Tumor gene expression analysis of synovial sarcoma patients treated with NY-ESO-1 TCR T cells (NCT01343043) [Immune]. Tumor gene expression analysis of synovial sarcoma patients treated with NY-ESO-1 TCR T cells (NCT01343043) [Immune]

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. 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. ***