Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, USA.
J Ovarian Res. 2012 Jan 20;5(1):3. doi: 10.1186/1757-2215-5-3.
We sought to identify candidate serum biomarkers for the detection and surveillance of EOC. Based on RNA-Seq transcriptome analysis of patient-derived tumors, highly expressed secreted proteins were identified using a bioinformatic approach.
RNA-Seq was used to quantify papillary serous ovarian cancer transcriptomes. Paired end sequencing of 22 flash frozen tumors was performed. Sequence alignments were processed with the program ELAND, expression levels with ERANGE and then bioinformatically screened for secreted protein signatures. Serum samples from women with benign and malignant pelvic masses and serial samples from women during chemotherapy regimens were measured for IGFBP-4 by ELISA. Student's t Test, ANOVA, and ROC curves were used for statistical analysis.
Insulin-like growth factor binding protein (IGFBP-4) was consistently present in the top 7.5% of all expressed genes in all tumor samples. We then screened serum samples to determine if increased tumor expression correlated with serum expression. In an initial discovery set of 21 samples, IGFBP-4 levels were found to be elevated in patients, including those with early stage disease and normal CA125 levels. In a larger and independent validation set (82 controls, 78 cases), IGFBP-4 levels were significantly increased (p < 5 × 10-5). IGFBP-4 levels were ~3× greater in women with malignant pelvic masses compared to women with benign masses. ROC sensitivity was 73% at 93% specificity (AUC 0.816). In women receiving chemotherapy, average IGFBP-4 levels were below the ROC-determined threshold and lower in NED patients compared to AWD patients.
This study, the first to our knowledge to use RNA-Seq for biomarker discovery, identified IGFBP-4 as overexpressed in ovarian cancer patients. Beyond this, these studies identified two additional intriguing findings. First, IGFBP-4 can be elevated in early stage disease without elevated CA125. Second, IGFBP-4 levels are significantly elevated with malignant versus benign disease. These findings provide the rationale for future validation studies.
我们试图确定用于检测和监测卵巢癌的候选血清生物标志物。基于患者来源肿瘤的 RNA-Seq 转录组分析，使用生物信息学方法鉴定高表达分泌蛋白。
使用 RNA-Seq 定量分析乳头状浆液性卵巢癌转录组。对 22 个冷冻肿瘤进行配对末端测序。使用程序 ELAND 处理序列比对，使用 ERANGE 处理表达水平，然后进行生物信息学筛选分泌蛋白特征。使用 ELISA 测量良性和恶性盆腔肿块妇女的血清样本和化疗期间妇女的系列样本中的 IGFBP-4。使用 Student's t Test、ANOVA 和 ROC 曲线进行统计分析。
胰岛素样生长因子结合蛋白（IGFBP-4）在所有肿瘤样本中所有表达基因的前 7.5%中始终存在。然后，我们筛选了血清样本以确定肿瘤表达增加是否与血清表达相关。在最初的 21 个样本发现组中，发现 IGFBP-4 水平在患者中升高，包括早期疾病和正常 CA125 水平的患者。在更大的独立验证组（82 名对照，78 例病例）中，IGFBP-4 水平显着升高（p < 5×10-5）。与良性肿块妇女相比，恶性盆腔肿块妇女的 IGFBP-4 水平高约 3 倍。ROC 灵敏度为 73%，特异性为 93%（AUC 0.816）。在接受化疗的妇女中，平均 IGFBP-4 水平低于 ROC 确定的阈值，且 NED 患者低于 AWD 患者。
这项研究是我们首次使用 RNA-Seq 进行生物标志物发现的研究，鉴定 IGFBP-4 在卵巢癌患者中过度表达。除此之外，这些研究还发现了另外两个有趣的发现。首先，IGFBP-4 可以在没有 CA125 升高的早期疾病中升高。其次，IGFBP-4 水平在恶性与良性疾病之间显着升高。这些发现为未来的验证研究提供了依据。
