Biomedical Research Institute (INCLIVA), Valencia, Spain.
Department of Physiology, Faculty of Medicine, University of Valencia, Valencia, Spain.
Clin Epigenetics. 2019 Feb 20;11(1):33. doi: 10.1186/s13148-019-0626-0.
Pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC) varies between 30 and 40% approximately. To provide further insight into the prediction of pCR, we evaluated the role of an epigenetic methylation-based signature.
Epigenetic assessment of DNA extracted from biopsy archived samples previous to NAC from TNBC patients was performed. Patients included were categorized according to previous response to NAC in responder (pCR or residual cancer burden, RCB = 0) or non-responder (non-pCR or RCB > 0) patients. A methyloma study was performed in a discovery cohort by the Infinium HumanMethylation450 BeadChip (450K array) from Illumina. The epigenetic silencing of those methylated genes in the discovery cohort were validated by bisulfite pyrosequencing (PyroMark Q96 System version 2.0.6, Qiagen) and qRT-PCR in an independent cohort of TN patients and in TN cell lines.
Twenty-four and 30 patients were included in the discovery and validation cohorts, respectively. In the discovery cohort, nine genes were differentially methylated: six presented higher methylation in non-responder patients (LOC641519, LEF1, HOXA5, EVC2, TLX3, CDKL2) and three greater methylation in responder patients (FERD3L, CHL1, and TRIP10). After validation, a two-gene (FER3L and TRIP10) epigenetic score predicted RCB = 0 with an area under the ROC curve (AUC) = 0.905 (95% CI = 0.805-1.000). Patients with a positive epigenetic two-gene score showed 78.6% RCB = 0 versus only 10.7% RCB = 0 if signature were negative.
These results suggest that pCR in TNBC could be accurately predicted with an epigenetic signature of FERD3L and TRIP10 genes. Further prospective validation of these findings is warranted.
新辅助化疗（NAC）后三阴性乳腺癌（TNBC）的病理完全缓解（pCR）率约为 30%至 40%。为了更深入地了解 pCR 的预测，我们评估了表观遗传甲基化标志物的作用。
对接受 NAC 治疗的 TNBC 患者的活检存档样本中提取的 DNA 进行表观遗传评估。根据患者对 NAC 的反应将其分为应答者（pCR 或残留肿瘤负担，RCB=0）和非应答者（非 pCR 或 RCB>0）。在发现队列中，通过 Illumina 的 Infinium HumanMethylation450 BeadChip（450K 芯片）进行甲基组学研究。在独立的 TNBC 患者队列和 TN 细胞系中，通过亚硫酸氢盐焦磷酸测序（PyroMark Q96 系统版本 2.0.6，Qiagen）和 qRT-PCR 验证了发现队列中这些甲基化基因的表观遗传沉默。
发现队列和验证队列分别纳入了 24 例和 30 例患者。在发现队列中，有 9 个基因存在差异甲基化：6 个基因在非应答者中呈现较高的甲基化（LOC641519、LEF1、HOXA5、EVC2、TLX3、CDKL2），3 个基因在应答者中呈现较高的甲基化（FERD3L、CHL1 和 TRIP10）。验证后，一个由两个基因（FER3L 和 TRIP10）组成的表观遗传评分预测 RCB=0 的曲线下面积（AUC）为 0.905（95%CI=0.805-1.000）。具有阳性表观遗传双基因评分的患者，RCB=0 的比例为 78.6%，而评分阴性的患者，RCB=0 的比例仅为 10.7%。
这些结果表明，基于 FERD3L 和 TRIP10 基因的表观遗传标志物可以准确预测 TNBC 的 pCR。需要进一步的前瞻性验证这些发现。
