Tumor-stromal crosstalk and macrophage enrichment is associated with chemotherapy response in bladder cancer

This dataset provides a spatial transcriptomic atlas of bladder cancer tissue treated ex vivo with standard chemotherapy. Tumor specimens from eight bladder cancer patients were excised and treated for 48 hours with gemcitabine and cisplatin (GemCis) or medium control (MSC), followed by formalin fixation and paraffin embedding. Spatial gene expression profiling was performed using the NanoString GeoMx Digital Spatial Profiler Whole Transcriptome Atlas (WTA), capturing expression of over 18,000 transcripts. Tumor regions were identified by cytokeratin (CK) staining and analyzed alongside adjacent stroma (CK-negative). Chemotherapy treatment led to significant transcriptomic alterations, including downregulation of pathways related to substance uptake (e.g., endocytosis) and metabolism (e.g., glycolysis), and upregulation of cell death pathways. Cellular deconvolution using xCell revealed stromal M2 macrophage enrichment in chemotherapy-resistant samples, suggesting a microenvironmental contribution to resistance. Overall design: Fresh tumor tissue from eight patients with bladder cancer was obtained and divided into two conditions: treatment with gemcitabine/cisplatin (GemCis) or medium control (MSC), incubated for 48 hours ex vivo. Post-treatment, tissues were formalin-fixed, paraffin-embedded, and processed using the NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) assay. Regions of interest (ROIs) were selected based on immunohistochemical cytokeratin (CK) staining to distinguish tumor cells (CK-positive) from stroma (CK-negative). Two technical replicates per condition and region were collected. Standard GeoMx WTA workflow was applied, with downstream analysis including differential expression, pathway analysis, caspase-3 immunohistochemistry for treatment response classification, and xCell-based deconvolution to profile immune cell populations. The resulting data provide spatial resolution of transcriptomic changes in response to chemotherapy and insights into mechanisms of chemoresistance in bladder cancer.

本数据集提供了经标准化疗离体处理的膀胱癌组织的空间转录组图谱（spatial transcriptomic atlas）。本研究从8名膀胱癌患者体内获取肿瘤标本，将其离体后分别用吉西他滨联合顺铂（gemcitabine and cisplatin, GemCis）或培养基对照（medium control, MSC）处理48小时，随后进行福尔马林固定与石蜡包埋。采用NanoString GeoMx数字空间分析仪全转录组图谱（Whole Transcriptome Atlas, WTA）进行空间基因表达谱分析，可覆盖超过18000个转录本（transcripts）的表达量检测。通过细胞角蛋白（cytokeratin, CK）染色标记肿瘤区域，并与相邻的CK阴性肿瘤间质区域一并进行分析。化疗处理可引发显著的转录组学改变：包括物质摄取相关通路（如内吞作用（endocytosis））与代谢通路（如糖酵解（glycolysis））的下调，以及细胞死亡通路的上调。采用xCell进行细胞反卷积（cellular deconvolution）分析后发现，化疗耐药样本中存在肿瘤间质M2型巨噬细胞（M2 macrophage）富集现象，提示肿瘤微环境（microenvironment）对化疗耐药存在调控贡献。实验整体设计：本研究获取8名膀胱癌患者的新鲜肿瘤组织，将其分为两组：分别采用吉西他滨联合顺铂（GemCis）或培养基对照（MSC）处理，离体孵育48小时。处理后的组织经福尔马林固定、石蜡包埋后，采用NanoString GeoMx DSP全转录组图谱（WTA）检测体系进行上机处理。基于免疫组化（immunohistochemical）细胞角蛋白（CK）染色筛选感兴趣区域（Regions of Interest, ROIs），以区分肿瘤细胞（CK阳性）与肿瘤间质区域（CK阴性）。每个实验条件与区域均设置两个技术重复样本。本研究采用标准GeoMx WTA实验流程，下游分析包括差异表达分析（differential expression）、通路分析（pathway analysis）、用于化疗应答分类的半胱氨酸天冬氨酸蛋白酶3（caspase-3）免疫组化检测，以及基于xCell的细胞反卷积分析以解析免疫细胞群体组成。本数据集所得数据可提供化疗应答相关转录组变化的空间分辨率信息，并为膀胱癌化疗耐药机制研究提供新的见解。