Deep Visual Proteomics and spatial transcriptomics reveal the landscape of tumor malignancy in borderline ovarian cancer

Women of reproductive age can develop serous borderline tumors (SBT) characterized by the uncontrolled growth of epithelial cells that do not invade the stroma. Despite a good prognosis after surgery, SBT may recur as low-grade serous cancer (LGSC), which is invasive and responds poorly to current standard chemotherapy. SBT and LGSC have overlapping genomic changes, but a putative transition sequence is poorly understood. Here, we employ Deep Visual Proteomics (DVP), a recently introduced single cell type specific spatial technology, to elucidate the evolution of this cancer at the molecular level. We show that the transition of SBT to LGSC occurs in the epithelial compartment through an intermediary stage with micropapillary features (SBT-MP) which involves a gradual increase in MAPK signaling. Proteomics identified several neuronal proteins, including the splicing factor NOVA2, that are exclusive to LGSC and its corresponding metastasis. In the stroma we observed major differences between non-invasive and invasive phenotypes. An acute inflammatory response was only found in SBT-MP. Spatial transcriptomics complemented the insights gained from proteomics, showing an increase in c-Met signaling, mRNA splicing in the epithelium, and HIF1α/angiogenesis in stroma between SBT and the more invasive phenotypes. Inhibiting the most prominently regulated pathways validated our results and suggested an FDA-approved FOLR1 inhibitor as a potential therapeutic strategy. Knockdown or inhibition of the top hits identified using spatial proteomics and transcriptomics confirmed their functional significance regulating migration and invasion. Combining spatial proteomics with transcriptomics is a promising approach to gaining mechanistic insights into tumor transformations and identifying novel treatment strategies.

育龄女性可发生浆液性交界性肿瘤（serous borderline tumors, SBT），其特征为上皮细胞不受控增殖但不侵袭间质。尽管术后预后良好，SBT可复发为低级别浆液性癌（low-grade serous cancer, LGSC），后者具有侵袭性且对当前标准化疗应答不佳。SBT与LGSC存在重叠的基因组改变，但二者的潜在转化序列仍未明确。本研究采用深度可视化蛋白质组学（Deep Visual Proteomics, DVP）——一项新近开发的单细胞类型特异性空间技术——解析该癌症在分子层面的演化过程。我们发现，SBT向LGSC的转化发生于上皮组分中，通过伴微乳头状特征的中间阶段（SBT-MP）实现，该过程伴随MAPK信号通路的逐步增强。蛋白质组学分析鉴定出多种仅存在于LGSC及其对应转移灶的神经元蛋白，包括剪接因子NOVA2。在间质组分中，我们观察到非侵袭性与侵袭性表型间存在显著差异。急性炎症反应仅见于SBT-MP阶段。空间转录组学补充了蛋白质组学的研究发现，显示在SBT与更高侵袭性表型之间，上皮组分中c-Met信号通路、mRNA剪接活动显著增强，间质组分中HIF1α/血管生成相关通路激活。抑制调控最为显著的通路验证了本研究的结论，并提示一款已获美国食品药品监督管理局（FDA）批准的FOLR1抑制剂可作为潜在治疗策略。敲低或抑制通过空间蛋白质组学与转录组学筛选得到的核心靶点，证实了其在调控细胞迁移与侵袭过程中的功能重要性。将空间蛋白质组学与转录组学相结合，是解析肿瘤转化机制、发掘新型治疗策略的极具前景的研究路径。