Supplementary Material for: Origin of residual tumor masses in BRCA1/2-driven ovarian carcinomas treated by neoadjuvant chemotherapy: selection of preexisting BRCA1/2-proficient tumor cells but not the gain of second ORF-restoring mutation

Introduction: Tubo-ovarian carcinomas (OCs) are highly sensitive to platinum-based neoadjuvant chemotherapy (NACT) but almost never demonstrate complete pathologic response. Methods: We analyzed paired primary and residual tumor tissues from 30 patients with hereditary BRCA1/2-driven OCs (BRCA1: 17; BRCA2: 13), who were treated by carboplatin/paclitaxel NACT (median number of cycles: 3, range 3-6). BRCA1/2 and TP53 genes were analyzed by the next-generation sequencing (NGS). The ratio between TP53 mutation-specific vs. wild-type reads was considered to monitor the proportion of tumor and non-tumor cells in the tissue sample, and the ratio between BRCA1/2 mutated and wild-type reads was used to estimate the presence of cells with the loss or retention of heterozygosity (LOH or ROH, respectively). Results: All 30 OCs had BRCA1/2 LOH in primary tumor and carried somatic TP53 mutation. Twenty-eight OCs had sufficient tumor cell cellularity in the post-NACT tissue to evaluate the ratio between mutated and wild-type BRCA1/2 alleles. Five (18%) out of 28 informative tumor pairs showed transition from LOH to ROH during NACT presumably affecting all or the vast majority of residual tumor cells. There were no signals of the emergence of a second open reading frame (ORF) restoring BRCA1/2 mutation. Conclusion: Chemonaive BRCA1/2-driven carcinomas may contain a fraction of tumor cells with preserved BRCA1/2 heterozygosity. NACT can cause a selection of pre-existing BRCA1/2-proficient tumor cells, without gaining secondary reversal BRCA1/2 mutations.

引言：输卵管卵巢癌（Tubo-ovarian carcinomas, OCs）对铂类新辅助化疗（platinum-based neoadjuvant chemotherapy, NACT）高度敏感，但几乎从未出现完全病理缓解。方法：本研究分析了30例遗传性BRCA1/2驱动型输卵管卵巢癌患者的配对原发与残留肿瘤组织（其中BRCA1突变型17例，BRCA2突变型13例），所有患者均接受卡铂/紫杉醇新辅助化疗（中位疗程数为3，范围3~6）。采用下一代测序（next-generation sequencing, NGS）分析BRCA1/2与TP53基因。以TP53突变型与野生型测序reads的比例监测组织样本中肿瘤细胞与非肿瘤细胞的占比，以BRCA1/2突变型与野生型测序reads的比例评估肿瘤细胞存在杂合性缺失（loss of heterozygosity, LOH）或杂合性保留（retention of heterozygosity, ROH）的情况。结果：30例输卵管卵巢癌的原发肿瘤均存在BRCA1/2杂合性缺失，且携带体细胞TP53突变。其中28例患者的新辅助化疗后残留肿瘤组织具有足够的肿瘤细胞占比，可用于评估BRCA1/2突变型与野生型等位基因的比例。28例可评估的肿瘤配对样本中，有5例（18%）在新辅助化疗过程中发生了从杂合性缺失向杂合性保留的转变，推测该转变影响了全部或绝大多数残留肿瘤细胞，未观察到可恢复BRCA1/2突变功能的第二个开放阅读框（open reading frame, ORF）出现的迹象。结论：初治BRCA1/2驱动型癌可能存在一定比例的BRCA1/2杂合性保留的肿瘤细胞。新辅助化疗可筛选预先存在的BRCA1/2功能正常的肿瘤细胞，且不会产生继发性回复BRCA1/2突变。