In the 1980s, UCLA cellular biologist Leonard Rome noticed odd, barrel-shaped structures present in almost all cells. The hollow particles were filled with RNA and a handful of proteins. Naming them vaults, Rome has tried to understand their purpose ever since.
Though vaults remain enigmatic, their unique structure recently inspired a separate team. Led by Fei Chen at the Broad Institute of MIT and Harvard, the scientists engineered vaults to collect and store messenger RNA (mRNA) molecules for up to a week. The mRNA vaults they created act like ledgers that detail which genes are turned on or off over time.
In several tests, opening the vaults and reading the mRNA stored within shed light on gene activity that helps cancer cells evade treatment. The method, called TimeVault, also tracked the intricate symphony of gene expression that pushes stem cells to mature into different cell types.
The work is “superpowerful” and “very innovative,” Jiahui Wu at the University of Massachusetts, who was not involved in the study, told Science.
Jay Shendure, an expert in cellular recorders at the University of Washington, agrees. It took “some creativity and some guts” to transform vaults into time capsules, he told Nature.
A Cell’s Life
Each cell is a metropolis humming with activity. Proteins zoom across its interior to coordinate behaviors. Structures called organelles churn out new proteins or recycle old ones to keep cells healthy. Scores of signaling molecules relay information from the environment to the nucleus, where our DNA resides. All this information causes the cell to turn certain genes on or off, allowing it to adapt to a changing biological world.
Scientists have long tried to spy on these intricate cellular processes. Using a common tool, they can tag molecules with glow-in-the-dark protein markers and track them under the microscope. This provides real-time data but only for a handful of proteins over a relatively short time.
Another approach takes snapshots of which genes are active in single cells or groups of cells, usually at the beginning and end of an experiment. Here, scientists extract mRNA, a molecule that carries gene expression information, to paint an overall picture of a cell’s current state. Comparing genetic activity between one point of time and another provides insight into the cell’s history. But unlike a video, these snapshots can’t capture nuanced changes over time.
More recently, a slew of cell recorders based on the gene editor CRISPR have galvanized the field. These tools encode information about cellular events into DNA, essentially forming a “video” of events inside cells that can be retrieved later by sequencing the DNA. Genomic recordings are relatively stable and have been used to map cell lineages—a bit like reconstructing a family tree—and record specific cell signals, such as those responding to viral infection, inflammation, nutrients, or other stimuli. But because they directly write into DNA, the process takes time and could trigger off-target effects.
Enter the Vault
Instead of tinkering with the genetic blueprint, mRNA may be a safer choice. These molecules carry protein-making instructions from DNA and have a relatively short lifespan. In other words, they reflect all the active genes in a cell at any moment, making them perfect candidates for a time capsule. But without protection, they’re rapidly destroyed—often within hours.
The team first tried to stabilize mRNA molecules by tethering them to a bacterial protein. It didn’t work. But after serendipitously stumbling across a YouTube channel by the Vault Guy, also known as Leonard Rome, they had an out-of-the-box idea. Cellular vaults are known to encapsulate some of life’s molecules. Could they also keep mRNA safe?
Vaults are made of 78 copies of a long protein. These proteins are woven into a barrel-shaped shell with a mostly hollow interior. To make their vault-based time capsule, the team first made a protective protein cap for the mRNA. This stabilized the molecules. The cap also links up with a slightly tweaked vault protein, engineered to tether captured mRNA molecules into a vault.
The team built in a switch too. TimeVault starts recording when cells are dosed with a chemical and stops as soon as the chemical washes out. Viewing the recording of gene activity is simple. The team retrieves the vaults and sequences all of the mRNA inside. TimeVault reliably stores the molecules for at least a week in multiple types of cells in petri dishes.
In a test, the technology faithfully captured mRNA in cells exposed to heat or low oxygen. Both are common ways to stress cells and force them change their gene expression. The mRNA profiles captured by TimeVault matched genetic responses measured using other methods, suggesting the recorder functions with high fidelity.
Another test showcased the time capsule’s power to observe complex diseases, such as lung cancer. Some tumor cells thwart medications and survive treatment. These cells don’t contain mutations that lead to drug resistance, suggesting they’re able to escape in other ways.
Using TimeVault, the team logged the cells’ activity before treatment began and discovered a ledger of genes, some previously not linked to cancer, that protect tumors from common therapies. By comparing gene expression from before and after treatment, they homed in on several overactive genes. Shutting these down boosted a cancer drug’s ability to kill more tumor cells, with one chemical cocktail lowering resistance to the cancer treatment.
The team is just beginning to explore TimeVault’s potential. One idea is to capture mRNA for longer periods of time from a single cell to record its unique genetic history. They’re also eager to re-engineer the technology so it works in mice, allowing scientists to capture an atlas of gene expression in living animals.
“By linking past and present cellular states, TimeVault provides a powerful tool for decoding how cells respond to stress, make fate decisions, and resist therapy,” wrote the team.
