NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE193729 Query DataSets for GSE193729
Status Public on Apr 20, 2022
Title TTFields treatment effects on newly diagnosed Glioblastoma patients in peripheral T lymphocytes
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We report the application of RNA-based sequencing technology for high-throughput profiling of T cell enriched peripheral blood mononuclear cells. By sequencing in total of 12 pairs GBM patient samples, we extracted TCRαβ V(D)J sequences from the deep RNA-seq of T cells isolated from the 24 PBMCs to determine if TTFields treatment affected TCR diversity, using the Simpson’s diversity index (DI), which is the average proportional abundance of TCR clones based on the weighted arithmetic mean. Of the 12 patients, 9 exhibited negative log fold change (logFC) of TCR DI after TTFields, indicating clonal expansion. Notably, in all but 1 patient, the top 200 most abundant clones post TTFields, which accounted for 38.1% to 100% (median 67%) of detectable clones, showed substantial expansion compared to pre-TTFields T cells, and inversely correlated with the DI. Thus, TTFields treatment is associated with adaptive immune activation as evidenced by clonal expansion of peripheral T cells.
 
Overall design Examination of TTFields treatment effects in T cell enriched peripheral blood mononuclear cells.
 
Contributor(s) Tran DD, LE SB, Chen D
Citation(s) 35199647
Submission date Jan 14, 2022
Last update date Dec 04, 2022
Contact name SON B LE
E-mail(s) sble@usc.edu
Phone 3522843026
Organization name University of Southern California
Street address 1645 Amberwood Drive, Unit 11
City SOUTH PASADENA
State/province CA
ZIP/Postal code 91030
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (24)
GSM5819414 Peripheral T cells of patinet #7 before TTF treatment
GSM5819415 Peripheral T cells of patinet #7 after TTF treatment
GSM5819416 Peripheral T cells of patinet #9 before TTF treatment
Relations
BioProject PRJNA797422

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE193729_RAW.tar 7.4 Mb (http)(custom) TAR (of TXT)
GSE193729_consolidated_count_table.csv.gz 2.2 Mb (ftp)(http) CSV
GSE193729_consolidated_count_table_translated.csv.gz 2.1 Mb (ftp)(http) CSV
GSE193729_consolidated_tpm_table.csv.gz 9.0 Mb (ftp)(http) CSV
GSE193729_consolidated_tpm_table_translated.csv.gz 9.0 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap