Jan 25, 2017

Most comprehensive single cell analysis of AML gene expression to date

Kariena Dill

Existing methods for single cell RNA-sequencing face practical challenges when scaling to tens of thousands or more cells in throughput. Plate-based approaches and microfluidics platforms have cumbersome and time-consuming workflows, limited throughput, and require prior knowledge of cell markers. Published academic droplet-based techniques can streamline workflows and allow for high-throughput, however, the hardware is challenging to construct and the protocols are not always robust.

To overcome these shortcomings and unlock the potential of single-cell transcriptomics for biological and clinical research, 10x has developed the Chromium™ Single Cell 3’ Solution, a droplet-based system that enables 3’ mRNA digital counting of transcripts from thousands of cells. With its flexible throughput, this powerfully scalable tool can encapsulate 700-70,000 cells in 10 minutes and has a cell capture efficiency of over 65% for rare cell types in heterogeneous populations. Plus, the Chromium™ Single Cell 3’ Solution features a simple and comprehensive workflow that allows users to quickly and easily prepare sequencing-ready cDNA libraries in less than 7 hours.

Jason Bielas, principal investigator for the Bielas Laboratory at the Fred Hutchinson Cancer Research Center, is focused on finding new practices and technologies "to prevent disease, advance treatment, and increase patient survival," especially in areas limited by available technology. To this end, Bielas partnered with 10x Genomics to validate and tailor this new single-cell RNA-sequencing platform. Researchers collected transcriptome data from approximately 250,000 single cells across 29 samples. Results validated the sensitivity of the system as well as its ability to characterize large and complex cell populations.

Next, the researchers employed the Chromium Single Cell 3’ Solution to analyze precious clinical samples from patients with acute myeloid leukemia who had undergone bone marrow transplantation. The system’s rapid cell encapsulation and high cell capture efficiency enabled researchers to analyze gene expression patterns of nearly 70,000 cells in a single experiment to determine host and donor chimerism at single cell resolution and to compare immune cell subpopulation changes in patients before and after transplant.

In an article on the Fred Hutch news page, Dr. Jerald Radich, a Fred Hutch physician-scientist and co-author on the study, explained how this new technique will enable researchers to learn more about the cellular interactions that drive cancer development and relapse after treatment.

"Cancer is essentially an ecosystem. This is one of the ways you can understand more about what’s really going on [in the cancer ecosystem] ...Once you start understanding what the ecosystem does, and what it takes to keep the cancer at bay, then you can start manipulating that, potentially therapeutically,"

Dr. Radich sees promise in the new technology for understanding mechanisms that drive relapse in Leukemia patients while Dr. Bielas is resurrecting an old project - examining the different types of immune cells that slip into tumors and their association with tumor progression and patient outcomes. There are many other possible applications for the technique, as Dr. Bielas said. "It’s kind of endless."

Read more about the impact and implications of these results:

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