Data Sheet 1_A comprehensive analysis of the tryptophan metabolism-related gene signature to predict the prognosis of esophageal squamous cell carcinoma based on multi-omics.xlsx

BackgroundTryptophan (Trp) metabolism plays a vital role in tumor development and outcomes. However, Trp in esophageal squamous cell carcinoma (ESCC) remains poorly understood. We aimed to explore the role and mechanism of Trp metabolism in ESCC.
MethodsWe integrated single-cell RNA (scRNA) sequencing, bulk transcriptome, proteomics, and microbiome data from public databases. Tryptophan-related cell populations and their interactions were explored using the “seurat” R package at the single-cell level. Least absolute shrinkage and selection operator (LASSO) and univariate Cox regression were used to select prognostic TrpGs and construct a risk model. The overall survival, immune infiltration, checkpoint expression, drug sensitivity, and microbiota composition between high- and low-risk groups were evaluated. Independent prognostic factors were identified via multivariate Cox analysis and validated by qPCR analysis, and a nomogram was constructed for survival prediction.
ResultsWe identified 28 differentially expressed tryptophan-related genes (DE-TrpGs), and fibroblasts emerged as the cell type with the highest TrpG score, although reduced in ESCC. Eighteen DE-TrpGs showed downregulation in tumor fibroblasts at the single-cell level. Fibroblast-epithelial communication involved the LAMININ, HSPG, and AGRN pathways. Five prognostic TrpGs (MAOA, AKR1A1, ALDH9A1, HAAO, and ALDH2) were selected to construct the risk model. The expression of MAOA, AKR1A1, ALDH9A1, HAAO, and ALDH2 was significantly downregulated in ESCC tumor tissues compared to non-tumor tissues. High-risk patients showed poorer overall survival (OS), distinct immune cell infiltration, elevated expression of KIR2DL1, LGALS9, TNFRSF18, and TNFRSF4, increased sensitivity to imatinib and axitinib, resistance to multiple chemotherapeutics, and reduced Fusobacteria and Tenericutes abundance. HAAO, ALDH2, and lymph node stage were identified as independent prognostic factors and were used to develop a predictive nomogram.
ConclusionWe identified a Trp metabolism-associated fibroblast population in the ESCC tumor microenvironment (TME) and developed a five-gene TrpG signature for prognostic prediction in ESCC patients.

研究背景
色氨酸（Tryptophan, Trp）代谢在肿瘤发生发展与预后转归中发挥关键作用。然而，食管鳞状细胞癌（esophageal squamous cell carcinoma, ESCC）中色氨酸代谢的相关研究仍较为匮乏。本研究旨在探讨色氨酸代谢在食管鳞状细胞癌中的作用及潜在机制。

研究方法
本研究整合了来自公共数据库的单细胞RNA（single-cell RNA, scRNA）测序、批量转录组、蛋白质组学及微生物组数据。在单细胞层面，我们采用‘Seurat’R包分析色氨酸相关细胞群及其相互作用网络。通过最小绝对收缩和选择算子（Least absolute shrinkage and selection operator, LASSO）回归与单变量Cox回归筛选预后相关色氨酸基因（TrpGs），并构建预后风险模型。我们进一步评估了高低风险组间的总生存期、免疫浸润特征、免疫检查点表达水平、药物敏感性及微生物群组成差异。通过多变量Cox分析筛选独立预后因子，并经qPCR实验验证，同时构建用于生存预测的列线图（nomogram）。

研究结果
本研究共鉴定出28个差异表达色氨酸相关基因（differentially expressed tryptophan-related genes, DE-TrpGs）。成纤维细胞成为色氨酸基因评分最高的细胞类型，但其在食管鳞状细胞癌组织中的丰度显著降低。在单细胞层面，有18个差异表达色氨酸相关基因在肿瘤成纤维细胞中呈下调表达趋势。成纤维细胞-上皮细胞通信涉及层粘连蛋白（LAMININ）、硫酸乙酰肝素蛋白聚糖（HSPG）及聚集蛋白聚糖（AGRN）通路。最终筛选出5个预后相关色氨酸基因（MAOA、AKR1A1、ALDH9A1、HAAO及ALDH2）以构建风险模型。与正常对照组织相比，食管鳞状细胞癌肿瘤组织中MAOA、AKR1A1、ALDH9A1、HAAO及ALDH2的表达水平显著下调。高风险组患者的总生存期（overall survival, OS）更短，免疫细胞浸润模式存在显著差异，KIR2DL1、LGALS9、TNFRSF18及TNFRSF4的表达水平显著升高，对伊马替尼（imatinib）和阿昔替尼（axitinib）的敏感性增强，而对多种化疗药物产生耐药，且梭杆菌门（Fusobacteria）和柔膜菌门（Tenericutes）的丰度显著降低。经多变量Cox分析筛选，HAAO、ALDH2及淋巴结分期被确定为独立预后因子，并据此构建了预测性列线图。

研究结论
本研究在食管鳞状细胞癌肿瘤微环境（tumor microenvironment, TME）中鉴定出一种与色氨酸代谢相关的成纤维细胞群，并开发了一个包含5个色氨酸基因的特征标签，用于食管鳞状细胞癌患者的预后预测。