The discovery that 20,000–24,000 protein-encoding genes exist in the haploid human genome (a key finding of the Human Genome Project) fueled initiatives to map gene interactions and characterize the genetic circuitry in cells.
Radiation hybrid mapping, a strategy in which high-dose X-rays randomly introduce chromosomal breaks that shatter the DNA into tiny fragments, was initially used to generate high-resolution physical maps of the human genome.
The strength of this strategy is its ability to identify genetic markers that are close to each other. The closer two genetic markers are to each other on the chromosome, the more likely it is that they will be located on the same chromosomal fragment. Moreover, the frequency of breakage between markers can be used to reveal their order on the chromosome.
“We realized that we could ask a different question from the one that radiation panels had previously explored,” says Desmond J. Smith, M.D., Ph.D., professor of molecular and medical pharmacology at University of California, Los Angeles. Dr. Smith and colleagues proposed that radiation hybrid mapping data from mammalian cells could be used to delineate genetic survival networks for proliferation.
Central to this endeavor was the concept that if an extra copy of a gene may lead to cell death, this toxic effect could be blocked by an additional copy of another, distant gene. “And if that was true, we could expect to see the two genes co-inherited more often than expected by chance in the panel of radiation hybrid cells,” says Dr. Smith.
By looking at all potential pair-wise interactions between all the genes from the genome, investigators in Dr. Smith’s lab delineated an unbiased network of interactions involved in cell proliferation and survival, and subsequently applied this knowledge to address a question relevant to genetic circuits that underlie malignancies. Some cancers have a survival advantage as a result of copy number changes, such as the amplification of genes that increase cell proliferation and the deletion of genes that block proliferation.
“Most investigators examined these copy number variations in isolation,” says Dr. Smith. The question that investigators in Dr. Smith’s lab addressed extended beyond the simple characterization of isolated copy number variations (CNVs) in cancer. “We wanted to know whether the amplification of a gene affected in cancer is accompanied by the amplification of a distant gene somewhere else in the genome,” says Dr. Smith.
This strategy helped characterize the survival network of cancer cells, which is a subset of the survival network that is unveiled by the radiation hybrid data. In addition, this strategy bypassed one of the most significant challenges in characterizing copy number changes, the frequent involvement of multiple genes, which historically made it difficult to point toward the specific genes contributing to the resulting phenotypes.
“This is not the case for radiation mapping hybrid panels, where X-rays fragment the DNA and the resolution is very high,” says Dr. Smith. Overlapping the cancer interaction network with the radiation hybrid network provides opportunities to better understand, at single-gene resolution, the involvement of specific genes in disease. “We hope that these networks can ultimately be exploited for cancer treatment,” says Dr. Smith.