Project Summary:
Millions of antibody sequences from both healthy individuals and patients with a variety of immune-mediated
disorders are now freely available to the research community. This has been made possible by support primarily
provided by NIAID for the research projects themselves and for the databases that curate the data. To maximize
the benefits of this financial support, the Institute now funds efforts to use the curated data to explore new
initiatives which are beyond the scope of the original research projects. We propose to use approximately one
million of these antibody sequences to test a hypothesis concerning rare antibody sequences that was first
proposed over 35 years ago but which now can be examined on a large scale by means of these NIAID supported
databases. The expansion of the antibody repertoire by V(D)J gene rearrangement, N-nucleotide addition, and
somatic hypermutation (SHM) introduces non-germline encoded sequence changes throughout the antibody
variable domain. Many of these sequences are either totally absent from, or very rare in, the human proteome.
It is already clear that these “foreign” sequences are common in V regions of antibodies even from healthy human
controls, so it is unlikely that the majority are immuno-pathogenic. However, there is reason to test the
hypothesis that a small subset of these forbidden/rare pentapeptides will be clinically immunogenic, i.e., will
be able to induce immune responses that should be absent from normal antibodies. If this can be confirmed, it
will help us address at least two major challenges now facing medical immunology. First is the persistent problem
of immunogenicity in new therapeutic antibodies which substantially raises the cost of development of these
agents and limits their efficacy in patients. If the proposed work is successful and the immunogenic
pentapeptides are identified, it could lead to the development of new algorithms that more accurately predict the
immunogenicity of therapeutic antibodies prior to expensive clinical trials. Second is the need for more specific
and effective therapies for autoimmune diseases such as SLE, MS, and type 1 diabetes. A large body of evidence
indicates that many of the self-reactive, pathogenic autoantibodies contain idiotopes in their structures which
are recognized by anti-idiotypic antibodies. Further, it appears that the presence or absence of these anti-
idiotypic antibodies may in part be responsible for periods of remission or active disease. Few idiotope structures
are known, but it seems reasonable that these immunogenic segments in antibody variable regions may also
contain the foreign pentapeptides; this could serve as a tool for identifying idiotopes in the sequences of
pathogenic self-reactive antibodies. A major outcome of the proposed studies is a bioinformatics research tool,
the Penta-Scope, which will take as input the sequences of large numbers of antibodies and return the frequencies
of their component pentapeptides in human and murine proteomes. This tool will be made freely available online
for other investigators to use in studies of antibody structure and/or immunogenicity.
