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Series GSE250037 Query DataSets for GSE250037
Status Public on Dec 19, 2023
Title Expanded T lymphocytes in the cerebrospinal fluid of multiple sclerosis patients are specific for Epstein-Barr virus infected B cells
Organism Homo sapiens
Experiment type Other
Summary Our hypothesis is that a major fraction of the expanded clones of T lymphocytes in the cerebrospinal fluid (CSF) are specific for autologous EBV-infected B cells. We obtained blood and CSF samples from 8 relapsing-remitting patients in the process of diagnosis. We stimulated cells from the blood with autologous EBV-infected lymphoblastoid cell lines (LCL), EBV, varicella zoster virus, influenza, and candida, and sorted the responding cells with flow cytometry after 6 days. We sequenced the RNA for T cell receptors (TCR) from CSF, unselected blood cells, and the antigen-specific cells. We used the TCR Vβ CDR3 sequences from the antigen-specific cells to assign antigen specificity to the sequences from the CSF and blood. LCL-specific cells comprised 13.0±4.3% (mean±standard deviation) of the total reads present in CSF and 13.3±7.5% of the reads present in blood. The next most abundant antigen specificity was flu, which was 4.7±1.7% of the reads in the CSF and 9.3±6.6% in the blood. The prominence of LCL-specific reads was even more marked in the top 1% most abundant CSF clones with statistically significant 47% mean overlap with LCL.
 
Overall design T cell receptor sequences from cerebrospinal fluid, peripheral blood mononuclear cells (PBMC), and proliferating CD3+ cells from PBMC stimulated with Epstein-Barr virus, autologous EBV-infected cell lines, varicella zoster virus, influenza, or candida.
 
Contributor(s) Lindsey JW, Gottlieb A
Citation(s) 38190525
Submission date Dec 12, 2023
Last update date Mar 19, 2024
Contact name John William Lindsey
E-mail(s) john.w.lindsey@uth.tmc.edu
Phone 7135007135
Organization name University of Texas Health Science Center At Houston
Street address 6431 Fannin St, Ste 7.044 MSB, Neurology Dept
City Houston
State/province TX
ZIP/Postal code 77030-1501
Country USA
 
Platforms (1)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (107)
GSM7971729 subject MS1 CSF cells, ex vivo
GSM7971730 subject MS1 PBMC, ex vivo
GSM7971731 subject MS1 PBMC, stimulated with autologous LCL
Relations
BioProject PRJNA1051639

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Supplementary file Size Download File type/resource
GSE250037_BF100CDR3.xlsx 1.7 Mb (ftp)(http) XLSX
GSE250037_BF1101CDR3.xlsx 2.1 Mb (ftp)(http) XLSX
GSE250037_BF1102CDR3.xlsx 662.3 Kb (ftp)(http) XLSX
GSE250037_BF1103CDR3.xlsx 1.4 Mb (ftp)(http) XLSX
GSE250037_BF1104CDR3.xlsx 1.1 Mb (ftp)(http) XLSX
GSE250037_BF87CDR3.xlsx 2.2 Mb (ftp)(http) XLSX
GSE250037_BF88CDR3.xlsx 1.7 Mb (ftp)(http) XLSX
GSE250037_BF89CDR3.xlsx 2.1 Mb (ftp)(http) XLSX
GSE250037_BF92CDR3.xlsx 2.7 Mb (ftp)(http) XLSX
GSE250037_BF93CDR3.xlsx 2.1 Mb (ftp)(http) XLSX
GSE250037_BF94CDR3.xlsx 1.3 Mb (ftp)(http) XLSX
GSE250037_BF95CDR3.xlsx 1.7 Mb (ftp)(http) XLSX
GSE250037_BF96CDR3.xlsx 1.8 Mb (ftp)(http) XLSX
GSE250037_BF97CDR3.xlsx 1.8 Mb (ftp)(http) XLSX
GSE250037_BF98CDR3.xlsx 1.1 Mb (ftp)(http) XLSX
GSE250037_BF99CDR3.xlsx 1.7 Mb (ftp)(http) XLSX
GSE250037_RAW.tar 461.9 Mb (http)(custom) TAR (of XLSX)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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