For many years, scientists believed that transfer RNAs are simple shuttles that bring amino acids to ribosomes. But a growing number of studies find that they can alter important cellular processes by influencing gene expression, including helping cancers grow. Now, researchers have found that tRNAs can speed up or slow breast cancer metastasis by accelerating the translation of growth genes.
In a study published in Nature Cancer on December 12, a team from the Rockefeller University and the University of California, San Francisco reports that tumor cells exhibit elevated levels of tRNAs that are required to assemble growth-promoting proteins. And in a twist, slightly different tRNAs that carry the same amino acid can have opposing effects on metastasis.
“It’s truly fascinating how cancer cells can manipulate the genetic code to their own advantage,” says Hannah Benisty, a cancer biologist at the Centre for Genomic Research in Spain who was not involved in the study. “The authors have done an impressive job of examining the role of tRNAs in cancer using a variety of experimental approaches,” she adds, noting that the results validate previous findings that tRNAs can regulate gene expression.
Transfer RNAs: not just simple shuttles
First described in the 1960s, tRNA molecules are cross-shaped nucleotide loops that attach to an amino acid on one arm and recognize a specific mRNA codon with another. Canonically, their sole purpose was to act as the principal translators of the genetic code. It’s only in recent years that a fuller picture of tRNA biology has begun to emerge, says Marsha Rosner, a cancer biologist at the University of Chicago who was not involved in the study. She first observed a likely link between cancer and tRNAs more than a decade ago, but was unable to establish a direct, causal connection at the time. She says that tRNAs are considered “workhorses in the cell and not genes that can be regulated in some way, and this [study] shows that they really can” regulate genes.
Previous studies linked irregular tRNA levels to metastatic growth, but why and how tRNAs behave in such an odd fashion in cancer cells remained unclear. This mystery intrigued Sohail Tavazoie, a cancer biologist at the Rockefeller University who coauthored the new study.
Lisa Earnest-Noble, a postdoc in his lab, quantified and compared levels of several different types of tRNAs in cultured human metastatic breast cancer cells and normal human breast tissue cells using CHIP-Seq and tRNA profiling. In doing so, she found that cancer cells have higher levels of a leucine-shuttling tRNA compared to normal cells. The tRNA in question recognizes the codon GAU on an mRNA molecule.
But even more surprisingly, Tavazoie says, she found that different tRNAs that carry the same amino acid (called isoacceptors) don’t necessarily follow the same pattern. Lower than normal levels of another leucine courier that recognizes the codon UAU were observed in the cancerous cells. As levels of the leucine-carrying GAU tRNA went up, levels of the UAU tRNA went down, meaning the levels of the two isoacceptors became polarized. “The fact that they go in the opposite directions allows the cancer cells to become optimized for metastasis,” says Tavazoie. Analyzing samples taken from human breast cancer patients, Earnest-Noble found elevated levels of patient samples, observing the same tRNA was elevated in human breast cancers and finding that a higher degree of polarization was associated with more aggressive disease.
The fact that they go in the opposite directions allows the cancer cells to become optimized for metastasis.
—Sohail Tavazoie, The Rockefeller University
The team followed up on this observation with a slew of tests in mouse breast cancer models, first disrupting the production of the two tRNAs using CRISPR and RNAi. Lowering the amount of GAU tRNA subsequently stunted cancer cell growth, adding more evidence that cancer cells take advantage of tRNAs to fuel their metastasis. Meanwhile, inhibiting UAU tRNA translation had the opposite effect, indicating that it might act as a suppressor for cancer growth. “That means that you can take a tRNA and turn its levels down, and you get more metastasis,” says Tavazoie.
“What was nice is they were able to get rid of specific tRNAs to really demonstrate their function,” says Rosner—something her team didn’t have the technology to do when she observed a possible connection between tRNAs and cancer years earlier—“and that’s extremely important for showing that this isn’t something that just happens, there’s a purpose for it.”
Lastly, the researchers performed genome-wide analyses to search for genes that code for mRNAs that are rich in GAU and UAU codons, which might benefit from more of their tRNAs being around. They also used ribosome profiling to take a snapshot of the proteins being actively made inside the cell in both normal and metastatic human breast tissue cells.
They found that growth-promoting genes contain large numbers of GAU codons and few UAU codons, and, in cancerous cells, ribosomes churned out more proteins from these GAU-rich genes. “All of these approaches clearly showed . . . the impact of these tRNAs on cancer metastasis,” says Tavazoie.
The authors say that the findings might help create or improve tRNA-based treatments for metastatic cancers, some of which are already clinically available. They want to continue to look into the mechanism by which this polarized expression of tRNAs occurs. “If we can figure out how this tRNA polarization happens,” says Tavazoie, “we could perhaps develop an approach to controlling metastatic disease.”
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