Interesting Antibody Papers.

Below are several antibody papers that should be of interest to those dealing with antibody engineering, be it computational or experimental. The running motif in this post will be humanization, or the process of engineering a mouse antibody sequence which binds to a target to look ‘more human’ so as to reduce the immune response (if you need an early citation on this issue, here it is).

We present two papers which talk about antibody humanization directly, one from structural point of view (Choi et al. 2015), the other one highlighting issues facing antibody engineers  mining for information (Martin & Rees, 2016). The third paper (Collins et al. 2015) takes a step back from the issues presented in the other papers and talks broadly about the nature of mouse sequences raised in the lab.

Humanization via structural means [here] (Bailey-Kellogg group). The authors introduce a novel methodology named CoDAH to facilitate humanization of antibodies. They design an approach which makes a tradeoff between sequence and structural humanization scores. The sequence score used is the Human String Content (Laza et al. 2007, Mol Immunol), which calculates how similar the query (murine) sequence is to short stretches of human sequences (mostly germilne). In line with the fact that T-Cells are one of main drivers of anti-biologics immunity, they define the sequences stretches to be 9-mer, as recognized by T-Cells. For the structural score, they use Rotameric energy as calculated by Amber. They demonstrate that constructs designed using their score express and retain affinity towards the target antigen, however they do not appear to prove that the new sequences are not immunogenic.

Extracting data from databases for humanization [here] (Martin group and Rees consulting). The main purpose of this manuscript is to warn potential antibody engineers of the pitfalls of species mis-annotations. They point out that in a routine ‘humanization’ pipeline where we aim to find human sequences given a mouse sequence, a great number of seemingly good ‘human’ templates are not human at all (sources as diverse as IMGT or PDB). This might lead to errors down the line if the engineer does not double check the annotations (unfortunate but true). Many of such annotations arise because the cells in which mouse antibodies are expressed are human cells or because the sequences are chimeric — in either case the annotation would not read mouse or chimeric, but erroneously ‘human’. NB. Another thing to watch in this publication is the fact that authors are working on a sequence database of their own: EMBLIG which is said to collect data from EMBL-ENA (nucleotide repository from EMBL). Hopefully in their database, authors will address the issues that they point out here.

What can we say about antibodies produces by laboratory mice? [here] (Collins group). Authors of this manuscript have addressed the issue that the now available High Throughput Sequencing (HTS) overlooked mouse repertoires. Different mice strains have different susceptibilities to diseases (Houpt, 2002, J Imunol; which might mean that you need to think twice which mice strain to choose for a given target). Currently known antibody repertoire of mice is based on the sequencing of two strains, BALB/c and C57BL/6. Here the authors apply HTS to two strains (BALB/c and C57BL/6) of laboratory mice (eight mice per strain) to get a better snapshot of antibody gene usage. Specifically, they pay close attention to the different genes combinations (VDJ) in the sequences that they obtain. Authors conclude that the repertoires between the two strains are strikingly different and quite restricted — which might mean that the laboratory mice were under very specific pressures (read inbred/overbred). All in all, the VDJ usage numbers that they produce in this publication are a useful reference to know which sequence combinations might be used by antibody engineers.