High expression of the vacuole membrane protein 1 (VMP1) is a potential marker of poor prognosis in HER2 positive breast cancer

BackgroundFusion genes result from genomic structural changes, which can lead to alterations in gene expression that supports tumor development. The aim of the study was to use fusion genes as a tool to identify new breast cancer (BC) genes with a role in BC progression.MethodsFusion genes from breast tumors and BC cell lines were collected from publications. RNA-Seq data from tumors and cell lines were retrieved from databanks and analyzed for fusions with SOAPfuse or the analysis was purchased. Fusion genes identified in both tumors (n = 1724) and cell lines (n = 45) were confirmed by qRT-PCR and sequencing. Their individual genes were ranked by selection criteria that included correlation of their mRNA level with copy number. The expression of the top ranked gene was measured by qRT-PCR in normal tissue and in breast tumors from an exploratory cohort (n = 141) and a validation cohort (n = 277). Expression levels were correlated with clinical and pathological factors as well as the patients’ survival. The results were followed up in BC cohorts from TCGA (n = 818) and METABRIC (n = 2509).ResultsVacuole membrane protein 1 (VMP1) was the most promising candidate based on specific selection criteria. Its expression was higher in breast tumor tissue than normal tissue (p = 1x10-4), and its expression was significantly higher in HER2 positive than HER2 negative breast tumors in all four cohorts analyzed. High expression of VMP1 associated with breast cancer specific survival (BCSS) in cohort 1 (hazard ratio (HR) = 2.31, CI 1.27–4.18) and METABRIC (HR = 1.26, CI 1.02–1.57), and also after adjusting for HER2 expression in cohort 1 (HR = 2.03, CI 1.10–3.72). BCSS was not significant in cohort 2 or TCGA cohort, which may be due to differences in treatment regimens.ConclusionsThe results suggest that high VMP1 expression is a potential marker of poor prognosis in HER2 positive BC. Further studies are needed to elucidate how VMP1 could affect pathways supportive of tumorigenesis.

研究背景：融合基因（fusion gene）源自基因组结构变异，可引发基因表达异常，进而促进肿瘤发生发展。本研究旨在以融合基因作为研究工具，筛选在乳腺癌（breast cancer, BC）进展中发挥功能的新型乳腺癌相关基因。
研究方法：我们从已发表文献中搜集乳腺癌组织及乳腺癌细胞系中的融合基因。从公共数据库调取肿瘤及细胞系的RNA测序（RNA-Seq）数据，使用SOAPfuse工具进行融合基因分析，或委托第三方完成该分析流程。对同时在肿瘤组织（n=1724）与细胞系（n=45）中鉴定到的融合基因，通过实时荧光定量聚合酶链反应（quantitative real-time polymerase chain reaction, qRT-PCR）及测序技术进行验证。依据纳入mRNA水平与拷贝数相关性在内的筛选标准，对融合基因所包含的单个基因进行排序。选取排序首位的基因，采用qRT-PCR检测其在正常组织及乳腺癌组织中的表达水平，检测队列包括探索性队列（n=141）与验证性队列（n=277）。分析该基因的表达水平与临床病理特征及患者生存结局的相关性。后续在癌症基因组图谱（The Cancer Genome Atlas, TCGA）队列（n=818）及分子分类学乳腺癌国际协作组（Molecular Taxonomy of Breast Cancer International Consortium, METABRIC）队列（n=2509）中对研究结果进行验证。
研究结果：依据特定筛选标准，空泡膜蛋白1（vacuole membrane protein 1, VMP1）为最具潜力的候选基因。VMP1在乳腺癌组织中的表达水平显著高于正常组织（p=1×10^-4）；在所有分析的4个队列中，其在人表皮生长因子受体2（human epidermal growth factor receptor 2, HER2）阳性乳腺癌组织中的表达水平显著高于HER2阴性乳腺癌组织。VMP1高表达与队列1的乳腺癌特异性生存（breast cancer specific survival, BCSS）显著相关（风险比（hazard ratio, HR）=2.31，95%置信区间（confidence interval, CI）1.27~4.18），且在METABRIC队列中同样观察到该关联（HR=1.26，CI=1.02~1.57）；在校正HER2表达状态后，队列1中该关联仍具有统计学意义（HR=2.03，CI=1.10~3.72）。队列2及TCGA队列中未观察到VMP1表达与BCSS的显著关联，该结果可能与不同队列间治疗方案的差异有关。
结论：本研究结果表明，VMP1高表达可作为HER2阳性乳腺癌不良预后的潜在标志物。后续仍需开展深入研究，以阐明VMP1调控肿瘤发生相关通路的具体分子机制。