Tag Archives: antibody

Benford’s law and OAS

Benford’s law is an observation that in numerical data (produced by many kinds of process), the leading digit tends to be small. Wikipedia tells you that it in datasets obeying Benford’s law, the number 1 appears as the leading digit about 30% of the time while 9 appears less than 5% of the time (p(n) = log10(1+1/n) where n is the leading digit). Wikipedia further lists multiple kinds of data where this tends to be true such as electricity bills, population numbers and physical and mathematical constants, and particularly where data can be described by a power law.

Power laws and antibodies have been co-discussed in reference to network descriptions of antigen-experienced BCR repertoires [1], which are often described as scale-free to use the network terminology (following a power law). This means a few highly-connected nodes in the network and lots of nodes with few or no connections. This is an obvious candidate for Benford’s law.

This is of no practical relevance, but I wondered if I could see Benford’s law in other kinds of data besides clone counts in the Observed Antibody Space (OAS). For example, I looked at the leading digit in the number of sequences in all of the data units in OAS. It looks like a good fit for Benford’s law (though with more density at the smaller leading digits) and has a chi-squared value of 0.007 (Figure 1A).

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Antibody Engineering and Therapeutics Conference

I was invited to speak at the Antibody Engineering and Therapeutics Conference (presenting mine and Matt’s recently published epitope profiling paper), in San Diego (December 12th – 16th). Unfortunately, the pandemic had other ideas so I decided not to travel but luckily the conference was hybrid. 

The conference included 1 day of pre-conference workshops and 4 days of presentations from academic and industry, with livestreaming of the initial keynotes (including one from Charlotte). Remaining talks were recorded and made available after the conference. I’ve highlighted a few of my favourite talks and conference themes, with links to papers where available.

Naturally, a lot of the presented research related to covid-19. I was speaking in the ‘Antibody Repertoires and Covid-19’ session, where there were interesting presentations from Professor Eline Luning Prak from the University of Pennsylvania and Elaine Chen from Vanderbilt University analysing antibody responses in covid-recovered individuals, and comparing vaccine responses in covid-recovered vs covid-naiive individuals. Other talks around SARS-CoV-2 vaccines included Dr Laura Walker from Adimab/Adagio Therapeutics comparing BCR repertoire responses to different types of vaccinations, and the effect of using different booster types.

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Do antibodies care about sex?

In a recent OPIG antibody meeting, the topic of immune system differences between men and women came up. I thought this was cool and something I hadn’t read about, so what a brilliant topic for a blog most. This post is a high-level overview – I’ve listed the papers I’ve used at the bottom of this post so please consult them for more details!

Differences between males and females can lead to pretty big disparities in disease prevalence and outcomes. For example, non-reproductive cancers occur predominantly in males, whilst the majority of autoimmune disease occurs in females. Many factors may be impacting this, including environmental, genetic and hormonal influences, and much more research is required to fully understand these processes. Here I focus on sex-based biology, rather than gender, though both can influence the immune response.

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Bioinformatics Hackathon Reflection

A week ago I participated in Copenhagen Bioinformatics Hackathon 2021, a hackathon focusing on machine learning and proteins, as a mentor for a challenge proposed by our group. The whole experience was fun, but I am also sitting here contemplating over a lot of things I wish I had done differently. For this blog text, I therefore want to highlight two changes which I believe would have greatly improved my challenge and which can hopefully also work as an inspiration for others presenting a hackathon challenge. 

Going into this event I had some experience from a few hackathons I had previously attended. Based on this, I wanted to create a challenge containing two parts. First, a simple task which everyone would be able to create a solution for, and second, a more challenging addition to the first task for more experienced participants. I decided to go with the challenge of predicting which heavy and light chains can form a pair, where the additional challenge was to try to visualize which residues were relevant for this interaction. Together with OAS containing a really nice positive dataset of paired chains, I thought this was going to be an amazing challenge, but as soon as the event began I started seeing the flaws of the challenge.

