fetal and neonatal period by limiting maternal iron intake from gestational day (G) 2 through postnatal day (P) 7. Choline (5.5 g/kg) was given to half of the pregnant dams during G11-18. This paradigm produced four comparison groups (Iron-sufficient [IS], Iron-deficient [ID], IS+choline [ISch], and ID+choline [IDch]). Hippocampi were collected from P65 males and analyzed for changes in chromatin conformation and histone H3K9me3 enrichment. ATAC-seq results accounted for 22% and 24%, whereas H3K9me3 enrichment accounted for 1.7% and 13% of differences in ID- and IDch-altered gene expression. These epigenetic changes were annotated onto gene networks regulating synaptic structure and plasticity, neuroinflammation, and reward circuits. The low correlation between gene dysregulation and changes in ATAC or H3K9me3 signatures indicate involvements of other epigenetic modifications. This study provides a genome-wide findings of stable epigenetic changes and lays a foundation for further analyses to elucidate more fully iron-dependent epigenetic mechanisms that underlie iron deficiency, choline supplementation, and their interactions in mediating long-term neural gene dysregulation. SIGNIFICANCE STATEMENTEarly-life iron deficiency can lead to long-term neurocognitive dysfunction and persistent neural gene dysregulation, despite prompt iron replenishment, suggesting that iron deficiency results in long-term neuroepigenomic changes. This study combined RNA-seq, ATAC-seq, and ChIP-seq to provide the epigenetic basis for gene dysregulation due to fetal-neonatal iron deficiency and prenatal choline supplementation. We found that early-life iron deficiency alters epigenetic regulation of genes involved in neuronal development, cell signaling, neuroinflammation, and reward-related cognition. While choline supplementation to iron-deficient animals partially reverses these effects, it also leads to dysregulation of genes in iron-sufficient animals. The patterns of gene dysregulation were positively correlated with differences in chromatin accessibility and negatively correlated with repressive histone H3K9me3 modification. Our results indicate that these changes at the epigenetic level partially account for the long-term hippocampal gene dysregulation.

neuroscience↗

bioRxiv2020

Quinomycin A reduces cyst progression in Polycystic Kidney Disease

Polycystic kidney disease (PKD) is a genetic disorder that affects cilia homeostasis and causes progressive growth of tubular-derived cysts within the kidney. Efforts to find safer drugs for PKD have increased in the past few years after the successful launch of tolvaptan, the first approved drug to combat autosomal dominant PKD progression. Here we investigate the effects of Quinomycin A on progression of PKD. Quinomycin A is a bis-intercalator peptide that has previously shown to be effective against cancer progression. Quinomycin A treatment decreased cyst progression of human ADPKD primary renal epithelial cells grown in a 3D collagen gel to form cysts. In an orthologous mouse model of PKD, Quinomycin A administration reduced kidney to body weight ratios, and reduced cystogenesis. This was accompanied by decreased cell proliferation and fibrosis. Quinomycin treatments efficiently reduced the expression of Notch pathway proteins, RBPjk and HeyL in kidneys of PKD mice. Interestingly, Quinomycin treatments also normalized cilia lengths of collecting duct cyst-lining renal epithelia of PKD mice. This is the first preclinical study to our knowledge that demonstrates Quinomycin A has protective effects against PKD progression, in part by reducing Notch signaling and renal epithelial cilia lengths. Our findings suggest Quinomycin A has potential therapeutic value for PKD patients.

genetics↗

bioRxiv2020

Repeated morphine exposure activates synaptogenesis and other neuroplasticity-related gene networks in the prefrontal cortex of male and female rats

BackgroundOpioid abuse is a chronic disorder likely involving stable neuroplastic modifications. While a number of molecules contributing to these changes have been identified, the broader spectrum of genes and gene networks that are affected by repeated opioid administration remain understudied. MethodsWe employed Next-Generation RNA-sequencing (RNA-seq) to investigate changes in gene expression in adult male and female rats prefrontal cortex (PFC) following daily injection of morphine (5.0 mg/kg) for 10 days. Ingenuity Pathway Analysis (IPA) was used to analyze affected molecular pathways, gene networks, and associated regulatory factors. Results90% of differentially expressed genes (DEGs) were upregulated in both males and females, with a 35% overlap between sexes. A substantial number of DEGs play roles in synaptic signaling and neuroplasticity. Although broadly similar, some differences were revealed in the gene ontology networks enriched in females and males (e.g., the endocannabinoid pathway in females and neuroinflammation in males). ConclusionsOur results cohere with findings from previous studies based on a priori gene selection, while identifying broader gene networks activated by repeated opioid exposure. Our results also reveal novel genes and molecular pathways that are upregulated by repeated morphine exposure.

neuroscience↗

bioRxiv2020

Thm2 interacts with paralog, Thm1, and sensitizes to Hedgehog signaling in postnatal skeletogenesis

