Tumor heterogeneity in relapsed or metastatic breast, ovarian and colorectal cancer

Cancer is a genetic disease. Genetic changes or mutations that alter the function of genes, can provide a cell with a selective growth advantage compared to its surrounding cells. Next-generation sequencing is revolutionizing the characterization of these (epi)genetic alterations and is gaining influence on therapy choice and prediction of prognosis. This manuscript describes the results and interpretations derived of genetic characterizations on three different cancer cohorts:

A first part investigates genetic heterogeneity after first-line chemotherapy in high-grade serous ovarian cancer. Most high-grade serous ovarian cancer patients benefit from platinum therapy, yet progressively develop resistance through subsequent relapses. The aim of this study was to investigate which aberrations are involved in acquired platinum resistance byprofiling 31 high-grade serous ovarian tumors before and after first-line platinum therapy. Subsequently, a pair-wise analysis was performed to map the changes occurring during disease progression and to identify possible mechanisms of therapy resistance. Already after a single line of platinum, there is huge variability between primary and recurrent tumors, advocating that in high-grade serous ovarian cancerbiopsies need to be collected at relapse to tailor treatment options to the underlying genetic profile. Nevertheless, all primary platinum-sensitive high-grade serous ovarian tumorsremained homologous recombination-deficient, irrespective of whether they became resistant to second-line platinum, further suggesting these tumors qualify for second-line PARP inhibitor treatment. Finally, chromosomal instability contributes to acquired resistance after a single line of platinum therapy.

On a second cohort, phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number alterations was performed.Distant metastatic disease is the main cause of breast cancer mortality. The aim of this study was to investigate the contribution of tumor heterogeneity to metastasis by profiling and comparing the primary tumor site with multiple matched metastases collected during autopsy of 10 breast cancer patients. Combining the allelic frequencies of somatic mutations with copy number information allowed to infer tumor clonality and reconstruct the phylogenetic evolution. We found that the major route of metastatic progression seems to be a cascading dissemination starting from the primary tumor and then from metastasis to metastasis but we also observed multiple seeding events and horizontal re-seeding in de novo metastatic patients.

A third cohort was characterized to determine the genomic landscape of metastatic colorectal cancer treated with bevacizumab. Since its approval, bevacizumab (Avastin® - Roche) has been widely administered to metastatic colorectal cancer patients (both those with or without K-ras/Braf mutations) as a first line treatment in combination with chemotherapy. However, several clinical investigations over the past years showed clear evidence for a very heterogeneous response amongst patients. The aim of this study was to profile 200 patients, treated with bevacizumab, in order to determine the genomic landscape and to investigate possible predictive biomarkers that help to select patients with the greatest treatment benefit. We identified 3 copy number subtypes differing in copy number burden due to copy number instability. Tumors belonging to intermediate-to-high instability subtypes (CNA subtypes 2 and 3) had improved outcome following chemotherapy and bevacizumab versuschemotherapy alone compared to CNA subtype 1 tumors with a very low copy number burden. These copy number subtypes overlapped with the consensus molecular subtypes (CMS) in colorectal cancer and experiments with CMS2 and CMS4 xenografts, clustered in CNA subtypes 2 and 3 showed an increase response to BVZ.