Microarray gene expression analysis of cells isolated from malignant pleural effusions (MPE) from patients with non-small cell lung cancer (NSCLC)

Abstract

7369 Background: Many patients with advanced NSCLC are diagnosed via needle biopsy, providing little tissue for molecular profiling of their cancer. MPE may offer an easily accessible source of cancer cells in these patients. Methods: We collected pleural fluid from 14 patients with advanced NSCLC and MPE. Cells were isolated and treated as follows: 1) total RNA extraction (n=6); 2) positive selection of malignant cells using immunomagnetic beads coated with Ber-EP4 antibody followed by total RNA extraction (n=5); 3) both immunobead and non-immunobead methods (n=3). Cytologic examination was performed in all cases. RNA quality and quantity were assessed using the Agilent 2100 bioanalyzer system (Agilent Technologies, Palo Alto, CA). Cases with RNA suitable for gene expression analysis were assayed using oligonucleotide-based microarray (Affimetrix chips U133A and B). Results: All patients in the study had carcinoma cells by cytology, except one. The MPEs in 3 of 14 patients (21%) yielded RNA suitable for microarray analysis, including the patient whose MPE was cytologically negative for cancer. The presence of good quality RNA did not appear to correlate with specimen cellularity, the percentage of tumor cells versus other types of cells seen on cytologic examination, the time interval between collection and extraction, or whether or not immunobead separation was performed. Two cases that were cytologically positive for cancer had a much higher level of Mucin 5b (a specific tracheobronchial mucin) gene expression than the patient with cytologically negative MPE. Conclusion: RNA of sufficient quality for gene microarray expression analysis can be obtained from cells in MPE using a variety of techniques. More studies are required to determine whether the RNA signal obtained is cancer-specific. No significant financial relationships to disclose.