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AIRR Community Meeting V – December 2020

We attended the virtual Adaptive Immune Receptor Repertoire (AIRR) Community Meeting in early December. The three day conference is usually held every 18 months and covered a range of research talks, software demonstrations and poster presentations on the latest TCR and BCR (antibody) research. While we missed certain elements that were present at the last AIRR community meeting (namely focaccia), it was a really interesting meeting with technology all running very smoothly.

Given our current research on SARS-CoV-2 antibodies, we particularly enjoyed the work presented by Armita Nourmohammad from the University of Washington on “Dynamics of BCR in Covid”, based on the preprint on medRxiv. The research identified 34 significantly expanded rare clonal lineages shared among patients with SARS-CoV-2, which are potential candidates for covid response. In particular, the analysis includes an assessment of whether an antibody sequence identified in different individuals (known as a shared or public sequence) is likely to be found due to inherent biases in antibody recombination. Shared antibody sequences which are calculated as  unlikely to be shared are potentially a response to a shared exposure such as SARS-CoV2, rather than randomly found in the antibody repertoire. In this way, Nourmohammed and colleagues identified ‘rare’ antibodies which were identified in more individuals than would statistically be expected, and therefore might be worthy of further experimental analysis.

A theme common across a short talk and poster by Hadas Neuman (Bar-Ilan) and a poster by Kenneth Hoehn (Yale), was class-switching dynamics revealed by phylogenetic inference (from IgM to IgA in the human gut in the former, and IgE and IgG4 in a paediatric patient with peanut allergy in the latter). Kenneth Hoehn’s poster also looked at B-cell differentiation during HIV infection – this can all be read about in this preprint. The methods developed in the paper for discrete trait analysis of differentiation, isotype switching and B-cell migration are implemented in the new R package dowser (https://bitbucket.org/kleinstein/dowser) which is part of the Immcantation suite (http://immcantation.org).

It was also really nice to see evidence of the burgeoning use of single-cell sequencing for immune repertoire profiling, with posters by Igor Snapkov (UiO), Indu Khatri (Leiden University Medical Centre), Nick Borcherding (Washington University in St. Louis) all using single-cell technologies, and a talk by Ivelin Georgiev on LIBRA-seq. 

If you missed the conference and have had your interest piqued, some of the conference talks are available at the AIRRC youtube channel.

We look forward to AIRRC6, Dec 7 – 11, 2021!

Sarah and Eve

Re-educating myself about the light chain

I have an unconscious habit of personification, and I always see the antibody light chain as lazy for not contributing more residues to binding interfaces (obviously a generalisation – e.g. insertions in CDRL4 in anti-HIV bNAbs [1]). Perhaps this is why I have a personal preference for the more diverse [2] heavy chain with its specificity-determining [3] CDR3. Having written this down, I realised it’s actually pretty weird to consider an antibody chain as a person and I ought to re-educate myself about the role that light chains play.

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New avenues in antibody engineering

Hi everyone,

In this blog post I would like to review an unusual antibody scaffold that can potentially give rise to a new avenue in antibody engineering. Here, I will discuss a couple of papers that complement each others research.

My DPhil is centered on antibody NGS (Ig-seq) data analysis. I always map an antibody sequence to its structure as the three-dimensional antibody configuration dictates its function, the piece of information that cannot be obtained from just the nucleotide or amino acid sequence. When I work with human Ig-seq data, I bear in mind that antibodies are composed of two pairs of light and heavy chains that tune the antibody towards its cognate antigen. In the light of recent research discoveries, Tan et al., found that antibody repertoires of people that live in malaria endemic regions have adopted a unusual property to defend the body from the pathogen (1). Several studies followed up on this discovery to further dissect the yet uncharacterized property of antibodies.

