The next wave in the biological research revolution


Josh Ryu, director of technology and co-founder of Rebus Biosystems

For decades, biomedical researchers have pursued a reductionist strategy, investigating DNA, RNA, proteins, and other cellular actors in isolation. These studies have been of critical importance, providing lists of vital pieces to guide further exploration. Now, however, biology has entered a new era, in which scientists must take more contextual approaches to understanding the fundamental units of life: cells.

But to really understand how cells work, we need to explore their relationships in time and space. It is not enough to study tumor cells on their own: we need to examine the microenvironments that help them survive and spread. The same goes for the brain. We can’t just look at how neurons, astrocytes and microglia work, we have to understand how they work together.

Reductionism is giving way to more holistic examinations of how cells interact, and the spatial context has taken center stage.

The next wave of the biological revolution: space omics

Advances in omics (genomics, transcriptomics, proteomics, etc.) have revolutionized biology in the 21st century. We have advanced from researching individual characteristics in a small number of cells to performing multiplex analyzes in many cells, from qualitative analyzes to quantitative analyzes.

But no matter how fruitful the omics have been, they have relied heavily on cells that have become detached from their native tissues. Crucial cell-to-cell interrelationships, and the biological ideas they provide, have been largely lost. Now, space omics, which allows multiplex quantitative analysis in intact tissues, has emerged as the next wave of the biological research revolution.

Various approaches to spatial omics have been developed. The most powerful combine high-resolution microscopy with assays that probe individual cell characteristics, such as RNA transcripts, into their original context.

When it comes to understanding how cells work, both on their own and in the tissues where they live and work, seeing is believing.

Resolution and performance: the best of both worlds

Microscopy has been a vital research tool for over four centuries. Until recently, however, scientists had had to make key commitments. Over a specific period of time, they may see a reduced number of high-resolution cells or a larger group of lower-resolution cells. But now it is possible to get the best of both worlds: resolution and performance.

The resolution can be defined differently. For some, it means pixel size. Although the pixel size of any imaging system contributes to the image quality, it does not clearly differentiate between separate objects. This metric is the optical resolution, which is controlled by the optics of the instrument.

At low resolution, two highly adjacent molecules may appear as one, disregarding quantitative accuracy. If the optics cannot separate two neighboring molecules, the pixel size becomes irrelevant. Ultimately, optics is the crucial ingredient that makes true high resolution possible.

However, in conventional optical microscopy, there is a fundamental limitation imposed by lens physics: resolution cannot be improved without drastically sacrificing image performance. In unicellular biology, innovation in optical imaging is highly desirable to deliver high resolution simultaneously with high performance. Synthetic aperture optics (ODS), which combines high-resolution structured lighting with a low-magnification lens, are a promising solution to this need.

High resolution, combined with a large field of view, allows researchers to see what happens at the individual molecule level in [thousands of] cells during a single experiment. They can see information at the anatomical level to know the structure of the tissue, as well as analyze quantitative data from a single molecule.

In other words, scientists can now see the forest and the trees.

Correct optics + correct test = high quality data

Optical systems for image-based space omics are just one part of the story. Seeing cellular features, such as RNA transcripts, requires an assay. There are many options, but not all are the same.

The most common RNA assay uses fluorescently labeled oligonucleotide probes that bind to target molecules, a technique called fluorescence. in situ hybridization (FISH).

FISH has many variations, but single molecule FISH (smFISH) is especially potent. Multiple probes are created for each target gene, and researchers only see the signal when multiple probes are joined. This guarantees a high specificity, which together with the high sensitivity of the technique have made it the gold standard for the analysis of gene expression.

While smFISH is quite useful, it is also incredibly complex. Researchers need a lot of experience to make the trial work reliably. Also, reagents are expensive and analyzing more than a few genes at a time can be laborious.

These drawbacks have limited the impact of smFISH on space omics. Laboratories can only analyze a few cells at a time, and even that takes weeks or months to produce results. Recent advances combining advanced optics and automated smFISH have changed the game in a few years.

What does the future hold for us?

The explosion of unicellular sequencing and early work in space omics using low-resolution techniques have created an avalanche of discoveries that now need further research and validation. Instruments that combine advanced optics and smFISH are ready to deliver previously unimaginable biological knowledge.

The automation of these tools will democratize space omics, allowing researchers from different disciplines and backgrounds to get the critical spatial context they need to answer their most important biological questions.

About Josh Ryu

Josh Ryu is the co – founder and chief technology officer of Rebus Biosystems. During his time at MIT, he was one of the original developers of the company’s core technology, Synthetic Aperture Optics (ODS). Josh co-founded Rebus Biosystems in 2018 and served as CEO of the company from its inception until 2020, when he assumed his current role. Josh earned his doctorate. from the Harvard-MIT Division of Health Science and Technology.

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