Browsing by Author "Wei, Xiaoran"

Now showing 1 - 6 of 6
  • Thumbnail Image
    Applying Proteomics and Computational Approaches to Identify Novel Targets in Blast-Associated Post-Traumatic Epilepsy
    Browning, Jack L.; Wilson, Kelsey A.; Shandra, Oleksii; Wei, Xiaoran; Mahmutovic, Dzenis; Maharathi, Biswajit; Robel, Stefanie; VandeVord, Pamela J.; Olsen, Michelle L. (MDPI, 2024-03-01)
    Traumatic brain injury (TBI) can lead to post-traumatic epilepsy (PTE). Blast TBI (bTBI) found in Veterans presents with several complications, including cognitive and behavioral disturbances and PTE; however, the underlying mechanisms that drive the long-term sequelae are not well understood. Using an unbiased proteomics approach in a mouse model of repeated bTBI (rbTBI), this study addresses this gap in the knowledge. After rbTBI, mice were monitored using continuous, uninterrupted video-EEG for up to four months. Following this period, we collected cortex and hippocampus tissues from three groups of mice: those with post-traumatic epilepsy (PTE+), those without epilepsy (PTE−), and the control group (sham). Hundreds of differentially expressed proteins were identified in the cortex and hippocampus of PTE+ and PTE− relative to sham. Focusing on protein pathways unique to PTE+, pathways related to mitochondrial function, post-translational modifications, and transport were disrupted. Computational metabolic modeling using dysregulated protein expression predicted mitochondrial proton pump dysregulation, suggesting electron transport chain dysregulation in the epileptic tissue relative to PTE−. Finally, data mining enabled the identification of several novel and previously validated TBI and epilepsy biomarkers in our data set, many of which were found to already be targeted by drugs in various phases of clinical testing. These findings highlight novel proteins and protein pathways that may drive the chronic PTE sequelae following rbTBI.
  • Thumbnail Image
    Atypical Neurogenesis, Astrogliosis, and Excessive Hilar Interneuron Loss Are Associated with the Development of Post-Traumatic Epilepsy
    Gudenschwager-Basso, Erwin Kristobal; Shandra, Oleksii; Volanth, Troy; Patel, Dipan C.; Kelly, Colin; Browning, Jack L.; Wei, Xiaoran; Harris, Elizabeth A.; Mahmutovic, Dzenis; Kaloss, Alexandra M.; Correa, Fernanda Guilhaume; Decker, Jeremy; Maharathi, Biswajit; Robel, Stefanie; Sontheimer, Harald; VandeVord, Pamela J.; Olsen, Michelle L.; Theus, Michelle H. (MDPI, 2023-04-25)
    Background: Traumatic brain injury (TBI) remains a significant risk factor for post-traumatic epilepsy (PTE). The pathophysiological mechanisms underlying the injury-induced epileptogenesis are under investigation. The dentate gyrus—a structure that is highly susceptible to injury—has been implicated in the evolution of seizure development. Methods: Utilizing the murine unilateral focal control cortical impact (CCI) injury, we evaluated seizure onset using 24/7 EEG video analysis at 2–4 months post-injury. Cellular changes in the dentate gyrus and hilus of the hippocampus were quantified by unbiased stereology and Imaris image analysis to evaluate Prox1-positive cell migration, astrocyte branching, and morphology, as well as neuronal loss at four months post-injury. Isolation of region-specific astrocytes and RNA-Seq were performed to determine differential gene expression in animals that developed post-traumatic epilepsy (PTE+) vs. those animals that did not (PTE−), which may be associated with epileptogenesis. Results: CCI injury resulted in 37% PTE incidence, which increased with injury severity and hippocampal damage. Histological assessments uncovered a significant loss of hilar interneurons that coincided with aberrant migration of Prox1-positive granule cells and reduced astroglial branching in PTE+ compared to PTE− mice. We uniquely identified Cst3 as a PTE+-specific gene signature in astrocytes across all brain regions, which showed increased astroglial expression in the PTE+ hilus. Conclusions: These findings suggest that epileptogenesis may emerge following TBI due to distinct aberrant cellular remodeling events and key molecular changes in the dentate gyrus of the hippocampus.
