Tumor intrinsic and extrinsic determinants of ER+ breast cancer dissemination

Lise Mangiante
Postdoctoral Scholar, Stanford Cancer Center

Introduction: Breast cancer is a highly heterogeneous disease, stratified clinically by the expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2). Despite advances in treatment, a significant proportion of patients, particularly those with ER-positive (ER+) subtypes, face persistent risks of distant metastases and mortality decades after diagnosis. Previously, we established a genome-driven breast cancer classification scheme that defines 11 integrative subgroups (ICs) with distinct molecular features and clinical trajectories. Specifically, we identify four subgroups of ER+ disease (IC1, IC2, IC6, IC9) with a persistent risk of lethal distant relapse up to two decades after diagnosis, each with focal copy number drivers and two distinct subgroups of triple-negative disease (Curtis et al. Nature 2012; Rueda et al. Nature 2019). These findings nominate new therapeutic strategies, however, it is not known how mutational processes and genomic architecture differ across the ICs to sculpt the development and evolution of disease, nor how their microenvironments differ.

Methods: To investigate the tumor-intrinsic and extrinsic factors underpinning breast cancer progression and immune evasion, we analyzed a meta-cohort of 2,877 breast tumors, including 1,865 whole-genome and 1,824 whole-transcriptome sequences. This dataset spans ductal carcinoma in situ, primary invasive, and metastatic breast cancer, with 812 samples profiled using both modalities. We employed a containerized bioinformatics workflow to characterize copy number alterations, structural variations, mutational signatures, as well as the impact on genetic mechanisms of immune escape and the tumor-immune microenvironment (TME) (Houlahan, Mangiante et al. Nature, doi: 10.1038/s41586-024-08377-x). Encouraged by the interconnection of genomic archetypes with distinct TME subtypes, single-cell spatial transcriptomic profiling was also performed on 267 clinically curated ER+ breast cancer patients, encompassing 936 tissue images and capturing over one million cells. Quantitative spatial omic analyses were used to define 16 cell types, six spatial niches, and 1,252 spatial features (Mangiante et al. In preparation).

Results: Our integrative analysis revealed that high-risk ER+ and HER2+ tumors acquire focal copy number alterations and complex structural variants early in disease progression and are associated with immune-depleted microenvironments, persisting from primary to metastatic stages. In contrast, triple-negative tumors displayed global genomic instability and an immune-enriched profile, with increased immune depletion during metastasis. Spatial transcriptomic profiling of ER+ tumors identified significant differences in cell type organization between high-risk and typical-risk groups. Four cancer cell archetypes were defined, each with distinct spatial associations within the tumor microenvironment, with notable evolution from primary to metastatic lesions in spatial features and archetype distributions.

Conclusion: This comprehensive study underscores the interplay of tumor-intrinsic genomic alterations and tumor-extrinsic microenvironmental factors in shaping breast cancer progression and immune evasion. High-risk ER+ and HER2+ subgroups exhibit persistent immune suppression driven by complex structural variants, while spatial transcriptomics highlights distinct cellular and spatial niches predictive of relapse. These findings provide a foundation for developing personalized therapeutic strategies targeting both the genomic drivers and microenvironmental features of breast cancer.