Biology subjects

Liu, S. X.

Publications and source records attributed to Liu, S. X..

9 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↗

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↗

bioRxiv2023

chronODE: A framework to integrate time-series multi-omics data based on ordinary differential equations combined with machine learning

Most functional genomic studies are conducted in steady-state conditions, therefore providing a description of molecular processes at a particular moment of cell differentiation or organismal development. Longitudinal studies can offer a deeper understanding of the kinetics underlying epigenetic events and their contribution to defining cell-type-specific transcriptional programs. Here we develop chronODE, a mathematical framework based on ordinary differential equations that uniformly models the kinetics of temporal changes in gene expression and chromatin features. chronODE employs biologically interpretable parameters that capture tissue-specific kinetics of genes and regulatory elements. We further integrate this framework with a neural-network architecture that can link and predict changes across different data modalities by solving multivariate time-series regressions. Next, we apply this framework to investigate region-specific kinetics of epigenome rewiring in the developing mouse brain, and we demonstrate that changes in chromatin accessibility within regulatory elements can accurately predict changes in the expression of putative target genes over the same time period. Finally, by integrating single-cell ATAC-seq data generated during the same time course, we show that regulatory elements characterized by fast activation kinetics in bulk measurements are active in early-appearing cell types, such as radial glial and other neural progenitors, whereas elements characterized by slow activation kinetics are specific to more differentiated cell types that emerge at later stages of brain development.

bioinformatics↗

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↗

bioRxiv2021

Youthful and age-related matreotypes predict drugs promoting longevity

The identification and validation of drugs that promote health during aging ( geroprotectors) is key to the retardation or prevention of chronic age-related diseases. Here we found that most of the established pro-longevity compounds shown to extend lifespan in model organisms also alter extracellular matrix gene expression (i.e., matrisome) in human cell lines. To harness this novel observation, we used age-stratified human transcriptomes to define the age-related matreotype, which represents the matrisome gene expression pattern associated with age. Using a youthful matreotype, we screened in silico for geroprotective drug candidates. To validate drug candidates, we developed a novel tool using prolonged collagen expression as a non-invasive and in-vivo surrogate marker for C. elegans longevity. With this reporter, we were able to eliminate false positive drug candidates and determine the appropriate dose for extending the lifespan of C. elegans. We improved drug uptake for one of our predicted compounds, genistein, and reconciled previous contradictory reports of its effects on longevity. We identified and validated new compounds, tretinoin, chondroitin sulfate, and hyaluronic acid, for their ability to restore age-related decline of collagen homeostasis and increase lifespan. Thus, our innovative drug screening approach - employing extracellular matrix homeostasis - facilitates the discovery of pharmacological interventions promoting healthy aging. HighlightsO_LIMany geroprotective drugs alter extracellular matrix gene expression C_LIO_LIDefined young and old human matreotype signatures can identify novel potential geroprotective compounds C_LIO_LIProlonged collagen homeostasis as a surrogate marker for longevity C_LI

pharmacology and toxicology↗

bioRxiv2020

A non-canonical EZH2 function sensitizes solid tumors to genotoxic stress

Drugs that block the activity of the methyltransferase EZH2 are in clinical development for the treatment of non-Hodgkin lymphomas harboring gain-of-function EZH2 mutations that enhance its polycomb repressive function. In contrast, in castration-resistant prostate cancer (CRPC) we have previously reported that EZH2 plays a non-canonical role as a transcriptional activator. In this setting, we now show that EZH2 inhibitors can also block the non-canonical activity of EZH2 and inhibit the growth of CRPC cells. Gene expression and epigenomic profiling of cells treated with EZH2 inhibitors demonstrated that rather than de-repressing tumor suppressor genes silenced by PRC2, EZH2 inhibitors downregulate a set of DNA repair genes that are directly regulated by EZH2. In addition, genome-wide CRISPR/Cas9-mediated loss-of-function screens in the presence of EZH2 inhibitors identified these DNA repair genes to underlie the growth-inhibitory function of these compounds. Interrogation of public data from diverse solid tumor types expressing wild-type EZH2 showed that expression of DNA damage repair genes is significantly correlated with cellular sensitivity to EZH2 inhibitors. Consistent with these findings, treatment of CRPC cells with EZH2 inhibitors dramatically enhanced their sensitivity to genotoxic stress. These studies reveal a previously unappreciated mechanism of action of EZH2 inhibitors and provide a mechanistic basis for potential new combination cancer therapies.

cancer biology↗

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↗

bioRxiv2018

Reducing False Positives in CRISPR/Cas9 Screens from Copy Number Variations

CRISPR/Cas9 knockout screens have been widely used to interrogate gene functions across a wide range of cell systems. However, the screening outcome is biased in amplified genomic regions, due to the ability of the Cas9 nuclease to induce multiple double-stranded breaks and strong DNA damage responses at these regions. We developed algorithms to correct biases associated with copy number variations (CNV), even when the CNV profiles are unknown. We demonstrated that our methods effectively reduced false positives in amplified regions while preserving signals of true positives. In addition, we developed a sliding window approach to estimate regions of high copy numbers for cases in which CNV information is not available. These copy number estimations can subsequently be used to effectively correct CNV-related biases in CRISPR screening experiments. Our approach is integrated into the existing MAGeCK/MAGeCK-VISPR analysis pipelines and provides a convenient framework to improve the precision of CRISPR screening results.

bioinformatics↗