What drives cancer?

New method to find important genome mutations in cancer

What drives cancer?

tumours_300.jpg
Development of benign and malignant tumours in the double transgenic mice at early ages. (A) Medulloblastoma in the inferior surface of the telencephalon of mouse PLND8.y. This tumor expressed MYC, a hallmark of medulloblastoma, as seen in (B). (C) A rhabdomyosarcoma in mouse PLND25.1 positively stained with a KRAS G12D-specific antibody as shown in (D). (E) Lymphoid infiltration or small cell carcinoma in the spleen of mouse PLND15.x1. (F) A non-small cell lung tumor with morphological features of bronchoalveolar carcinoma in mouse PLND21. (Magnification: E x 100; A, B, D, and F x 200; C x 400.)

A new method has been developed to screen thousands of gene mutations for their ability to cause cancer. The method will mean that researchers can more rapidly find the most important mutations in tumour samples.

Cancer is a disease in which the genome is ravaged by mutations. It is known that several mutations are most often required for development of cancer, but the high levels of DNA damage in many tumours can make it difficult to determine which mutations are involved in causing the cancer (driver mutations) and which are unimportant side-effects of the disease (passenger mutations).

The new method, published in Proceedings of the National Academy of Sciences this week, 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. 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."

Dr Pentao Liu, Investigator at the Wellcome Trust Sanger Institute

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.

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, 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."

Professor Allan Bradley, Director of the Wellcome Trust Sanger Institute

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.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."

Dr Pentao Liu, Investigator at the Wellcome Trust Sanger Institute

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.

Notes to Editors
Publications
  • A DNA transposon-based approach to validate oncogenic mutations in the mouse.

    Su Q, Prosser HM, Campos LS, Ortiz M, Nakamura T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2008;105;50;19904-9

Funding

This work was supported by The Wellcome Trust.

Collaborating Institutions
  • Wellcome Trust Sanger Institute, Hinxton, Cambridge, England
  • The Cancer Institute, Japanese Foundation for Cancer Research, 3-10-6 Ariake, Koto-ku, Tokyo, Japan
  • Department of Anatomy and Cell Biology, University of Iowa, 51 Newton Road, Iowa City, IA, USA
  • Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Republic of Singapore
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