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Answer by Tirumalai Kamala:

We don’t know for sure how any conjugate vaccine works. There are two prevailing hypotheses. The whats and whys of conjugate vaccines set the stage for their hows.

Why Conjugate vaccines
A conjugate vaccine has two main components, a sugar and a protein. The sugar is usually derived from the cell wall of encapsulated bacteria like Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitidis. Encapsulated means they have a thick polysaccharide (sugar) coat. These bacteria cause local infection, primarily in upper airways. If we don’t stop them there, they can get into blood and cause severe disease such as meningitis or pneumonia. They are extracellular, i.e. they replicate in interstitial fluids, in the spaces between cells. Complement and macrophages usually get rid of extracellular bacteria except here their thick sugar coats render these encapsulated bacteria impervious to such killing. On the other hand, neutralizing antibodies specific for these sugars can bind and clear them, preventing their bloodstream spread. Problem is how to make sugar-specific antibodies that can do this.

What are Conjugate Vaccines?
Some B cells called Innate B cells can and do make low-affinity IgM antibodies against sugars. While these appear to be sufficient to prevent bloodstream spread in adults, there’s something different about babies less than 2 years of age. Two prevailing hypotheses attempt to explain this difference:
a) Babies lack these Innate B cells (also called Marginal Zone B cells) until about two years of age.
b) Babies’ noses (or maybe another body site) are only colonized by a cross-reactive environmental (benign) bacterium by two years of age or so. This cross-reactive bacterium primes these or other B cells to make neutralizing antibodies ready to stop the disease-causing bacteria.

While we still don’t know why babies don’t make sufficient antibodies to sugar alone to prevent meningitis or pneumonia, the upshot is that bacterial sugar-alone vaccines are adequate (not optimal, only adequate) in adults but useless in babies. We need a different type of vaccine to prevent disease from these bacteria in babies, especially since they are quite susceptible to these diseases. How to do that?

Enter need for conjugate vaccines
In order to make high-affinity neutralizing anti-sugar antibodies, we need another type of B cell, the Classical (or Follicular or Germinal Center; GC) B cell.

Dogma I. Classical (Follicular; GC) B cells need T cell help.

Dogma II. T cells respond to peptides, not sugars.

We seem stuck but good. Solution? Glue the sugar to a protein, preferably a protein that our T cells respond to strongly. Such T cells will get activated and help sugar-specific B cells. Never mind whether and how such help could actually happen. This was the idea behind the sugar-protein conjugate design of conjugate vaccines.

Did this approach work? Yes, and how. We stuck sugars from Haemophilus influenzae, Streptococcus pneumoniae or Neisseria meningitidis to proteins such as Tetanus toxoid (Act-HIB, for e.g.) and Diphtheria Toxoid (Prevnar13, for e.g.). Such vaccines protect both babies and adults from bacterial meningitis.

The pneumococcal conjugate vaccine has sugars from several Streptococcus pneumoniae strains conjugated to diphtheria toxoid. There are about 90 different Streptococcus pneumoniae strains in the world while approved pneumococcal conjugate vaccines have sugars from 7, 10 or 13 strains, typically those most prevalent in humans in different parts of the world.

How do conjugate vaccines work?
Let’s look at the two prevailing hypotheses now.

Hypothesis I: Conventional idea (from Neonatal and Infantile Immune Responses to Encapsulated Bacteria and Conjugate Vaccines)

Hypothesis II: Paradigm-changing idea (from A novel mechanism for glycoconjugate vaccine activation of the adaptive immune system)

Let’s go through step by step (steps 6 and 7 are the only ones different between the two hypotheses).

  1. Let’s make the vaccine X+Y. Polysaccharide (sugar) is X (blue). Conjugate (protein) is Y (red).
  2. X specific-B cell binds to the X part of the X+Y vaccine with its receptor (B Cell Receptor; BCR).
  3. B cell internalizes the bound X(+Y) + BCR.
  4. Bound X(+Y) + BCR dissociates inside the B cell.
  5. B cell digests bound X(+Y). This generates sugar bits (X alone), peptide bits (Y alone) and sugar-peptide bits (Yx).
  6. Hypothesis I: X-specific B cell presents Y peptides to a Y-specific CD4 T cell inside a MHC II molecule.
  7. Hypothesis II: X-specific B cell presents Yx peptides to a Yx-specific CD4 T cell inside a MHC II molecule.
  8. Some more details activate the T cell (Not relevant for this answer).
  9. Activated Y-specific (Hypothesis I) or Yx-specific (Hypothesis II) T cells help X-specific B cells make X-specific antibodies.
  10. What is T cell help exactly? (same for both hypotheses)
    a) Help B cell Class Switch Recombination to switch from making IgM to IgG.
    b) Help B cell Somatic Hypermutation to exponentially increase antibody affinity.

Any proof for conventional hypothesis I? Not really.
Unconventional hypothesis II? Yes, in a mouse model. However, as far as I know, no one else has generated independent data for Hypothesis II since the original publication in 2011.

The big deal about these hypotheses? Both overturn different aspects of the central tenets of T and B cell function.

  1. A tenet of T and B cell function is cognate T cell help. Y-specific T cell helps a Y-specific B cell. In Hypothesis I we have non-cognate T cell help. Y-specific T cell helping an X-specific B cell.
  2. Another tenet of T cell function is that T cell receptors bind to peptides. Hypothesis II turns that on its head by suggesting that T cell receptors can bind to peptides that have sugar pieces stuck to them.

What is the mechanism of action of Pneumococcal conjugate vaccine?