Old Dog Reveals New Tricks

For decades, scientists have believed that messenger RNA (mRNA) serves only to shuttle information from genes to sites in the cell where proteins are made. But it now appears that these messengers are multitaskers, also playing a role in their own regulation. A study in the June 24 issue of Nature reports that this new and surprising function may constitute an additional layer of control that cells use to suppress tumor growth. The discovery is all the more intriguing because it is based on genetic material that has long been labeled “junk.”

Senior author Pier Paolo Pandolfi, the George C. Reisman professor of medicine at HMS and Beth Israel Deaconess Medical Center, and his colleagues have found that a stretch of human DNA—formerly called junk because it does not code for protein—indirectly regulates a critical tumor suppressor protein, called PTEN. This molecule, which controls the cycle of cell division, preventing the cell from multiplying too rapidly, is one of the most commonly lost tumor suppressors in human cancer. Researchers in the Pandolfi lab had previously shown that even a 20 percent reduction in the levels of this molecule could lead to tumor growth.

The stretch of DNA that influences PTEN is almost identical to the PTEN gene. It is so close, in fact, that it is called a “pseudogene” and designated PTENP1. A pseudogene closely resembles a protein-coding gene but is different enough to be incapable of coding for a functional protein.

As the investigation demonstrated, pseudogenes are far from useless. There had been some indication of this in previous work, which showed that levels of pseudogenes correlate to disease and therefore might play a role in regulating protein-coding genes. Pandolfi, who is chief of the Division of Genetics in the Department of Medicine at BID, and his colleagues showed that the DNA blueprint of PTENP1 yields an mRNA with the key task of suppressing cancer.

According to postdoctoral fellow Leonardo Salmena, a first author on the paper, “We’re not changing the central dogma, we’re just adding a new branch to it.” Salmena’s co–first author is former postdoc Laura Poliseno.

During the course of DNA transcription, when the blueprint of a DNA strand is processed into mRNA, the mRNAs assembled from the gene and the pseudogene collect in the cell and compete for binding partners. One of these partners is microRNA (miRNA), which as a group forms another layer of gene regulation. Strands of miRNA bind with mRNAs that have a complementary genetic sequence. This interaction inactivates the mRNAs, preventing them from generating protein.

The result in terms of PTEN is a check on tumor growth. The mRNA transcribed from the pseudogene PTENP1 serves as a decoy for complementary miRNA binding. The more miRNA that binds with PTENP1 mRNA transcripts, the less that binds with PTEN transcripts (see figure below), increasing the amount of PTEN protein in the cell and strengthening its tumor suppressor function.

Fine-tuning protein levels. Both protein-coding genes and noncoding pseudogenes can be transcribed into strands of messenger RNA (mRNA) that contain information affecting protein production, a new study has found. Regulatory microRNAs (miRNAs) stop protein-coding mRNAs from being turned into proteins by binding to the mRNAs’ 3’ untranslated region (3’ UTR). Pier Paolo Pandolfi and colleagues at HMS report on a case in which pseudogene mRNAs compete for miRNA binding in the cell, providing an additional layer of control for the availability of a particular tumor suppressor protein.

“These findings have really transformed the way by which we think about, and do research in the lab,” said Pandolfi. “The findings represent for us a radical change of perspective on how genes operate. It never occurred to me that I would observe such a transformative phase in my career. We are astonished, but also excited about this unexplored dimension. We now attribute a putative function to any RNA, coding and noncoding, and importantly, we can predict it.”

The researchers went on to show that PTENP1 is selectively lost in dozens of colon cancer lines. They have proposed that, rather than be classified as a pseudogene, PTENP1 be reclassified as a “bona fide tumor suppressor gene.” They have coined a name for this new regulatory mechanism: competitive endogenous RNA, or ceRNA. It appears that every expressed element that makes up the set of all RNA transcripts, including long noncoding RNAs, has the potential to work through this mechanism.

According to Frank Furnari, an associate investigator at the Ludwig Institute for Cancer Research and an associate professor at the University of California, San Diego, School of Medicine, “The study by Poliseno and colleagues adds a new mechanism to the multiple ways the function of this and other tumor suppressor genes can be abrogated. The question now is: How many genes implicated in cancer fall under the category of [ceRNA] regulation?”

For more information, students may contact Pier Paolo Pandolfi at ppandolf@bidmc.harvard.edu.

Conflict Disclosure: The authors declare no conflicts of interest.

Funding Sources: The National Institutes of Health; the authors are solely responsible for the content of this work.