Identification and characterization of progenitor circulating tumor cells of leptomeningeal and brain metastases

• Applicant: Dr. André Franken
• Subject Area: Gynaecology and Obstetrics ; Hematology, Oncology
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 578715613

Breast cancer (BC) is the most frequent cancer type and leading cause of cancer associated death among women. Brain metastases (BMs) occur in approximately one third of women with advanced metastatic BC (mBC), making BC the second most common cause of BMs. As new therapeutic advances increasingly succeed in suppressing cancer progression systemically, recurrence of disease within the central nervous system is emerging as a major cause of cancer relapse and mortality. Among different forms of BMs, the leptomeningeal carcinomatosis (LC) is associated with a particularly poor outcome with a median survival of only 4 months for patients receiving state-of-the-art treatment. At the time of a BM or an LC diagnosis, most patients have already developed metastases outside the central nervous system. This suggests that brain metastasis mostly occurs as a secondary metastasis founded by circulating tumor cells (CTCs) that spread from already established metastases in e.g., the bones. Profound knowledge on the biology and molecular features of the brain metastasis initiating CTCs (BMICs) is still lacking. In my preliminary work I have established a workflow for the detection, isolation and molecular characterization of CTCs from the cerebrospinal fluid (CSF) which enables a liquid biopsy from the brain. In a proof-of-concept analysis on one patient I found that CSF-CTCs present very clonal chromosomal aberrations different to those of CTCs from blood. In a longitudinal analysis of CTCs from that patient, CTCs closely related to the CSF-CTCs were detected 13 months before the diagnosis of the brain metastasis. Based on the pattern of chromosomal aberrations, these CTCs can be considered as BMICs. Based on that, I hypothesize that LCs are characterized by the expansion of a single or very few BMICs, which are present in the blood before the diagnosis of the brain metastases. Further, I hypothesize that these BMICs can be detected by a longitudinal CTC analysis and their characterization will reveal molecular features of CTCs with the capacity to colonize to the brain. To address this, I composed an exceptionally unique cohort of 14 mBC patients with metastasis to the brain - 9 presented an LC - after several years of longitudinal CTC sampling. The clonal composition of each patients BM or LC will be deciphered by low pass whole exome sequencing (LPS). Next, I aim to identify BMICs by analysis of the clonal evolution by LPS. The BMICs will then be analyzed in further detail: By RNA Sequencing I will unravel the development of brain metastasis incompetent CTCs to BMICs to CSF-CTCs that adapted to the brain environment and grew out to an LC. Based on the findings I aim to reveal a signature of BMICs. The profound understanding of BMICs will lead to identifying CTCs having the capacity to colonize the brain and particularly the meninges and will uncover potential vulnerabilities that may be used to obviate the development of BMs in patients at risk in future.

• DFG Programme: Research Grants