NEW YORK (GenomeWeb) – Dutch bioinformatics software company Enpicom seeks to build a business around ready-to-use software that will initially support target discovery and development in the immunotherapy space, with plans to expand into clinical applications such as patient stratification and treatment monitoring.
The newly minted limited liability company, based in Amsterdam, the Netherlands, has tapped Jos Lunenberg to serve as its CEO and plans to hire additional staff in the coming weeks, bringing its total headcount to six employees. Lunenberg joins Enpicom after serving as co-owner and chief business officer for Genalice, a bioinformatics company that offers tools for sequence alignment, data correlation, and clinical decision support.
Enpicom's ImmunoGenomiX platform will include individual software modules for different markets. Lunenberg said that the company's first such product will be available next year, a research-use-only software solution for immunotherapy. The planned solution will enable researchers to analyze sequence data from samples prepared via various sample prep protocols and sequenced on various sequencing instruments, he said. It will fill a current need in the market for more flexible tools that let customers pick and choose which resources they want to use in their immunotherapy research.
Currently, customers have two options when it comes to analysis tools for immunotherapy, according to Lunenberg. "You have all kinds of open-source tools that you have to script together to make a workflow from start to finish … depending on your research or clinical question," he said. The alternative is to purchase analysis solutions that come prepackaged with assays developed and sold by companies such as Adaptive Biotechnologies.
The problem with the first option is that it requires customers to have sufficient computing experience. Furthermore, the interfaces to many open-source solutions are not the most user-friendly. In terms of existing commercial assays, some clients already have their preferred sample prep protocols and sequencing instruments, so they don't require the full assay solution offered by Adaptive Biotechnologies, for example, Lunenberg said, because all they want is the data analysis. Unwilling or unable to cobble together their own informatics pipelines, some customers turn to existing commercial solutions sold by bioinformatics firms like Genalice, but those tools are not designed for the unique requirements of the immunotherapy development market, he said.
Enpicom's solution is designed to analyze sequences from patients' B-cells and T-cells to gain accurate snapshots of their immune systems at a given time point. One of the challenges for existing software solutions in terms of analyzing this type of data is the level of variability in the T-cell and B-cell repertoires of cancer patients, for example, Lunenberg explained. "There is [so much] variability in the genes that are coding for the T-cell receptor and the B-cell receptor … that standard procedures to do alignment and variant calling on these parts of the DNA don't work," he said. "You have to have totally different algorithms for it."
One other challenge for the market is a shift towards RNA-based B- and T-cell analysis. However, "what most companies on the market currently have is a DNA-based assay, and a lot of potential customers don't want that," Lunenberg said. Moreover, current assays focus largely on T-cell receptor beta chains but clients that Enpicom has spoken to have also expressed interest in analyzing T-cell receptor alpha-chains as well as gamma- and delta-chains, which software solutions offered with existing assays do not support, he added.
Enpicom is currently developing its solutions in collaboration with various small and medium-sized enterprises and academic institutions. Its first solution will target customers working in the oncology research space but the company hopes to have a clinically-focused, validated solution on the market within two years. It will also gradually explore immunotherapy applications in disease areas outside the oncology domain for example in the autoimmune diseases area as they gain traction.
"What we want to bring to market is a solution that is flexible on the front end, that can basically pick up any kind of data coming from any kind of sequencing machine [from samples] prepared with any kind of sample preparation protocol, because that [currently] doesn't exist," Lunenberg said. In addition, the company wants to make measurements over time. "If you want to monitor a patient, you need to be able to correctly interpret the data that you observe at different time points, or do a differential analysis between patients. That is something that is not available yet, but there is a clear need," based on conversations with people in the field.
That ability to monitor patients' disease development over time will be a key feature of Enpicom's clinical solution, helping to point clinicians towards more effective treatments for the patients in their care. For example, clinicians could use the solution to monitor dominant T-cell clones present in patients' tumors prior to starting chemotherapy, during treatment, and post treatment. "They'll be able to detect at a much earlier stage whether there is a breakthrough or whether there is still residual disease and make clinical decisions earlier," Lunenberg explained.
Enpicom's product portfolio grows out of work done under its initial business model. The company spun out of Vrije Universiteit Amsterdam in 2015. It was originally set up as a partnership between Nicola Bonzanni and Alvise Trevisan, now the company's CSO and CTO, respectively, to provide tailored bioinformatics solutions for clients. One of those customers was Kite Pharma, a biopharmaceutical company that focuses on developing cancer immunotherapy products and was recently acquired by Gilead Sciences for $11.9 billion. Enpicom initially developed the solutions it is now bringing to market for use at Kite Pharma.
"We started working with them mainly on getting an algorithm on sequence selection and categorization for one of our projects involving T-cell receptors," said Markwin Velders, Kite Pharma's vice president of operations and managing director. Their solution "helped us to order large datasets into valuable and accessible [information]. It helped us select the right sequences to continue with." In addition, Kite also used Enpicom's solutions to ensure that sequences that it selected for further study did not infringe on any existing patents, he said. Velders also highlighted the software's ease of use as one of its key benefits.
Enpicom plans to offer its solutions under a license-based model but is not disclosing prices at this time. Initially, customers will have to install Enpicom's solutions locally if they purchase them but the company is open to exploring partnerships with existing bioinformatics companies, such as DNAnexus, that have cloud-based platforms, Lunenberg said. "It doesn’t make sense to do things like that yourself if there are platform providers that have a good stake in the market and [whose] products are already ready [and being used] by many of our potential customers."
That list of potential customers includes researchers in academia working on new immunotherapies, as well as biotechnology and pharmaceutical companies. Later on, when Enpicom's clinical solution comes to market, the company hopes to see its products peddled in clinics as well, and not just for cancer applications. "[There] is value [in] T-cell repertoire and B-cell repertoire analysis in the field of autoimmune diseases and organ transplantation, to observe whether the immune system is recovering well or not [for example]," Lunenberg said. So "that is a second audience that we can identify."
Meanwhile, Kite Pharma continues to use the Enpicom-developed solution internally, Velders said, and the companies are still in contact regarding software development in general. It is not clear how the partnership will proceed under Kite's new ownership – Velders declined to comment on the combined company's plans moving forward.
Enpicom is also partnering with companies and academic institutions currently developing immunotherapies to create assays that cover tools for sample prep through to analysis using Enpicom's solutions. It has also set up a Eurostars consortium with several immunotherapy developers, data management companies, and a university medical center in Europe to work on validating its solutions. It has applied for grant funding from Eureka, a pan-European intergovernmental research and development funding initiative, to support those efforts. Enpicom also received an early-phase loan of an undisclosed amount from the Dutch Ministry of Economic Affairs, which it is using to support product development and expand its team.