The human protein atlas blog

Epitope mapping and development of therapeutic antibodies

Affinity proteomics Antibody Antibody Microarray cells Epitope mapping Human Protein Atlas Life Science

Johan Rockberg

Within the Human Protein Atlas project, antibodies are used to study the localization of protein in human tissues and cells. To generate the antibodies recombinant expression clones are produced from human RNA pools by cDNA synthesis, cloning and plasmid purification. These clones produce what is called Protein Epitope Signature Tags (PrESTs), a selected part of the target protein that should be recognized by antibodies.

Johan Rockberg, Associate Professor in antibody technology and directed evolution at KTH - Royal Institute of Technology in Stockholm, Sweden is the group leader for the epitope mapping and therapeutic antibodies group within the Human Protein Atlas.

"I have a M. Sc in chemical engineering from KTH and University of Sydney and joined the Human Protein Atlas Project in 2003, right in the beginning. Since I took courses in computational and information science in parallel with chemical engineering it was natural to pursue a career in bioinformatics."

After completion of his master degree Johan joined the Human Protein Atlas aiming to develop software to define the part of a protein that should be selected as PrESTs and best suited to generate antibodies.

"This was a very exciting project, to try to understand the connection between antigen and antibodies."

After developing the software Johan developed a method for epitope mapping, to further understand how antigens and antibodies are correlated, a project that became the foundation of his PhD thesis.

"I started off as a bioinformatician and developed into an experimental scientist, and today almost all of my work is done experimentally."

Johan has been devoting his scientific career to trying to understand and characterize antibodies not only for research use but also extend their use to therapeutic applications. For example he performs epitope mapping using a combination of platforms including: (i) cellsurface display of target directed peptide or folded domain libraries using staphylococcal display, (ii) suspension bead arrays for mapping using overlapped or alanine mutated synthetic peptides, and (iii) large scale synthetic peptide arrays.

These methods have been also used within precision medicine, to explore if a drug will be useful for treatment of a specific patient or not, in recent paper.

In addition to investigating how to design the best antibodies possible, Johan Rockberg and his group are also involved in optimizing the production of full-length active human proteins to be used for therapy. The proteins used in the Human Protein Atlas project are produced in an E.coli-system, but for the last five years Johan has worked on a project developing mammalian cell factories to be used to produce protein drugs. The group mainly make use of Chinese Hamster Ovary (CHO) cells, because they are known to produce large amounts of protein, can take up foreign DNA easily and are easily grown in a large scale. They do not work equally well for all proteins however.

"Our goal is to make these cells even better at producing proteins to allow for the next-generation biologics, which today fail to produce at high enough levels, to reach their patients. We have developed a method to measure protein secretion and are using new gene editing techniques such as CRISPR-Cas9 to modify cells to give higher quantity and quality of protein, Johan explains." Since January 1, Johan is also responsible for developing the next generation platforms for bioproduction in human cells. In this project, selected human cell lines are modified for improved expression, secretion and posttranslational modifications of biopharmaceuticals.

"In this project we work in close collaboration with the industry, and it is exciting to get the whole perspective and feel that we can complement each other. "

Today, Johan´s group consists of five PhD students, one lab manager and two technicians.

"They are my team, and they are great!"

Frida Henningson Johnson

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