Researchers at Beth Israel Deaconess Medical Center (BIDMC) have found more evidence that RNA that does not code for protein does likely play an important role in the cell. Reporting in Nature, the scientists demonstrate that such RNA orchestrates the functions of cellular parts in a tissue-dependent manner. The following video is a lecture from the NIH about how such non coding RNAs can regulate the genome.
Only two percent of the human genome encodes for proteins, which make up all the various parts and components of our bodies. The remainder of the genome had been largely written off in the early days of genetics, and it was termed junk DNA. But many researchers knew there had to be more to it than that, and after the genome was sequenced and many genes were characterized, those non-coding parts of the genome began to get a lot more attention. It has been found that some of those regions gets transcribed into RNA, and there have been a multitude of names for those molecules, one of which is long non-coding RNA (lncRNA).
"Whether such small, hidden polypeptides are actually functional, or represent 'translational noise' within the cell is still relatively unclear," explained senior author of the work, Pier Paolo Pandolfi, MD, PhD, Director of the Cancer Center and Cancer Research Institute at BIDMC. "Our team set about trying to understand to what extent lncRNA molecules might actually encode functional polypeptides, and how important such peptides might be."
For this study, the scientists utilized computational approaches to identify potential molecules that lncRNAs could encode, and then applied mass spectrometry to find out if each molecule had indeed been translated into a protein. "With this approach we actually identified many expressed hidden polypeptides and went on to characterize one in particular," Pandolfi explained. The lncRNA they characterized is LINC00961, which encodes a 90 amino acid polypeptide.
The team found that the peptide LINC00961 codes for works to modulate the function of the mTORC1 protein complex, which is vital to the cell as a sensor of nutrient levels, and a regulator of a variety of cell functions like growth and proliferation, metabolism and translation. Dysfunction in the complex can lead to cancer. Since it seemed that LINC00961 blocks the ability of the mTORC1 complex to sense amino acid stimulation, the researchers termed the molecule SPAR (Small regulatory Polypeptide of Amino acid Response).
Further research indicated that SPAR is highly expressed in many tissues including muscle. The investigators determined that in mince, SPAR aids in the regulation of muscle repair and regeneration through its influence on mTORC1. Experiments showed that LINC00961 expression is blocked after muscle injury in mice, SPAR is consequently reduced and mTORC1 activity is elevated, promoting tissue healing.
"The experimental approach we used allowed us to eliminate expression of the SPAR polypeptide, while maintaining expression of the host lncRNA," said lead author of the work Akinobu Matsumoto, PhD, research fellow at the Cancer Center at BIDMC. "We are able to ascribe this function to the coding function of the lncRNA rather than any non-coding function it may also have." The findings suggest that therapeutic strategies that restrict expression of SPAR in injured muscle may promote a more rapid regeneration of tissue.
While lncRNAs might not code for protein, this works indicates that they could have many different functions and are very important for cells. They may exert their actions through small peptides that can alter the action of larger cellular components.
mTORC1 is often implicated in human disease such as cancer, and the team hopes to find additional cellular functions that SPAR may act upon, and whether it has a role in disease. Because these peptides work in a tissue-specific manner, they could be valuable as drugs.
"An ability to target such modulators could be of great advantage from a therapeutic perspective, allowing for control of mTORC1 activity in cells or tissues that express such modulators while not affecting its activity and function in other tissue and cell types," explained co-author John Clohessy, PhD, Instructor in Medicine at BIDMC and a senior member of Pandolfi's research team.
"We are very excited about this discovery," said Pandolfi. "It represents a new and startling mechanism by which important sensory pathways can be regulated within cells, and we believe it will have important implications for how we approach the design of therapies and treatments in the future."
The following is a brief interview with Pier Pandolfi about some aspects of his work and how they might impact cancer therapies.