DisCo: Boosting the efficiency of single-cell RNA sequencing

Date:
February 14, 2022
Source:
Ecole Polytechnique Fe'de'rale de Lausanne
Summary:
Bioengineershave found a way to radically increase the efficiency
of single-cell RNA-sequencing, a powerful tool that can 'read'
the genetic profile of an individual cell.



FULL STORY ========================================================================== Single-cell RNA sequencing, or "scRNA-seq" for short, is a technique that allows scientists to study the expression of genes in an individual cell
within a mixed population -- which is virtually how all cells exist in
the body's tissues. Part of a larger family of "single-cell sequencing" techniques, scRNA- seq involves capturing the RNA of a single cell and,
after multiple molecular conversion reactions, sequencing it. Since RNA is
the intermediate step from gene (DNA) to protein, it provides an overview
about which genes in that particular cell are active and which are not.


========================================================================== Because scRNA-seq captures the activity of all genes in the cell's genome
- - thousands of genes at once -- it has become the gold standard for
defining cell states and phenotypes. This kind of data can reveal rare
cell types within a cell population, even types never seen before.

Cost and efficiency But scRNA-seq isn't just a tool for basic cell
biology; it has been widely adopted in medical and pharmacological
research as it is capable of identifying which cells are actively dividing
in a tissue, or which are reacting to a particular drug or treatment.

"These single-cell approaches have transformed our ability to resolve
cellular properties across systems," says Professor Bart Deplancke at
EPFL's School of Life Sciences. "The problem is that they are currently tailored toward large cell inputs." This isn't a trivial problem,
as scRNA-seq methods require over a thousand cells for a useful
measurement. Dr Johannes Bues, a researcher in Deplancke's group,
adds: "This renders them inefficient and costly when processing small, individual samples such as small tissues or patient biopsies, which tends
to be resolved by loading bulk samples, yielding confounded mosaic cell population read-outs." The DisCo solution


========================================================================== Bues, with Marjan Bio?anin and Joern Pezoldt, also in Deplancke's group,
have now developed a new method that allows scRNA-seq to efficiently
process samples with fewer cells. Published in Nature Methods, the
method is dubbed "DisCo" for "deterministic, mRNA-capture bead and cell co-encapsulation dropleting system." Unlike usual single-cell methods
that rely on passive cell capture, DisCo uses machine-vision to actively
detect cells and capture them in droplets of oil and beads. This approach allows for continuous operation, and also renders scaling and serial
processing of cell samples highly cost efficient.

As shown in the study, DisCo features precise particle and cell
positioning, and controls droplet sorting through combined machine-vision
and multilayer microfluidics. All this allows for continuous processing
of low-input single cell suspensions at high capture efficiency (over 70%)
at speeds that can reach 350 cells per hour.

To further showcase DisCo's unique capabilities, the researchers tested
it on the small chemosensory organs of the Drosophila fruit fly, as
well as on individual intestinal crypts and organoids. The latter are
tiny tissues grown in culture dishes closely resembling actual organs --
a field that EPFL has been spearheading for years.

The researchers used DisCo to analyze individual intestinal organoids
at different developmental stages. The approach painted a fascinating
picture of heterogeneity in the organoids, detecting various distinct
organoid subtypes of which some had never been identified before.

"Our work demonstrates the unique ability of DisCo to provide
high-resolution snapshots of cellular heterogeneity in small, individual tissues," says Deplancke.

========================================================================== Story Source: Materials provided by
Ecole_Polytechnique_Fe'de'rale_de_Lausanne. Original written by Nik Papageorgiou. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Johannes Bues, Marjan Biočanin, Joern Pezoldt, Riccardo
Dainese,
Antonius Chrisnandy, Saba Rezakhani, Wouter Saelens, Vincent
Gardeux, Revant Gupta, Rita Sarkis, Julie Russeil, Yvan
Saeys, Esther Amstad, Manfred Claassen, Matthias P. Lutolf,
Bart Deplancke. Deterministic scRNA-seq captures variation in
intestinal crypt and organoid composition. Nature Methods, 2022;
DOI: 10.1038/s41592-021-01391-1 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/02/220214111824.htm

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