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Patrik Ståhl: Method for Single-Cell Resolved Transcriptomics

Patrik Ståhl: Method for Single-Cell Resolved Transcriptomics
Postdoctoral associate, Frisén lab, Science for Life Laboratory, Karolinska Institute, Science for Life Laboratory
Recommended by Joakim Lundeberg, Science for Life Laboratory, KTH Royal Institute of Technology

Stahl.jpgPatrik Ståhl is a methods developer from way back. His PhD work focused on general genomics and he's ridden the wave over into transcriptomics. Currently, he and his colleagues are working on a spatially resolved transcriptomics method that he said allows single-cell resolution.

Typically transcriptomic analysis is an analysis of an average: A tissue is ground up and its RNA extracted. That RNA gives an overall view of what's going on in that tissue.

Instead, Ståhl's approach relies on overlaying tissue on a microarray surface that is embedded with a number of barcoded features that tell the researchers just where in the tissue a transcript is present.

"It's a totally new method and basically we can get a single-cell resolution in that way, and we can analyze tens of thousands of samples in the same experiment at that resolution," Ståhl said, noting that he and his colleagues are in the process of publishing this work. "Obviously, we are very excited [and] we think that this could really be a huge hit."

But methods aren't always a huge hit. One of the challenges of being a methods developer is the low citation rate, especially if the tool hasn't widely caught on. Plus, Ståhl said, methods papers typically cite fewer papers than other biomedical papers.

On the other hand, it offers the ability to try to make commercially viable tools, which he said appeals to his entrepreneurial spirit.

And on the side, Ståhl writes for a Swedish biotech publication, called Life Science Sweden, where he writes product reviews and other articles. This, he added, helps keep him up to date on all the new products.

Paper of note

As his spatial transcriptomic approach hasn't been published yet, Ståhl noted that he has also worked on methods to visualize DNA. He and his colleagues published a series of papers, the first one in Genomics in 2007, on their method using magnetic beads to capture DNA and increase its size, making it visible to humans. This approach, Ståhl said, has potential to be used for rapid, onsite diagnostic tests.

Looking ahead

The field, Ståhl said, is moving toward more targeted and higher quality assays as some applications don't require the full spread of data generated by transcriptome or genome sequencing.

"I think that these bench-top sequencing experiments, for instance, or, as we all anticipate nanopore, more compact, simpler-to-use instruments, I think those are the future," he added. "That's where everyone wants to go, I think, towards a little bit more intelligent experiments concerning more focused assays."

And the Nobel goes to…

If Ståhl were to take home the Nobel Prize, he hopes that it would be for his new transcriptomics method. "It would be fun actually if it proved that the method we are working on would really impact the field," he said. "That would be fun."