I was recently a panelist at the 31st Protein Structure Determination in Industry Meeting (PSDI...
In the fast-paced world of cryo-EM methods, remarkable advancements can occasionally go unnoticed amidst the constant stream of new research, particularly when they are not published in a top-tier journal. One such example is a revolutionary 'structure-to-gene' method, published by the Ward group at Scripps Research in January 2022, in the journal Science Advances. I want to write about it because I found that awareness is low even in the cryo-EM community, let alone amongst people who are engaged in antibody discovery research. And I've chosen to spotlight this 'structure-to-gene' paper in the first scientific cryoDuck blog post because it perfectly embodies the very essence of innovation, ingenuity, and bold thinking that we at cryoDuck strive to foster. So let's take a look together.
What is cryoEMPEM?
The structure-to-gene technique employs Electron Microscopy Polyclonal Epitope Mapping (EMPEM) to accelerate the discovery of therapeutic antibodies. CryoEMPEM itself is a revolutionary approach in its own right. CryoEMPEM is a powerful method for visualizing polyclonal antibody responses elicited by vaccination or infection. EMPEM starts by collecting blood samples from animals or individuals who have been either vaccinated or infected. The next step is to isolate polyclonal antibodies from the serum and to complex them with their antigen. These very heterogenous complexes are then imaged by cryo-EM to map epitopes of the polyclonal mixture. This reveals the diversity of epitopes recognized by the antibodies and can give insights into which ones might be most effective in neutralizing the pathogen. This can then be used to inform the rational design of new vaccine constructs, which are optimized for antigen integrity, manufacturability, and neutralizing antibody response. However, the real breakthrough comes when EMPEM is used for the discovery of monoclonals.
Going from cryoEMPEM maps to handpicked monoclonals
The 'structure-to-gene' method expands the applicability of cryoEMPEM to the identification of specific monoclonals. It takes a hybrid approach that uses the structural restraints from cryoEMPEM maps and next-generation sequencing (NGS) data of antigen-specific B cell repertoires for identification of monoclonal antibodies. While the 3-4 Å reconstructions of polyclonal-derived antigen-antibody complexes are often too ambiguous to directly determine antibody sequences, these sequences can be inferred by reconciling heterogenous cryo-EM density maps with NGS data obtained from antigen-binding B cells.
The present method differs dramatically from conventional monoclonal antibody discovery practices that rely on individual B cell sorting, hybridoma techniques, and phage display technologies. In traditional antibody isolation techniques, a bottleneck often emerges during the screening of monoclonal libraries to spot clones exhibiting the preferred epitope specificity. However, this new approach starts with detailed epitope data for antigen-specific polyclonal antibodies, enabling researchers to selectively choose antibodies based on their desired epitope and binding orientation.
Clovertex for all your cryo-EM computing ducks
Bringing such an application into the mainstream of antibody discovery so that researchers can discovery better antibodies in a fraction of time, would of course be disruptive. But the future of this particular next-gen cryo-EM application and all other ones depends on further workflow improvements and method developments. It will require streamlining and miniaturization of sample preparation, more efficient cryo-EM workflows, advances in orthogonal technologies like NGS, and above all better structure-to-sequence algorithms with slick implementations thereof. Perhaps you can guess who is eager to help with getting all these ducks in a row. And that's why I want to present you one special partner in the cryoDuck ecosystem.
Given the paramount importance of scientific computing for cryo-EM, and particularly for next-gen cryo-EM, I am thrilled to announce our collaboration with Clovertex, Inc. With deep roots in the fields of both cryo-EM and genomics, Clovertex brings a unique blend of IT and scientific expertise to the table. Their experience enables them to craft intricate, innovative workflows tailored to the unique requirements of cryo-EM. This collaboration empowers cryoDuck to offer its customers and partners a comprehensive, fully managed computing solution, thereby providing a competitive edge in this fast-evolving field and the ability to bring ground-breaking methods to fruition.
Useful links
1. From structure to sequence: Antibody discovery using cryoEM (Science Advances).
3. Clovertex fully managed computing for pharma and biotech.
