The immune system's B cells create antibodies that can mount a response against just about anything — either destroying a pathogen or instructing the rest of the immune system to go after the offender. But what happens when these antibodies malfunction? Researchers at Boston Children's Hospital have identified the previously unknown mechanism for how immune cells can go back and self-edit the genes that code for these antibodies, essentially recycling them into newer versions.
The workings of this new mechanism, published in Nature, were uncovered in the laboratory of Frederick Alt, PhD , of the Program in Cellular and Molecular Medicine at Boston Children's and a Howard Hughes Medical Center Investigator. The research team found that when they gave a developing B cell the genetic instructions for problematic antibody genes, the cell used a different DNA editing mechanism to fix the antibody than the one used to initially create the antibody.
"For decades we've known how antibody gene segments are cut and pasted, but our studies have shown that these gene segments are actively brought together over long distances in chromosomes in a conveyer belt like process that could work in three-dimensions," said Alt. "This is a culmination of many years of my lab's work."
To get a truly varied immune response, antibodies are made from a combination of repeated gene pieces, known as Variable, Diversity, and Joining (V(D)J) gene segments, that are each slightly different. These are rearranged, mixed up, and pieced together to form two identical larger, heavy chains and two identical smaller, light chains that make up the Y-shaped antibody. The heavy chains contain all three kinds of gene segments, but the light chains contain only V and J pieces.
Alt's team showed how the developing B cells initially form antibodies by long-range edits in the genome that create heavy chains and light chains stitched together from V, D, and J or V and J gene segments. Researchers previously knew that B cells could edit problematic antibodies, but they could only speculate the mechanism.
"If the light chains don't pair properly with the heavy chains because something is wrong with the antibody, we found that an unexpected secondary editing mechanism takes over, essentially swapping out the light chain and often replacing it with a nearby new one that often may be related," said Alt.
In this newly discovered secondary editing process, the V and J gene segments get cut and pasted by an enzyme — known as RAG. The Alt lab showed that the RAG enzyme scans the DNA in a single direction and only cuts at certain places where RAG luring signals pair up and draw in RAG. The luring signals stick closest to each other at the beginning of the gene segments, where the cuts occur. After the enzyme finds its first cut/paste swap during secondary editing, the remaining V and J gene segments in either direction of the DNA can mix up and swap to make a new antibody light chain. This new one is often related to the first draft, but potentially no longer defective or autoreactive.
"For us this is an exciting story that adds another layer to what our lab has learned about both how gene segments packaged in chromatin can be actively captured over long chromosomal distance and joined to make our immense antibody repertoires," said Alt. "The information we have gained from the new technologies we developed to view these mechanisms has provided a major leap in our understanding of antibody diversification mechanisms, far beyond the static one-dimensional descriptions long presented in textbooks."
