Genomic profiling of circulating biomarkers and matched primary tumors from breast cancer patients.

• Applicant: Zbigniew Czyz, Ph.D.
• Subject Area: Gynaecology and Obstetrics ; Hematology, Oncology
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 465250727

Despite significant therapeutic progress, prognosis for patients with luminal B, HER2-overexpressing and triple negative breast cancers (TNBCs) remains poor. Genetic instability as well as primary and acquired resistance arising from intratumor heterogeneity are recognized as highly important reasons for therapy failure. Identification of actionable mutations in primary tumors (PTs) can be used to detect potential therapy targets for patients showing no or only partial response to standard treatment. However, basing therapy decision upon primary tumor data ignores changes of mutational profiles during treatment or in systemically spreading cancer cells, which may genetically differ from bulk PTs. In addition, genetic background of patients may have a profound impact on the outcome of treatment. Therefore, in this project we will analyze the profiles of pharmacogenetic (PGx) germline sequence variations as well as the landscape of somatic actionable mutations in both primary and systemic cancer. For this purpose, we propose to analyze PT, germline DNA specimens as well as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) – biomarkers representative of highly aggressive disease – for the presence of actionable genetic alterations.We hypothesize that ctDNA/CTCs inform best about actionable changes emerging during the treatment. However, analysis of CTCs remains challenging due to their phenotypic diversity, which impairs CTCs detection. Literature data and own results indicate that the presence of CTCs displaying a mesenchymal phenotype, which is often overlooked by conventional detection methods, is linked to an aggressive course of disease and poor prognosis in early and metastatic breast cancer. To more accurately assess the clinical value of CTCs for therapy selection, we will determine (actionable) somatic mutations in primary tumors and corresponding epithelial and mesenchymal CTCs collected from a cohort of 15 metastatic and 60 non-metastatic, high-risk breast cancers patients. For this purpose, we will utilize our proprietary method for isolation of epithelial and mesenchymal CTCs and adopt the FDA approved MSK-IMPACT assay to identify druggable oncogenic mutations in CTCs before and after treatment. In addition, the IMPACT method will be modified to enable detection of germline variants annotated as drug metabolism modifiers. Data resulting from profiling of PTs, CTCs and the corresponding germline samples will be used to determine patients-specific sequence markers for subsequent targeted screening of serially collected ctDNA samples. In summary, comparative analysis of localized cancer with early systemic seeds detected in blood throughout the treatment will inform about the most relevant source of information to predict clinical outcome and uncover targets for personalized treatment of patients at high risk of progression.

• DFG Programme: Research Grants
• International Connection: Poland
• Partner Organisation: Narodowe Centrum Nauki (NCN)
• Cooperation Partner: Dr. Aleksandra Markiewicz