Comprehensive characterization of pre- and post-treatment samples of breast cancer reveal potential mechanisms of chemotherapy resistance

When locally advanced breast cancer is treated with neoadjuvant chemotherapy, the recurrence risk is significantly higher if no complete pathologic response is achieved. Identification of the underlying resistance mechanisms is essential to select treatments with maximal efficacy and minimal toxicity. Here we employed gene expression profiles derived from 317 HER2-negative treatment-naïve breast cancer biopsies of patients who underwent neoadjuvant chemotherapy, deep whole exome and RNA-sequencing profiles of 22 matched pre- and post-treatment tumors, and treatment outcome data to identify biomarkers of response and resistance mechanisms. Molecular profiling of treatment-naïve breast cancer samples revealed that expression levels of proliferation, immune response and extracellular matrix (ECM) organization combined predict response to chemotherapy. Triple negative patients with high proliferation, high immune response and low ECM expression had a significantly better treatment response and survival benefit (HR 0.29, 95% CI 0.10-0.85; p=0.02), while in ER+ patients the opposite was seen (HR 4.73, 95% CI 1.51-14.8; 0=0.008). The characterization of paired pre-and post-treatment samples revealed that aberrations of known cancer genes were either only present in the pre-treatment sample (CDKN1B) or in the post-treatment sample(TP53, APC, CTNNB1). Proliferation-associated genes were frequently down-regulated in post-treatment ER+ tumors, but not in triple negative tumors. Genes involved in ECM were upregulated in the majority of post-chemotherapy samples. Genomic and transcriptomic differences between pre- and post-chemotherapy samples are common and may reveal potential mechanisms of therapy resistance. Our results show a wide range of distinct, but related mechanisms, with a prominent role for proliferation- and ECM-related genes.EGA study EGAS00001005876

局部晚期乳腺癌接受新辅助化疗（neoadjuvant chemotherapy）后，若未获得完全病理缓解，复发风险将显著升高。明确潜在的耐药机制，对于筛选疗效最大化、毒性最小化的治疗方案至关重要。本研究纳入317例接受新辅助化疗的HER2阴性初治乳腺癌活检样本的基因表达谱，以及22例配对的治疗前后肿瘤标本的深度全外显子组测序（whole exome sequencing, WES）和RNA测序（RNA-sequencing, RNA-seq）谱，并结合治疗结局数据，以识别化疗应答相关生物标志物及耐药机制。对初治乳腺癌样本的分子谱分析显示，增殖、免疫应答及细胞外基质（extracellular matrix, ECM）相关基因的表达水平联合可预测化疗应答情况。三阴性乳腺癌患者中，若增殖水平高、免疫应答强且ECM表达低，则化疗应答及生存获益显著更佳（风险比HR=0.29，95%置信区间CI=0.10~0.85；p=0.02）；而ER阳性乳腺癌患者则呈现相反趋势（HR=4.73，95%CI=1.51~14.8；p=0.008）。对配对治疗前后样本的特征分析显示，已知致癌基因的变异仅存在于治疗前样本（如CDKN1B），或仅存在于治疗后样本（如TP53、APC、CTNNB1）。增殖相关基因在治疗后ER阳性肿瘤中常出现下调，但在三阴性肿瘤中未观察到此现象。多数化疗后样本中，ECM相关基因呈现上调表达。化疗前后样本间的基因组与转录组差异普遍存在，这或可揭示治疗耐药的潜在机制。本研究结果显示，存在多种独立但相关的耐药机制，其中增殖相关及ECM相关基因发挥了关键作用。本研究隶属于EGA数据库收录项目EGAS00001005876