CHICAGO – Following a year of growth in 2020, Dutch bioinformatics firm Enpicom sees 2021 as the year in which it diversifies into multiomics and begins to unlock some of the promise of personalized medicine, while its clients continue to address the COVID-19 pandemic.
Based in s'Hertogenbosch, the Netherlands, Enpicom makes a bioinformatics technology called ImmunoGenomix (IGX), a cloud-based, software-as-a-service (SaaS) platform to manage, store, analyze, visualize, and interpret T and B cell repertoire sequencing data. While it can integrate information from other sources, it was built specifically to handle molecular immunomics data.
"The SaaS approach eliminates deployment time, substantially reduces maintenance costs, and ensures that users always have access to the latest version of the IGX Platform," according to a company spokesperson.
In November, Enpicom expanded its partnership with Neogene Therapeutics, a developer of personalized neoantigen T-cell therapies fresh off a $110 million Series A fundraising round, which is adopting IGX to manage and analyze T cell sequencing data. Enpicom said that it has customized its platform to help the technology fit the workflow of Amsterdam-based Neogene.
Last month, Enpicom and MiLaboratories announced a strategic partnership to integrate MiLaboratories' MiXCR immune repertoire sequencing software into IGX. Solana Beach, California-based MiLaboratories produces a human T cell receptor profiling kit, immune cell profiling services, and software tools and algorithms to analyze immune cell profiles.
Enpicom was founded as a limited liability company in 2017 by CEO Jos Lunenberg, CTO Alvise Trevisan, and CSO Nicola Bonzanni, after being spun out of Vrije Universiteit Amsterdam two years earlier. The firm now has about 30 employees.
According to Lunenberg, algorithms developed to process other parts of the genome simply do not work well for immunomics data. "This particular small piece of DNA or RNA is unique because it's so diverse," he said.
"There was a chance to bring something unique to market, because there's a lot of companies out there who concentrate on the other parts" of the genome according to Lunenberg. He noted that immunotherapy and antibody development are fast-growing segments of the pharmaceutical industry at the moment, in part because of the worldwide race to develop and administer effective COVID-19 vaccinations.
"Anybody with an interest in immunology, very basic to translational, to more clinical, related to immunotherapy development or discovery potentially can benefit from a product like ours," Luneberg said.
Bonzanni said that Neogene is trying to develop personalized therapies using T cell receptors.
"This of course, offers many challenges," he said, not the least of which is data management, as data volume explodes when having to look at sequences for each individual.
"On top of that, they have a proposition which is based on immunogenomics. They developed TCRs … and therefore they need a specialized system for that kind of data," Bonzanni said.
"There is where our platform shines because it's not a generic genomics platform. It's a platform for organizing that specific kind of data," he said.
Lunenberg noted that Neogene is just one company in the burgeoning market for neoantigen therapeutic development, though that firm has been in the news for its recent fundraise.
Enpicom itself is funded by venture capital, and most recently added a €1.1 million ($1.4 million) follow-on in May 2020 to its €1.2 million Series A round that closed in March 2019.
The company also has received some grants from the European Commission and individual European countries and localities.
Enpicom took another step forward in precision medicine in September when it announced the Princess Margaret Cancer Centre, part of Toronto-based University Health Network, as a user of IGX. Specifically, the laboratory of Princess Margaret senior scientist Trevor Pugh hopes to make comprehensive genome analysis part of a routine clinical test to choose therapies for cancer patients.
According to Enpicom, the Pugh Lab is trying to understand the clinical implications of clonal shifts in cancer and non-cancerous cells alike, using technologies including cell-free DNA, immune repertoire sequencing, and single-cell RNA sequencing. "IGX offers us flexibility, ease of use, data integration, and data sharing possibilities — all criteria that we consider extremely important to properly support our scientific work," Pugh said in a statement.
Institutions as large as Princess Margaret Cancer Centre — as well as the international scientific consortia they belong to — require data management and sharing capabilities, Lunenberg said.
"The same is true for antibody developers," he said. "You have a lot of service providers in the field of antibody development [that] also need to be able to share the results of their discovery work with their clients."
Lunenberg said that the data management capability in IGX is "broadly applicable."
Enpicom released version 2.0 of IGX in April 2020. That release supports single-cell sequencing data and bulk sequencing data workflows in tandem.
Enhancements in V2.0 include the IGX-Compare app, which allows users to compare any two data sets to visualize and prioritize matching clones; and more extensive data support, supporting the upload of readily annotated clone tables from, for instance, 10x Genomics or Adaptive Biotechnologies. The new version also features more clonotype grouping definitions and V/J gene usage plotting, the company said.
Another platform update is expected early this year. Enpicom said that it would "expand the available functionalities even further, offering an intuitive end-to-end solution for antibody developers."
In 2021, Enpicom will be looking to incorporate more downstream analysis by launching a module that eventually will contain three different apps, according to Bonzanni. He did not offer more details.
Bonzanni did say, however, that Compare is proving to be useful in development of COVID-19 therapies and vaccines. For example, a researcher might see whether something in the immune system might explain why some patients infected with the novel coronavirus develop severe symptoms, while others do not.
"What the Compare app allows you to do is to compare a large amount of sequences," Bonzanni said. This is important, he explained, because there is no true reference genome in immunomics.
"There can be billions of possibilities. There is not such a thing as a complete database of references that you can just go out there and look into it. That's why you need this kind of special algorithm," Bonzanni said.
"It allows you to compare across different individuals, different samples, different repertoires, and different immune systems," Bonzanni continued. "Understanding what are the differences is the key to potentially developing new vaccines or diagnostics."
Enpicom software currently is completely targeted toward researchers, but Bonzanni noted that the company would eventually like to get its software into clinical settings.
Immunomics and immunogenomics may represent niche spaces now, but Enpicom expects those interrelated fields to grow exponentially in the near future.
"Our immune system conserves the history of all our diseases. It's sort of a library of all these diseases," Bonzanni said. It also serves as a compendium of "solutions" to those conditions for those who overcome them.
"You can imagine a future which might or not be very far away, in which you will be able to look at the immune system of a person and perhaps uncover what are the diseases that this person had in the [past]" and might develop in the future, Bonzanni explained.