Project description:Clinically Isolated Syndromes (CIS)represent the first clinical episode of an inflammatory demyelinating disorder suggestive of MS. Most CIS will develop relapsing-remitting MS (RR), characterized by clinical and inflammatory attacks followed by periods of recovery and stability. With time, most RR-MS subjects will evolve to secondary progressive MS (SP), with advancing neurological impairment in absence of recognizable relapses. A small fraction of MS subjects experience worsening of neurologic function from the onset and are thus defined primary progressive MS (PP). We analysed PBMC transcriptomes relative to 41 healthy subjects, 47 CIS, 49 RR, 22 SP and 27 PP patients and applied a semi-automated pipeline in R Bioconductor platform to perform preprocessing and differential expression analysis.
Project description:Purpose: The goal of this study is to compare and examine the transcriptional profiles in spleen(SP) Tfh cells versus Peyer's patches(PP) Tfh cells by mRNA sequencing. Methods: Tfh cells (CD4+CXCR5+PD1+GITR-CD44+) were sorted by a MoFlo-Astrios (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. A library for mRNA sequencing was prepared using the SMART-Seq mRNA Kit/NEXtera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. Sequencing was performed with Novaseq 6000 (Illumina). Results: For alignment and transcript quantification of raw RNA sequencing data, STAR (v2.7.10b) and RSEM(v1.3.3) were used. To normalize the expected read counts while accounting for differences in sequencing depth and gene length, GeTMM method was applied. Differentially expressed genes (DEGs) analysis was conducted using DESeq2 R package (DESeq2 version 1.42.1; R version 4.1.2) (Log2 fold-change > 1 and P < 0.01). Conclusions: Our study presents comparative gene expression analysis of Tfh cells from SP and PP in wild type SPF mice. We concluded that PP-Tfh cells express higher levels of Tfh related genes. The data reported here also provide supplementary files of read counts and GeTMM
Project description:Vitamin B12 is an essential micronutrient that functions in two metabolic pathways: the canonical propionate breakdown pathway and the methionine/S-adenosylmethionine (Met/SAM) cycle. In Caenorhabditis elegans, low vitamin B12, or genetic perturbation of the canonical propionate breakdown pathway results in propionate accumulation and the transcriptional activation of a propionate shunt pathway. This propionate-dependent mechanism requires nhr-10 and is referred to as “B12-mechanism-I”. Here, we report that vitamin B12 represses the expression of Met/SAM cycle genes by a propionate-independent mechanism we refer to as “B12-mechanism-II”. This mechanism is activated by perturbations in the Met/SAM cycle, genetically or due to low dietary vitamin B12. B12-mechanism-II requires nhr-114 to activate Met/SAM cycle gene expression, the vitamin B12 transporter, pmp-5, and adjust influx and efflux of the cycle by activating msra-1 and repressing cbs-1, respectively. Taken together, Met/SAM cycle activity is sensed and transcriptionally adjusted to be in a tight metabolic regime.
