Correlating Genotype and Phenotype of Metastatic Cancer Cells In Vivo Using Nanolaser Optical Barcode

Project Summary. The complex dynamics of metastatic cancer, which include processes like plasticity, immune evasion, and therapy resistance, pose significant challenges to effective treatment. While emerging single-cell sequencing technologies now aid in understanding the genetic heterogeneity and clonality, as well as the unique genome expression of individual cancer cells within tumor microenvironments, these methods often fail to fully capture the behavior of living cells, such as migration, division, and regulation of volume and mass. The primary technical bottleneck lies in the inability to read DNA barcodes in live cell states and the limited number of unique fluorescence barcode colors available. Addressing these limitations is crucial for enhancing our comprehension of metastatic cancer and improving treatment outcomes. The proposed K25 project aims to develop a single-cell assay for correlating genome, transcriptome, and dynamic behaviors of metastasis cancer cells in an in vivo mice model using laser particles (LPs). These biocompatible particles emit ultrabright narrowband laser emission, creating unique optical barcodes for a massive number of migrating cancer cells, enabling real-time tracking in vivo and compilation of data from different assays. The project comprises three primary aims: 1. Employing LP to create workflows that correlate single cell sequencing with real-time observations of cancer cell mass, volume, and migration using optical microscopy. 2. Creating multiplet LPs, multiple LPs within one body, to ensure the enduring uniqueness of barcodes for long-term, in vivo tracking of cancer cells. 3. Integrating advancements to enable multidimensional single-cell assays within an in vivo metastatic breast cancer model, linking migration and immune cell interaction data from imaging with single-cell DNA and mRNA sequencing results. The project's key innovations involve correlating the genotype and phenotype of migrating cells, integrating cutting-edge LP technology into in vivo cancer studies, and analyzing high-dimensional single-cell data. Aims 1 and 2 operate independently, while Aim 3 is designed to anticipate potential pitfalls and explore alternative approaches. Each aim is supported by preliminary data. The project spans five years, focusing on application to an in vivo model. Expected outcomes include successfully correlating genotype, genome expression profile, and optical phenotypes with single-cell resolution, as well as uncovering novel insights into tumor metastasis and therapeutic responses. Furthermore, the mentoring and training provided by the advisory team empower the principal investigator of this project, with strong backgrounds in nanophotonics and chemistry, not only to contribute significantly to cancer research but also to advance their career toward independent academic positions.