HC8: B-cell development and antibodies

SARS-CoV2

The SARS-CoV2 (COVID-19) virus can bind to the ACE2 receptor molecule. SARS-CoV2 has a spike protein, the S1 domain of this protein can bind to the ACE2 receptor in the respiratory tract and intestines. When the virus arrives, the following happens:

1. Multiple spike proteins bind to different types of ACE2 molecules
2. The virus has a small genome of only 30.000 base pairs → it needs human cells to proliferate
3. Depending on the antibodies available, the virus is blocked a little
4. If the epitopes on the spike proteins aren't blocked, the virus invades the human cells
5. If everything goes well, antibodies that are fully blocking destroy the virus after a few days

Diversity

Every lymphocyte is different, because during development T-cells and B-cells preform rearrangements of immunoglobulin genes. Different parts of V-, J- and D-regions are coupled. This process can reach a diversity of 2 x 10⁶. The diversity can grow even more at the junction site where V, D and J are coupled → junctional diversity. Here, there is an enormous deletion and inversion of nucleotides which increases the diversion up to 10¹²-10¹⁴.

There are several molecular processes in precursor B-cells and peripheral B-cells:

1. The process of rearrangement takes place in the bone marrow
2. Immature B-cells go into the periphery
3. Immature B-cells arrive in the lymph node via arteries and exit the blood stream
4. The immature B-cells arrive in the germinal center
5. The immature B-cells come into contact with an antigen
6. Under support of T-cells, proliferation, somatic hypermutation and class switch recombination of the B-cells takes place → plasma cells and memory B-cells are created
   • This process takes a few days
7. Antibodies are created

Somatic hypermutation:

Somatic hypermutation takes place in the gene segments that coat particles for the variable domains:

• The heavy chain's VDJ-exon
• The light chain's VJ-exon

There are 3 contact spots per antibody chain → complementary determining regions (CDRs). These are the spots where the mutation takes place during the germinal center response. Different rounds of mutation ensure that the antibody can fit into the epitope:

• There is an increased diversity
• The affinity for the antigen is increased

Class switch recombination:

Class switch recombination is critical to change the effective function of an antibody. These functions take place in the constant domains of antibodies, for instance whether an antibody is brought easily onto the epithelial layer. IgA plays a very important role in this process.

CSR exclusively takes place in immunoglobulin genes. A portion of the heavy chain locus is removed from the chromosome, and the gene segments surrounding the deleted portion are rejoined to retain a functional antibody gene that produces antibodies of a different isotype. This can occur multiple times and does not happen randomly → antibody genes are produced to create antibodies according to the B-cells that are most busy at the moment.

Immune monitoring

In total, there are more than 250 blood leukocyte subsets. These sets are monitored for infections, like SARS-CoV2:

1. There are 10¹²-10¹⁴types of B-cell
2. An antigen arrives → the response at the germinal center starts
3. Proliferation, somatic hypermutation and class switch recombination occurs
   • If this process goes on for a long time, it means it's hard to produce the correct plasma cells
4. Plasma cells and memory B-cells are created

This process is different per age group:

• There is an enormous increase in B-lymphocytes the first 2 years of life
• In adults, the amount of B-lymphocytes has decreased substantially

In case of COVID-19, blood lymphocyte analysis of usually healthy patients shows a huge increase in the amount of plasma cells. Afterwards, the peak decreases again. Nasal line fluid analysis is applied for research → antibodies in the nose are checked for specific antibodies against the virus.

Binding interaction sites

There is a huge difference in binding interaction sites of the SARS-CoV2 and SARS-CoV1 spike proteins:

• SARS-CoV1 has 8 interaction sites
• SARS-CoV2 has 18 interaction sites → the affinity for SARS-CoV2 for human molecules is over 8 x 10^-10 → such affinity hasn't been found in nature before

In the SARS-CoV2 spike protein, there are 2 regions that have an enormous site of interaction:

• DIR-1
  • The strongest
• DIR-2

Together, this surface is huge. Recently, it has been discovered that antibodies do not completely target both dominant interaction regions → all the current antibodies only cover one side of the synaps. Ideally, there'd be a set of antibodies that blocks the full synaps. Antibodies should preferably have the IgA class in dimer format.