  • Thumbnail Image
    EGR1 recruits TET1 to shape the brain methylome during development and upon neuronal activity
    Sun, Zhixiong; Xu, Xiguang; He, Jianlin; Murray, Alexander; Sun, Ming-an; Wei, Xiaoran; Wang, Xia; McCoig, Emmarose; Xie, Evan; Jiang, Xi; Li, Liwu; Zhu, Jinsong; Chen, Jianjun; Morozov, Alexei; Pickrell, Alicia M.; Theus, Michelle H.; Xie, Hehuang David (2019-08-29)
    Life experience can leave lasting marks, such as epigenetic changes, in the brain. How life experience is translated into storable epigenetic information remains largely unknown. With unbiased data-driven approaches, we predicted that Egr1, a transcription factor important for memory formation, plays an essential role in brain epigenetic programming. We performed EGR1 ChIP-seq and validated thousands of EGR1 binding sites with methylation patterns established during postnatal brain development. More specifically, these EGR1 binding sites become hypomethylated in mature neurons but remain heavily methylated in glia. We further demonstrated that EGR1 recruits a DNA demethylase TET1 to remove the methylation marks and activate downstream genes. The frontal cortices from the knockout mice lacking Egr1 or Tet1 share strikingly similar profiles in both gene expression and DNA methylation. In summary, our study reveals EGR1 programs the brain methylome together with TET1 providing new insight into how life experience may shape the brain methylome.
  • Thumbnail Image
    Immunoregulatory and neutrophil-like monocyte subsets with distinct single-cell transcriptomic signatures emerge following brain injury
    Gudenschwager Basso, Erwin K.; Ju, Jing; Soliman, Eman; de Jager, Caroline; Wei, Xiaoran; Pridham, Kevin J.; Olsen, Michelle L.; Theus, Michelle H. (2024-02-03)
    Monocytes represent key cellular elements that contribute to the neurological sequela following brain injury. The current study reveals that trauma induces the augmented release of a transcriptionally distinct CD115+/Ly6Chi monocyte population into the circulation of mice pre-exposed to clodronate depletion conditions. This phenomenon correlates with tissue protection, blood–brain barrier stability, and cerebral blood flow improvement. Uniquely, this shifted the innate immune cell profile in the cortical milieu and reduced the expression of pro-inflammatory Il6, IL1r1, MCP-1, Cxcl1, and Ccl3 cytokines. Monocytes that emerged under these conditions displayed a morphological and gene profile consistent with a subset commonly seen during emergency monopoiesis. Single-cell RNA sequencing delineated distinct clusters of monocytes and revealed a key transcriptional signature of Ly6Chi monocytes enriched for Apoe and chitinase-like protein 3 (Chil3/Ym1), commonly expressed in pro-resolving immunoregulatory monocytes, as well as granule genes Elane, Prtn3, MPO, and Ctsg unique to neutrophil-like monocytes. The predominate shift in cell clusters included subsets with low expression of transcription factors involved in monocyte conversion, Pou2f2, Na4a1, and a robust enrichment of genes in the oxidative phosphorylation pathway which favors an anti-inflammatory phenotype. Transfer of this monocyte assemblage into brain-injured recipient mice demonstrated their direct role in neuroprotection. These findings reveal a multifaceted innate immune response to brain injury and suggest targeting surrogate monocyte subsets may foster tissue protection in the brain.
