New Sequencing Instrument provides powerful research in small package

Tapestri instrument
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New Sequencing Instrument provides powerful research in small package

By Alissa Kocer

The Sequencing and Genomic Technologies (SGT) Core Facility has a new instrument on its bench. It might not look like much --  a small box just over a foot tall and less than a foot wide with a small door on the top and an even smaller screen on the front – but the Tapestri Platform by MissionBio is anything but weak.

Tapestri is the only system capable of single cell multi-omics. “It’s the only instrument in the lab that can do single cell assays, in particular DNA assays,” Nicolas Devos, director of SGT said. “Down the road, we will also be able to conduct protein and RNA assays on the same cells.” It can simultaneously provide both genotype and phenotype data from the same cell across thousands of cells. 

For Dan Snellings, graduate student in Doug Marchuk’s lab, that’s huge. “Being able to simultaneously look at DNA, RNA and protein in single cells is massive for the omics world and for precision medicine, cancers and really specific research,” he said. “This is a really big deal.”

Snellings has been working with Doug Marchuk, the James B. Duke Professor of Molecular Genetics and Microbiology, on somatic mutations in cerebral cavernous malformations (CCMs). CCMs cause mulberry-like lesions in the brain and look like balloons filled with blood. Some lesions are very small and may not cause any problems, but some can become large and cause stroke and even death.

To try to understand what causes some lesions to stay small and others to grow, Marchuk and Snellings decided to sequence CCM tissues the lab had acquired through biobanks. Since biobanks provide frozen samples, the lab couldn’t isolate intact cells. Instead, they had to pull out nuclei from the samples and needed a platform that would allow for single nucleus studies, which is when they learned about SGT’s acquisition of Tapestri.

Through single nucleus sequencing on Tapestri, Marchuk and Snellings validated their findings that two mutations are occurring in the same group of cells. “They are getting two somatic mutations that are knocking out both copies of that gene,” Snellings said. “So those genes can’t make any functional protein in those cells, which causes the cerebral cavernous malformations.”

The team also decided to sequence the CCMs on an oncopanel to compare them to various oncogenes related in cancer. They found that 70% of their CCM samples had a somatic activating mutation in PI3-kinase, which is the second most commonly mutated gene in cancer. “We never knew about this,” Marchuk said. “We thought it was just the CCM genes getting mutated.”

Some patients have hundreds of these CCMs in their brain, and while there have been many ideas on how to treat these lesions without surgery, discovering that they are related to cancer opens up new avenues for treatment as cancer drug development is a much larger market. Outside collaborators with Marchuk’s team made a mouse model of CCM and showed that the immunosuppressant drug Rapamycin, which inhibits PI3-kinase signaling, is very effective at preventing CCM formations. “This is a promising new therapy candidate for CCMs that is based on our work,” Marchuk said.

This research has been published in Nature.

While the Marchuk lab was the first to use the new Tapestri platform, Sequencing and Genomics Technology Director Nicolas Devos expects that this new machine will be helpful to a variety of investigators. “This will allow for much more single cell analysis work to be done at Duke,” Devos said, “and will help people who are asking very specific questions about individual cells.”

To learn more about Tapestri or to set up a consultation, visit the Sequencing and Genomic Technology website.

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Daniel Snellings discusses cerebral cavernous malformations

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