Abstract A1-18: Attacking the SAGA of tumor heterogeneity: The development of a novel technique to provide spatiotemporal genomic profiling of rare cancer cells

Abstract

Abstract Intratumoral heterogeneity can dictate a patient's response to therapy and overall survival. In fact, rare sub-populations within the bulk of a tumor are often considered the drivers of cell proliferation, survival, and metastasis. Though major efforts are underway to address this, very few have attempted to address heterogeneity by precisely selecting living cells within a physiologically relevant environment. This approach would not only provide the ability to select cells of interest based upon dynamic behaviors but also allow genomes to be mapped back to individual cells or cell sub-populations. We now report the development of a technique termed spatiotemporal genomic analysis (SAGA), which combines live cell confocal imaging and genomics in a novel way in order to precisely select living, rare cell populations that are maintained within a physiologically relevant environment for downstream genomic analyses. While widely applicable, we utilized SAGA to specifically address the question as to whether certain cells within an invasive chain have different genomic expression patterns. Collective cell invasion occurs within tumors of various in vivo mouse models as well as patient tumors and thus is a relevant mechanism of tumor metastasis. Collective invasion also displays phenotypic heterogeneity, with leader cells that pioneer invasion into the microenvironment with follower cells immediately following the leaders. Using 3-D cancer cell spheroids, we precisely selected as few as 10 leader cells with SAGA, extracted them from the bulk of the spheroid, and compared their gene expression pattern to that of follower cells using an Affymetrix microarray. The array identified over 150 transcripts that are significantly up- or downregulated in leader cells compared to follower cells. Pathway analysis showed that alterations in genes within the cell adhesion and Wnt signaling pathways are significantly enriched in leader cells compared to follower cells, illustrating the validity of SAGA to identify biologically relevant genomic information on rare cell populations. In addition to genomic analyses, SAGA allows cells of interest to be cultured post-selection, and thus a normally rare cell population can be amplified and maintained. Therefore, we now possess novel leader as well as follower cell lines that maintain their original phenotypes over time. The leader cells show highly dynamic invasive patterns, while follower cells have limited invasive capabilities when cultured alone. Interestingly, reintroducing limited numbers of leader cells into the follower cell cultures can promote invasion in the follower cells. Thus, our data show that SAGA can precisely select living cells based upon dynamic behaviors for genomic analysis and can be used to amplify rare cell populations for subsequent molecular, cellular, and proteomic analyses. Therefore, this method has the potential to impact the field of tumor heterogeneity by uncovering genomic signatures of rare yet dynamic subpopulations within a heterogeneous cancer population. Citation Format: Jessica Konen, Adam I. Marcus. Attacking the SAGA of tumor heterogeneity: The development of a novel technique to provide spatiotemporal genomic profiling of rare cancer cells. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-18.