Molecular Profiling of Tumor Cells in Cerebrospinal Fluid and Matched Primary Tumors from Metastatic Breast Cancer Patients with Leptomeningeal Carcinomatosis

Abstract

Although leptomeningeal carcinomatosis is a well-established clinical syndrome, virtually nothing is known about the tumor cells responsible for this particularly aggressive metastatic process. To isolate cerebrospinal fluid-derived tumor cells (CSFTC) from 15 patients with metastatic breast cancer diagnosed with leptomeningeal carcinomatosis, CSF samples were subjected to a two-step method involving immunomagnetic enrichment and fluorescence-activated cell sorting (IE/FACS), a technique previously used for isolating circulating tumor cells (CTC) from blood. CSFTCs were subjected to genome-wide copy number analysis by array comparative genomic hybridization. Genomic profiling was successfully performed for 13 of 15 patients (87%). Copy number analysis in CSFTCs revealed genomic alterations commonly observed in primary breast cancer and CTCs, indicating their malignant origin. Interestingly, 12 (92%) harbored high-level gains on the 8q24 locus, which includes the MYC oncogene. Comparison of CSFTCs against corresponding archival primary tumors in six patients revealed clonal relationships with some divergence. Good concordance among serial samples attested to the reproducibility of the assay. Our approach for isolation and molecular analysis of CSFTCs yielded new insights into the molecular nature of these cells. Further genomic and functional analyses may help elucidate mechanisms by which tumor cells metastasize to the central nervous system. Cancer Res; 73(23); 7134-43. Ó2013 AACR.

Evaluation and consequences of heterogeneity in the circulating tumor cell compartment

“…Sampling at multiple time-points to evaluate genetic evolution based on CNA profiles was performed in three studies [36, 80, 116]. Dago and colleagues thoroughly analyzed CNA of multiple single CTCs of one patient with prostate cancer by WGS at various time points.…”

Molecular characterization of cerebrospinal fluid tumor cells associated with leptomeningeal carcinomatosis

“…In this paper, we highlight our recent study on the isolation and detailed genomic profiling of CSFTCs [10] . We also include a brief review of the literature pertaining to genomic analysis of CSFTCs, which has primarily involved fluorescence in situ hybridization (FISH) assays.…”

“…We subjected the IE/FACS-isolated cells to different molecular assays, including gene expression and copy number analysis [10] .…”

“…The scatter plots of the log2 ratio values for each sample pairs are shown on the upper right side of the box. Adapted from [10] . EPCAM and down-regulation of PTPRC (encodes CD45) expression (Figure 1).…”

Maximizing derivable information from cytologic specimens for pathologic and molecular diagnostics

“…10 In fact, molecular analysis from a variety of cytology formats (fluids, washes, aspirations, and cell blocks) have been documented to be reliable sources for molecular analysis. [11][12][13][14][15] Looking to further increase the value of cytology specimens, we have developed a microfluidic platform from which the cells in a cytologic specimen can be viewed for diagnostic purposes and later recovered for molecular analysis, all in the context of a formalin-free environment. Herein we demonstrate the utility of applying microfluidics to the cytologic evaluation of cells and the recovery of highemolecular weight DNA from those same cells.…”