This article has been reviewed according to Science X's editorial process and policies. Editors have highlighted the following attributes while ensuring the content's credibility: In recent years, scientists have developed methods to measure a cell's transcriptome, or all the RNA produced by a cell, to study the cell's identity and genetic activity. However, these methods rely on killing the cell to access the bits of RNA within and offer only a one-time snapshot.
Now, researchers at the Broad Institute and MIT have invented a "cellular self-reporting" approach that lets living cells share their own transcriptomes so scientists can analyze them without killing the cells. Described in the journal Cell, the live-cell transcriptomic method relies on virus-like particles, which cells use to package and deliver RNA to the culture medium in which they are bathed. Scientists can simply sample the medium to isolate the RNA and do this repeatedly to reveal how gene activity in the same cell population changes as the cells mature or respond to perturbations.
The researchers applied their method to a variety of cellular model systems, demonstrating its potential to help reveal how cells go awry over time in disease and how drugs affect cells. "Our lab focuses our time and resources on developing tools that will actually get used and make a real impact on the broader field," says study senior author Paul Blainey, who is a core member of the Broad and a professor of biological engineering at MIT. "It's so gratifying to see this concept come to fruition, which was complete science fiction when we started.
It's a great example of the innovative impact long-term, high-risk, high-reward research can have." The effort to build the new method began more than a decade ago, when the Blainey lab set out to find a new way to do RNA sequencing without killing cells. "The existing methods were a bit medieval and involved stabbing cells or cutting pieces off of them," recalls Blainey. Inspired by the performance of molecular technologies such as CRISPR-based technology and their ease of adoption, Blainey and study first author Jacob Borrajo committed to developing a molecular method they knew would be challenging and take time but would also make the approach scalable and easy for other labs to perform.
The team found inspiration in retroviruses, which over millions of years evolved the ability to package their RNA genomes in protein shells to spread from one infected cell to another. To build their method, the team engineered mammalian cells to express a retroviral structural protein that can encapsulate not only viral RNA but also a cell's RNA. Integrated into the cell's membrane, the viral protein can recruit cellular RNA, form a shell around it to create a virus-like particle and bud off from the membrane to enter the liquid medium around the cell.
The scientists then take a sample of the medium, isolate the RNA and sequence it to get a view of the transcriptome from that cell population—all without destroying or damaging the cells. "Compared to methods using robotics or mechanical biopsies of cells, our molecularly encoded solution could be much more broadly enabling for the average life science or biomedical lab, particularly for the time-dynamic questions that we hope to elucidate with this technology," says co-first author Mohamad Najia, research fellow in the Blainey lab and the lab of George Daley at Boston Children's Hospital. Najia and Borrajo led the work along with co-first author Anna Le, a postdoc in the Blainey lab.
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