Dataset for: Estrogen receptor mutations and splice variants determined in liquid biopsies from metastatic breast cancer patients

Mutations and splice variants in the estrogen receptor (ER) gene, ESR1, may yield endocrine resistance in metastatic breast cancer (MBC) patients. These putative endocrine resistance markers are likely to emerge during treatment and therefore its detection in liquid biopsies, such as circulating tumor cells (CTCs) and cell-free DNA (cfDNA), is of great interest. This research aimed to determine if ESR1 mutations and splice variants occur more frequently in CTCs of MBC patients progressing on endocrine treatment. In addition, the presence of ESR1 mutations was evaluated in matched cfDNA and compared to CTCs. CellSearch-enriched CTC fractions (≥5/7.5 mL) of two MBC cohorts were evaluated, including 1) patients starting first-line endocrine therapy (n=43, baseline cohort) and 2) patients progressing on any line of endocrine therapy (n=40, progressing cohort). ESR1 hotspot mutations (D538G and Y537S/N/C) were evaluated in CTC-enriched DNA using digital PCR and compared with matched cfDNA (n=18 baseline cohort; n=26 progressing cohort). Expression of ESR1 full-length and 4 of its splice variants (∆5, ∆7, 36KD and 46KD) was evaluated in CTC-enriched mRNA. It was observed that in the CTCs, the ESR1 mutations were not enriched in the progressing cohort (8%), when compared to the baseline cohort (5%) (P=0.66). In the cfDNA, however, ESR1 mutations were more prevalent in the progressing cohort (42%) than in the baseline cohort (11%) (P=0.04). Three of the same mutations were observed in both CTCs and cfDNA, 1 mutation in CTCs only and 11 in cfDNA only. Only the ∆5 ESR1 splice variant was CTC-specific expressed, but was not enriched in the progressing cohort. In conclusion, sensitivity for detecting ESR1 mutations in CTC-enriched fractions was lower than for cfDNA. ESR1 mutations detected in cfDNA, rarely present at start of first-line endocrine therapy, were enriched at progression, strongly suggesting a role in conferring endocrine resistance in MBC.

雌激素受体（estrogen receptor, ER）编码基因ESR1的突变与剪接变体，可能引发转移性乳腺癌（metastatic breast cancer, MBC）患者出现内分泌治疗抵抗。这类潜在的内分泌治疗抵抗标志物很可能在治疗过程中出现，因此针对循环肿瘤细胞（circulating tumor cells, CTCs）、循环游离DNA（cell-free DNA, cfDNA）等液体活检样本的检测受到广泛关注。本研究旨在明确，接受内分泌治疗后出现疾病进展的MBC患者，其CTCs中ESR1突变与剪接变体的检出频率是否更高。此外，本研究还对匹配样本的cfDNA中ESR1突变的存在情况进行了评估，并与CTCs的检测结果进行对比。本研究对两个MBC队列中经CellSearch技术富集的CTC组分（≥5个/7.5mL）进行了分析，其中队列1为接受一线内分泌治疗的初治患者（基线队列，n=43），队列2为经任意线内分泌治疗后出现疾病进展的患者（进展队列，n=40）。采用数字PCR技术对CTC富集样本的DNA进行ESR1热点突变（D538G、Y537S/N/C）检测，并与匹配的cfDNA样本进行对比（基线队列n=18，进展队列n=26）；同时对CTC富集样本的mRNA进行检测，分析ESR1全长型及其4种剪接变体（Δ5、Δ7、36KD、46KD）的表达情况。研究结果显示，与基线队列（5%）相比，进展队列CTC中ESR1突变的检出率仅为8%，两组差异无统计学意义（P=0.66）。而在cfDNA中，进展队列的ESR1突变检出率（42%）显著高于基线队列（11%，P=0.04）。在CTC与cfDNA中共检出3种相同突变，仅在CTC中检出1种突变，仅在cfDNA中检出11种突变。仅Δ5型ESR1剪接变体在CTC中特异性表达，但在进展队列中未出现富集。综上，CTC富集组分中ESR1突变的检测灵敏度低于cfDNA。cfDNA中检出的ESR1突变在一线内分泌治疗初始阶段极少出现，却在疾病进展阶段显著富集，强烈提示其在MBC内分泌治疗抵抗的发生中扮演重要角色。