Abstract 5316: Multi-platform spatial profiling reveals intra-tumor heterogeneity in intrinsic subtypes and immune markers in breast tumors from Kenyan patients
Authors: Mustapha Abubakar, Shahin Sayed, Hela Koka, Scott Lawrence, Karun Mutreja, Xing Hua, Viviane Oluoch, Veronica Ngundo, Zaitun Ajuoga, Difei Wang, Chad Highfill, Petra Lenz, Maria Brown, Aaron M. Rozeboom, Kristine Jones, Amy Hutchinson, Belynda Hicks, Paul S. Albert, Francis Makokha, Stefan Ambs, Jonine Figueroa, Jianxin Shi, Xiaohong Rose Yang
Journal: Cancer Research (2025)

Breast cancer is a highly heterogeneous disease at the clinical, population, and molecular levels. Using key molecular markers, breast cancer can be classified into at least four major intrinsic subtypes: luminal A, luminal B, HER2-enriched, and basal-like or triple-negative. These subtypes are associated with distinct risk factors, clinical behaviors, treatment responses, and outcomes. Recent research highlights the importance of the breast tumor microenvironment (TME) in shaping tumor evolution and cancer progression. Both tumor and TME cells within an individual patient often exhibit substantial intratumoral heterogeneity (ITH), the extent of which may impact accurate tumor classification and treatment response, but has not been well characterized especially in women of African Ancestry. The goal of this study was to comprehensively investigate ITH of intrinsic subtypes and immune TME markers in breast cancer patients from an East African population. Specifically, we employed the Nanostring GeoMxTM platform to quantify 44 key breast cancer intrinsic and immune subtyping markers in spatially defined regions of breast tumors from 31 Kenyan breast cancer patients. We found that all 31 tumors exhibited some degree of ITH, with a third of them showing substantial ITH. Cell composition (epithelial vs. stromal), spatial location of TME immune cells (tumor-leading edge, proximity to tumor or stroma), and intrinsic subtype (specifically, basal-like vs. luminal A) all contributed significantly to ITH of these markers. When comparing results to those obtained from an in-situ multiplex staining platform InSituPlex (ultivue) and bulk Nanostring nCounter RNA expression, all generated from the same set of cases, we found that intrinsic or immune subtyping by bulk approaches, which is heavily influenced by the predominant subtypes within a tumor, may lead to inaccurate classification when substantial ITH exists. Similarly, sampling-based approaches like tissue microarrays (TMAs) or region-of-interest (ROI)-based assays are also likely to be subjective to inaccurate and inconsistent measurements of immune markers due to sampling bias. In low-resource settings, in-situ assays combined with multi-region scoring may offer a more accurate yet practical alternative to bulk or single-cell assays, which are often costly and technically challenging. Citation Format: Mustapha Abubakar, Shahin Sayed, Hela Koka, Scott Lawrence, Karun Mutreja, Xing Hua, Viviane Oluoch, Veronica Ngundo, Zaitun Ajuoga, Difei Wang, Chad Highfill, Petra Lenz, Maria Brown, Aaron M. Rozeboom, Kristine Jones, Amy Hutchinson, Belynda Hicks, Paul S. Albert, Francis Makokha, Stefan Ambs, Jonine Figueroa, Jianxin Shi, Xiaohong Rose Yang. Multi-platform spatial profiling reveals intra-tumor heterogeneity in intrinsic subtypes and immune markers in breast tumors from Kenyan patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5316.