Paul Evan D, Huraiová Barbora, Valková Natália, Matyasovska Natalia, Gábrišová Daniela, Gubová Soňa, Ignačáková Helena, Ondris Tomáš, Gala Michal, Barroso Liliane, Bendíková Silvia, Bíla Jarmila, Buranovská Katarína, Drobná Diana, Krchňáková Zuzana, Kryvokhyzha Maryna, Lovíšek Daniel, Mamoilyk Viktoriia, Mancikova Veronika, Vojtaššáková Nina, Ristová Michaela, Comino-Méndez Iñaki, Andrašina Igor, Morozov Pavel, Tuschl Thomas, Pareja Fresia, Kather Jakob N, Čekan Pavol
MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia.
MultiplexDX, Inc, Rockville, MD, USA.
Nat Commun. 2025 Jan 2;16(1):226. doi: 10.1038/s41467-024-55583-2.
Current assays fail to address breast cancer's complex biology and accurately predict treatment response. On a retrospective cohort of 1082 female breast tissues, we develop and validate mFISHseq, which integrates multiplexed RNA fluorescent in situ hybridization with RNA-sequencing, guided by laser capture microdissection. This technique ensures tumor purity, unbiased whole transcriptome profiling, and explicitly quantifies intratumoral heterogeneity. Here we show mFISHseq has 93% accuracy compared to immunohistochemistry. Our consensus subtyping and risk groups mitigate single sample discordance, provide early and late prognostic information, and identify high risk patients with enriched immune signatures, which predict response to neoadjuvant immunotherapy in the multicenter, phase II, prospective I-SPY2 trial. We identify putative antibody-drug conjugate (ADC)-responsive patients, as evidenced by a 19-feature T-DM1 classifier, validated on I-SPY2. Deploying mFISHseq as a research-use only test on 48 patients demonstrates clinical feasibility, revealing insights into the efficacy of targeted therapies, like CDK4/6 inhibitors, immunotherapies, and ADCs.
目前的检测方法无法应对乳腺癌复杂的生物学特性，也无法准确预测治疗反应。在一个包含1082份女性乳腺组织的回顾性队列中，我们开发并验证了mFISHseq，它将多重RNA荧光原位杂交与RNA测序相结合，并由激光捕获显微切割技术引导。这项技术确保了肿瘤的纯度、无偏倚的全转录组分析，并能明确量化肿瘤内的异质性。在这里，我们展示了与免疫组织化学相比，mFISHseq的准确率达到93%。我们的共识亚型分类和风险组减少了单个样本的不一致性，提供了早期和晚期的预后信息，并识别出具有丰富免疫特征的高风险患者，这些特征在多中心、II期、前瞻性I-SPY2试验中可预测对新辅助免疫治疗的反应。我们确定了推定的抗体药物偶联物（ADC）反应性患者，这在I-SPY2上验证的19个特征的T-DM1分类器中得到了证明。对48名患者仅作为研究用途进行mFISHseq检测，证明了其临床可行性，揭示了对靶向治疗（如CDK4/6抑制剂、免疫疗法和ADC）疗效的见解。
