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

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. This dataset consists of 22 tumor samples collected from synovial sarcoma patients pre or post treatment with NY-ESO-1 TCR T cells in trial NCT01343043. There are 11 pre-infusion samples from 10 patients; 1 patients had two samples tested in replicate, results were averaged for downstream analysis. There are 5 at-progression samples. Six 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 Pathway Panel *** Submitter declares that individual raw reads are not provided in order to protect patient privacy. ***

经转导以表达靶向NY-ESO-1的高亲和力T细胞受体的自体T细胞（letetresgene autoleucel，简称lete-cel）在转移性滑膜肉瘤的治疗中展现出潜力，总体应答率达50%。但可预测应答与耐药性的生物标志物仍有待进一步明确。在45例滑膜肉瘤患者中，我们分析了lete-cel治疗应答（临床试验编号NCT01343043）与肿瘤基因表达之间的关联。对治疗后肿瘤样本的分析显示，lete-cel发生浸润且巨噬细胞相关基因表达下调，提示肿瘤微环境发生重塑。本数据集包含临床试验NCT01343043中，接受NY-ESO-1 TCR T细胞治疗前后的滑膜肉瘤患者所采集的22份肿瘤样本。其中10例患者提供了11份输注前样本；1例患者提供了2份重复检测样本，下游分析中对其结果取平均值。另有5份为疾病进展时采集的样本。由于样本采集时间与分析侧重点，有6份样本被排除在下游分析之外，详细信息参见样本说明。针对每份样本，使用5张厚度为4μm的未染色切片进行宏观组织剖分，随后开展RNA提取。RNA提取物采用Quant-iT RiboGreen RNA试剂与试剂盒进行定量（包含RNA纯度评估），并通过Agilent RNA Pico芯片分析评估RNA质量。使用NanoString nCounter®系统对RNA进行分析，同一份提取物同时开展两套NanoString检测：nCounter®泛癌免疫分析面板（PanCancer Immune Profiling Panel）与nCounter®泛癌通路分析面板（PanCancer Pathway Panel）。针对通过质量控制的样本，分别基于泛癌免疫面板与泛癌通路面板的基因原始nCounter计数进行归一化处理；采用R包"NanoStringNorm"（R版本4.0.3），并设置如下参数：CodeCount = 'geo.mean'，Background = 'mean.2sd'，SampleContent = 'housekeeping.geo.mean'，round.values = TRUE，take.log = TRUE。nCounter® PanCancer Pathway Panel***提交者声明，为保护患者隐私，未提供原始测序读长数据。***