PO.ET03.05 · 实验与分子治疗
整合多组学与空间转录组学揭示肿瘤-基质共进化驱动BRAF-V600E胆管癌的dabrafenib耐药
Integrated multi-omics and spatial transcriptomics reveal tumor stroma co-evolution driving dabrafenib resistance in BRAF-V600E cholangiocarcinoma
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
背景：BRAF-V600E突变是胆管癌（CCA）中最具治疗可操作性的致癌改变之一。尽管BRAF抑制剂如Dabrafenib已显示出临床获益，但CCA中的反应往往是短暂的，与黑色素瘤或甲状腺癌相比，疾病复发迅速且侵袭性高。此类治疗诱导适应的潜在机制仍知之甚少。
方法：我们建立了一个dabrafenib耐药的BRAF-V600E CCA模型及其药物敏感对照，随后进行了整合的转录组学、蛋白质组学和代谢组学分析。同时，对配对的治疗前和复发后CCA患者标本进行了空间转录组学（ST）分析，以在空间上解析肿瘤微环境（TME）内的恶性细胞、癌症相关成纤维细胞（CAF）和CD45⁺免疫细胞。
结果：多组学整合鉴定出3,562个差异表达基因、1,986种蛋白质和数百种代谢物，它们共同揭示了一种TME驱动的耐药表型。耐药恶性细胞表现出上皮-间质转化（EMT）和异生物质解毒通路的激活，而CAF经历了深刻的PPAR驱动的脂肪酸代谢重编程和CYP450富集，将基质转变为一个营养丰富且使药物失活的生态位。与此同时，CD45⁺区室表现出KRAS/E2F信号、慢性炎症和代谢耗竭的转录特征。引人注目的是，补体和凝血级联在所有三个区室中空间共定位并同步激活，提示存在一种免疫逃逸和基质屏障形成的统一机制。
结论：我们的发现揭示，BRAF-V600E CCA中获得性dabrafenib耐药源于内在EMT和外在TME重塑的共进化。CAF代谢轴和共享的TME-凝血通路成为可操作的脆弱性，为克服复发性CCA治疗耐药的联合策略提供了机制依据。
查看英文原文 English abstract
Background: BRAF-V600E mutation represents one of the most therapeutically actionable oncogenic alterations in cholangiocarcinoma (CCA). Although BRAF inhibitors such as Dabrafenib have demonstrated clinical benefit, responses in CCA are often transient, with rapid disease recurrence and high invasiveness compared to melanoma or thyroid cancer. The mechanisms underlying such therapy-induced adaptation remain poorly understood.
Methods: We established a Dabrafenib-resistant BRAF-V600E CCA model and its drug-sensitive counterpart, followed by integrated transcriptomic, proteomic, and metabolomic profiling. In parallel, spatial transcriptomics (ST) was performed on paired pre-treatment and post-recurrence CCA patient specimens to spatially dissect malignant cells, cancer-associated fibroblasts (CAFs), and CD45⁺ immune cells within the tumor microenvironment (TME).
Results: Multi-omics integration identified 3,562 differentially expressed genes, 1,986 proteins, and hundreds of metabolites that collectively revealed a TME-driven resistance phenotype. Resistant malignant cells displayed activation of epithelial-mesenchymal transition (EMT) and xenobiotic detoxification pathways, while CAFs underwent profound PPAR-driven fatty acid metabolic reprogramming and CYP450 enrichment, transforming the stroma into a nutrient-rich and drug-inactivating niche. Concurrently, the CD45⁺ compartment exhibited transcriptional signatures of KRAS/E2F signaling, chronic inflammation, and metabolic exhaustion. Strikingly, Complement and Coagulation Cascades were spatially co-localized and synchronously activated across all three compartments, suggesting a unified mechanism of immune evasion and stromal barrier formation.
Conclusions: Our findings reveal that acquired Dabrafenib resistance in BRAF-V600E CCA arises from the co-evolution of intrinsic EMT and extrinsic TME remodeling. The CAF metabolic axis and shared TME-Coagulation pathway emerges as actionable vulnerabilities, offering a mechanistic rationale for combination strategies to overcome therapeutic resistance in recurrent CCA.
利益披露 Disclosure
N. Chiang, None..
Y. Hou, None..
C. Hsieh, None..
C. Cheng, None..
C. Shen, None.