Ciliopathies are genetic syndromes that link osteochondrodysplasias to dysfunction of primary cilia. Primary cilia extend from the surface of bone and cartilage cells, to receive extracellular cues and mediate signaling pathways. Mutations in several genes that encode components of the intraflagellar transport-A ciliary protein complex have been identified in skeletal ciliopathies, including THM1. Here, we report a role for genetic interaction between Thm1 and its paralog, Thm2, in skeletogenesis. THM2 localizes to the ciliary axoneme, but unlike its paralog, Thm2 deficiency does not affect ciliogenesis and Thm2-null mice survive into adulthood. Since paralogs often have redundant functions, we crossed a Thm1 null (aln) allele into the Thm2 colony. After 5 generations of backcrossing the colony onto a C57BL6/J background, we observed that by postnatal day 14, Thm2-/-; Thm1aln/+ mice are smaller than control littermates. Thm2-/-; Thm1aln/+ mice exhibit shortened long bones, narrow ribcage, shortened cranium and mandibular defects. Mutant mice also show aberrant architecture of the tibial growth plate, with an expanded proliferation zone and diminished hypertrophic zone, indicating impaired chondrocyte differentiation. Using microcomputed tomography, Thm2-/-; Thm1aln/+ tibia were revealed to have reduced cortical and trabecular bone mineral density. Deletion of one allele of Gli2, a major transcriptional activator of the Hedgehog (Hh) pathway, exacerbated the small phenotype of Thm2-/-; Thm1aln/+ mice and caused small stature in Thm2-null mice. Together, these data reveal Thm2 as a novel locus that sensitizes to Hh signaling in skeletal development. Further, Thm2-/-; Thm1aln/+ mice present a new postnatal ciliopathy model of osteochondrodysplasia.

developmental biology↗

bioRxiv2019

MetAP2 inhibition reduces food intake and body weight in a ciliopathy mouse model of obesity

The ciliopathies Bardet-Biedl Syndrome and Alstrom Syndrome are genetically inherited pleiotropic disorders with primary clinical features of hyperphagia and obesity. Methionine aminopeptidase 2 inhibitors (MetAP2i) have been shown in preclinical and clinical studies to reduce food intake, body weight, and adiposity. Here we investigated the effects of MetAP2i administration in a mouse model of ciliopathy produced by conditional deletion of the Thm1 gene in adulthood (Thm1 cko). Thm1 cko mice show decreased hypothalamic pro-opiomelanocortin expression as well as hyperphagia, obesity, metabolic disease and hepatic steatosis. In obese Thm1 cko mice, two-week administration of MetAP2i reduced daily food intake and reduced body weight 17.1% from baseline (vs. 5% reduction for vehicle). This was accompanied with decreased levels of blood glucose, insulin and leptin. Further, MetAP2i reduced gonadal adipose depots and adipocyte size and improved liver morphology. This is the first report of MetAP2i reducing hyperphagia and body weight, and ameliorating metabolic indices in a mouse model of ciliopathy. These results support further investigation of MetAP2 inhibition as a potential therapeutic strategy for ciliary-mediated forms of obesity.

pharmacology and toxicology↗

bioRxiv2019

Genetic interaction of mammalian IFT-A paralogs regulates cilia disassembly, ciliary protein trafficking, Hedgehog signaling and embryogenesis

Primary cilia are sensory organelles that are essential for eukaryotic development and health. These antenna-like structures are synthesized by intraflagellar transport protein complexes, IFT-B and IFT-A, which mediate bi-directional protein trafficking along the ciliary axoneme. Here using mouse embryonic fibroblasts (MEF), we investigate the ciliary roles of two mammalian orthologues of Chlamydomonas IFT-A gene, IFT139, namely Thm1 (also known as Ttc21b) and Thm2 (Ttc21a). Thm1 loss causes perinatal lethality, and Thm2 loss allows survival into adulthood. At E14.5, the number of Thm1;Thm2 double mutant embryos is lower than that for a Mendelian ratio, indicating deletion of Thm1 and Thm2 causes mid-gestational lethality. We examined the ciliary phenotypes of mutant MEF. Thm1-mutant MEF show decreased cilia assembly, shortened primary cilia, a retrograde IFT defect for IFT and BBS proteins, and reduced ciliary entry of membrane-associated proteins. Thm1-mutant cilia also show a retrograde transport defect for the Hedgehog transducer, Smoothened, and an impaired response to Smoothened agonist, SAG. Thm2-null MEF show normal ciliary dynamics and Hedgehog signaling, but additional loss of a Thm1 allele impairs response to SAG. Further, Thm1;Thm2 double mutant MEF show enhanced cilia disassembly, and relative to Thm1-null MEF, increased impairment of IFT81 retrograde transport and of INPP5E ciliary import. Thus, Thm1 and Thm2 have unique and redundant roles in MEF. Thm1 regulates cilia assembly, and together with Thm2, cilia disassembly. Moreover, Thm1 alone and together with Thm2, regulates ciliary protein trafficking, Hedgehog signaling, and embryogenesis. These findings shed light on mechanisms underlying Thm1-, Thm2- or IFT-A-mediated ciliopathies.

genetics↗