Only
by viewing a Seurat painting at close range can you appreciate the
hidden complexities of pointillism—small, distinct dots of pure color
applied in patterns to form an image from a distance. Similarly,
biologists and geneticists have long sought to analyze profiles of genes
at the single cell level but technology limitations have only allowed a
view from afar until now.
Research published in the July 22 issue of Nature Biotechnology,
shows for the first time that a novel genomic sequencing method called
Smart-Seq can help scientists conduct in-depth analyses of clinically
relevant single cells. Smart-Seq has many possible applications,
including helping scientists to better understand the complexities of
tumor development. This is vitally important as many clinically
important cells exist only in small numbers and require single cell
analysis. The study was conducted by a team of researchers from the
Ludwig Institute for Cancer Research, the Karolinska Institutet in
Sweden, the University of California, San Diego and Illumina Inc.
“While
our results are preliminary, we showed that it is possible to do
studies of individual, clinically relevant cells,” says biomedical
scientist Rickard Sandberg, researcher at the Ludwig Institute for
Cancer Research and principal investigator at the Department of Cell and
Molecular Biology, Karolinska Institutet. “Cancer researchers around
the world will now be able to analyze these cells more systematically to
enable them to produce better methods of diagnosis and therapy in the
future.”
Previous
research showed that it is common for one gene to give rise to several
forms of the same protein through different cut-and-paste configurations
of its raw copy. The phenomenon, known as splicing, means that cells
from the same tissue are not so homogenous as previously thought.
The
research team has now taken its study a step further and developed a
method for the complete mapping of the gene expression of individual
cells. In showing which genes are active, it is now possible to
accurately describe and study differences in gene expression between
individual cells from the same tissue.
“Scientists
have been waiting for a long time for such a method to come along, but
technical limitations have made it difficult to produce a sufficiently
sensitive and robust method,” says Dr. Sandberg. “The method has several
areas of applications including cancer research where it can be used to
study which cell types form cancer tumors in individual patients.”
In
the study, scientists studied tumor cells in the blood system of a
patient with recurring malignant melanoma. Once they had identified the
tumor cells in a regular blood test, the team used Smart-Seq to analyze
their gene expression. By using this method, researchers could show that
the tumor cells had activated many important membrane proteins that are
understood to be responsible for their ability to evade the body’s
monitoring system and spread in the blood or lymph.
The
study was conducted with the support of several funding bodies,
including the European Research Council, the Swedish Research Council,
the Foundation for Strategic Research, the Åke Wiberg Foundation and the
National Institutes of Health (NIH).
Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells
