Spatial proteomics of breast ductal carcinoma in situ reveal distinct regional differences

Breast ductal carcinoma in situ is a common non-invasive clinical finding that can progress to invasive breast cancer (IBC). Spatial proteomics can provide an additional dimension to our understanding of this disease and its capacity to progress. A subset (n = 103 patients) of a previously established cohort of primary DCIS specimens with known clinical outcomes was analyzed using a multiplexed proteomic platform (Nanostring GeoMx) for simultaneous quantitative measurement of 53 antigens. 1262 spatially distinct regions of interest (ROIs) (1226 ROIs after filtering) were collected, including inside DCIS epithelium, adjacent stroma, co-existing benign breast epithelium, and biopsy sites. We identified two predominant subgroups of DCIS, ER high/HER2 low and ER low/HER2 high. Levels of tumor associated proteins varied between benign and DCIS, between ER + and ER- patients, and between different regions within the DCIS epithelium. In addition, we identified several immune-related antigens (CD127, CD8, and PD-L2) within the DCIS epithelium that are associated with invasive progression. Comparison of antigen levels in matched ipsilateral breast events (both DCIS recurrences and IBC) demonstrates an effect of hormonal therapy on the phenotype of subsequent cancers. This study adds a spatially resolved proteomic dimension to our understanding of DCIS, its microenvironment, and its propensity to progress to IBC.