CAR-T, and related cell therapies such as TCR, are an exciting new field of biologics drug discovery targeting cancer. Two CAR-T therapies, Kymriah (Novartis) and Yescarta (Gilead / Kite Pharma) have been approved to date, and there are more than 100 companies working to develop additional CAR-T treatments. CAR-T treatments are a “living therapeutic” utilizing a patient’s own T lymphocyte cells, that have been augmented through genetic modification with a cancer-targeting CAR (Chimeric Antigen Receptor). This truly represents personalized medicine!
Research to develop new CARs, along with associated regulatory mechanisms, is an extremely active and exciting field. CARs are artificial antigen receptors proteins, comprised of sub-domains of various naturally occurring and artificial entities. As with any new area of drug discovery research, rapid advances are being made, and agility in research programs is paramount. The Dotmatics Informatics Platform is ideally suited to support this exciting field of drug discovery.
Intellectual property protection and tracking candidate CAR complexes
As the name indicates, CARs are complexes comprised of multiple sub-domains, constructed through recombinant biology. While there is an ever-increasing variety of types, current therapeutic CARs are constructed from four distinct domains: an antibody single-chain variable region (scFv) for antigen recognition and binding, a spacer region to facilitate binding of the scFv and receptor aggregation, a transmembrane domain for targeting and placement of the CAR in the cell plasma membrane, and an intracellular signaling domain, including co-stimulatory regions, to generate the immune response once the CAR binds to a target cancer cell. A CAR research project will involve multiple parent versions of these domains, as well as many child variants (i.e., residue variations) of each of them, leading to challenges of tracking the many potential permutations of the sub-domains. Dotmatics Bioregister is ideally suited to managing this complexity, allowing each sub-domain, and their variants, to be registered and tracked individually, as well the CAR entity type, and all its variations, that they make up. Tracking, including managing lineages and relationships with physical samples, is critical to establishing intellectual property protection for your candidate therapeutics.
CAR and sub-domain analysis, visualization and design
It’s critical to be able to view both the entire sequence of a CAR as well as the subdomains, perform alignments, and analyze the potential or actual effects of residue substitutions, insertions and deletions. By analyzing experimental data from CAR variants, molecular biologists can determine the effects of these changes and make predictions on which additional changes will confer positive properties in new variants. Dotmatics Vortex has the power, and breadth of capabilities, to allow scientists to perform these critical tasks. Vortex can easily handle the data volumes used in CAR-T research programs, while still allowing each residue, of each candidate complex, to be individually addressable for analysis.
Experimental data capture – supporting standard processes and novel science
Developing a CAR is an involved process, requiring careful coordination to design and build the sub-domains, and test the effectiveness of each complete candidate receptor. It is critical that project experiments are captured in an electronic laboratory notebook (ELN) to preserve the full details of the work done. This further contributes to IP protection given the importance of process reproducibility to biologic drug discovery. Dotmatics already has preconfigured ELN protocols for many common laboratory workflows utilized in biologics drug discovery, such as animal immunization, protein production and purification, and various molecular biology workflows. But CAR research for drug discovery is a rapidly evolving field, meaning new science is being developed to support it. The Dotmatics ELN is designed to have the flexibility needed to support emerging scientific methods. Existing protocols can be extended to support newly designed workflows, and the ELN can also be used in a simple “paper-on-glass” mode to capture first-time experiments and associated documents.
Capturing and analyzing assay data
Once you have candidate CAR entities created, you’ll be performing primary and secondary screening to assess their potential and investigate the effects of variations and combinations of sub-domains. As always, collecting and processing the data, and performing first level analysis is critical, and minimizing error-prone manual tasks is essential to generating the highest quality data possible. Dotmatics Studies provides advanced capabilities including the ability to automate much, if not all, of the workflow from when plates are first placed into the readers, through to first-pass QA analysis, curve fitting and categorization of results. Working with lab automation and Internet of Things (IoT) vendors, Dotmatics has a proven track record of supporting seamless, end-to-end assay workflows.
Managing physical samples and batches
As the research progresses, you will create multiple samples and batches of individual CAR candidates. The conceptual representation of these is managed in Bioregister, and the corresponding physical representation is managed in Dotmatics Inventory, with cross-referencing between them, so you always know where to find a given entity. If you choose to use a different inventory system, APIs in Bioregister and throughout the Dotmatics Platform should allow you to make and maintain these relationships (limitations may exist on the other system).
Organizing research data and tracking project progress
As with any drug discovery research program, CAR-T research is complex and generates huge amounts of data, which is stored in multiple databases and file-shares. Aggregating the data to allow a comprehensive project view can be a labor-intensive, onerous task, meaning that often project decisions are made on incomplete or out-of-date information. Dotmatics Browser solves this problem, allowing all project data to be viewed together in configurable views that always have the most up-to-date information. For example, as soon as an ELN experiment is signed-off (or otherwise meets organizational business rules), the information is available in Browser. Similarly, with increasingly automated assay systems, screening data, perhaps generated overnight at a CRO, are available as soon as you log in to the system.