Cancer begins in the genes: When certain genes become over or under active, the ensuing deregulation of cell growth, reproduction and death leads to cancer. But researchers attempting to identify specific genetic markers that signify a predisposition to cancer or hoping to find a gene-based cure have been largely disappointed.
One reason for this, says Dr. Amos Tanay of the Weizmann Institute’s Computer Science and Applied Mathematics Department, is that scientists may have been conducting too narrow a search. In a recent study published in the online journal PLoS Genetics, Tanay and a team of scientists – including mathematicians and geneticists from three different research groups – turned their sights on a large “gene desert,” using powerful new methods to comb a vast stretch of genomic information for variations that may increase cancer risk, as well as providing possible new targets for treatment.
The long expanses of chromosomal DNA known as gene deserts are basically devoid of the genes that code for protein production, but they’re hardly barren. Genes make up only a fraction of the DNA in our cells; scientists have come to realize in recent years that much of the so-called “non-coding” DNA influences gene activity at various stages, forming a complex system of checks and balances that regulates the process.
One such gene desert, a long segment of chromosome 8, had been implicated in cancer. The region, called 8q24, is half a million bases (“letters” of the gene code) long, and at first there was little way to make sense of the finding. “But the newest revolution in DNA sequencing technology enabled us to examine the entire region in a single experiment and to zoom in on the really important cancer-related genetic variations,” says Tanay.
Together with his research students Gilad Landan and Rami Jaschek, as well as Gerhard Coetzee and Li Jia of the University of Southern California, Matthew Freedman of Harvard University and others, Tanay used the new rapid sequencing and microarray methods together with the advanced analysis techniques they developed, to map an area of the chromosome covering millions of bases. Their search was for activity in single-nucleotide polymorphisms, or SNPs (pronounced “snips”) – places where the DNA codes tend to vary among people by one or two letters.
After they had succeeded in assembling a color-coded map of the region, the scientific team was able to identify “hot spots” – regions of unusual activity. Next they zoomed in on these hot spots, isolating suspect sequences and inserting them into cells in the lab to see how these would affect cell function.
Several of the DNA sequences the researchers identified were indeed seen to be “enhancers” – bits of code for ratcheting up gene activity. Enhancers created by modifying normal DNA sequences to make them similar to those in cancer patients were much more active than the normal variants. This allowed the researchers to narrow down the list of genetic variations suspected of promoting cancer from many thousands to just a few.
But how can a change in one nucleotide amid half a million letters cause cancer? And which gene (or genes) was being enhanced by the newly discovered variants? The answers might be found just past the outskirts of the 8q24 gene desert, where a gene called Myc is located. Heightened Myc activity is associated with many types of cancer, so a connection is likely.
Myc may be the SNP’s nearest gene neighbor, but they’re still “kilometers” apart as far as DNA sequences go. Nonetheless, Tanay and Landan believe that they communicate directly, with the whole DNA strand folding over to bring the two into physical contact. It’s a phenomenon recently witnessed in another 8q24 DNA sequence, and they think such folding might be fairly common in the cancer genome, enabling distant bits of code – even those residing way out in the middle of gene deserts – to directly regulate the genes. “We’re used to thinking of the genetic code as an orderly sequence, but it appears to be more like spaghetti – or like the Internet, with hyperlinks all over the place,” says Tanay. “We’re starting to untangle these processes, and our findings seem to point to new directions for more effective prevention, diagnosis and treatment.”
Dr. Amos Tanay’s research is supported by Pascal and Ilana Mantoux, Israel.
The Math of Life
Born on Moshav Moledet in Israel, Dr. Amos Tanay earned his B.Sc. and M.Sc. in mathematics from Tel Aviv University. While in graduate school, he headed a research team that developed algorithms for an optimization company, Schema Group, then cofounded an optical networks technology start-up, Optivera Technologies, and headed its R&D effort for two years. However, Tanay soon decided his true interest was biological research, and he returned to Tel Aviv University, obtaining his Ph.D. in computational biology in 2005. After conducting postgraduate research in Rockefeller University’s Center for Studies in Physics and Biology, he joined the Weizmann Institute as a senior scientist in 2007. The thrill of science, for Tanay, is that “there’s always something new. You can ask big questions and find answers, but those answers will always lead to a new set of questions.”
Tanay is married and the father of three children. He is a keen jazz musician in his scarce spare time.
 Michael Kertesz and Dr. Eran Segal. Focus on targets.jpg "(l-r) Michael Kertesz and Dr. Eran Segal. Focus on targets")
Skeletons (and other Organs) in the Cell Family Tree
The method, developed over several years in the lab of Prof. Ehud Shapiro of the Institute’s Biological Chemistry, and Computer Science and Applied Mathematics Departments, uses mutations in specific genetic markers to determine which cells are most closely related and how far back they share a common parent cell, to create a sort of family tree for cells. Shapiro and members of his lab, including Drs. Shalev Itzkovitz and Rivka Adar, together with Prof. Nava Dekel and research student Yitzhak Reizel of the Biological Regulation Department, used their method to see if ova could be descended from bone-marrow stem cells. Their findings indicated that any relationship between the two types was too distant for one to be an ancestor of the other.
These scientists also found, surprisingly, that the ova of older mice had undergone more cell divisions than those of younger mice. This could be the result of replenishment during adulthood; but an alternate theory holds that all eggs are created before birth, and those that undergo fewer divisions are simply selected earlier on for ovulation. Further experimentation, says Shapiro, will resolve the issue.
A number of papers published by Shapiro, his team and collaborators in recent months have demonstrated the power and versatility of this method. One study, for instance, lent support to the notion that the adult stem cells residing in tiny crypts in the lining of the colon do not harbor, as thought, “immortal DNA strands.” Immortal strands may be retained by dividing stem cells if they always relegate the newly synthesized DNA to the differentiating daughter cell and keep the original strand in the one that remains a stem cell.
A second study addressed an open question about developing muscle cells. Here they found that two kinds of progenitor cell – myogenic cells, which eventually give rise to muscle fiber, and non-myogenic cells – found within the same muscle are more closely related than similar cells in different muscles.
One immediate advantage of the cell lineage analysis method developed by Shapiro’s team is that it is non-invasive and retrospective, and as such can be applied to the study of human cell lineages. Most other studies of development rely on genetically engineered lab animals in which the stem cells are tagged with fluorescent markers. In addition to providing a powerful new research method that does not rely on such markers, Shapiro believes that it could one day be adapted as a diagnostic tool that might, for instance, reveal the history of an individual’s cancer and help doctors determine the best course of treatment.
Dr. Eran Segal's research is supported by the Cecil and Hilda Lewis Charitable Trust; the Carolito Stiftung; the Kahn Family Research Center for Systems Biology of the Human Cell; and the European Research Council.
Prof. Ehud Shapiro's research is supported by the Paul Sparr Foundation; Miel de Botton, UK; the Carolito Stiftung; and the European Research Council. Prof. Shapiro is the incumbent of the Harry Weinrebe Professorial Chair of Computer Science and Biology.