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Series GSE168826 Query DataSets for GSE168826
Status Public on Mar 13, 2021
Title TCR beta sequencing of blood and tumor samples from EG7.OVA bearing wildtype mice with OT-1 T cell transfer
Organism Mus musculus
Experiment type Other
Summary We report the application of TCRβ sequencing to understand T cell repertoire of matched blood and tumor samples pre and post treatment in EG7.OVA tumor bearing mice with OT-1 cell transfer. TCRβ sequencing demonstrated that OT-1 (CASSRANYEQYF) was the most abundant T-cell clone in both blood and tumors of mRBC‑OVA-4-1BBL-IL-12 treated mice. To investigate the effects of mRBC‑OVA-4-1BBL-IL-12 on immune memory, the T cell repertoire was also analyzed before and after EG7.OVA and EL4 tumor rechallenge in cured and treatment-naive mice. TCRβ sequencing on T cells in peripheral blood showed that OT-1 clones increased in frequency after EG7.OVA challenge in previously cured mice. OT-1 frequency did not increase in treatment-naïve mice after tumor challenge, indicating that the tumor alone is insufficient to drive OT-1 cell expansion. We also evaluated the frequencies of unique TCRβ sequences in T cell clones that significantly expanded post EL4 challenge (EL4 responsive TCR). Increased frequency of EL4-responsive TCRs upon each tumor challenge (EG7.OVA and EL4) was associated with complete responders (mice that rejected EL4 challenge), suggesting that T-cell-mediated protection against parental tumor antigens was generated prior to EL4 challenge. Partial responders (delayed tumor growth compared with naïve mice) had increases in EL4-responsive TCR frequencies after EL4 challenge but not during the EG7.OVA rechallenge, whereas the non-responder (tumor growth similar to naïve mice) had minimal increases in TCR frequencies upon EL4 challenge. Overall, the ability to control EL4 tumors correlated with the expansion of EL4-responsive TCR clones.
Overall design TCR repertoire analyses of matched blood and tumor samples, pre and post mRBC-OVA-4-1BBL-IL-12 treatment as well as pre and post EG7.OVA and EL4 challenge in cured mice in a murine lymphoma model with OT-1 T cell transfer
Submitter claims they are unable to provide raw fastq files:
The authors state "Raw data were processed using the standard immunoSEQ Analyzer from Adaptive Biotechnologies Corporation (third party CRO), and this third party does not release raw data."
Contributor(s) Zhang X, Chen TF, Salzberg A, Nixon M
Citation(s) 33976146
Submission date Mar 12, 2021
Last update date May 19, 2021
Contact name Anna Salzberg
Organization name Rubius Therapeutics
Street address 399 Binney St UNIT 300
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (81)
GSM5170838 Naive pre EG7.OVA tumor challenge blood - Mouse 1 RUB157_1_1_Naive_preblood
GSM5170839 Naive pre EG7.OVA tumor challenge blood - Mouse 2 RUB157_1_2_Naive_preblood
GSM5170840 Naive pre EG7.OVA tumor challenge blood - Mouse 3 RUB157_1_3_Naive_preblood
BioProject PRJNA714102

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Supplementary file Size Download File type/resource
GSE168826_RAW.tar 24.1 Mb (http)(custom) TAR (of FASTA, TSV)
Raw data not provided for this record
Processed data provided as supplementary file

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