Project description:Rasmussen encephalitis is a unilateral encephalitis characterized by treatment-resistant epilepsy and progressive cognitive and motor decline. MRI reveals inflammation and neuropathology reveals reactive astrocytes, microglial activation, microglial nodules, T cell infiltration, and neuronal loss.
Despite the abundant evidence of altered signaling pathways in Rasmussen brain tissue and associated genetic variants, the mechanisms remain poorly understood, and it is uncertain which are a part or result of the underlying cause
In Rasmussen brain tissue, we identified by RNAseq altered immune signaling pathways, immune cell type annotation enrichment, and by whole exome sequencing HLA variants more common to Rasmussen. These findings demonstrate immune cell infiltration associated with innate and adaptive immune responses, as well as HLA variants that may increase vulnerability to RE.
Project description:We performed whole-genome transcriptome analysis of Rasmussen Encephalitis of the early disease stages for an overview of differentially expressed pathways leading to widespread neuroinflammation and degeneration.
Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.
Project description:T-cell receptor (TCR) diversity is generated through V(D)J recombination, which are essential for adaptive immunity. Although many methods have been applied, a simple method to detect TCR rearrangement at the DNA level remains lacking. Here we introduce HTGTS-TCR-seq, a novel approach derived from high-throughput genome-wide translocation sequencing (HTGTS), to comprehensively and unbiasedly analyze TCR recombination. Unlike multiplex PCR requiring extensive V-J segment primers, HTGTS-TCR-seq enables unbiased TCR profiling through targeted enrichment and deep sequencing by a single primer. This method identifies biased V(D)J segment usage in developing T cells through V/J primer-based amplification and provides unique complementarity determining region 3 (CDR3) profiles in mature T cells via J primers. HTGTS-TCR-seq detects rearrangement at both alleles, enabling quantification of DJβ and VβDJβ rearrangement products with productive and nonproductive profile. Applied to human peripheral blood mononuclear cells (PBMCs), HTGTS-TCR-seq reveals a shared CDR3 motif between humans and mice. HTGTS-TCR-seq is a robust tool for T cell immunity research, with potential application in immune responses analysis, cancer research, and autoimmune diseases investigation.
Project description:Transcriptional profiling of human mesenchymal stem cells comparing normoxic MSCs cells with hypoxic MSCs cells. Hypoxia may inhibit senescence of MSCs during expansion. Goal was to determine the effects of hypoxia on global MSCs gene expression.
Project description:Gene methylation profiling of immortalized human mesenchymal stem cells comparing HPV E6/E7-transfected MSCs cells with human telomerase reverse transcriptase (hTERT)- and HPV E6/E7-transfected MSCs. hTERT may increase gene methylation in MSCs. Goal was to determine the effects of different transfected genes on global gene methylation in MSCs.
