ClonMapper: A multifunctional cell barcoding platform for tracking heterogeneous cancer cells
Conventional DNA barcoding allows quantification of clonal dynamics in heterogeneous cell populations but requires destructive sequencing, preventing further study of specific clonal lineages. To overcome this, we engineered ClonMapper, a molecular platform with expressed gRNA barcodes that enables tracking of clonal dynamics using high-resolution genomic sequencing and clonally-resolved single cell transcriptomic analysis. ClonMapper gRNA barcodes also act as actuators, enabling clone-specific gene expression control and isolation of desired lineages. By integrating gRNA barcodes with synthetic gene circuits, the system allows programmable, clone-specific gene expression in live cells.
Heterogeneity in Chemotherapeutic Response
In a cancer cell line model integrated with the ClonMapper DNA barcoding technology, changes in RNA expression and abundance of individual clonal subpopulations can be tracked across treatment with chemotherapy. These types of data can provide insight into the heterogenous chemotherapeutic resistance and transcriptomic response of cancer cell subpopulations. Current projects include tracking the resistance and response to targeted inhibitor treatments in patient-derived TNBC cell models, and investigating the influence of cell-cell fusion on chemotherapeutic resistance and heterogeneity.
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Systems Approaches to Cell-Cell Fusion in Cancer
Well-studied in processes that produce detectable multinucleated cells, cell-cell fusion is more challenging to study in the context of tumor biology. Post-fusion cancer cells can revert to single-nucleated states with recombined genomes, complicating their detection and characterization. Fusion initially results in whole-genome doubling, often followed by aneuploidy, both key drivers of tumor evolution. However, the role of cell-cell fusion in cancer progression and treatment response has been understudied due to limited experimental systems for tracking and analyzing individual fusion events.
We are leading efforts in the development and implementation of molecular and computational tools to unveil the hidden roles of homotypic cell-cell fusion in cancer cell state transitions under naive and chemotherapeutic conditions. |
Analyzing the Clonal Dynamics and Metastatic Potential of Isolated Subpopulations within TNBC cells
While progress has been made to understand the molecular underpinnings of metastasis, it is not clear how subpopulations of cells with different invasive potential may interact and impact tumor expansion and chemoresistance. This project investigates the metastatic potential, proliferation, and chemoresistance of subpopulations in the HCC1806 and MDA-MB-231 cell lines using ClonMapper to track the clonal composition of isolated subpopulations.
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Understanding the Role of Metabolism in Triple-Negative Breast Cancer Clonal Populations
Despite significant advances in understanding cancer cell metabolism, different metabolic conditions and their impact on the interactions between subpopulations of cells with diverse metabolic preferences, chemoresistance, tumor composition, and heterogeneity remain unclear. ClonMapper technology, RNA sequencing, and ecological modeling will be utilized to explore the influence of nutrient availability on clonal selection, sensitivity to chemotherapeutics, and cell-cell interactions in triple-negative breast cancer cell lines.
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