LeGO-Teknik reveals that the neurogenesis pathway is a clone-specific hallmark of brain metastasis in breast cancer

Abstract

Breast cancer exhibits substantial inter- and intra-patient heterogeneity. Yet the molecular features underlying this diversity and their roles in tumour progression are not yet fully elucidated. Within a primary tumour, certain clones possess a unique capacity to metastasize to distant organs, such as the brain, and this propensity may be associated with specific gene expression profiles. To investigate this phenomenon, we developed a new optical barcoding library, LeGO-Teknik, compatible with high resolution imaging, flow cytometry, single-cell RNA sequencing and machine learning computational methods. Using this new tool, we systematically assessed the fitness and organ tropism of multiple human breast cancer clones in spontaneous metastasis assays. Linking transcriptomic profiles of individual cancer cells to their clonal identities and metastatic behaviours, we identified that clones predisposed to forming brain metastases exhibit distinct molecular signatures. Notably, individual cells from these clones showed enriched expression of neurogenesis-related genes. Using SCENIC transcription factor analysis, we found that some of these features are driven by the transcription factor SOX4. This hallmark, likely due to a process of cellular reprogramming, is a remarkable example of organ mimicry during clonal selection. Together, this work provides critical insights into brain metastasis and highlights the potential for identifying predictive biomarkers and therapeutic targets for metastatic breast cancer.