Integrated multi‐regional multiomic profiling of breast phyllodes tumours reveals peritumoural immune activation and stromal remodelling

BACKGROUND: Breast malignant phyllodes tumours are rare fibroepithelial neoplasms arising from periductal stromal cells, characterized by rapid progression and a high recurrence rate. The poor prognosis largely stems from the lack of effective therapeutic strategies, underscoring the insufficient understanding of their molecular mechanisms and therapeutic targets. Moreover, most previous studies have mainly focused on the tumour core, while the molecular features of the surrounding peritumoural tissue remain insufficiently explored. METHODS: To address this problem, we collected 66 phyllodes tumour specimens from 22 patients, including benign, borderline and malignant subtypes. For each case, paired samples were obtained from the tumour core and peritumoural regions. Multi-regional genomic, transcriptomic and digital pathology analyses were performed to characterize spatial patterns of tumour evolution. In addition, multiplex immunofluorescence was applied to validate the spatial distribution of key cellular and molecular features. RESULTS: Malignant phyllodes tumours exhibited markedly enhanced proliferative activity compared with benign and borderline counterparts. Malignant tumours were also characterized by a distinctly immune activated peritumoural niche encasing an immune excluded tumour core. Specifically, the peritumoural regions displayed abundant lymphocyte infiltration and close immune cell clustering, whereas the intratumoral compartments were largely devoid of immune cells. Enhanced angiogenesis and collagen remodelling were observed in the peritumoural compartment. In malignant phyllodes tumour patients, a more pronounced spatial immune segregation phenotype may be associated with a lower risk of recurrence. CONCLUSION: These results provide an integrated view of phyllodes tumour progression and identify immune exclusion as a defining feature of malignancy. The unique biological characteristics of the peritumoural region may serve as valuable therapeutic targets, offering potential for combined anti-angiogenesis agents and immunotherapy strategies to overcome the immune excluded microenvironment of malignant phyllodes tumours.