If a tumour is made up of cells with many different genomes, a single drug might not kill them all. A technique developed by a team of DTU researchers makes it possible to identify cancer cells on the genetic level—potentially paving the way for tailored and more effective treatments.
“The technique known as optical mapping provides large-scale information about the genome,” explains Rodolphe Marie, Associate Professor at DTU Health Tech.
“It works like a map of the world with forests, lakes, and mountains, but without the finer details like roads, houses, and towns. By comparing optical maps from a single cell with a reference map for the average human cell, we can pinpoint differences between them. This information can reveal genomic heterogeneity within a tumour and may even indicate how cells have developed into tumours.”
Optical mapping of DNA from a single cell consists of four steps: First, a cell is captured, and long fragments of its DNA are extracted. Then the DNA fragments are dyed with a fluorescent dye.
The DNA molecules are then heated. The dye sticks better in some places than others, depending on the DNA sequence. This leaves a barcode-like pattern on the molecules.
Finally, the molecules are stretched and images of them are taken under a microscope in order to read the ‘barcodes’ that work like fingerprints.
One of the challenges with standard DNA sequencing methods is that they require many copies of the genome. Since there is only one version of the genome in each cell, the first step is to copy the genome several times. However, copy errors often occur and may obscure the results.
Another challenge is that each copy of the DNA molecule is randomly cut up into smaller pieces just a few hundred base pairs long. However, the genome is coded on 48 DNA molecules in two-nanometres-thick fibres up to eight centimetres long. Reading the DNA sequence from one end to the other will therefore provide the best results.
Optical mapping can provide a sketch-style ‘fingerprint’ of the underlying sequence of DNA molecules which are up to one million base pairs long—i.e. much longer than the short read sequences of traditional DNA sequencing. The long fragments make it possible to detect structural variations ranging from a few thousand and up to several hundred thousand base pairs long.
Individualized cancer treatment
The entire process was performed on a disposable ‘lab-on-a-chip’—an important technological aspect of the researchers’ work, as the plastic chip reduces the use of expensive chemicals and minimizes the risk of contamination of the sample.
The challenge now is to be able to analyse several DNA molecules at a time with the aim of mapping all DNA from a single cell, as the ability to sequence the genome at cell level can lead to a more effective and individualized cancer treatment in the long term. At present, the work is still in the research phase and the solution is not yet ready for use in hospitals.
Four-step optical mapping of DNA
The ‘barcode’ generated by the method acts as a fingerprint: The fingerprint identifies which part of the reference genome a DNA molecule is closely related to. And it can even detect differences between the depicted DNA molecule and the reference genome.
1. First, a cell is captured, and long fragments of its DNA are extracted. (At the bottom of the figure)
2. Then the DNA fragments are dyed with a fluorescent dye (to the right of the figure).
3. The DNA molecules are then heated. The dye sticks better in some places than others, depending on the DNA sequence. This leaves a barcode-like pattern on the molecules (at the top of figure).
4. Finally, the molecules are stretched and images of them are taken under a microscope in order to read the ‘barcodes’ (to the left of the figure).