January 28, 2009
ROCKVILLE, MD and NEW YORK, NY—January 27, 2009— Researchers from the J. Craig Venter Institute (JCVI) and the Ludwig Institute for Cancer Research (LICR) have uncovered new genomic alterations that lead to gene fusions in a breast cancer cell line by using 454 Life Sciences sequencing technology. The work, led by Qi Zhao of JCVI and Otavia L. Caballero, of LICR, is being published the week of January 26 in the early online edition of the Journal of the Proceedings of the National Academy of Sciences (PNAS).
Previous studies have shown that gene fusions are key gene alteration events in the development and progression of many kinds of cancers. The discovery of the best known gene fusion, BCR-ABL, led to the development of Gleevec® for the treatment of chronic myelogenous leukemia and other cancers.
In this proof of concept study the researchers focused on the transcriptome, a subset of genes in the genome that code for proteins. It has long been known that cancers arise from various types of genomic changes in certain cells. Continued advances and cost efficiencies of next generation DNA sequencing technologies are enabling this more precise and detailed examination of changes in the human genome that could be directly involved in cancer.
The JCVI/LICR researchers began with a well-characterized breast cancer cell line, HCC1954 and performed high-throughput transcriptome sequencing. Previous studies on this cell line have uncovered certain types of genetic mutations and chromosomal abnormalities associated with breast cancer. By conducting the in-depth transcript sequencing in this study and comparing these data to the previous studies a clearer picture is emerging of all the expressed genes some of which present in altered forms in the cancer cell line.
The team began by generating more than half a million 454 reads of cDNA sequences. After extensive data mining, the team uncovered 496 sequences that indicate chromosomal translocations. Of these 496, the team characterized 208 as inter-chromosomal abnormalities and 210 were intra-chromosomal abnormalities. From here the team performed more detailed validation experiments with a control cell line (HCC1954 BL).
Through further analysis the team confirmed six inter-chromosomal changes and one intra-chromosomal change that have the potential to affect the protein producing ability of at least nine genes. The researchers also discovered that chromosome 8 in the cancer cell line seemed to be very involved in some of the genomic rearrangements. This data confirms earlier studies showing that genomic instability in this area is implicated in breast and prostate cancers.
Most genes involved in the discovered chromosomal rearrangement events in this study have been implicated in cancers, such as the MRE11A protein that is associated with mutations in many types of tumors including in breast cancer. The team also identified the SAMD12 gene as being involved in both inter- and intra-chromosomal rearrangements. While not previously thought to play a role in the development of cancer, this study showed that this gene might be implicated in cancer.
The team concluded that transcriptome sequencing with next generation sequencing technologies such as the 454 Life Sciences platform is very adept at finding genomic rearrangements and mutations associated with cancers. With deeper sequencing coverage this approach could be a powerful and efficient way to discover all events associated with expressed genes including gene fusions, somatic mutations and alternative trans-splicing that lead to the development of cancer.
Robert Strausberg, Ph.D., Deputy Director of the JCVI and leader of the Human Genomic Medicine team noted, “This approach reveals alterations in the cancer genome within the active genes of cancer cells. Through the comparison with related normal cells we can glean those that are specific to cancer cells, thereby revealing their unique biology, as well as suggesting new approaches to detection, diagnosis and treatment of cancers.”
According to Andrew Simpson, Ph.D., Scientific Director of the LICR, “These studies are an important component of the Hilton-Ludwig Cancer Metastasis Initiative, focused on preventing and treating cancer metastasis. This program brings together interdisciplinary teams of expert scientists, working together to improve the lives of cancer patients. The current study represents one aspect of our teams’ creative approach in revealing previously unknown features of cancer that together will provide a platform for cancer prevention and intervention.”