Abstract 2852: Mapping single cell spatial 3D genome landscape of localized and metastatic breast cancer sub-types
Authors: Shyamtanu Chattoraj, Huy Nguyen, Jude Dunne
Journal: Cancer Research (2025)

Abstract Metastatic breast cancer is the most aggressive form of breast cancer leading to poor disease-free patient survival and accounting for 90% of all breast cancer-related deaths. The specific mechanisms that promote metastasis are not fully understood owing to the complex interplay between cancer cells and their surrounding microenvironment. This microenvironment involves clonal and sub-clonal heterogeneity in genomic, transcriptomic and protein signaling network across different cancer cell sub-populations. Understanding the molecular mechanism behind cancer metastasis demands state of the art single cell and spatial technologies that can provide deeper insight on disease progression. Since, cancer is heavily influenced by genetic changes, the study of the 3D- genome organization in single cells helps to improve 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 disease research. In this abstract, we present a novel jebFISHTM protocol on the PaintScapeTM platform that can be used to understand differences in global 3D genome organization among several localized and metastatic breast cancer cell lines at single cell, sub-population and population level. Using a highly multiplexed genome wide panel of chromosomal targets, 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 will also show the signature of specific 3D genome structural alterations and interchromosomal interactions related to breast cancer metastasis compared to normal breast cells. In addition, we investigated differences in global 3D genome architecture of different breast cancer sub-types such as HER2 enriched vs triple negative breast cancer cells. We will show how different breast cancer sub-types carry specific chromosomal instability and differential interchromosomal interaction patterns at single cell, sub-chromosomal and sub-population level. We envision this study will improve our understanding on breast cancer disease progression 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. We propose that this study serves as proof-of-principle and is generalizable to other types of cancers where changes in 3D genome organization may occur at different cancer stages. Citation Format: Shyamtanu Chattoraj, Huy Nguyen, Jude Dunne. Mapping single cell spatial 3D genome landscape of localized and metastatic breast cancer sub-types [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 2852.