The immune system is made of complex networks of interactions between secreted proteins or proteins expressed on the cell surface. These proteins are encoded by germline genes or result, for immunoglobulins and T cell receptors, from random recombinations of several genes that create a repertoire of varied molecules capable of selective interactions. This repertoire is composed in humans of several hundred million different clones that are partly selected to interact preferentially with molecules that are foreign to us (the non-self) and to avoid reactions with our own molecules (the self). However, this selection is very imperfect because of the complexity of the molecular representation of the self. The mechanisms we study are mostly a consequence of the composition of immune repertoires and the directed evolutionary systems we use are largely inspired by the immune system.
Immunogenicity of therapeutic proteins and antibodies.
| Team leader Bernard Maillère
+ 33 1 69 08 94 47 |
Therapeutic proteins and antibodies represent an ever-increasing share of drugs. Among the ten best-selling molecules in the world, eight are antibodies. These molecules have the advantage of being very specific to their target and not very toxic. Unfortunately, they also have the disadvantage of being potentially immunogenic, i.e. of triggering an immune response. The antibodies that patients might produce and that are directed against a therapeutic protein could decrease the pharmacokinetics of the protein, neutralize its therapeutic activity or trigger allergic or autoimmune symptoms. Because of the major role of CD4 T cells in the initiation and regulation of the immune response, the quantification of the repertoire of naive CD4 T cells specific to therapeutic molecules and the identification of the sequences that these cells recognize (T cell epitopes) allows us to better understand the origin of the immunogenicity of therapeutic molecules.
By identifying the epitopes of several therapeutic antibodies, we have shown that the T cell epitopes of therapeutic antibodies are present in the mutated parts of the variable sequences (1-3). We have also demonstrated the existence of CD4 T cells specific for lowly expressed proteins in the body such as hormones and growth and replacement factors, explaining immunogenicity of their recombinant form (4-7).
Current work focuses on the characterization of the diversity of the specific repertoires of therapeutic proteins, the effector or regulatory phenotype of CD4 T lymphocytes specific to therapeutic proteins as well as on the development of a strategy to create de-immunized molecules, i.e. no longer inducing an immune response.
Antibody Engineering and immunogenicity
The Antibody Engineering and Immunogenicity team of DMTS/SIMoS develops new antibody-based ligands for various applications, whether therapeutic, imaging or diagnostic. The team is particularly interested in designing high affinity antibodies with controlled selectivity but also with low immunogenicity to allow administration in humans while limiting the risks of immunogenicity.
The team has developed tools for molecular engineering of proteins coupling a high-throughput screening method, the Yeast Surface Display, with high-throughput NGS sequencing methods (8). In particular, it implements the Deep Mutational Scanning approach aimed at identifying the main amino acids in the protein sequence that have a functional role. The DMS data allow us to understand the protein/protein interfaces (such as epitopes or paratopes) (9, 10). They are also used to guide the engineering of optimized molecules, notably for affinity maturation or antibody selectivity engineering.
These technologies are the basis for the creation of the antibody engineering service company Deeptope:
http://deeptope.com
Synthetic biology and evolution
The toolbox of the Synthetic Biology and Evolution (SBE) team includes many technologies of molecular biology, some of which have been developed by the team itself. The main applications are in the field of DNA assembly, microbial genomic engineering and evaluation of molecular interactions in the intracellular context and continuous evolution. A central technology in our activities is a quantitative bacterial two-hybrid system with low stochasticity, good dynamic range and good correlation with affinity. This technology, developed by our team, is also applied in the development of a continuous evolution system inspired by retroviruses such as HIV (patent EP20305531).