  • Thumbnail Image
    Mechanism and Function of TrkB.T1 Astrocyte Expression
    Wei, Xiaoran (Virginia Tech, 2024-07-23)
    Astrocytes are the most abundant glial cell type in the central nervous system (CNS). Most astrocytes are born during the early postnatal period in the rodent brain and mature alongside neurons, demonstrating remarkable morphological structural complexity, and attaining maturity in the second postnatal month. We have shown that astrocyte morphogenesis is regulated in part by brain-derived neurotrophic factor (BDNF) via signaling through the truncated tropomyosin receptor kinase B (TrkB) receptor. TrkB is the primary receptor for BDNF which is broadly expressed and released by neurons in developing and mature brain. TrkB has two predominant isoforms expressed in central nervous system (CNS), the full length TrkB (TrkB.FL) receptor and truncated TrkB (TrkB.T1) receptor. We recently demonstrated in the adult rodent cortex that TrkB.T1 is largely specific to astrocytes and over 90% of all Ntrk2 expression in astrocytes attributed to TrkB.T1. In contrast TrkB.FL is the predominant isoform expressed by neurons. It is not known how astrocytes and neurons regulate their specific TrkB isoform expression, although previous studies in bulk frontal cortical tissue from human postmortem samples indicate that DNA methylation level in promoter region and 3' UTR region of NTRK2 is negatively correlated with TrkB.T1 expression levels, but not with TrkB.FL expression. The mechanism of TrkB.T1 isoform-specific expression and the role of TrkB.T1 in astrocyte developmental process are unknown. In this dissertation, we aimed to determine in the DNA methylation contributes to isoform specific expression of TrkB.T1. We thus profiled the 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in neurons, astrocytes and microglia utilizing nanopore sequencing. We identified robust differences in cell-type specific TrkB isoform expression is associated with significantly different 5mC and 5hmC patterns in neurons and astrocytes. Further, we investigated the role of TrkB.T1 in cortical astrocyte developmental processes and astrocyte function during early postnatal development (postnatal day (P) 8, P14, P28 and P60). RNA sequencing of TrkB.T1 deficient astrocytes isolated at these timepoints revealed aberrant gene expression in astrocyte maturation, while pathway analysis indicated disruptions in synapse organization, neurotransmitter transport and exocytotic processes. Subsequent functional secretory proteomics highlighted disruptions in metabolism and lipid regulation, particularly cholesterol transport, suggesting potential implications for synapse formation. We observed dysregulated spine density in the motor and somatosensory cortices from TrkB.T1-deficient astrocytes relative to control astrocytes. These findings suggest that TrkB.T1 deficiency adversely affects normal astrocyte development, which in turn affects neuronal synapse development. This study provides new insights into the role of BDNF/TrkB.T1 signaling in CNS development and lays the groundwork for evaluating astrocyte BDNF/TrkB.T1 signaling in neurological diseases.
  • Thumbnail Image
    Recursive Motif Analyses Identify Brain Epigenetic Transcription Regulatory Modules
    Banerjee, Sharmi; Wei, Xiaoran; Xie, Hehuang David (Elsevier, 2019-04-09)
    DNA methylation is an epigenetic modification modulating the structure of DNA molecule and the interactions with its binding proteins. Accumulating large-scale methylation data motivates the development of analytic tools to facilitate methylome data mining. One critical phenomenon associated with dynamic DNA methylation is the altered DNA binding affinity of transcription factors,which plays key roles in gene expression regulation. In this study,we conceived an algorithm to predict epigenetic regulatory modules through recursive motif analyses on differentially methylated loci. A two-step procedure was implemented to first group differentially methylated loci into clusters according to their correlations in methylation profiles and then to repeatedly identify the transcription factor binding motifs significantly enriched in each cluster. Weapplied this tool on methylome datasets generated for mouse brainswhich have a lack of DNA demethylation enzymes TET1 or TET2. Compared with wild type control, the differentially methylated CpG sites identified in TET1 knockout mouse brains differed significantly from those determined for TET2 knockout. Transcription factors with zinc finger DNA binding domains including Egr1, Zic3, and Zeb1 were predicted to be associated with TET1 mediated brain methylome programming, while Lhx family members with Homeobox domains were predicted to be associated with TET2 function. Interestingly, genomic loci from a co-methylated cluster often host motifs for transcription factors sharing the same DNA binding domains. Altogether, our study provided a systematic approach for epigenetic regulatory module identification and will help throw light on the interplay of DNA methylation and transcription factors.