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| Status |
Public on May 16, 2022 |
| Title |
Tumor gene expression analysis of synovial sarcoma patients treated with NY-ESO-1 TCR T cells (NCT01343043) [Immune] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Autologous T cells transduced to express a high affinity T-cell receptor specific to NY-ESO-1 (letetresgene autoleucel, lete-cel) show promise in the treatment of metastatic synovial sarcoma, with 50% overall response rate. Biomarkers predictive of response and resistance remain to be better defined. In 45 synovial sarcoma patients, we analyzed the association of response to lete-cel (NCT01343043) with tumor gene expression.
Analysis of tumor samples post-treatment illustrated lete-cel infiltration and decreased expression of macrophage genes, suggesting remodeling of the tumor microenvironment.
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| Overall design |
This dataset consists of 23 tumor samples collected from synovial sarcoma patients pre or post treatment with NY-ESO-1 TCR T cells in trial NCT01343043. There are 13 pre-infusion samples from 10 patients; 3 patients had two samples tested in replicate, results were averaged for downstream analysis. There are 5 at-progression samples. Five samples were excluded from downstream analysis due to time of collection and focus of analysis (see Sample notes for more details). For each sample, five 4-µm unstained slides were used for macrodissection and subsequent RNA extraction. RNA extract was quantified (including assessment of RNA purity) using the Quant-iT RiboGreen RNA Reagent and Kit, and RNA quality was assessed using Agilent RNA Pico chip analysis. RNA was analyzed using the NanoString nCounter® system, with 2 sets of NanoString assays (nCounter® PanCancer Immune Profiling Panel and nCounter® PanCancer Pathway Panel) run on the same extract. The normalization for raw nCounter counts of expressed genes was separately done for QC-passed samples in PanCancer immune and PanCancer pathway panel using the R-package “NanoStringNorm” (R version 4.0.3) with a set of parameters; CodeCount = ‘geo.mean’, Background = ‘mean.2sd’, SampleContent = ‘housekeeping.geo.mean’, round.values = TRUE, take.log = TRUE.
nCounter® PanCancer Immune Profiling Panel
*** Submitter declares that individual raw reads are not provided in order to protect patient privacy. ***
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| Contributor(s) |
Gyurdieva A, Chang Y, Houseman EA, Kim J, Dhusia K, Eleftheriadou I |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
May 13, 2022 |
| Last update date |
May 16, 2022 |
| Contact name |
Uma Saxena |
| E-mail(s) |
uma.x.saxena@gsk.com
|
| Phone |
6175841270
|
| Organization name |
Glaxosmithkline
|
| Street address |
1000 Winter Street
|
| City |
Waltham |
| State/province |
MA |
| ZIP/Postal code |
02451 |
| Country |
USA |
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| Platforms (1) |
| GPL32232 |
NanoString nCounter PanCancer Immune Profiling Panel (NS_CancerImmune_V1.1) |
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| Samples (23)
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| GSM6142429 |
Sample 07670055C0013R (cancer immune panel) |
| GSM6142430 |
Sample 07670058C0013R (cancer immune panel) |
| GSM6142431 |
Sample 07670059C0015R (cancer immune panel) |
| GSM6142432 |
Sample 07670062C0013R (cancer immune panel) |
| GSM6142433 |
Sample 07670064C0023R (cancer immune panel) |
| GSM6142434 |
Sample 07670067C0011R (cancer immune panel) |
| GSM6142435 |
Sample 07670076C0023R (cancer immune panel) |
| GSM6142436 |
Sample 08950109C0004R (cancer immune panel) |
| GSM6142437 |
Sample 08950113C0004R (cancer immune panel) |
| GSM6142438 |
Sample 08950114C0004R (cancer immune panel) |
| GSM6142439 |
Sample 08950116C0004R (cancer immune panel) |
| GSM6142440 |
Sample 08950117C0004R (cancer immune panel) |
| GSM6142441 |
Sample 08950118C0004R (cancer immune panel) |
| GSM6142442 |
Sample 08950121C0004R (cancer immune panel) |
| GSM6142443 |
Sample 08950124C0004R (cancer immune panel) |
| GSM6142444 |
Sample 07670056C0013R (cancer immune panel) |
| GSM6142445 |
Sample 07670063C0024R (cancer immune panel) |
| GSM6142446 |
Sample 08950124C0005R (cancer immune panel) |
| GSM6142447 |
Sample 07670061C0025R (cancer immune panel) |
| GSM6142448 |
Sample 07670079C0028R (cancer immune panel) |
| GSM6142449 |
Sample 07670080C0030R (cancer immune panel) |
| GSM6142450 |
Sample 08950118C0005R (cancer immune panel) |
| GSM6142451 |
Sample 07670091C0043R (cancer immune panel) |
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| This SubSeries is part of SuperSeries: |
| GSE202981 |
Tumor gene expression analysis of synovial sarcoma patients treated with NY-ESO-1 TCR T cells (NCT01343043) |
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| Relations |
| BioProject |
PRJNA837943 |
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