Genetic and Epigenetic Diversity of Tumors

Introduction

Tumors are large systems of cells that have lost their normal cooperative behavior and proliferate in an uncontrolled manner. Tumor development is an evolutionary process, in which somatic cells that acquire malignant mutations outcompete normal cells of the tissue. Cells can be altered genetically by point mutations or genomic rearrangements, and epigenetically by changing methylation status or histone modifications. The relationship between genetic and epigenetic changes in cancer cells is largely unknown.

Tumorgenesis proceeds through a series of clonal expansions. The evolutionary dynamics of these selective sweeps are amenable to mathematical modeling and this approach has provided important insights into the somatic evolution of cancer. Most models predict a certain degree of genetic diversity within the tumor, especially at low frequencies. However, this prediction has been almost impossible to test so far, because of technical limitations of Sanger sequencing. By contrast, deep sequencing, a new generation of high-throughput shotgun sequencing technologies, puts the question of tumor diversity within experimental reach. This massively parallel sequencing approach produces millions of reads in a single run, and a mixed sample can be analyzed directly.

A combined deep sequencing and mathematical modeling approach to the somatic evolution of cancer

We use a combined deep sequencing and mathematical modeling approach to assess the diversity of solid tumors. Employing a two-step procedure, we first conduct genome-wide screening experiments using target enrichment and sequencing followed by bioinformatics analyses in order to identify somatic mutations and epigenetic changes (DNA methylation) in the primary carcinoma. In the second step, we will use ultra-deep sequencing to assess the genetic and epigenetic diversity of the tumor at selected loci.

The data produced in the second deep sequencing experiment will first be analyzed with the goal of quantifying tumor diversity from the huge set of error-prone sequence reads. Next, we use the diversity estimates for testing model predictions regarding the evolutionary dynamics of cancer. This analysis will provide insight into the dynamics of carcinogenesis and metastasis formation. Comparing the same estimates between genetic and epigenetic changes will elucidate the contribution of genetic and epigenetic changes to disease progression.

Overall, this study will provide the first direct experimental evidence and the first comprehensive quantitative analysis of genetic and epigenetic diversity within solid tumors. We develop and establish several experimental and computational techniques that pave the way for future tumor genetics and epigenetics studies. 

People Involved

Moritz Gerstung
Prof. Dr. med. Holger Moch
Prof. Dr. Niko Beerenwinkel
Dr. Christian Beisel

Funding