Several studies have been published linking epigenetic mechanisms to gene functions in cancer, autoimmune disease, as well as biological processes like aging. With the release of the EpiFinder family of products, newly-minted start-up Epigenica hopes to improve scientists’ ability to capture and extract insights from the epigenome. 

This week, the Solna, Sweden-based company announced the launch of the EpiFinder platform, its patented high-throughput, multiplexing, quantitative ChIP-seq technology platform. The company also unveiled EpiFinder Genome, its flagship product and first commercial kit of its kind. According to the company, the kits can be used to target up to eight common and rare markers including DNA methylation in up to 24 samples or independent replicates. It’s a cut above some kits currently on the market that can only profile one sample against one marker. The company also claims that its technology can generate up to 192 genome-wide profiles in a fraction of the time it takes to perform 192 parallel ChIP-seq experiments. 

Describing the release, Epigenica CEO and co-founder Mohamad Takwa, PhD, said, “The development of these technologies has been a true labor of love for our team and marks an important milestone for Epigenica as we advance our mission to bring unprecedented scale, speed, and affordability to the rapidly growing field of epigenetics.”

According to Björn Reinius, an associate professor at the Karolinska Institute with a research focus on X-chromosome inactivation, who beta-tested EpiFinder Genome, the kit is well-suited for researchers with limited prior experience with ChIP-seq or similar methods for obtaining high-quality ChIP-seq data.

Democratizing the epigenome

Takwa met his Epigenica co-founder and CSO Simon Elsässer, PhD, nearly seven years ago when they both worked on a medtech project. They reconnected four years ago when Elsässer reached out to discuss an idea for an epigenetic profiling project. 

They ultimately decided to work together to co-found Epigenica to commercialize the technology they’d worked on, Takwa told GEN. This decision was driven by what they believed was a need in the market for a technology that could democratize epigenetic profiling and generate quantitative data at scale.

While EpiFinder Genome is the first product they are launching, the Epigenica team plans to ultimately offer a range of kits that provide genome-wide detail with high sequencing depth to global quantifications based on low-depth sequencing. All products made by the company will be able to generate epigenetic data at a lower price point than is currently possible with the gold-standard kits, according to Takwa. In fact, Epigenica’s throughput, and multiplexing capabilities are the company’s main advantage over other players in the market, he said. “Also this scale makes it so that we really have a price advantage as well [because] when you do many profiles at the same time, you reduce the price and the time as well.” 

At the core of Epigenica’s platform are two proprietary technologiesits hmqChIP-seq technology and its Ligation-sensitive Amplification with Coded Adaptor (LACODE) design and barcoding technology, which the company claims significantly improves on current DNA barcoding approaches. It does this by avoiding the formation of dimers where two adapters bind to each other resulting in increased background noise, Takwa explained. With the LACODE technology, only barcodes that successfully bind to DNA are translated, while all others are eliminated. This both reduces background noise and offers greater specificity compared to current approaches.

Both technologies were developed at the Karolinska Institute. Details of an early version of the technology were published in Cell Press in 2019. That paper described an application of their ChIP-sequencing technology to quantify histone modification patterns in mouse embryonic stem cells. In addition to the kits, Epigenica has also developed an open-source, custom-designed software for analyzing data generated using EpiFinder Genome. Details of the company’s analysis pipeline are shared in a 2022 bioRxiv paper. In it, the scientists describe a user-friendly workflow for transforming raw sequencing files into normalized data for quantitative downstream analysis. Takwa added that the company also has additional publications in the works.

The primary target markets for the kits are scientists in biomedical research laboratories as well as pharmaceutical companies developing drugs that target the epigenome. Other customers include scientists working on research into aging and longevity. Customers can now purchase EpiFinder Genome kits from Epigencia. Each kit comes with instructions for preparing the samples for sequencing. For now, customers have to do their own sequencing but Epigenica plans to begin offering sequencing services to support customers who don’t have their own capabilities in-house, Takwa said. For now, once the customers have generated their data, they can upload it to the company analysis pipeline, which converts the sequencing data into normalized quantitative data. 

Besides offering a sequencing service, Epigenica also plans to add new products to the Epifinder family in the near future. All products will share some features including high-throughput, multiplex capabilities, and access to the company’s data analysis tools. But each product will offer a different level of profiling or will be optimized to work with different starting materials such as liquid biopsies. 

Upcoming products include one called EpiFinder Global which Takwa says will be the first ChIP-seq global profiling technology. It will offer higher throughput and more multiplexing capabilities than existing technologies. Another upcoming product is EpiFinder c-Nuc, which will be a genome-wide profiling kit for capturing data from circulating nucleosomes in the blood. Both products should be on the market in early 2025. 

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