Low Cost Method Examines Single Leukemic Cells

Cells are packed with genetic information that can be used to improve treatment of diseases such as cancer, but the ribonucleic acid (RNA) sequencing methods typically used today have one limitation in that they do not identify in which cells the genetic activity is taking place.

Scientists at the KTH Royal Institute of Technology (Stockholm, Sweden) and their colleagues developed a new method they used to examine individual tumor cells in patients with chronic lymphocytic leukemia (CLL), an important advance considering the team found the leukemia tumors to be comprised of cells with entirely different gene expressions. They used cryopreserved peripheral blood mononuclear samples derived from three CLL patients. All cases were diagnosed and classified according to recently revised iwCLL criteria44 with a typical CLL immunophenotype.

Individual cells were sorted on a specially made glass surface and using analysis of RNA molecules with next-generation sequencing, from which one can tell which genes are active. The spatial information on the glass surface tells which cell a specific RNA molecule is to be found in. The FACS sorter utilized for analyses and single-cell sorting was a BD Influx. Images of sorted and stained cells on barcoded microarrays were recorded using a Metafer Vslide scanning system installed on an Axio Imager Z2 LSM700 microscope.

The method enabled massive microarray-based barcoding of expression patterns in single cells, termed MASC-seq. This technology enabled both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell transcriptomes per day at a low cost of USD 0.13/cell, which is two orders of magnitude less than commercially available systems. The novel approach provides data in a rapid and simple way. Therefore, MASC-seq has the potential to accelerate the study of subtle clonal dynamics and help provide critical insights into disease development and other biological processes.

Joakim Lundeberg, PhD, a professor of Gene Technology and senior author of the study, said, “We found that CLL cells do not consist of a single cell type, but of a number of sub-clones that exhibit entirely different gene expression. With this new, highly cost-effective technology, we can now get a whole new view of this complexity within the blood cancer sample. Molecular resolution of single cells is likely to become a more widely-used therapy option.” The study was published on October 14, 2016, in the journal Nature Communications.

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