For decades, biomedical researchers pursued a reductionist strategy, investigating DNA, RNA, proteins and other cellular players in isolation. These studies have been critically important, providing vital parts lists to guide further exploration. Now, however, biology has entered a new age, in which scientists must adopt more contextual approaches to understand the fundamental units of life – cells.
But to truly understand how cells operate, we must explore their relationships in time and space. It’s not enough to study tumor cells on their own – we must examine the microenvironments that help them survive and spread. The same is true in the brain. We can’t simply observe how neurons, astrocytes and microglia work, we need to understand how they work together.
Reductionism is giving way to more holistic examinations of how cells interact, and spatial context has taken center stage.
The Biology Revolution’s Next Wave: Spatial Omics
Advances in omics (genomics, transcriptomics, proteomics, etc.) have revolutionized biology in the 21st century. We’ve progressed from investigating individual features in small numbers of cells to conducting multiplex analyses across many cells – from qualitative analyses to quantitative analyses.
But as fruitful as omics have been, they’ve largely relied on cells that have been disassociated from their native tissues. Crucial cell-to-cell interrelationships – and the biological insights they provide – have largely been lost. Now, spatial omics, which enables multiplex quantitative analyses in intact tissues, has emerged as the next wave in the biological research revolution.
Several spatial omics approaches have been developed. The most powerful unite high-resolution microscopy with assays that probe individual cellular features, such as RNA transcripts, in their original context.
When it comes to understanding how cells function, both on their own and in the tissues where they live and work, seeing is believing.
Resolution and Throughput: The Best of Both Worlds
Microscopy has been a vital research tool for more than four centuries. However, until recently, scientists have had to make key compromises. In a specific time frame, they could either view a small number of cells at high resolution or a larger cell group at lower resolution. But now it is possible to get the best of both worlds: resolution and throughput.
Resolution can be defined differently. For some, it means pixel size. While the pixel size in any imaging system contributes to image quality, it does not clearly differentiate separate objects. That metric is optical resolution, which is controlled by the instrument’s optics.
With low resolution, two closely adjacent molecules may appear as one, undercutting quantitative accuracy. If the optics cannot separate two neighboring molecules, pixel size becomes irrelevant. Ultimately, optics are the crucial ingredient that makes true high resolution possible.
However, in conventional optical microscopy, there’s a fundamental limitation imposed by the physics of the lens – improving resolution cannot be achieved without dramatically sacrificing imaging throughput. In single-cell biology, innovation in optical imaging is highly desired that delivers high resolution simultaneously with high throughput. Synthetic Aperture Optics (SAO), which combines high-resolution structured illumination with a low magnification lens, is a promising solution to such a need.
High resolution, combined with a large field of view, allows researchers to see what’s happening at the individual molecule level in [thousands of] cells during a single experiment. They can view anatomical level information to learn about tissue structure, as well as analyze quantitative single-molecule data.
In other words, scientists can now see the forest AND the trees.
Right optics + Right assay = High quality data
Optical systems for image-based spatial omics are only part of the story. Seeing cellular features, such as RNA transcripts, requires an assay. There are many choices, but they are not all created equal.
The most common RNA assay uses fluorescently tagged oligonucleotide probes that bind to target molecules, a technique called fluorescent in situ hybridization (FISH).
FISH has many variations, but single-molecule FISH (smFISH) is particularly powerful. Multiple probes are created for each gene target, and researchers only see the signal when multiple probes bind. This ensures high specificity, which along with the technique’s high sensitivity has made it the gold standard for gene expression analysis.
While smFISH is quite useful, it is also incredibly complex. Researchers need tremendous expertise to make the assay work reliably. In addition, reagents are expensive and analyzing more than a few genes at a time can be laborious.
These downsides have limited smFISH’s impact in spatial omics. Labs 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 just a few short years.
What does the future hold?
The explosion in single-cell sequencing and early work in spatial omics using low-resolution techniques has created an avalanche of discovery that now needs to be further investigated and validated. Instruments that combine advanced optics and smFISH are poised to deliver previously unimaginable biological insights.
Automating these tools will democratize spatial omics, allowing researchers from different disciplines and technical 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 (SAO). Josh co-founded Rebus Biosystems in 2018 and served as the company’s Chief Executive Officer from its founding through 2020 when he took on his current role. Josh earned his Ph.D. from the Harvard-MIT Division of Health Sciences and Technology.