115025 Pathobody: A proteogenomic pipeline for capture and sequencing and production of pathogen-specific antibodies

AbSano has changed the patient criteria for inclusion in the study so that we now include patients who have had COVID and have additionally taken a vaccine. We have seen that this gives the highest number of B cells in the FACS sample. AbSano has generated and tested the TSN (concentration) for the B-cell selection, as well as defined conditions for labeling by FACS. Absano has also tested and defined the conditions for the B-cell cultures, conditions which have now been put into use. ELISA analyses, which test for: antibody production, antibody specificity and neutralization capacity, are now done for each individual B-cell culture. GenXPro has worked on the development of sequencing protocols for antigen-binding fragments from antibodies. They have developed and tested preparation protocols for the NGS library. This was done in two steps, first the experiments were designed and developed, and then this knowledge was used to analyze the test sequences. Erasmus MC has received ~2000 FACS selected B cells for 10x Genomics sequencing. Sequencing is still ongoing. Erasmus MC has also worked on the validation of the affinity enrichment from supernatants from the B-cell samples. They have carried out a successful affinity enrichment where they were able to identify immunoglobulin-related peptides via proteomics analysis. They were able to show that proteomics data could be matched with available NGS data from the reference culture, thus confirming a good workflow. Pubgene has carried out a literature analysis for current COVID antibodies, their status with regard to clinical studies, target sequence for the antibodies, scientific findings and patent situation. PubGene has also developed methods and routines that allow monitoring of scientific progress within the field. Pubgene has started work on database design and framework for storage, mapping and analysis of the various data elements that are expected from the various analyzes from the various experiments. This gives us a good basis for data handling, storage and analysis of future data from the project