Hi everyone!

Today is the day for another blog post from me. Here, I would like to give you an update on new studies, which were deposited in the Observed Antibody Space (OAS) resource and take a closer look at one of these studies. To date, we have curated 57 studies in OAS, where we provide raw nucleotide and numbered amino acid sequences for download. These amino acid sequences have been filtered using ANARCI parsing, which ensures that the sequences align to respective species HMM profiles and do not have unusual indels and frameshifts. More than 660 million numbered amino acid sequences are deposited in OAS, where every sequence keeps a link to its corresponding nucleotide sequence. Recently we added two more studies to OAS: Sheng et al., (2017) and Setliff et al., (2018). We numbered roughly 2.8 and 46 million sequences in Sheng et al., and Setliff et al., studies respectively. In this blog post, I would like to talk more about the uniqueness of Setliff et al., data.

Most studies deposited in OAS interrogate immune system dynamics in response to vaccination or in disease states. HIV is the most studied disease state using next-generation sequences of antibody gene repertoires (Ig-seq). These Ig-seq studies gleaned repertoire dynamics insights from individuals already infected with the virus. Longitudinal Ig-seq studies of HIV infection progression allows scientists to track the development of efficacious broadly neutralizing antibodies e.g. in Doria-Rose et al., (2014). Some studies also interrogated antibody repertoires of “elite” HIV controllers after 15 year of infection (Wu et al., 2015). Setliff et al., research also provides longitudinal analysis of HIV progression in six individuals. In contrast to the rest of HIV studies found in OAS, Setliff et al., performed Ig-seq on the individuals before they contracted the virus. This allowed for investigation of antibody repertoire changes in early stages of HIV infection. The clonotype overlaps were very low before HIV infection as well as 6 months and 3 years after infection within six individuals. This suggested that sequence turnover was high (Figure 1).

Figure 1. Clonotype overlaps in 6 B-cell donors at three different time points (before, 6 months and 3 years after HIV infection).

V gene and CDR-H3 length usages remained almost unaltered in individuals throughout disease progression. This was an unexpected finding as HIV, which has a very high mutation rate, causes a chronic debilitating disease. It is known that HIV broadly neutralizing antibodies have CDR-H3 lengths longer than 30 amino acids. Perhaps, 3 years of infection was not yet enough for the immune system to generate broadly neutralizing antibodies in these six individuals.

Next, the authors investigated the clonotype overlaps between all six individuals. They found that the number of shared clonotypes was significantly higher between the individuals after 3 years of infection. This shows that antibody repertoire sequences have a higher level of convergence after 3 years (Figure 2).

Figure 2. Clonotope overlaps between 6 B-cell donors at different disease progression time points

To investigate if representative sequences from the convergent clonotypes are HIV specific, the authors created paired Ig-seq datasets from another two individuals who were HIV-positive for 3 years. The paired Ig-seq data holds information of both heavy and light chains, which allows researchers to express antibodies with a correct structural paratope. In other words, when you carry out a single heavy chain Ig-seq data, and you isolate a sequence believed to be target specific, the next step is to find a suitable light chain to express this antibody (in this examples, I was not considering single chain antibodies (VHH)). However, the two different light chains can change the structure of the paratope dramatically, so the antibody loses its pharmacodynamics properties. In this work, the authors isolated two representative sequences from large overlapping clonotypes formed between paired and heavy chain Ig-seq datasets. These isolated sequences were converted into full-length IgG molecules and their binding properties were confirmed with ELISA. This shows that largely expanded shared clonotypes can contain antibody sequences directed against a common antigen.

Overall, it is exciting to see more and more Ig-seq data being generated that provides insights into antibody biology. I am planning to deposit a new Ig-seq study on OAS really soon. This study holds about 30 million sequences from human Ig-seq experiment. If you know about Ig-seq studies, which are not currently included in OAS, let me know and I will fix that  🙂 .

Thank you.

Best,

Alex

References:

1. Sheng, Z., C. A. Schramm, R. Kong, J. C. Mullikin, J. R. Mascola, P. D. Kwong, and L. Shapiro. 2017. Gene-specific substitution profiles describe the types and frequencies of amino acid changes during antibody somatic hypermutation. Front. Immunol. 8.
2. Setliff, I., W. J. McDonnell, N. Raju, R. G. Bombardi, A. A. Murji, C. Scheepers, R. Ziki, C. Mynhardt, B. E. Shepherd, A. A. Mamchak, N. Garrett, S. A. Karim, S. A. Mallal, J. E. Crowe, L. Morris, and I. S. Georgiev. 2018. Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection. Cell Host Microbe .
3. Doria-Rose, N. A., C. A. Schramm, J. Gorman, P. L. Moore, J. N. Bhiman, B. J. DeKosky, M. J. Ernandes, I. S. Georgiev, H. J. Kim, M. Pancera, R. P. Staupe, H. R. Altae-Tran, R. T. Bailer, E. T. Crooks, A. Cupo, A. Druz, N. J. Garrett, K. H. Hoi, R. Kong, M. K. Louder, N. S. Longo, K. McKee, M. Nonyane, S. O’Dell, R. S. Roark, R. S. Rudicell, S. D. Schmidt, D. J. Sheward, C. Soto, C. K. Wibmer, Y. Yang, Z. Zhang, J. C. Mullikin, J. M. Binley, R. W. Sanders, I. A. Wilson, J. P. Moore, A. B. Ward, G. Georgiou, C. Williamson, S. S. A. Karim, L. Morris, P. D. Kwong, L. Shapiro, and J. R. Mascola. 2014. Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies. Nature 508: 55–62.
4. Wu, X., Z. Zhang, C. A. Schramm, M. G. Joyce, Y. Do Kwon, T. Zhou, Z. Sheng, B. Zhang, S. O’Dell, K. McKee, I. S. Georgiev, G. Y. Chuang, N. S. Longo, R. M. Lynch, K. O. Saunders, C. Soto, S. Srivatsan, Y. Yang, R. T. Bailer, M. K. Louder, J. C. Mullikin, M. Connors, P. D. Kwong, J. R. Mascola, and L. Shapiro. 2015. Maturation and diversity of the VRC01-antibody lineage over 15 years of chronic HIV-1 infection. Cell 161: 480–485.