Labeling cells with barcodes: New CRISPR technology reveals how cells communicate

In recent years, small extracellular vesicles (sEVs) have captured the attention of scientists due to their critical role in cell-to-cell communication and disease progression. These nanosized particles, released by cells, were once dismissed as biological waste.

Today, they are recognized as vital components in processes ranging from normal tissue maintenance to the spread of conditions like cancer and neurodegenerative diseases. Despite their significance, understanding the mechanisms behind their formation and release has posed significant challenges for researchers—until now.

A novel breakthrough, leveraging CRISPR gene-editing technology, is revolutionizing how scientists study sEVs. This innovative approach, known as CIBER (CRISPR-assisted individually barcoded sEV-based release regulator), enables researchers to investigate thousands of genes simultaneously.

By tagging sEVs with unique RNA “barcodes,” CIBER offers unparalleled insights into the molecular processes regulating sEV release, setting the stage for advancements in biotechnology and disease treatment.

Extracellular vesicles, which include sEVs, are small, membrane-enclosed particles released by cells into their surroundings. Their size, origin, and cargo determine their classification. sEVs, typically 30–200 nanometers in diameter, are among the smallest but most intriguing members of this group. These vesicles transport biomolecules—such as RNA, proteins, and lipids—between cells, acting as communication messengers.

The cargo they carry dictates their function. In healthy tissue, sEVs help maintain balance and promote healing. However, in disease states, these vesicles can exacerbate harmful conditions.

For instance, cancer cells use sEVs to promote metastasis, while neurodegenerative diseases like Alzheimer’s leverage them to spread toxic proteins. As a result, understanding how sEVs are formed and released could unlock new therapeutic pathways.

Studying sEVs has long been hindered by technical limitations. Traditional methods require separating cells into individual wells, altering a gene in each, and then analyzing the released sEVs. This process is time-intensive and only scratches the surface of the complex networks regulating sEV behavior.

Moreover, sEVs are highly heterogeneous, with subpopulations differing in their origins, cargo, and release mechanisms. Untangling this diversity has proven nearly impossible with conventional tools.

Further complicating matters, many genes implicated in sEV release also influence critical cellular functions like viability. Distinguishing sEV-specific effects from broader cellular impacts adds another layer of difficulty. These challenges have left researchers with an incomplete understanding of sEV biology—until the advent of CIBER.

CIBER streamlines the study of sEVs, combining CRISPR-based gene editing with high-throughput screening. The system works by using guide RNA to knock out specific genes in cells. Each altered gene is “barcoded” into the sEVs the cell releases, allowing researchers to track and measure sEV production.

This innovative method allows thousands of genes to be studied in a single experiment, drastically reducing the time and effort required.

“We have established a new high-throughput screening platform named CIBER,” explained Associate Professor Ryosuke Kojima from the University of Tokyo. “This system allows a single experimenter to implement a genome-wide screening of sEV release regulators within several weeks to a couple of months, which is superefficient compared to the conventional methods.”

The beauty of CIBER lies in its ability to analyze complex interactions in a pooled setting. By studying cells collectively rather than in isolation, researchers can identify both individual and combined effects of various genes on sEV release. The technique also enables the study of sEV subpopulations, offering a more detailed picture of their diversity and behavior.

The potential applications of CIBER are vast. By identifying genes and pathways that regulate sEV release, scientists could develop targeted therapies for diseases where sEVs play a harmful role, such as cancer.

For example, blocking sEV release from tumor cells might limit their ability to spread to other tissues. Conversely, enhancing sEV production could pave the way for new drug delivery systems.

sEVs are naturally biocompatible and capable of carrying therapeutic molecules directly to target cells, making them ideal candidates for drug delivery. By fine-tuning their production, researchers could create vesicles tailored to deliver specific treatments with minimal side effects.

Beyond therapeutics, the CIBER system holds promise for basic science. “Barcoded sEVs could also be used to estimate cell population dynamics without destroying cells,” said Kojima. “Tracing the fate of barcoded sEVs can help us better understand sEV biology. We believe that CIBER screening has great potential.”

As the understanding of sEV biology deepens, the implications for precision medicine become clear. The ability to manipulate sEV release at a molecular level could revolutionize the treatment of complex diseases, enabling therapies that are not only more effective but also highly personalized.

The journey from discovery to application is still underway, but the strides made with tools like CIBER mark a significant leap forward. By unraveling the mysteries of sEVs, researchers are opening doors to new frontiers in medicine and biotechnology.

Note: Materials provided above by The Brighter Side of News. Content may be edited for style and length.

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