Monitoring of circulating tumor DNA and drug testing in organoids to tailor neoadjuvant and postneoadjuvant treatment in patients with early breast cancer

• Applicants: Professor Dr. Andreas Hartkopf; André Koch, Ph.D.; Professor Stephan Ossowski, Ph.D.; Dr. Christopher Schroeder
• Subject Area: Gynaecology and Obstetrics
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 497656430

Neoadjuvant systemic therapy (NAT) is increasingly used to optimize the treatment of primary breast cancer (PBC), as it allows in vivo monitoring of treatment response. Patients who do not achieve a pathological complete response (pCR., i.e. NAT has killed all invasive tumor in breast and lymph-nodes) often receive additional postneoadjuvant systemic therapy after surgery. However, the concept of NAT with consecutive postneoadjuvant treatment still has some limitations: (1) Surgery is required to verify whether a pCR has been achieved or not. (2) Postneoadjuvant therapy does not consider the characteristics of the residual tumor; hence, pCR is used as a prognostic marker to identify high-risk patients, but not to predict treatment efficacy. (3) Since a large proportion of patients do not experience distant recurrence despite residual tumor, many patients are overtreated with postneoadjuvant therapy. (4) As the primary tumor is removed after NAT, therapy monitoring is no longer possible during the postneoadjuvant treatment phase. Using circulating tumor DNA (ctDNA) from blood samples obtained before NAT, before surgery and during postneoadjuvant treatment / follow-up could address these challenges by predicting pCR more accurately and helping to better assess the risk of recurrence in non-pCR patients. Furthermore, molecular characterization of residual tumor tissue can help to identify therapeutic targets on the one hand; on the other hand, mutations potentially induced by NAT can be used to monitor the efficacy of postneoadjuvant treatment after surgery more sensitively. To this end, a targeted sequencing approach able to detect ctDNA based on characteristics (mutations) of the primary tumor before and after NAT is required. To verify druggable mutations and to develop postneoadjuvant strategies for patients in whom no such mutations were found, patient derived cancer organoids (PDOs) from residual tumor tissue after NAT are a promising functional test. By using blood/plasma samples, tumor tissue and PDOs (n=100 patients) that are already stored in our translational biobank we aim to assess whether ctDNA is detectable before NAT, directly after NAT (i.e. before surgery) and one year after NAT (i.e. after postneoadjuvant treatment). To identify mutations for ctDNA monitoring as well as druggable mutations in residual tumor tissue after NAT we will perform whole-exome-sequencing (WES) on tumor tissue before the start of NAT (core biopsies are routinely performed at that time-point) and on residual tumor tissue after NAT, obtained from surgery (approx. 50 patients who will not achieve pCR). PDOs from ten of these patients without pCR will be used for drug efficacy screenings, including drugs that have been identified from WES of primary tumor tissue. To better understand the observed efficacy of drug screening and to compare it with the predicted efficacy based on WES of the primary tumor, we will also perform WES of the PDOs.

• DFG Programme: Research Grants