Today is the day when I write a blog about an exciting research paper in the field of B-cell receptor (BCR) repertoires analysis. At OPIG, we (antibody people) are working hard to model and characterise antibody 3D configuration from its sequence. Significant progress has been made in modelling software development, so that we can predict antibody structures with high confidence. This task becomes considerably harder when we model the entirety of BCR repertoire sequences. Current methods of BCR repertoire sequencing operate primarily on the heavy chain only. This limits our capacity to generate refined 3D antibody models to just approximation of shapes of complementarity determining regions(CDRs).
Availability of cognate heavy/light chain pairing information is long-awaited in the structure prediction field. The first paired BCR repertoires were generated by DeKoskyet al.,[1, 2, 3] However, the short Illumina read length limited the scope of sequencing to just CDR3, FW4 and FW3 regions.
Year 2019 was special as the new technology has been widely introduced to BCR repertoire sequencing, 10x Genomics. It enabled researchers to obtain native full-length VH/VL sequence information from individual B-cells. The detailed description how 10xGenomics technology works is a topic that deserves a separate blog post. In this post, I briefly go through a recent paper in Cell by Setliff et al.,[4].
10xGenomics leverages molecular barcoding of VH and VL DNA sequences followed by short read sequencing with Illumina. Next, short-read genome assembler can be used to generate two separate contigs for identically barcoded VH and VL molecules. Setliff et al.,[4] took it one step further. They also used 10XGenomics barcode delivery beads to attach the DNA barcodes to VH, VL DNA sequences as well as to the surface of an antigen of interest. This enables sorting and sequencing antigen specific B-cells in parallel. In their study, they showed that their platform (LIBRA-seq) enables simultaneous screening and isolating of target-specific BCRs against multiple antigens.
Overall, LIBRA-seq has the potential to critically speed up and make drug discovery more efficient. There are still some limitations associated with 10xGenomics such as the number of B-cells being sequenced in one run. Well-established single chain sequencing can obtain unique sequences from million of B-cells, whereas 10xGenomics takes into analysis 10,000 B-cell per chip (8 chips are usually incorporated into a single run). Finally, new bioinformatics tools also urgently needed to enable smooth processing and analysis of 10xGenomics data, as I strongly believe that we shall see a sharp increase in 10xGenomics data availablity in 2020.
Thank you.
Until next time,
Alex
References
[1] Brandon J DeKosky, Gregory C Ippolito, Ryan P Deschner, Jason JLavinder, Yariv Wine, Brandon M Rawlings, Navin Varadarajan, Claudia Giesecke, Thomas Dorner, Sarah F Andrews, Patrick C Wilson, Scott P Hunicke-Smith, C Grant Willson, Andrew D Ellington, and George Georgiou. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire.Nature Biotechnology, 31(2):166–169, 2013.
[2] Brandon J DeKosky, Takaaki Kojima, Alexa Rodin, Wissam Charab, Gregory C Ippolito, Andrew D Ellington, and George Georgiou. In-depth determination and analysis of the human paired heavy-and light-chain antibody repertoire. Nature medicine, 21(1):86, 2015.
[3] Brandon J. DeKosky, Oana I. Lungu, Daechan Park, Erik L. Johnson,Wissam Charab, Constantine Chrysostomou, Daisuke Kuroda, Andrew D.Ellington, Gregory C. Ippolito, Jeffrey J. Gray, and George Georgiou. Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires.Proceedings of the National Academy of Sciences of the United States of America, 113(19):E2636–E2645, may 2016.
[4] Ian Setliff, Andrea R Shiakolas, Kelsey A Pilewski, Amyn A Murji, Rutendo E Mapengo, Katarzyna Janowska, Simone Richardson, Charissa Oosthuysen, Nagarajan Raju, Larance Ronsard, et al. High-throughput mapping of b cell receptor sequences to antigen specificity.Cell, 179(7):1636–1646,2019.
