The rapid mutations of B cells

One of the riddles of the immune system is how the system develops antibodies to bacteria and viruses, and how the components of these antibodies are kept in a kind of library in the genome. A new doctoral thesis sheds light on the subject

Life is a continuous struggle against threats, and the immune system is supposed to give us an answer to them.

The immune system is a very complex system, says Dr. Michal Barak from the Laboratory for Computational Biology in the Mina and Everard Goodman Faculty of Life Sciences, who dealt with this topic in her doctoral thesis under the guidance of Prof. Ramit Mer. One of the features of the cells of the immune system responsible for the production of antibodies is the rapid evolution they undergo all the time in response to new threats to the body, in that they develop mutations that are more suitable for antigens, which are markers that stick out from the faces of viruses or bacteria, and stimulate the creation of antibodies to these invaders. In her work, Barak developed a simulation that tries to imitate the process of creating antibodies. "The immunoglobulins (antibodies) expressed by B cells play a central role in the immune system. The goal of the study was to examine the evolution of immunoglobulins at the micro level (within the individual) and at the macro level (in the development of biological species). By using the techniques we developed for the study of immunoglobulins also for the RNA editing system, we gained insights into this process as well," Barak writes in her work.

"The laboratory deals with the application of methods from the field of computational biology to study the immune system," explains Barak. "We are trying, with the help of simulations and mathematical models, to predict its behavior in normal times and times of diseases in general and autoimmune diseases in particular - a situation in which the body attacks itself."

Natural vaccine

The detection system of the antibodies can be compared to two parts of an attachment that connect to each other. The higher the fit, the stronger the connection between the two parts. Each cell in the body displays on its envelope a kind of marker that associates it with the body in which it is found. Parts of the immune system know how to call these markers and thus identify the cell as belonging to the body. The antibody tries to identify protein forms that do not belong to the body and neutralize the cell or the virus that presents them. It does this by attaching the antibodies to the cell or virus, an action that neutralizes the invader and signals to other parts of the immune system that an invader is present in the body. However, in most cases the match is not exact. Every person (and every other vertebrate) has a unique collection of antibody markers. As the person develops, the immune system learns to recognize the bacteria and viruses it encounters, and thus the antibodies are created that provide more and more targeted protection, to the relevant virus. The immune system achieves this through a process called hyperevolution - rapid evolution that occurs in germinal centers located in the lymph nodes, spleen, intestines and other tissues.

The cells of the immune system are found in various tissues and even circulate in the body, damaging any cell or other factor that does not display the hallmarks of the body. They break down the invader into parts which they display on their membrane surface. Then they migrate to the lymph nodes and present the protein representing the cell or virus they ingested to the immune system cells that are there. If this is the first time the immune system has encountered this particular invader, then the B cells with the most appropriate antibody will wake up and start fighting the invader. The system will fill in the lack of a complete match, which causes the antibodies to bind weaker to the invader, with the help of offsetting a larger amount of antibodies. At this stage of primary infection, the disease caused by the virus or bacteria breaks out in the body. But that is not the end of the process. Within the lymph nodes there are germinal centers within which new B cells will develop from the existing pool of B cells in the body. At the same time as dealing with the invader, and even in a period of weeks afterwards, these cells undergo rapid evolution and try, by trial and error, to get as close as possible to matching the foreign agent. After the successful end of the war against the virus or bacteria, copies of this B cell will remain in the system for decades or even for life and will serve as memory cells, and when the invader comes again it will be possible to fight it easily, usually without the person feeling it at all.

The immune system, which adapts itself to threats, uses molecules that recognize the antigens to help it mount an immune response. The structure of the antibody allows it to fulfill its role. The antibody molecules contain two functionally separate regions: the variable region, which is used for antigen recognition, and the constant region for the function of the antibody.
The structure of the constant region (C) determines whether the antibody will remain attached to the B cell membrane or be secreted from it, and this region is also responsible for linking with other parts of the immune system. The structure of the variable region (V) is optimized for antigen binding.

Barak's work was designed to simulate components of the antigen binding process. The first part was a simulation of the development of the B cells in the germinal centers and the hyperevolution process they go through to adapt more and more to the antigen. This simulation was conducted with Dr. Gitit Lavia-Shaf.

"This simulation has greatly improved our understanding of the process of hyperevolution in the germinal centers," says Barak. "We assume that there is a germinal center where the antigen reaches. Its amount decreases over time as more B cells are exposed to it and bind to the antigen molecules. We have developed differential equations that describe the change in the amount of antigen over time and also the cloning of B cells suitable for fighting this antigen. During the process of hyperevolution, B cells divide at a high rate, and mutations are created in the region that is responsible for coding the variable part of the antibody at a rate several orders of magnitude greater than the normal rate of mutations in DNA. The process begins when several B-cells with different antibodies compete for binding to the antigen. As the match between the antibody and the antigen increases, so does the strength of the bond between them and the effectiveness of the antibody. When the cells divide and change, different antibodies are formed in the new cells. These antibodies also compete for binding to the antibody. At the same time, there is a process of selection in which cells with receptors that may endanger the body and cells with receptors whose degree of binding to the antibody is small are removed from the competition and even killed in order not to harm the body itself.

