Proteomic Landscapes of 3D and 2D Models of High-Grade Serous Ovarian Carcinoma: Implications for Carboplatin Response

High-grade serous ovarian carcinoma (HGSOC) is the most
common
form of ovarian cancer, and finding new treatments remains an unmet
need. While drug discovery is typically performed in two-dimensional
(2D) monolayers, three-dimensional (3D) culture systems better mimic
the in vivo conditions. However, a comprehensive comparison of 3D
versus 2D ovarian cancer models is lacking. Here, we quantitatively
compared the whole cell proteomic signatures of four ovarian cell
linesPEO1, PEO4, UWB1.289, and UWB1.289+BRCA1with
different status of BRCA genes grown in 2D and 3D. Using isobaric
labeling proteomics, we quantified 6404 proteins and identified 371
significantly and commonly altered proteins between 2D and 3D. Proteins
upregulated in 3D were enriched for transmembrane transport and NADH:ubiquinone
oxidoreductase complex I, while energy metabolism and cell growth
pathways also showed dimensionality-dependent changes. Notably, membrane-associated
proteins were downregulated in spheroids, particularly EGFR in PEO1.
Furthermore, the 3D culture modulated the response to carboplatin,
with an increased expression of drug resistance-associated proteins,
including NDUF family members in all spheroid models. These findings
underscore how culture dimensionality influences both the molecular
landscape and the chemotherapeutic response of HGSOC cells and highlights
candidate targets for overcoming carboplatin resistance.

高级别浆液性卵巢癌（High-grade serous ovarian carcinoma, HGSOC）是最常见的卵巢癌亚型，研发新型治疗手段仍存在未被满足的临床需求。传统药物研发通常以二维（2D）单层培养为模型开展，而三维（3D）培养体系则更能模拟体内生理微环境。然而，目前尚缺乏卵巢癌3D与2D模型的系统性对比研究。本研究对4株携带不同BRCA基因状态的卵巢癌细胞系——PEO1、PEO4、UWB1.289及UWB1.289+BRCA1——分别在2D及3D培养条件下的全细胞蛋白质组特征进行了定量比较。采用同位素标记蛋白质组学技术，共定量到6404种蛋白质，并鉴定出371种在2D与3D培养间显著且共差异表达的蛋白。在3D培养中上调的蛋白显著富集于跨膜运输及NADH:泛醌氧化还原酶复合物I相关通路，同时能量代谢与细胞生长通路也呈现出依赖培养维度的表达变化。值得注意的是，3D培养形成的细胞球中膜相关蛋白呈现下调趋势，其中PEO1细胞系中的表皮生长因子受体（EGFR）下调尤为显著。此外，3D培养可调控细胞对卡铂的化疗应答，所有细胞球模型中耐药相关蛋白（包括NDUF家族成员）的表达均出现上调。本研究结果明确了培养维度对高级别浆液性卵巢癌细胞分子图谱及化疗应答的影响，并为克服卡铂耐药提供了潜在候选靶点。