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Selected Publication:

Zhou, Q.
Tumor Genome Stratification and Network Analyses based on Non-invasive Liquid Biopsies.
PhD-Studium (Doctor of Philosophy); Humanmedizin; [ Dissertation ] Graz Medical University; 2020. pp. 125 [OPEN ACCESS]


Authors Med Uni Graz:
Bauernhofer Thomas
Höfler Gerald
Speicher Michael

Colorectal cancer is the third most commonly diagnosed malignancy worldwide. The mortality of colorectal cancer has been decreasing in recent decades due to improved diagnostic procedures, which allow the identification of patients with early-stage disease. However, the survival of patients with advanced diseases is still unsatisfactory. Recently, targeted therapies, e.g., anti-EGFR and anti-VEGF treatments, have shown promising results in late-stage colorectal cancer patients. However, the survival benefit of targeted therapies is usually limited to a few months, and acquired resistance occurs frequently. Liquid biopsy, which refers to the analysis of tumor content from a body fluid such as blood, has become a promising method for early diagnosis and the management of patients. In the project described in this thesis, we employed whole-genome sequencing of plasma DNA, which in patients with cancer contains circulating tumor DNA (ctDNA) to evaluate the tumor genome of patients with colorectal cancer (CRC). A focus was on those patients who received targeted treatment, to validate the usage of ctDNA for acquired resistance and patient outcome prediction, and also to determine novel resistance mechanisms. Using longitudinal plasma analyses, we studied the evolution of tumor genomes in a metastatic colorectal cancer cohort. Interestingly, two patients under anti-EGFR treatment showed focal amplification in resistance-related genes (i.e., KRAS and ERBB2) when the disease progressed. Moreover, focal amplification in CDK6 (resistance-related) was found in one patient under anti-ERBB2 treatment. These results suggested that liquid biopsy is a promising tool for identification of emerging focal amplifications, which may be associated with acquired resistance prediction. In addition to focal amplifications with established driver genes, we also identified recurrent focal amplifications, which had not yet been investigated in detail, such as an amplicon on chromosome 13q12.2. By analysis of CRC cases from the TCGA database, we confirmed that amplification of 13q12.2 was associated with more advanced stages. We first defined the minimally amplified region and then tested the function of all genes included with two in vitro cell models. We found evidence for POLR1D being the potential driver gene within the amplicon, which impacted cell proliferation by inducing the expression of some oncogenes (e.g., VEGFA and EREG). The upregulation of VEGFA, an essential regulator of angiogenesis, has been implicated in the resistance to bevacizumab treatment. Interestingly, by serial monitoring of two patients under bevacizumab treatment, we observed the emergence of the 13q12.2 amplification when the respective tumors developed resistance to the therapy. All the results indicated that POLR1D is the potential driver gene in 13q12.2 and plays a role in bevacizumab resistance. To this end, we confirmed that liquid biopsy as a non-invasive method applicable for acquired resistance and patient outcome prediction in the clinic. Liquid biopsy is also a useful tool in cancer research, which allows the identification of novel driver genes.

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