Relationship of adaptive subtyping and tumour heterogeneity of treatment response to neoadjuvant therapy in hormone receptor–positive HER2-negative early breast cancer: PENELOPE-B.
Authors: Denkert Carsten , Rachakonda Krishna , Filipits Martin , Weber Karsten , Marmé Frederik , Untch Michael , Witkiewicz Agnieszka K , Im Seock-Ah , DeMichele Angela , Pehl Anika , van 't Veer Laura , Jank Paul , Schem Christian , Fasching Peter A. , Reimer Toralf , Knudsen Erik S. , Liu Yuan , Rojo Todo Federico Gustavo , Turner Nicholas C. , Loibl Sibylle 
Published: May 2024

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Background: The concept of intrinsic subtyping has been an important step for understanding of breast cancer (BC) as a heterogenous disease. However, these subtypes are not adapted to therapy-induced molecular plasticity. We have evaluated a high-risk luminal BC clinical trial cohort to identify new additional adaptive BC subtypes based on molecular alterations induced during neoadjuvant chemotherapy (NACT). Methods: A total of 1250 ER+/HER2- BC patients (pts) with residual disease after NACT and increased risk (CPS-EG score of ≥3 or 2 with ypN+) were randomized into the PENELOPE-B (NCT01864746) trial to receive palbociclib or placebo. Biomarker analysis was performed in 1411 pre- or postNACT tumor samples including 540 paired samples using the HTG EdgeSeq Oncology Biomarker Panel targeting 2549 genes (HTG Molecular Diagnostics Inc.), with assessment of the absolute assignment of breast cancer intrinsic molecular subtype (AIMS). For a subcohort of 29 pts, we evaluated triplicate samples before and after NACT as well as at the time of metastatic disease. Results: In paired biopsies, a total of 335 genes were significantly different between the pre- and the postNACT cohort. With hierarchical unsupervised clustering of these 335 genes, we characterized five different tumor subtypes with highly significant iDFS survival differences (p<0.0001, n=539). We identified two large groups of tumors with excellent prognosis (adaptive cluster AC1 and AC2, together n=284, 6 events), as well as two groups with a poor prognosis; AC-3 (n=163, 82 events) and AC-4 (n=78, 29 events). The worst prognosis was observed in a small group of tumors with a pre-NACT Basal/HER2E AIMS subtype (n=14, 11 events). AC1 and AC3 are enriched for tumors with an AIMS subtype change from LumB to LumA during NACT, with improved iDFS for AC1. AC2 and AC4 are enriched for tumors with a constant LumA AIMS subtype before and after NACT, with improved iDFS for AC2. The low-risk adaptive subtypes AC1 and AC2 cover a total of 52.7% of pts with a combined event rate of 2.1%. In contrast, the best pretherapeutic conventional AIMS-subtype, preNACT LumA, covers 51.7% of pts, but still has an event rate of 15.4%. This suggests that adaptive subtypes are superior to classical AIMS subtypes for prediction of survival after NACT in luminal BC. Conclusions: Classical approach of intrinsic subtyping relies on constant gene expression, limiting its scope. Adaptive subtyping can complement the classical approach, focusing on those genes that are changed during therapy. Comparison of paired samples before and after therapy is superior to classical subtyping of baseline samples. This approach identified large subgroups of pts with excellent prognosis after NACT despite clinical high risk. This can be an important step to focus on high-risk pts for new neoadjuvant and post-neoadjuvant therapy concepts.