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| Status |
Public on Mar 13, 2018 |
| Title |
Impact of B16F0 exosomes on the transcriptome of CTLL2 cytotoxic T cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
While recent clinical studies demonstrate the promise of cancer immunotherapy, a barrier for broadening the clinical benefit is identifying how tumors locally suppress cytotoxic immunity. As an emerging mode of intercellular communication, exosomes secreted by malignant cells can deliver a complex payload of coding and non-coding RNA to cells within the tumor microenvironment. Here, we quantified the RNA payload within tumor-derived exosomes and the resulting dynamic transcriptomic response to cytotoxic T cells upon exosome delivery to better understand how tumor-derived exosomes can alter immune cell function. Exosomes derived from B16F0 melanoma cells were enriched for a subset of coding and non-coding RNAs that did not reflect the abundance in the parental cell. Upon exosome delivery, RNAseq revealed the dynamic changes in the transcriptome of CTLL2 cytotoxic T cells. In analyzing transiently co-expressed gene clusters, pathway enrichment suggested that the B16F0 exosomal payload altered mitochondrial respiration, which was confirmed independently, and upregulated genes associated with the Notch signaling pathway. Interestingly, exosomal miRNA appeared to have no systematic effect on downregulating target mRNA levels.
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| Overall design |
CTLL2 cells were grown in complete media for 24 hrs, and then stimulated with fresh B16F0 exosomes resuspended in PBS, to a final exosome concentration of 0.2 mg/ml. The transcriptome of untreated CTLL2 cells was assayed at 0, 0.5, 2, 4, and 8 hours after cells were placed in fresh media. There are 4 biological replicates at the 0 hour time point and 3 biological replicates at the 0.5, 2, 4, and 8 hour time points. The transcriptome of CTLL2 cells treated with B16F0 exosomes was assayed at 0.5, 2, 4, and 8 hours after addition of fresh media containing B16F0 exosomes. There were 3 biological replicates performed at each time point.
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| Contributor(s) |
Klinke DJ |
| Citation(s) |
29399967 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 CA193473 |
Integrative systems approach to identify local oncogenic modulation of the IL12 axis |
WEST VIRGINIA UNIVERSITY RESEARCH CORPORATION |
David John Klinke |
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| |
| Submission date |
Aug 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
David John Klinke |
| E-mail(s) |
David.Klinke@mail.wvu.edu
|
| Phone |
304-293-9346
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| Organization name |
West Virginia University
|
| Department |
Chemical Engineering
|
| Street address |
P.O. Box 6102
|
| City |
Morgantown |
| State/province |
WV |
| ZIP/Postal code |
26506-6102 |
| Country |
USA |
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| Platforms (1) |
| GPL18480 |
Illumina HiSeq 1500 (Mus musculus) |
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| Samples (28)
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| GSM2752325 |
untreated CTLL2 cells 0 hr rep 4 |
| GSM2752326 |
untreated CTLL2 cells 0.5 hr rep 1 |
| GSM2752327 |
untreated CTLL2 cells 0.5 hr rep 2 |
| GSM2752328 |
untreated CTLL2 cells 0.5 hr rep 3 |
| GSM2752329 |
B16F0 exosome-treated CTLL2 cells 0.5 hr rep 1 |
| GSM2752330 |
B16F0 exosome-treated CTLL2 cells 0.5 hr rep 2 |
| GSM2752331 |
B16F0 exosome-treated CTLL2 cells 0.5 hr rep 3 |
| GSM2752332 |
untreated CTLL2 cells 2 hr rep 1 |
| GSM2752333 |
untreated CTLL2 cells 2 hr rep 2 |
| GSM2752334 |
untreated CTLL2 cells 2 hr rep 3 |
| GSM2752335 |
B16F0 exosome-treated CTLL2 cells 2 hr rep 1 |
| GSM2752336 |
B16F0 exosome-treated CTLL2 cells 2 hr rep 2 |
| GSM2752337 |
B16F0 exosome-treated CTLL2 cells 2 hr rep 3 |
| GSM2752338 |
untreated CTLL2 cells 4 hr rep 1 |
| GSM2752339 |
untreated CTLL2 cells 4 hr rep 2 |
| GSM2752340 |
untreated CTLL2 cells 4 hr rep 3 |
| GSM2752341 |
B16F0 exosome-treated CTLL2 cells 4 hr rep 1 |
| GSM2752342 |
B16F0 exosome-treated CTLL2 cells 4 hr rep 2 |
| GSM2752343 |
B16F0 exosome-treated CTLL2 cells 4 hr rep 3 |
| GSM2752344 |
untreated CTLL2 cells 8 hr rep 1 |
| GSM2752345 |
untreated CTLL2 cells 8 hr rep 2 |
| GSM2752346 |
untreated CTLL2 cells 8 hr rep 3 |
| GSM2752347 |
B16F0 exosome-treated CTLL2 cells 8 hr rep 1 |
| GSM2752348 |
B16F0 exosome-treated CTLL2 cells 8 hr rep 2 |
| GSM2752349 |
B16F0 exosome-treated CTLL2 cells 8 hr rep 3 |
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| This SubSeries is part of SuperSeries: |
| GSE102951 |
Expression data from parental B16F0 cells and B16F0 exosomes |
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| Relations |
| BioProject |
PRJNA399762 |
| SRA |
SRP116047 |
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