Karyotype diversification in colorectal cancer

From the moment of conception, every human being is in the process of developing cancer. Whether or not you will ultimately be diagnosed with this disease is simply a matter of whether something else kills you first. Cancer is not one disease. Rather, the radical growth of malignant cells represents a phenotypical extreme of cells that escape homeostasis. There are astronomically many potential combinations of genetic, epigenetic and environmental influences that can push cells into malignancy. Therefore, not only is every type of cancer different, but every instance of cancer is its own unique disease. The standardized treatments given to patients with similar types of malignancy are simplified abstractions, born from our lack of understanding of optimal treatment. The development of personalized cancer treatment options is one of the defining goals of modern medicine. Fundamental research plays an important role in progressing toward this goal, since without a true understanding of cancer biology we cannot hope to develop truly personalized treatment protocols.

This thesis describes technological advances aimed at investigating fundamental cancer biology using patient derived organoids as a model system. Patient derived organoid culture protocols allow in vitro culture of three-dimensional (3D) wild-type and malignant tissue structures. By allowing differentiated outgrowth in 3D space, organoid culture protocols more accurately recapitulate tissue composition, density and cell division dynamics of human tumors in vivo. When combined with fluorescent live cell imaging, patient derived tumor organoids provide spectacular tools to support fundamental cancer research.

One of the protocols we developed is called 3D Live-Seq, which combines imaging of tumor organoid outgrowth and single-cell sequencing of each imaged cell to reconstruct evolving tumor karyotypes (the number of chromosomes or sub chromosomal fragments per cell) across consecutive cell generations. By using 3D Live-Seq, we showed that advanced colorectal cancer cells continuously generate both singular and very complex chromosome errors during outgrowth of a tumor. Collectively, these cells represent a body of genetic diversity from which treatment resistant or more aggressive subclones may emerge during disease progression.