Abstract
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.
Data availability
Clinical and raw Nanostring expression data are available as part of the supplementary material of this report. The time-to-event data and the RNAseq data used to determine ER and HER2 status were made public as part of a prior publication and can be accessed through the Human Tumor Alas Network (HTAN) [https://humantumoratlas.org/explore] and subset using the patient manifest available on Mendeley [https://data.mendeley.com/datasets/tbzv5hpvw5/3]. The code to reproduce the analyses presented in this paper, including that needed to join these external data sets with the raw Nanostring expression data, along with the apptainer definition file to reproduce the computing environment used to conducted the analyses are available through [https://gitlab.oit.duke.edu/dcibioinformatics/pubs/marks-nanostring-dcis]. We note that an analysis-ready version of the data, which includes these external time-to-event data and ER and HER2 status variables, is also provided as part of the supplementary material of this report.
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Funding
Research reported in this publication was supported by National Cancer Institute of the National Institutes of Health under award number R01 CA185138-01 (ESH); U2C CA-17-035 Pre-Cancer Atlas (PCA) Research Centers (ESH); UO1 CA214183 (JRM); DOD BC132057 (ESH); BCRF 19–074 (ESH); P30CA014236 (YD, ABS, KO) and Duke Cancer Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
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J.M. and S.H. conceived and were responsible for the overall study design. J.M., L.K., L.S., A.H., R.F., and J.N. conducted the experimental portion of the study and primary data collection. Y.D., A.S., and K.W. were responsible for data analysis. Y.D. and A.S. prepared the figures. S.N. provided input on interpretation of the data. J.M., Y.D., A.S., K.W. and S.H. wrote the main manuscript text. All authors reviewed the manuscript.
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Marks, J.R., Dai, Y., King, L.M. et al. Spatial proteomics of breast ductal carcinoma in situ reveal distinct regional differences. Sci Rep (2026). https://doi.org/10.1038/s41598-026-43486-9
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DOI: https://doi.org/10.1038/s41598-026-43486-9
