Abstract 5241: Mapping spatial 3D genome landscape of breast cancer cells in different tumor immune microenvironments using onco-immune co-culture as a model

One of the leading causes of tumor cell heterogeneity is the complex nature of the tumor immune microenvironment involving crosstalk between different signaling pathways of cancer cells and immune cells. For cancer cells to grow into a primary tumor and then metastasize into secondary tumors, they must avoid or overcome the attack of different types of immune cells, including macrophages, natural killer (NK) cells, and T lymphocytes. For example, cancer cells can polarize macrophages from “tumor killing” to “tumor promoting” type using specific signaling molecules. Such tumor immune crosstalk is dependent on the clonal and sub-clonal heterogeneity in genomic, transcriptomic and protein signaling networks across different cancer cell sub-populations, immune cells and its surrounding microenvironment. Since structural aberrations affect gene dysregulation, the study of the 3D- genome organization in single cells can help in better understanding of disease progression and prognosis. The genome is organized and packaged in a highly structured manner inside the nucleus of mammalian cells and exhibits dynamic reorganization throughout disease progression. Understanding this 3D organization at the single-cell level with high spatial resolution is crucial for immune-oncology disease research such as investigating tumor-immune cell interactions. In this abstract, we present a novel jebFISHTM protocol on the PaintScapeTM platform that can be used to investigate immune cell modulated differences in global 3D genome organization among different localized and metastatic breast cancer cell lines at single cell, sub-population and population level. Using a genome wide panel of chromosomal targets on an onco-immune co-culture system involving different breast cancer cell lines and CD4+ T-cells or macrophages, we will show disruption in chromosome territory, radius of gyration, chromosomal instability between localized and metastatic breast cancer cells at single cell and sub-population level. We observed signatures of specific 3D genome structural alterations and interchromosomal interactions in cancer cells and/or immune cells, related to the effect of different types of immune response. We will show how the 3D architecture of key genomic loci and its associated regulatory elements belonging to major cancer signaling pathways exhibit specific signatures including differential folding, chromosomal instability, differential interchromosomal interaction and structural variation patterns at single cell, sub-chromosomal and sub-population level. We envision this study will improve our understanding on breast cancer tumor immune microenvironment and provide deeper insight into the underlying genomic heterogeneity of single cancer cells and sub-populations which might help to design better treatment options in the future. Citation Format: Jude Dunne, Huy Nguyen, Shyamtanu Chattoraj. Mapping spatial 3D genome landscape of breast cancer cells in different tumor immune microenvironments using onco-immune co-culture as a model [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 5241.