Gene expression workflow to analyze residual leukemic cells in Chronic Lymphocytic Leukemia

Background: In chronic lymphocytic leukemia, a better understanding of leukemic cell characteristics after treatment would help to design specific therapeutic approaches aimed at preventing clinical relapse. Gene arrays have become a powerful approach to perform gene expression profiling; nevertheless, to work with residual cells entails an intensive labor. The aim of this study was to set forth an effective gene expression approach to analyze residual leukemic cells.

Methods: Leukocytes from CLL patient's samples were sorted by flow cytometry using a 6-color panel. The quality and quantity of RNA isolated from different inputs of cells were compared by two silica column protocols: RNeasy Micro and RNeasy Mini. RNA amplifications were carried out according to two manufacturer's protocols: Ovation Pico SL and Ovation Pico WTA. A total of 3.5 μg of cDNA was labeled and hybridized to Human Gene 2.0 ST arrays.

Results: RNA extracted from low number of input cells by RNeasy Micro showed similar RNA integrity number to that obtained from RNeasy Mini; however, the RNA quantity was higher using the RNeasy Micro Kit. In addition, those RNA samples obtained with RNeasy Micro and amplified with Ovation Pico WTA showed good quality to proceed for a gene array study, independently of the number of input cells (range: 1 × 10⁴ -5 × 10⁵ cells).

Conclusions: We observed that this workflow is a feasible approach to obtain genomic material extracted from leukemic cells as little as 1 × 10⁴ cells and it can be useful to carry out gene expression profile experiments to characterize residual leukemic cells in chronic lymphocytic leukemia.