It is possible to describe the development of B cells during the hyperevolution process in the form of a tree, which begins with the first cell, which is a B cell that is not optimally suited to the particular virus, and continues through the modification of the antibody gene in the DNA of the B cell, which is designed to adapt to the antigen in a series of mutations in the region responsible for binding with the antigen .

Barak explains: "The problem of wood production is an NP COMPLETE problem, meaning a very difficult problem for computers, which cannot be solved in a reasonable amount of time. Therefore, in the next part of the study, we wrote an algorithm that tries to find the most probable tree without entering into calculations that are impossible for a computer to run. In light of the experiments we conducted, it seems that the algorithm describes the results in a fairly good approximation. The algorithm uses a series of assumptions that lead it to reject the biologically implausible trees in the initial stage, the main one of which is that the size of the tree is minimal - that is, a minimal number of mutations can produce all the sequences of the antibodies found in the sample."

"The use of trees was done in order to compare the way in which the different sequences were created in the simulation compared to sequences that are sampled in people," adds Barak. "In the trees that are created in the simulation, all the mutations are known and so is the exact structure of the tree. On the other hand, in the sequences of antibodies taken from people, there are no stages of the hyperevolution and only the cells that survived it and were found in the sample are present. The algorithm we created allows us to generate the complete tree from the partial information of the sample. Using a comparison between the trees of the model and the trees created from a real blood sample of people (sick and healthy), we found a way to check which step in the hyperevolution process is defective in various diseases (for example, mutations that do not stop even after the antigen is eliminated or an antibody selection mechanism that does not work properly)."

Another part of the research deals with the development of the organization of the code for creating antibodies in DNA during evolution. In the genome there are regions that are assigned to libraries that contain copies that are slightly different from each other. of the parts that make up the antibody. The antibody itself is built like an aggregate. You take a part from here and a part from there and put them together, but not always in exactly the same way. The goal of this biological process is to produce diversity unlike any other cell in the body, where the goal is to produce an identical cell to replace a cell that has ended its life, for example a muscle cell. This variation is then amplified in the hyperevolution process that occurs only after actual exposure to the antigen.

Immune system cells, B cells and T cells (which this study did not deal with) circulate in the body. Although all B cells originate from the same genome, they express completely different antibodies and each of them will be able to bind to a different antigen. B cells that attach too easily to the body's own cells will be killed, all other cells will survive and cover the space of the different possible structures of foreign antigens.

"The arrangement in the genome of the gene libraries for antibodies is found in different forms in different animals. In some of them - especially in more ancient animals - the libraries contain complete antibody genes without the need to connect different parts. In others, the different parts of the antibody are distributed in different libraries. We have created a simulation that will show how the antigen libraries in contemporary organisms have evolved from a single primary antibody. The libraries were created by mutations that duplicate the antibody coding in the genome and delete genes or create mutations in the copies of the antibody genes. These processes are able to produce a high level of diversity in the antibodies encoded in the genome."

"The ambition in the future is that the evolutionary tree of the antibodies, which will be taken from a sample of blood or tissue of the patient, can be a diagnostic tool, but that still requires time. Today it is possible to sequence a genome for about 4,000 dollars. As soon as it will be possible to do things like this more easily and at a cheaper price, it will be possible to perform a blood test and know immediately if the person is currently sick and if so, how his immune system reacts to the drugs, and thus adjust a more correct drug to him. Biology is converging in the direction of developing personalized medicines for a disease that actually occurs in the body. The algorithm we created for finding the hyperevolutionary tree of antibodies was also found to be useful in a completely different biological field - that of RNA editing. RNA editing, in which the base adenosine is replaced by inosine (Adenosine-to-Inosine RNA editing) occurs intensively in the human brain. The editing changes the original content of the copied genome, and some speculate that it is related to thought processes.

Despite the differences in the biological processes, the information analyzed in both cases - RNA editing and antibody development - shares certain similarities: the original DNA sequence is known, the length of the tested sequences is the same, not all mutations in the case of antibody genes or all RNA editing events are found as different sequences in the sampled information, and in both cases a representation of the information as a tree can lead to insights into the biological conditions of the system from which the information was obtained.

In a joint study with Dr. Erez Lebanon from Harvard University, we used editing trees and found that RNA editing is a source of great variation.

About the researcher

Barak went through a rather unique path at Bar-Ilan University. She did her first degree in physics and computers in general, in her master's degree she specialized in computational physics, while the doctorate she did with Ramit Mar deals with computational biology. "Computational biology and theoretical biology in general are relatively new fields. When DNA sequencing opened up to us huge amounts of information that classical biology had no tools to deal with, and the power of computers was increasing, biologists switched to using tools developed in physics such as differential equation models and computational models, which until recently were only used in a small part of biological research, such as in models ecological. Simulations with computational tools, which were used in physics, began to prove themselves effective in biology as well.

However, Barak estimates that the transition process of physicists and computer scientists to biology is about to end because a new generation of students studying bioinformatics and computational biology has arisen, who will be the next generation of researchers coming from biology.

The article was published in Galileo and in the Bar-Ilan University's journal Innovations