Malaria parasites in the erythrocytic stage produce RIFIN proteins that are displayed on the surface of the erythrocytes. The main function of RIFINs is to bind to the LAIR1 receptors that are found on the surface on the immune cells. The LAIR1 receptor is inhibitory, which leads to inhibition of the immune system. The endogenous ligand of the LAIR1 receptor is collagen, which is found on the surface of body cells. This is to make sure that the immune cells will not be activated against its own body. Activating the LAIR1 receptors is one of the escape mechanisms that the malaria parasite has evolved.

Tan et al., (1) showed that in an evolutionary arms race between human and malaria, our immune system has harnessed the property of RIFINs to bind to LAIR1 against the parasite itself. By doing single B cell isolation and sequencing, it was discovered that antibodies, which are the effector molecules of our immune system, can incorporate the LAIR1 protein in its structure. Taking into account our knowledge of antibody engineering, the idea of incorporating a 100 amino acid long protein into antibody structure is very hard to comprehend. Sequences of these antibodies showed that the LAIR1 insertion was introduced to CDR-H3. Recently, the crystal structure of this construct has become available (2). The crystal structure revealed that the LAIR1 insertion indeed is structurally functional. All 5 of antibody canonical CDRs interact with the LAIR1 protein and its linkers to accommodate the insertion. The CDR-L3 forms two disulfide bonds with the liker to orientate the LAIR1 protein in the way, it will interact with RIFINs. It is worth to stress that LAIR1 sequence differs from the wild type, but the structure is very similar (<0.5 RMSD). The change in sequence and structure is crucial to prevent the LAIR1 containing antibody from interacting with collagen, but only with RIFINs.

Pieper et al., (3) tried to interrogate the modality of LAIR1 insertions into antibody structures. It was performed by single cell sequences as well as NGS of the antibody shift region. It turns out that human antibodies can accommodate two types of insertion modalities and can form   camelid-like antibodies. The insertion of LAIR1 can happen to CDR-H3, leading to the loss of antibody binding to its cognate antigen. Another modality is the incorporation of the LAIR1 protein to the shift region of the antibody. This kind of insertion does not interfere with the Fv domain binding properties, which leads to creating of  bi-specific antibodies. The last finding was the insertion of the LAIR1 into antibody structure where D, J and most of V genes, and the light chain were deleted. The resultant scaffold is structurally viable and only possesses the heavy chain. Hence, it is the evidence that human antibodies can also form camelid-like antibodies. Interestingly, these insertions into the shift region are not exclusive to people that live in malaria endemic regions. By doing NGS of the shift domain from European donors, around 1 in 1000 antibody sequences had an insertion of varying lengths. These insertions are introduced from different chromosomes of both intergenic and genic regions.

To sum up, it is very intriguing that our immune system has evolved to create camelid-like and bi-specific antibodies. It will be very informative to try to crystallize these structures to see how these antibodies accommodate the insertion of LAIR1. Current antibody NGS data analysis primarily concentrates on the heavy chain due to sequencing technology limitations. It will be invaluable information if we could sequence the entire heavy chain as well as adjacent shift region to see how our immune system matures and activates against pathogens.

 

  1. Tan J, Pieper K, Piccoli L, Abdi A, Foglierini M, Geiger R, Maria Tully C, Jarrossay D, Maina Ndungu F, Wambua J, et al. A LAIR1 insertion generates broadly reactive antibodies against malaria variant antigens. Nature (2016) 529:105–109. doi:10.1038/nature16450
  2. Hsieh FL, Higgins MK. The structure of a LAIR1-containing human antibody reveals a novel mechanism of antigen recognition. Elife (2017) 6: doi:10.7554/eLife.27311
  3. Pieper K, Tan J, Piccoli L, Foglierini M, Barbieri S, Chen Y, Silacci-Fregni C, Wolf T, Jarrossay D, Anderle M, et al. Public antibodies to malaria antigens generated by two LAIR1 insertion modalities. Nature (2017) 548:597–601. doi:10.1038/nature23670