2 min readNew Method to find Important Genome Mutations in Cancer
A new method, published in Proceedings of the National Academy of Sciences, allows researchers to screen thousands of genes in hundreds of tissue at one time. The technique should allow cancer researchers to establish rapidly which mutations are drivers and which are passengers, leading more swiftly to identification of important targets for development of diagnostics and therapies.
“Genome-wide cancer studies are uncovering hundreds of mutations from tens of tissues, but we face a challenge in determining which are driving the development of cancer,” explains Dr. Pentao Liu, Investigator at the Wellcome Trust Sanger Institute. “Computer analyses can guide efforts, but give only a partial picture.”
“Our robust in vivo system should rapidly take us from many possible mutations to the small number of critical mutations, speeding work to understand the biology of cancer and to define important diagnostic or therapeutic targets.”
The activity of protein-coding genes is exerted through nearby regulatory sequences that do not themselves produce/code for protein but effectively control the activity of the adjacent gene. These promoter sequences act to switch a gene on or off, up or down, in the appropriate cells at the appropriate time.
According to the report, the novel system uses DNA transposons – unusual DNA sequences that can hop around a genome – to carry possible cancer gene segments into new locations in the mouse genome. Initially, the cancer genes are inserted into one location in the genome. The researchers then use a genetic trick to make the genes jump out of the genome and into multiple new locations. A transposon called Sleeping Beauty induces transposition of the cancer genes: if a cancer gene jumps close to a promoter, then it will be controlled by those sequences.
“The mice harbouring these transposons are free of disease because the cancer genes are silent before transposition,” explains Professor Allan Bradley, Director of the Wellcome Trust Sanger Institute, “but after transposition, the cDNAs are excised from the genome and reintegrate into new loci across the genome. The oncogene cDNAs have the opportunity to search the entire genome for the optimal regulatory elements, for the appropriate temporal points, and for the right cellular compartments to exert their oncogenic potential.”
“The transposons do our promoter selection for us.”
Sleeping Beauty DNA transposition creates combinations of activation of these genes, effectively ‘screening’ billions of cells in one mouse.
The team showed that many mice developed multiple tumours, including major human types such as carcinomas, sarcomas, and hematopoietic malignancies. The results show that the genes studied have the potential to cause cancer in different tissues or organs. They also show that the levels of activity of the cancer gene can be low: it is not necessary in many cases to drive high levels of activity.
“Our DNA transposon-based platform allows us to explore the oncogenic potential of thousands of genetic mutations in the mouse,” continues Dr. Liu. “Conventional transgenic research requires prior selection of which promoter sequence to use: ours is a largely unbiased approach that can scan many hundreds or thousands of promoters.”
The team is optimistic that their approach will add biological understanding to the flow of genomic information from projects such as the Sanger Institute’s Cancer Genome Project and the International Cancer Genome Consortium.
The study is the result of a collaboration between researchers at the Wellcome Trust Sanger Institute, the Japanese Foundation for Cancer Research, the Department of Anatomy and Cell Biology, University of Iowa, and the Institute of Molecular and Cell Biology, Singapore.