Genomics, transcriptomics and proteomics can all now be run at scale. Epigenomics, the study of how genes are switched on and off, has lagged behind, especially in liquid biopsy. In this Spotlight On, we look at Epigenica AB, a Swedish company building tools to measure epigenetics across many samples and marks at once.
Epigenica is working on a basic question for the field: how do you actually measure epigenetics at scale?
Why epigenomics hasn't scaled
Epigenetic changes control which genes are active. They play a part in everything from normal development to cancer and neurological disease. Even so, the tools for measuring them have held the field back:
Few options for running large numbers of samples.
Most methods look at only one or two marks at a time.
Workflows are complex and hard to scale up.
As a result, epigenomics is used far less widely than other omics. In some ways, it sits where genomics was 10 to 15 years ago: plenty of scientific interest, but not yet the tools to support large studies.
About Epigenica
Epigenica is based in Sweden and led by CEO Mohamad Takwa. Its product range is called the EpiFinder technology suite. The company was set up after early work with industry showed a clear gap: there were no quantitative epigenomic profiling tools that could handle large studies. The team has experience of scaling life science tools businesses before, including Olink's growth from start-up to an acquisition of around $3 billion.
The EpiFinder platform
Epigenica's platform has four parts, covering research from early discovery through to translational work:
Part: EpiFinder cNUC
Used for: Liquid biopsy and translational research
Part: EpiFinder GenomePro
Used for: Discovery research and drug development
Part: EpiFinder Analysis Services
Used for: Running studies from sample to data for customers
Part: Data processing and bioinformatics
Used for: Standard analysis and interpretation of the results
Most existing methods measure one epigenetic mark at a time. Epigenica's technology measures several in parallel, across many samples in one run. The main difference is that it can profile histone modifications and DNA methylation together in one workflow. Researchers get a fuller picture of gene regulation from a single experiment, instead of combining results from separate assays.
EpiFinder cNUC: epigenomics from a blood sample
EpiFinder cNUC is Epigenica's lead product. It profiles the epigenetic marks carried on circulating nucleosomes, small packages of DNA and protein found in plasma or serum.
Most liquid biopsy methods look for mutations or DNA methylation alone. cNUC also reads the histone marks on those nucleosomes, which show which gene programmes are active and which tissues the DNA came from. It is designed for research into:
Liquid biopsy biomarker discovery.
Cancer monitoring.
Disease stratification.
Precision medicine.
Early detection.
Results from a colorectal cancer study
In a recent colorectal cancer study, cNUC:
Produced genome-wide epigenomic profiles from as little as 200 µL of plasma.
Clearly separated cancer samples from controls using clustering and PCA.
Added fragmentomics and copy-number analysis from the same workflow.
Identified disease-linked gene regulation at the level of individual genes.
EpiFinder GenomePro: genome-wide profiling for drug discovery
GenomePro is built for quantitative, genome-wide epigenomic profiling in cells and tissue. It analyses histone modifications, DNA methylation and transcriptional regulators in one workflow.
Low input. It needs only 0.5 to 1 million cells, or 10 to 15 mg of tissue, per sample.
Less variation between samples. Samples are pooled early, so they are processed together and can be compared directly.
No spike-ins. Results are normalised to an input sample.
Flexible samples. It is validated for native cells, fixed cells and tissue.
Open-source analysis. Automated pipelines take raw FASTQ files through to quantitative datasets.
Lower cost per dataset. Running many samples and targets together cuts the cost of large studies.
Analysis services and bioinformatics
For teams without their own lab set-up, EpiFinder Analysis Services runs the whole study. That covers sample processing for cells, tissue and liquid biopsies, multiplex analysis and sequencing, data processing and standard data delivery. Further bioinformatics support is available if needed.
This lowers the cost and effort of getting started and gets results back faster. Epigenica also provides a bioinformatics layer to help researchers make sense of the data:
Standard, open-source pipelines from raw sequencing data to quantitative datasets.
Built-in quality control and interactive data exploration through its EpiPeak tool.
Copy number and fragmentomics analysis from the same genome-wide data.
Support for combining EpiFinder results with other omics data.
Together, these keep results consistent across experiments and shorten the time from data to biological findings.
Why it matters
DNA sequence alone doesn't explain how genes are controlled. Epigenomics adds that information, and it is relevant to:
How gene regulation works.
Disease biology, including cancer and neurological conditions.
Liquid biopsy and non-invasive testing.
Biomarker discovery.
Without tools that scale, much of this has stayed out of reach for large studies. Epigenica's aim is to make epigenomics a routine part of multi-omics research, alongside genomics and proteomics.
What it means for hiring
Growing a tools company the way Olink did depends on making the right leadership hires at the right time. Companies at this stage typically need:
Commercial leaders who can build sales in a market that is still developing, across pharma, academic and translational research.
Scientific and product leaders with experience in epigenomics, liquid biopsy or multi-omics assays.
Bioinformatics and data leaders who can make complex data usable for customers.
Executives and board members who have taken a life science tools company through rapid growth or acquisition.
Pharma and diagnostics companies building liquid biopsy and biomarker programmes need many of the same skills in their own teams.
What's next for Epigenica
With its products and services now in place, Epigenica is moving into a growth phase. The team is focused on:
Producing case studies and validation data.
Raising its profile in the epigenomics and multi-omics communities.
Meeting researchers at major conferences such as AACR.
You can find out more about the EpiFinder platform and analysis services on the Epigenica website.
