For the first time, scientists can view RNA molecules directly inside cells and tissue in minute detail and across the entire human genome concurrently, thanks to new technology created by a Yale research team.
The technique, known as Reverse-padlock Amplicon Encoding Fluorescence In Situ Hybridization (RAEFISH), solves a trade-off that researchers have long been forced to make: detail versus scope. Earlier tools required researchers to choose between seeing either a limited number of genes in high detail or seeing many genes but with a limited level of detail regarding their transcripts’ (RNAs’) location and how they interacted.
“We developed a technique that satisfies both needs at the same time,” said Siyuan (Steven) Wang, an associate professor of genetics and cell biology at Yale School of Medicine. “It solves the key limitations of previous technologies in the spatial transcriptomics field.”
The new technology is described in a study published in the journal Cell.
We’re in an era when the tools are becoming available to tackle a greater level of complexity.
Image-based spatial transcriptomics techniques directly image RNA molecules in cells and tissue to map RNA location and gene expression patterns.
The RAEFISH technique represents a powerful advance in this imaging process, the researchers say. They created it by designing special probes that attach to RNA molecules inside cells. The probes make copies of targeted RNAs, and fluorescent tags are added so the RNAs can be seen under a microscope.
The method, which was tested in human cells and in tissues from mouse liver, placenta, and lymph nodes, can identify different RNA molecules from more than 20,000 genes. RAEFISH was able to map cell types, show how cells organize, and reveal interactions between different cell types through their gene expression patterns.
This will help reveal not only which genes are active, but also where in a cell or tissue they’re working, the researchers say. In addition, the expanded view may also provide new insights into developmental and aging processes in complex tissue, and how many diseases develop and progress.
“We could potentially discover new therapeutic biomarkers to treat diseases such as cancer where it’s critical to understand how cancer cells interact with other cells in the surrounding tissue microenvironment,” Wang said.
Breakthroughs in imaging omics technology, such as RAEFISH, are driving the future of medical research today, fueling novel therapeutic interventions, Wang said.
“We’re in an era when the tools are becoming available to tackle a greater level of complexity,” he said. “Being able to now study gene expression and cell interactions in greater detail in the complexity of the native tissue environment, which will be helpful in investigating a range of diseases.”
The all-Yale team included researchers from the departments of genetics, immunobiology, pathology, and cell biology at Yale School of Medicine.
Grants from the National Institutes of Health and from the Pershing Square Sohn Cancer Research Alliance supported this research.
This research was done in partnership with the National Institutes of Health (NIH) through a grant that includes reimbursement for facilities and administrative expenses (also known as indirect cost reimbursements) that are necessary to ensure the safe conduct of research and compliance with federal regulations.
In February, the NIH announced it would dramatically cut such reimbursements to universities, including Yale. The courts have blocked the cuts, but the threat remains.
At stake is research that saves lives, strengthens the economy, and bolsters national interests. Yale projects in danger include research that saves infants born with heart defects, extends the lives of cancer patients, addresses mental health challenges, and prevents and slows the effects of Alzheimer’s disease.
