Minimal residual disease in breast cancer: detection and genomic characterization of disseminated cancer cells
Killinger K.1, Schneider E.1, Schmidt O.1, Czyz Z.2, Patwary N.1, Haunschild G.1, Rack B.3, Schlimok G.4, Klein C.A.1
1Universität Regensburg, Lehrstuhl für experimentelle Medizin und Therapieverfahren, Regensburg, Deutschland, 2Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Project Group, Personalized Tumor Therapy, Regensburg, Deutschland, 3Universität München, Abteilung für Frauenheilkunde und Geburtshilfe, München, Deutschland, 4Diakonissenkrankenhaus Augsburg, Hämatologie und Onkologie, Augsburg, Deutschland

Breast cancer (BC) contributes to 15% of all cancer related deaths globally with the leading cause of death being metastasis. The presence of disseminated cancer cells (DCCs) in bone marrow (BM) is associated with shortened survival. Our study aimed to investigate the prevalence and clinical significance of genomic changes in DCCs in a cohort of 343 patients, with no prior history of cancer, at the time of primary oncological surgery.
We screened BM for cytokeratin (CK)-positive cells. After single cell isolation we performed whole genome amplification (WGA). WGA products of sufficient quality were subjected to genetic analysis. First, we concentrated on the six most common oncogenic "drivers" (ERBB2, MYC, CCND1, FGFR1, TP53, and PIK3CA). We performed multiplex qPCR for amplification analysis of ERBB2, MYC, CCND1, and FGFR1 and Sanger-sequencing for somatic point mutation analysis of TP53 and PIK3CA. Finally, we analysed the prevalence of genetic changes within the biological subtypes.
38,5% of patients in our cohort had CK-positive cells. We successfully isolated 330 cells. Of these, 224 cells were of sufficient quality for further genomic analysis. Overall, 18.75% of 224 analysed cells showed at least one driver mutation (8.5% MYC, 5% ERBB2, 5% FGFR1, 1.4% CCND1, 12.1% TP53, 5.4% PIK3CA). Among BC subtypes, driver mutations were detected in 34.4% of cells isolated from triple-negative BC, in 18.7% of cells isolated from luminal-like BC and in 18.2% of cells from Her2-enriched BC. Later, we will investigate clinical relevance statistically and analyse copy number variations with aCGH and shallow genome sequencing.