DataSheet_3_A combined analysis of bulk and single-cell sequencing data reveals that depleted extracellular matrix and enhanced immune processes co-contribute to fluorouracil beneficial responses in gastric cancer.xlsx

Fluorouracil, also known as 5-FU, is one of the most commonly used chemotherapy drugs in the treatment of advanced gastric cancer (GC). Whereas, the presence of innate or acquired resistance largely limits its survival benefit in GC patients. Although accumulated studies have demonstrated the involvement of tumor microenvironments (TMEs) in chemo-resistance induction, so far little is known about the relevance of GC TMEs in 5-FU resistance. To this end, in this study, we investigated the relationship between TME features and 5-FU responses in GC patients using a combined analysis involving both bulk sequencing data from the TCGA database and single-cell RNA sequencing data from the GEO database. We found that depleted extracellular matrix (ECM) components such as capillary/stroma cells and enhanced immune processes such as increased number of M1 polarized macrophages/Memory T cells/Natural Killer T cells/B cells and decreased number of regulatory T cells are two important features relating to 5-FU beneficial responses in GC patients, especially in diffuse-type patients. We further validated these two features in the tumor tissues of 5-FU-benefit GC patients using immunofluorescence staining experiments. Based on this finding, we also established a Pro (63 genes) and Con (199 genes) gene cohort that could predict 5-FU responses in GC with an AUC (area under curve) score of 0.90 in diffuse-type GC patients, and further proved the partial applicability of this gene panel pan-cancer-wide. Moreover, we identified possible communications mediated by heparanase and galectin-1 which could regulate ECM remodeling and tumor immune microenvironment (TIME) reshaping. Altogether, these findings deciphered the relationship between GC TMEs and 5-FU resistance for the first time, as well as provided potential therapeutic targets and predicting rationale to overcome this chemo-resistance, which could shed some light on developing novel precision treatment strategies in clinical practice.

氟尿嘧啶，亦称5-FU，是治疗晚期胃癌（GC）中最常用的化疗药物之一。然而，先天或后天获得的耐药性在很大程度上限制了其在GC患者中的生存益处。尽管已有累积的研究表明肿瘤微环境（TMEs）在化疗耐药性诱导中的作用，但关于GC TMEs与5-FU耐药性的相关性至今知之甚少。为此，本研究利用结合TCGA数据库的批量测序数据和GEO数据库的单细胞RNA测序数据的分析方法，探讨了TME特征与GC患者5-FU反应之间的关系。我们发现，减少的细胞外基质（ECM）成分，如毛细血管/基质细胞，以及增强的免疫过程，如M1极化巨噬细胞/记忆T细胞/自然杀伤T细胞/B细胞的数量增加以及调节性T细胞的数量减少，是两个与GC患者5-FU有益反应相关的重要特征，尤其是在弥漫型患者中。我们进一步通过免疫荧光染色实验验证了这两个特征在5-FU获益的GC患者肿瘤组织中的存在。基于这一发现，我们还建立了一个包含63个基因的促（Pro）基因组和199个基因的抑（Con）基因组，该基因组可以预测弥漫型GC患者的5-FU反应，其AUC（曲线下面积）得分为0.90，并在泛癌范围内部分证明了该基因组的适用性。此外，我们还识别了由肝素酶和半乳糖凝集素-1介导的可能通信，这些通信可以调节ECM重塑和肿瘤免疫微环境（TIME）重塑。总之，这些发现首次揭示了GC TMEs与5-FU耐药性之间的关系，并提供了克服这种化疗耐药性的潜在治疗靶点和预测依据，这为临床实践中开发新的精准治疗策略提供了启示。