Comparison of gene expression and flow cytometry for immune profiling in chronic lymphocytic leukaemia

Abstract

Understanding how cancer and cancer therapies affect the immune system is integral to the rational application of immunotherapies. Flow cytometry is the gold standard method of peripheral blood immune cell profiling. However, the requirement for viable cells can limit its applicability, especially in studies of retrospective clinical cohorts. We aimed to determine if gene expression, analysed using the NanoString platform, could be used to quantify the immune populations present in cryopreserved peripheral blood mononuclear cell (PBMC) samples from patients with chronic lymphocytic leukaemia. Cell abundance scores derived from gene expression analysis were significantly correlated with the population frequency quantified by flow cytometry for all subsets analysed, including T cells, NK cells and Monocytes. This study demonstrates that gene expression analysis can be applied to cryopreserved PBMC and provides a concordant and complementary understanding of the immune profile to flow cytometry.