Pretreatment MRI reveals a latent, molecular-subtype-independent structural phenotype that organizes treatment trajectories and recurrence risk

Pathologic complete response and tumor shrinkage measure whether breast cancer responds to neoadjuvant therapy, but not whether that response was structurally favorable, persistent, or hidden beneath volume loss.

We built an outcome-blind longitudinal DCE-MRI manifold from I-SPY2 trajectories to test whether pretreatment imaging carries a structural response phenotype missed by conventional descriptors.

The dominant axis of response geometry was not recoverable from the full clinical and genomic stack -- age, receptor subtype, MammaPrint, PAM50, treatment arm, and tumor burden -- but became strongly recoverable once baseline structural entropy was added.

A constrained representation mapping recovered the same axes as unconstrained decomposition, establishing the structure as intrinsic rather than a post-hoc interpretation.

The phenotype persisted through therapy, and as treatment proceeded the volumetric signal faded while entropy stayed separated -- a crossover from burden to structural persistence.

Among complete responders, structurally disordered tumors could shrink more early yet remain structurally disordered, a volumetric deception invisible to endpoint labels.

External analyses in UCSF, I-SPY1, and Duke established recurrence relevance under representation-dependent boundaries, and a representation-family commensurability assessment showed why feature-name matching is insufficient: the same label can fail, transport, or entangle with extraction geometry.

Pretreatment MRI therefore exposes a structural response phenotype that endpoint-based language leaves invisible -- including, among complete responders, a pretreatment imaging signal of structurally distinct response states that awaits prospective validation.