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Are all the cancer cells the same?


February 21, 2019 – 09:44

Knowing the genetic variation in cancer cells can help us to develop targeted treatments.

Take two cancer and compare their genomes. Surprisingly, they can be quite different.

This genetic variation is one of the main characteristics of cancer, and one reason why cancer treatment is so hard.

If a tumor contains cells with a number of different genomes, one drug might not kill them all. However, knowing the genetic variation can help us to develop targeted treatments.

As part of our research, we have caught one cell of cancer on a plastic device (see figure), removed its DNA, and produced a rough graze of this DNA sequence.

Our results are published in the magazine Proceeding of National Academy of Sciences of the United States of America & # 39; (PNAS).

Optical mapping of DNA from one cell

We used a technique of the optical mapping name that provides large-scale information about the genome.

It works as a map of the world with forests, lakes and mountains, but without the more details such as roads, houses and small cities.

By comparing the optical maps of one cell with a reference map for the common human cell, we can identify differences between them. This information can help to reveal genomic heterogeneity within a tumor and can even indicate how cells have evolved into motors.

Optical DNA mapping of one cell consists of four steps:
• First of all, we hold cells and remove long pieces of DNA.
• Then we color DNA pieces with fluorescent color flow.
• After that we heat DNA molecules. The color is better in some places than others, depending on the DNA sequence. This leaves a pattern similar to a bar code on the molecules.
• Finally, we extend the image of the molecules under a microscope to read the barcodes.
We develop a low cost plastic device that integrates the four stages. The steps are shown in the figure below.

Barcode & # 39; works as fingerprint: It sets out which part of the genomics is a reference that is associated with a DNA molecule. And it can even reveal differences between the imaginary DNA molecule and the genome reference.

Optical mapping sequence

So why use optical mapping and just the usual DNA sequence that you might already be familiar with?

The following DNA sequential methods have the advantage of having a single pair solution, which means that all basic pairs can be identified in a DNA molecule. Given enough material, one can follow the whole genome of a human cell – about six billion centers – in a few days.

But there is a challenge to follow a single copy of a human genome. And that's all we have when we start with a single cell.

Human cells are loaded into one-use plastic device. One cell is caught, and its DNA is removed and stained with fluorescent color. The DNA is then heated to create a barcode, ie a fluorescent pattern that depends on its specific DNA sequence. Individual DNA pieces have been extended, and their barcodes have been imagined and analyzed. A comparison with a genome direction shows genetic changes in the specific cell that the DNA came from.

One of the challenges is that the following normal DNA methods require several copies of the genome. Since there is only one copy of the genome in each cell, the first step is to copy the multiple genome times. This is called expanding DNA and normal chemistry. But copying errors sometimes occur, which are unclear the results.

Another challenge is that all copies of the DNA molecule have to randomly crash into smaller pieces, only a few hundred basic pairs. These pieces will then be followed. Then, the results, readings & # 39; as they are called, are brought together to a full genome by matching partially overlapping readings.

It is also very difficult to find structural variations, such as repetitive patterns or embedded / missing genomic elements than the pair's reading distances. But this type of structural information can only be useful for choosing cancer therapies.

There is, at least in theory, a more prominent and efficient way of reading the DNA sequence. The genome has codes on 48 molecules of DNA, in two fiber thickness nanometer, up to eight centimeters long. So, why not read the DNA sequence from one end to the other?

Optical mapping almost does this: It provides fingerprints & # 39; rough of DNA's basic DNA molecule continuation of DNA molecules up to a million pairs. That is, much longer than the short extracts of DNA sequence. And optical mapping also avoids the expansion actions needed for DNA sequence.

The long sections make it possible to find structural variations that come from a few kilo-base pairs up to several pairs of 100 kilo-base. Smaller variations with DNA sequence can be found.

Therefore, both methods (sequencing and mapping) are complementary. And the same DNA molecule, in principle, can be mapped optically and then its sequence.

Towards more efficient and personal cancer treatment

The ability to follow the genome at one cell level could lead to more efficient and individual cancer treatments. But as we explain above, following the DNA of one cell still requires the use of current sequence techniques.

We have shown for the first time that optical mapping can detect large-scale genetic variations in a DNA molecule taken from one cell. And we do it without the expansion steps required by DNA sequence methods.

The process of preparing a sample was done exclusively on a single-use laboratory-chip device, starting from one cell and ending with useful genome data.

This is an important technological aspect of work, as the device reduces the use of expensive chemicals and reduces the risk of contamination.

To be clear, our work is still in the research period. Our device is not yet ready to be used in hospitals, and the challenge now is to increase output, so that we can analyze more DNA molecules at a time. The aim is to map all DNA from one cell.

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