Defining the Relationship Between Cellular and Extracellular Vesicle (EV) Content in Breast Cancer via an Integrative Multi-Omic Analysis

Much recent work has been dedicated to exploring the utility of extracellular vesicles (EVs) as circulating cancer biomarkers. This is driven by the understanding that the molecular cargo of EVs reflects their originating cell, meaning EVs may enable non-invasive tumour surveillance. Few attempts have been made, however, to empirically validate this assumption on the -omic level and define the relationship between the molecular phenotype of cells and EVs. To this end, we present an integrative multi-omic analysis of a panel of breast cancer cell lines and corresponding EVs. Transcriptomic analysis of the cells was first used to confirm that expression of disease-related transcripts remained stable following transition to a low serum EV production medium. Proteomic analysis of the EVs indicated that neither the ER nor PR protein could be directly detected in EVs, but cellular expression of ER could be indirectly inferred from the EV proteome. Transcriptomic analyses generally suggested a direct positive correlation between transcript levels in cells and EVs. Integrative analysis suggested that the EV proteome and transcriptome captured select hallmarks of aberrant pathway activity in the originating cells, supporting the potential use of EVs to non-invasively monitor molecular evolution in breast cancers. Sequencing of total RNA isolated from breast cancer cell-derived extracellular vesicles (EVs)

近年来诸多研究致力于探索细胞外囊泡（extracellular vesicles, EVs）作为循环癌症生物标志物的应用价值。该研究方向的核心逻辑在于，细胞外囊泡的分子载荷能够反映其来源细胞的特征，意味着细胞外囊泡可实现肿瘤的无创监测。然而，目前鲜有研究在组学层面通过实验验证这一假设，并阐明细胞分子表型与细胞外囊泡之间的关联。为此，本研究对一组乳腺癌细胞系及其对应的细胞外囊泡开展了整合多组学分析。首先通过对细胞的转录组学分析，确认在更换至低血清细胞外囊泡生产培养基后，疾病相关转录本的表达水平保持稳定。对细胞外囊泡的蛋白质组学分析显示，无法在细胞外囊泡中直接检测到雌激素受体（ER）与孕激素受体（PR）蛋白，但可通过细胞外囊泡蛋白质组间接推断细胞内雌激素受体的表达水平。转录组学分析整体表明，细胞与细胞外囊泡内的转录本水平呈直接正相关。整合分析结果显示，细胞外囊泡的蛋白质组与转录组能够捕捉到来源细胞中通路异常激活的部分特征，佐证了细胞外囊泡可用于无创监测乳腺癌分子演化的潜在应用价值。对从乳腺癌细胞来源的细胞外囊泡（EVs）中分离得到的总RNA进行测序