A prominent feature of a group of deadly inherited neurodegenerative diseases – including Huntington’s disease, certain forms of amyotrophic lateral sclerosis (ALS), and frontotemporal dementia – is the presence of “RNA foci,” abnormal clusters of RNA molecules that accumulate in the cell nucleus. Many researchers believe that these clusters are toxic to nerve cells, but it has not been clear how or why they form. Now, UC San Francisco researchers have drawn a link between distinctive genetic abnormalities in these diseases and the formation of RNA foci, work the scientists said may open avenues to the development of new drug treatments.
In addition, while previous research indicated that RNA somehow combined with proteins to form foci, the new UCSF work suggests these clusters can arise from RNA alone.
“We have contributed a new hypothesis of how RNA foci form in these disorders,” said UCSF’s Ronald Vale, PhD, professor in the Department of Cellular and Molecular Pharmacology and a Howard Hughes Medical Institute (HHMI) investigator, who led the new research. “Protein aggregation is a well-accepted cause of many neurodegenerative diseases, including Alzheimer’s and ALS, but our work suggests that aggregation of RNA, by itself, might also be a culprit in neurodegeneration.”
The new study, published online on May 31 in the journal Nature, focused on a group of disorders known as “repeat expansion” diseases. In these conditions, short strings of the DNA “letters” known as nucleotides are abnormally repeated several times. Over the course of an individual’s life, or across generations, the number of such repeats can expand, which may increase disease susceptibility and severity within families.
Although the first of these repeat expansion disorders was identified nearly three decades ago, and more than 30 now are known, how a repeating nucleotide sequence gives rise to disease is not well understood. Earlier studies were based on the idea that repeat expansions alter gene activation or protein production, but in some animal studies, a complete loss of the protein encoded by affected genes did not produce disease symptoms.
Another suspect is messenger RNA, which is copied from the DNA and used by the cell to guide protein production. Messenger RNA is made in the cell’s nucleus from a DNA template and normally transported out of the nucleus to make proteins.
Vale and UCSF postdoctoral fellow Ankur Jain, PhD, who performed the new experiments, found that each nucleotide repeat in RNA behaves like a small piece of molecular Velcro that can stick to repeats on other RNA strands. “When you have lots of tandem pieces of Velcro, that allows one RNA strand to stick to multiple other strands with similar repeats,” Vale said. “What you then get is many RNAs binding to one another to form a tangled gel,” a bit like microscopic gummy bears trapped in the nucleus.
Jain and Vale demonstrated this phenomenon in purified RNA in a test tube as well as when they artificially induced production of these disease-causing RNAs in cells in a dish. “You start that process of making the RNA in cells and then can watch the gels forming in the nucleus in a time-lapse movie,” Vale said.
Jain and Vale found that about 30 nucleotide repeats were needed to trigger formation of RNA gels, similar to the number of repeats associated with the emergence of disease symptoms. RNA gels did not form when Jain tested random nucleotide sequences that did not have disease-related repeating patterns.
“Now we want to tackle new therapeutics by focusing on strategies that act on RNA and that could dissolve these potentially pathological structures,” Vale said. By adding short bits of DNA known as “antisense” to tie up the specific RNA sequences, or alternatively, by applying the cancer chemotherapy drug doxorubicin — both of which inhibit the Velcro-like process of RNAs coming together — Jain was able to dissolve the gels in test tubes, in the cell-culture model of repeat expansion disorders, and even in living cells derived from patients.
“But doxorubicin targets all DNA and RNA in the cell, and has substantial side effects,” Jain said. “So we are looking for small molecules that specifically act on the disease-related sequences as potential therapeutics against these devastating conditions.”
The UCSF study was funded by HHMI and the Damon Runyon Cancer Research Foundation. Some of the experiments were carried out at the Marine Biological Laboratory in Woods Hole, Massachusetts, in another HHMI-funded laboratory.
UC San Francisco (UCSF) is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. It includes top-ranked graduate schools of dentistry, medicine, nursing and pharmacy; a graduate division with nationally renowned programs in basic, biomedical, translational and population sciences; and a preeminent biomedical research enterprise. It also includes UCSF Health, which comprises three top-ranked hospitals, UCSF Medical Center and UCSF Benioff Children’s Hospitals in San Francisco and Oakland, and other partner and affiliated hospitals and healthcare providers throughout the Bay Area.