High throughput phylogeography of tumors: how the tissue environment influences cancer evolution?

Introduction

The tumor microenvironment (TME) is a dynamic ecosystem wherein tumor cells, immune cells, and stromal cells interact and evolve. One of the primary characteristics of cancer progression is the diversification, selection, and expansion of tumor sub-clones in a manner that largely depends on the TME, e.g., through immune responses or metabolic crosstalk.

Advances in Research

Advances in single-cell and spatial genomics provide exciting opportunities for studying how tumors evolve in their tissue context. This technology lends an information-rich perspective on which cell subsets are present and how they might interact. However, fundamental questions remain challenging to study through this perspective, particularly regarding how single tumor cells are related sub-clonally.

Key Questions

• What characterizes the immediate cellular environment of successful subclones?

Development of Transcriptional Phylogeography

Here, we develop transcriptional phylogeography—a paradigm for studying tumor development in situ, on a transcriptome-wide scale, and at single-cell resolution. Our work will leverage studies by us and others that utilized CRISPR/Cas9 mutations coupled with single-cell RNA sequencing to infer the lineage structure of thousands of single cells at a time.

In-Situ Profiling

Adapting this system for in-situ profiling, we will generate the first of its kind phylogeography dataset of a tumor model. This data will allow us to identify tissue locations that harbor critical sub-clonal properties such as:

1. Unrestrained growth
2. Dedifferentiation
3. Metastatic seeding

By investigating these properties through the lens of high-throughput genomics, we will explore how the TME is associated with them.

Addressing Analytical Questions

We will also identify and offer solutions for outstanding analytical questions in this nascent area, including:

• Lineage inference given sparse data
• Characterizing the metabolic aspects of tumor-TME crosstalk

Conclusion

Together, these studies will help establish new causal links between the TME and tumor evolution and lay the foundation for transcriptional phylogeography analysis.