Accurate to the cell
The new tool uses RNA sequencing to map cellular and tissue functions
The Slide-seq method creates high–resolution maps of cellular relationships in tissues without using a microscope, writes the Broad Institute website (New tool uses RNA sequencing to chart rich maps of cellular and tissue function) with reference to Science (Rodriques et al., Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution).
A new technique developed by scientists from the Institute. Broad at the Massachusetts Institute of Technology and Harvard, gives an unprecedented insight into the cellular organization of tissues. This method, known as Slide-seq, uses genetic sequencing to build detailed three-dimensional tissue maps showing not only the variety of cell types, but also where they are located and what functions they perform.
Three-dimensional reconstruction of nine cubic millimeters of the mouse hippocampus, obtained using Slide-seq (colors denote different types of cells). Provided by Chen and Makosko Laboratories.
Since specialized imaging equipment is not required in this case, this technology can be used by scientists in various fields of biology, genetics and medicine who want to look at the cellular structure of tissues or observe where specific genes operate in a tissue, organ or even the whole organism.
Such a platform offers unprecedented insights into the cellular structure of tissues, the role played by genes in various tissues, as well as the effects of injuries or other disturbances on tissue, providing researchers with rich schemas of tissue functions.
In the 19th century, neuroscientist Santiago Ramon y Cajal amazed the scientific world with his detailed drawings of human tissues showing that the brain consists of individual cells. The development of antibodies in the mid-20th century allowed researchers to look at proteins – to see several at a time – in cells and tissues. In recent years, RNA sequencing has given scientists the opportunity to determine which types of cells are present in the tissue and which genes are included throughout the genome, but it does not help in determining the exact location of these cells.
Slide-seq can be considered as the latest achievement in this technological evolution.
The technique begins with a rubber-coated slide or "washer", which is filled with microparticles, or "beads", with unique DNA barcodes. Scientists sequentially generated data that later allows users to determine where the reading of the sequence in the array of "beads" comes from.
"This is similar to the cellular form of GPS," said Robert Stickels, co–author and graduate student at Macosko Laboratory. "When we created this technology, we wanted to simplify its use by our employees. We perform all operations to create images and arrays in advance, and provide arrays to the end user so that they do not need special knowledge in the field of microscopy."
In a few hours of working with arrays, researchers can transfer pieces of freshly frozen tissue to the surface of the ball and dissolve the tissue, leaving mRNA transcripts associated with the barcode of the balls. Then the RNA library with a barcode is sequenced on commercial devices. Software developed by the Broad Institute team and made available to end users assigns locations for each sequence reading, which can be built to create high-resolution maps of cell types or gene expression, with richer information than standard microscopic images.
To demonstrate the capabilities of the tool, the team used Slide-seq to localize cell types in the cerebellum and hippocampus in the mouse brain, highlighting detailed structures, including a layer of cells one cell thick. By applying Slide-seq to slices of the mouse cerebellum, the team identified bands of gene activity changes in the tissue, patterns that indicate spatially defined subpopulations that were not detected using the traditional method of sequencing individual cells.
The team also showed that Slide-seq can be useful for testing the effects of perturbations, when used to monitor the responses of specific cell types in a mouse model of traumatic brain injury. By filtering the data to demonstrate the expression of individual genes, they found that some genes are switched on in neurons based on proximity to injury even long after injury.
The researchers also demonstrated that superimposing a series of pieces of tissue can reveal three-dimensional tissue organization and cellular function, generating an animated three-dimensional reconstruction of the mouse hippocampus, which can be customized to display different cell types or the expression of individual genes.
"Single–cell RNA sequencing speaks really well about which cells are in your sample," said one of the first authors, Samuel Rodriquez, a member of Chen's lab and a graduate student at the Massachusetts Institute of Technology in the laboratory of extended associate member Ed Boyden. "But Slide–seq is a fundamentally new tool that adds a completely different dimension, telling us where the cells are in the tissue...".
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