In 1986, Leonard Rome and Nancy Kedersha discovered vaults, barrel-shaped particles made naturally by human cells, at the University of California, Los Angeles (UCLA). Despite studying the particles since their discovery, Rome and other scientists have failed to find their purpose. Now, scientists at the Broad Institute are using the mysterious structures to record the gene activity of cells.
Cross-section of human lung tissue under microscope. Adobe
Vaults are composed of 78 copies of a long molecule called major vault protein (MVP) which form a shell containing RNA of unknown function and some proteins that bind to the interior. Various hypotheses have been proposed for the function of these vaults, including that vaults help move molecules around inside cells or clear toxins. However, each hypothesis has failed to produce supporting evidence. Rome went on to co-found Vault Pharma, a company that works out of an incubator space at UCLA. The company is researching the use of vaults as vessels for delivering therapies.
A research team at the Broad Institute of MIT and Harvard is now engineering vaults to take in RNA and record nearly all gene activity in groups of cells for up to seven days. They published their findings in Science last week. This new method could help scientists investigate cellular processes, including how some cancer cells become resistant to drugs.
Existing methods of tracking gene activity have limitations. They can only track a few genes or only the genes that happen to be active at the time. Fei Chen, a biomedical engineer at the Broad Institute, asked a doctoral student to develop a better method. Their idea was to capture mRNA and store it so it could be read later.
mRNA usually breaks down within hours, so the team needed a way to protect the molecules. They first thought to connect Poly (A) binding protein (PABP), which naturally attaches to the end of mRNA, to more stable molecules. However, linking the PABP to bacterial proteins did not work. Then, Yu-Kai (Kevin) Chao, who was leading the project, suggested the use of vaults.
The team fused the gene for PABP with DNA encoding the MVP-binding subunit to an interior protein in a vault. When the altered PABP gene was added with the copy of the MVP gene, captured mRNAs ended up inside newly made vaults. The team was then able to open the vaults and sequence the mRNA.
The team was able to use the method to confirm known genetic responses to heat and low oxygen. They also used the method, which they call TimeVaults, to identify genes that enable some lung cancer cells to resist a drug by adding the TimeVaults to cancer cells and then exposing them to the drug. The team pinpointed protective genes that were active before treatment. Adding a second drug targeting one of these genes wiped out most of the resistant cells.
Chen’s lab now plans to see whether TimeVaults can record all active genes in a single cell. They also want to engineer the genes for TimeVaults for mice to test whether it works in living animals.
