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Startup Cartana Aims to Commercialize Spatial Gene Expression Technology

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SAN FRANCISCO (GenomeWeb) – Cartana, a Swedish startup that spun out of the Science for Life Laboratory in 2017, is developing in situ RNA sequencing technology that is based on research originally developed in Mats Nilsson's laboratory at SciLifeLab.

Malte Kühnemund, CEO of Stockholm-based Cartana, said that after the SciLifeLab researchers first described the technology in a 2013 Nature Methods study, the group began receiving requests for collaborations and decided to make the technology robust and optimize it to offer it as a service.

The company currently has eight full-time employees and expects to reach 10 to 12 employees by the end of the year. Last year, it raised SEK 10 million ($1 million) in financing, which will support further development of its technology, including a new sequencing chemistry, and the launch of its service facility, Kühnemund said.

Cartana's technology is based on using barcoded padlock probes to target genes of interest. The probes target cDNA and are amplified in situ using rolling circle amplification, followed by sequencing-by-ligation, also directly on the tissue.

Kühnemund said that currently, the main application of the technology is to study and map cell types that researchers have identified through single-cell RNA sequencing. "It's very complementary to single-cell RNA-seq technology," he said. While the latter can identify cell types in a high-throughput manner, Cartana's technology can map those cell types in a tissue by targeting certain marker genes, he added.

Cartana's first product is NeuroKit, which can identify more than 100 genes from a brain tissue section at single-cell resolution. Customers can either prepare their own samples using the Cartana kit and then send them to Cartana for in situ sequencing, or they can send their tissue slide to Cartana for the entire process of sample prep, sequencing, and image analysis.

"In the future, we want to also provide a sequencing kit, so customers can do the in situ sequencing part themselves," Kühnemund said. In order to get to that next step, however, the company would look to partner with an instrument company, he said. Already, the team has begun collaborating with an undisclosed partner to automate the image analysis.

In addition, Kühnemund said, the firm is working on developing a different sequencing chemistry. The current product and service makes use of the sequencing-by-ligation chemistry described in the original Nature Methods study, but the group is working on a new chemistry, details of which Kühnemund declined to disclose.

Last fall, researchers from SciLifeLab and University College London described in a paper published on the BioRxiv preprint server how they used the RNA in situ sequencing technology to map inhibitory neurons in an area of the mouse hippocampus that is important for memory. Cell types in that brain region have already been well characterized, so the researchers first validated that they were able to recapitulate what is already known.

For their experiment, the researchers selected a panel of 99 genes that can be used to identify cell types. Next, they created a set of padlock probes to target the genes. Each padlock probe contained so-called recognition arms  — two arms that matched a 40-bp sequence in mRNA molecule — as well as a 4-bp barcode, an anchor sequence, and a 20-bp hybridization sequence. In total, the team designed 755 probes.

They then converted mRNA to cDNA in situ and applied the padlock probe library. A ligation enzyme then circularized the probes that bound to the cDNA targets, followed by via rolling circle amplification. Finally, the amplification products, which contain hundreds of copies of the barcode, were analyzed via fluorescence imaging.

The researchers confirmed that the expression patterns for genes they targeted that had also been studied as part of the Allen Mouse Brain Atlas were consistent between both data sets.

Kühnemund said that analyzing brain cells would be a major application but noted that researchers have also applied the technology to study the development of embryonic stem cells. He said that the company is also working to develop a kit to target immune cell marker genes for applications in the growing immuno-oncology space, for example to map immune cells inside tumors and to study "how they react to certain therapies to understand why some work and some don't."

The spatial genomics field, while still nascent, has grown rapidly just over the last year. Another SciLifeLab spinout, Spatial Transcriptomics, was acquired by 10x Genomics last year, for example. Spatial genomics was also a big theme at this year's Advances in Genome Biology and Technology meeting, with 10x discussing its plans to commercialize technology derived from the Spatial Transcriptomics acquisition and NanoString Technologies presenting early-access data from its Digital Spatial Profiler, GeoMx. 

Kühnemund said that while the Cartana and Spatial Transcriptomics technologies were developed separately in two different SciLifeLabs groups, and while there is no business relationship between the companies, the two labs have collaborated and worked to combine their technologies in various research projects, including to study heart development.

In addition, Cartana is applying for grant funding through the EU's Horizon 2020 research program to contribute to the Human Cell Atlas project, he said. 

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