Vast hidden network regulates gene expression in cancer: Study illuminates the 'dark matter' of the genome

"The discovery of this regulatory network fills in a missing piece in the puzzle of cell regulation and allows us to identify genes never before associated with a particular type of tumor or disease," said Andrea Califano, PhD, professor of systems biology, director of the Columbia Initiative in Systems Biology, and senior author of the CUMC research team.

For decades, scientists have thought that the primary role of messenger RNA (mRNA) is to shuttle information from the DNA to the ribosomes, the sites of protein synthesis. However, these new studies suggest that the mRNA of one gene can control, and be controlled by, the mRNA of other genes via a large pool of microRNA molecules, with dozens to hundreds of genes working together in complex self-regulating sub-networks.

The findings have the potential to broaden investigations into how tumors develop and grow, who is at risk for cancer, and how to identify and inactivate key molecules that encourage the growth and spread of cancer.

For example, in the case of the phosphatase and tensin homolog gene (PTEN), a major tumor suppressor, deletions of its mRNA network regulators in patients appear to be as damaging as mutations of the gene itself in several types of cancer, the studies show.

The newly identified regulatory network (called the mPR network by the CUMC investigators) allows mRNAs to communicate through small bits of RNA called microRNAs. Researchers first realized about a decade ago that microRNAs, by binding to complementary genetic sequences on mRNAs, can prevent those mRNAs from making proteins. Turning this concept on end, the new studies reveal that mRNAs actually use microRNAs to influence the expression of other genes.

When two genes share a set of microRNA regulators, changes in expression of one gene affects the other. If, for instance, one of those genes is highly expressed, the increase in its mRNA molecules will "sponge up" more of the available microRNAs. As a result, fewer microRNA molecules will be available to bind and repress the other gene's mRNAs, leading to a corresponding increase in expression. Although such an effect had been previously elucidated, the range and relevance of this kind of interaction had not been characterized.

"It turns out that this type of microRNA-mediated regulation is commonplace in the cell, and thousands of genes are regulating one another through hundreds of thousands of microRNA-mediated interactions," says Pavel Sumazin, PhD, research scientist in systems biology and a first author of the CUMC paper. "This is similar in size and effect to other regulatory networks, such as transcriptional regulatory networks, where target genes are regulated by transcription factors."

In the CUMC study, Dr. Sumazin and his colleagues analyzed glioblastoma mRNA and microRNA expression data from the Cancer Genome Atlas, a public database, uncovering a regulatory layer comprising more than 248,000 microRNA-mediated interactions.

Looking specifically at the tumor suppressor gene PTEN, the researchers found that it is part of a sub-network of more than 500 genes. Of these genes, 13 are frequently deleted in glioblastoma and seem to work together through microRNAs to stop PTEN activity -- achieving the same result as if the tumors had inactivating mutations or deletions of PTEN itself.

The finding explains, at least in part, why all patients with glioblastoma do not share the same genetic profile. In about 80 percent of patients, their tumors have a deletion of PTEN. In most of the remaining 20 percent, PTEN is intact, but the gene is not expressed -- an observation that had confounded researchers. "This suggested that there must be some other mechanism by which PTEN can be completely suppressed," said Dr. Sumazin. "Now we know that there are at least 13 other genes -- none of which had ever been implicated in cancer -- that can 'gang up' on PTEN to suppress its activity, with different combination of deletions in different patients."

"This network helps explain the so-called dark matter of the genome," added Dr. Califano. "For years, scientists have been cataloguing all the genes involved in particular diseases. But if you add up all the genetic and epigenetic alterations that have been identified, even with high-resolution studies, there are still many cases where you cannot explain why a person has the disease. Now we have a new tool for explaining these genetic variations, for gaining a better understanding of the disease and, ultimately, for finding new treatments."

In another study published in Cell, Pier Paolo Pandolfi, MD, PhD, director of the Cancer Genetics Program at Beth Israel Deaconess Medical Center, and his colleagues linked about 150 new genes to PTEN in human prostate and colon cancer cell lines. In a second paper, the Pandolfi group showed that mutations in the PTEN-RNA network speeded up the growth of cancer in a mouse model of melanoma. The final related study in Cell, led by Irene Bozzoni at the Sapienza University of Rome, extends functional evidence of the new RNA network phenomenon to the normal differentiation of human muscle cells and to the large realm of human non-coding RNAs.

Dr. Sumazin's paper is titled, "An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma." The paper's other co-first authors include postdoctoral fellow Xuerui Yang and graduate student Hua-Sheng Chiu. Other co-authors include Wei-Jen Chung, Archana Iyer, David Llobet-Navas, Presha Rajbhandari, Mukesh Bansal, Paolo Guarnieri, and Jose Silva, all at CUMC.

This research was supported by the National Institutes of Health.