Building a tool that maps genes in cells

BIOTECH CartaNA’s technology has been described as Google Maps for finding how specific genes are expressed in the body. The technique is set to have a major impact on accelerating the development of new drugs.

“We usually refer to the technique as a kind of Google Maps for biological tissue. It identifies where individual genes are located in tissue, and with the help of gene expression, cells can also be identified,” says Francesca Bignami, CartaNA co-founder.

The technique is called in-situ-sequencing and has been developed over the past 20 years at Mats Nilsson’s lab at the SciLifeLab, (Science for Life Laboratory), research center.

In-situ-sequencing maps which genes are expressed in a particular cell directly in the tissue itself. By analyzing a cell’s DNA, the technique can show which RNA molecules are present in a cell. This provides better understanding of a range of diseases, from Alzheimer’s and Parkinson’s to cancer. The result of the sequencing is shown as fascinating and colorful images – see above image that shows sections of a mouse brain.

Quickly triggered international interest

A description of the technique was first published in 2013 in an article in Nature Biotech and generated considerable international interest in the research world. The lab was soon flooded with enquiries and proposals for collaborations, quickly raising the prospect of commercializing the technique.

This task was handed to Malte Kühnemund, who led the work of transforming the method into a shareable product. Kühnemund and co-founders Xiaoyan Qian and Thomas Hauling all worked under Mats Nilsson’s leadership. They were now joined by Francesca who is an engineer in biomechanics with a passion for innovation and entrepreneurship. She came to Karolinska Institutet (KI) in 2011 to participate in a research project that set out to map all KI’s innovations of the previous 15 years.

When Francesca with the other co-founders decided to launch Cartana in 2017, she was working on her doctorate at the Unit for Bioentrepreneurship at KI.

“My PhD gave me the opportunity to learn more about the innovation ecosystem in the life science industry and in Sweden. CartaNA has been the perfect environment where to put in practice the innovation theory studied during my doctoral education ”

For the launch, the team had help from Drive, KI Innovation’s business incubator.

“They helped us to understand our weaknesses, and what we needed to progress. We’ve had a lot of help from the whole region’s innovation ecosystem with all available networks,” she says.

“There’s no middle ground when you start a company, you have to go all in and work evenings and weekends. But I’m not complaining because I like it.”

Acquired by 10x Genomics

The strength of the technique and the team meant that CartaNA got off to a flying start, Francesca explains.

“The pace of change in biotech right now is extremely fast, it seemed a natural step to be able to continue developing our technology by joining the team at 10xGenomics” she says.

In the summer of 2020, CartaNA was acquired by 10x Genomics, which in 2018 also bought the gene analysis company Spatial Transcriptomics founded by Joakim Lundeberg, professor of genetic engineering at KTH, and Jonas Frisén, professor of stem cell research at KI.

“Our technologies complement each other. Both offer tools that can show which genes are expressed in a tissue but with different levels of detail. Thanks to the acquisition, we can now develop further together at 10x Genomics research center in Stockholm,” Francesca says.

All former CartaNA employees have joined 10x Genomics. Today, Francesca has a business development role while maintaining her links to KI, where, among other things, she has taught fellow researchers interested in starting companies.

“Now I hope to be able to share my knowledge further, perhaps through guest lectures for researchers and students,” she says.

Text: Magnus Trogen Pahlén.
Photo: Håkan Lindgren.