Dark Side of the Genome

Scientists have since learned that non-coding RNA comes in a variety of forms and serves many different biological functions. One example is ribosomal RNA, a key component of the protein assembling molecular machines known as ribosomes. Unfried is particularly interested in long non coding RNAs (lncRNAs). These are at least 200 nucleotides in length and chemically identical to protein-producing messenger RNAs. To date, more than 20,000 lncRNAs have been found within the human genome and more than twice as many are predicted to exist. Although their functions have yet to be fully elucidated, a growing body of evidence suggests that many are important for a wide range of biological processes, such as the regulation of protein production, and are relevant to human diseases like cancer.

Unfried grew up in Costa Rica and discovered his passion for research while studying the dengue virus as an undergraduate student in biochemistry. He first encountered lncRNAs as a doctoral student in the laboratory of Puri Fortes, a principal investigator at the University of Navarra in Spain. While probing for lncRNAs involved in cancer, Unfried zeroed in on one particular lncRNA that was associated with worse outcomes in patients with liver cancer. This molecule, which he dubbed NIHCOLE (short for “noncoding RNA induced in hepatocellular carcinoma with an oncogenic role in ligation efficiency”), appeared to only be highly expressed in liver cancer cells. Tissue and disease specificity is a common characteristic of lncRNAs, according to Unfried, making them ideal potential therapeutic targets.

Further assessments revealed that NIHCOLE was involved in repairing double-stranded breaks in DNA, a common (and the most toxic) form of DNA damage. The rapid proliferation of cancer cells makes them susceptible to this kind of impairment, but by protecting these cells against such harm, NIHCOLE actually enables them to proliferate unchecked, Unfried explains. By helping repair DNA damage, NIHCOLE also enables cancer cells to resist treatments such as radiotherapy, according to Fortes. “Our dream would be to give radiotherapy to patients while we decrease the levels of NIHCOLE, because this is really catastrophic for the cancer cells,” she says. “The experiments from Juan Pablo allowed us to propose a new therapy for liver cancer.”

The characteristics of NIHCOLE left Unfried wondering why this molecule was selected for during the process of evolution if all it does is help a tumour survive. What Unfried suspects is that lncRNAs like NIHCOLE, which appear to be specific in diseases, may play important roles during early development — particularly in highly proliferative tissue like testis, where sperm is produced, or in energy-guzzling organs such as the brain— then become silenced before reappearing in tumours or other diseases later in life. Supporting this notion, Unfried and his colleagues identified overlaps between the lncRNAs expressed in cancers and those found in healthy tissues in testis and the brain. “We think that these lncRNAs offer a fitness advantage and thus became part of the genome during evolution,” he says.

In his current position as a postdoc with Igor Ulitsky in the Department of Biological Regulation at Weizmann, Unfried is focused on identifying what lncRNAs do and how they carry out those functions. In the case of NIHCOLE, he has used atomic force microscopy to find that loops within its structure are key to its ability to bind the DNA repair machinery. Using a variety of methods, Ulitsky and Unfried hope to ultimately generate a kind of “codebook” that will lay out the diverse functions of lncRNAs and their mechanisms of action. Messenger RNAs are relatively simple in that their main function— protein production — is known. The repertoire of lncRNAs, on the other hand, remains largely unknown.

“The possibilities are so endless,” Unfried says. Unfried also suspects that lncRNAs may have played a central role in the evolution of higher primates. While many organisms, including some plants, have far more protein-coding genes than we do, the number of noncoding sequences tends to increase with organismal complexity. “The size of the non-coding genome is a better predictor of organismal complexity than protein coding genes,” Unfried says.

Preliminary evidence suggests lncRNAs may be the primary route through which organisms evolve new traits. “It’s a bit like the stock market,” Unfried explains. “It’s a very risky game to play with your building blocks, proteins, because they are essential, but you can mutate a lncRNA many times without consequences.” For this reason, some scientists hypothesize that lncRNAs may have been crucial to the evolution of complex organisms like humans. When Unfried eventually sets up his own lab, he hopes that a central focus will be trying to understand how lncRNAs allow the cell to play the evolution game. That, Unfried says, is “the wildest dream of my future.”