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Lecture notes Advanced Molecular Immunology and Cell Biology
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  • Course
  • Advanced molecular immunology and cell biology (AM_470656)
  • Institution
  • Vrije Universiteit Amsterdam (VU)

This document contains extensive lecture notes of the course Advanced Molecular Immunology and Cell Biology. It is fully written in English and contain images from the slides as well. This really helped me to prepare for the exam, resulting in a 9!

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Document information

  • December 15, 2023
  • 32
  • 2023/2024
  • Class notes
  • Prof. dr. r. mebius
  • All classes

Subjects

  • oncology
  • immunology
  • cell biology
  • biomedical sciences
  • molecular immunology
  • vu

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  • Vrije Universiteit Amsterdam (VU)
  • Biomedical Sciences
  • Advanced molecular immunology and cell biology (AM_470656)
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Lecture notes AMI
HC 1: Introduction 4-9-2023
24-10-2023 Writing assignment read on Canvas how to prepare for that. Read the 2 papers (displays
the structure). This assignment is in pairs.

Lectures are not mandatory but contain exam material.

Cell of the immune system
Why do we need an immune system? To get rid/destruction of dangerous pathogens
and fight infections = to keep us healthy.

Adaptive > BC and TC

- Use antigen receptors to recognize antigens.
- Variable
- Highly specific
- Improves during response (secondary/memory response is even better)
- Respond slow, 24/48 hours
- Started in secondary lymphoid organs (spleen, mucous-associated lymphoid
structure (MALS), tonsil). In the lymph, there is activation and travel via the
bloodstream (highly .. venules).
- Wound > immature DC takes up pathogens > DC gets matured > process
antigen > travel to the lymph nodes > mature DC activates BC/TC by presenting
antigens (here starts the adaptive response!).
o Good at phagocytosing = immature
o Presenting = mature

Innate > NK, Mast cells, neutrophils, MQ

- Use pattern recognition receptors (PRR) on bacteria and viruses. Activate
myeloid cells.
o MQ recognizes the cell-surface carbohydrates of bacterial cells but not
those of human cells.
o NK cell receptors recognize changes at the surface of human cells that
are caused by viral infections.
- Respond fast, within hours
- Fixed
- Limited specificities
- Constant response
- Distinguish self from non-self. An
infected cell changes its epitope that the
innate cells recognize.
- 2 responses
o Phagocytosis > destruction of
bacteria/pathogen
o Signalling (Toll-like receptors) >
produce cytokines that will help
the phagocytosis.

,Complement
Ab recognizes bacteria > opsonization of Ab-bacteria complex by MQ > phagocytosing + destruction
 phagocytosis is better this way. In combination with complement > it goes more efficiently.

- Factors present in serum, lymph, and
extracellular fluids.
- Synthesized by the liver
- Bind pathogens, causing them to undergo
phagocytosis.
- Without these factors, many bacteria would not
be phagocytosed.

3 pathways in complement activation:

1. Alternative pathway: The pathogen surface
creates a local environment conducive to
complement activation.
2. Lectin: mannose-binding lectin binds to the
pathogen.
3. Classical pathway: C-reactive protein or Ab
binds to specific Ag on the pathogen.
 All three lead to cleavage of C3 to C3a and C3b
> C3b covalently bound to the surface components of pathogens. This leads to opsonization,
perforation of the cell membrane, and recruitment of inflammatory cells (C5) > all leading to
the death of the pathogens.

The adaptive immune system
Specific! Has a memory! They recognize antigens (small peptides specific to the pathogen).
After binding AgR you get effector cells (TC produces soluble factors like granzymes,
cytokines, and cytotoxins; BC = plasma cell and produces antibodies > improves the immune
response by fine-tuning the Ab that bind antigens, so they improve binding to pathogens).

- BC mature in bone marrow. Ag recognition on the variable part. AgR and effector
molecule;
- TC mature in thymus. Have CD3 molecules. AgR is the TCR, and effector molecules are the
cytokines or granzymes.

They are required for the rearrangement of immunoglobulin (antibody) genes: RAG-enzyme
expression (recombinant-activation genes). Only lymphocytes express RAG enzymes.

BC diversity:

- Genes rearrangement gives diversity.
- More during immune response by somatic hypermutation.
- High-affinity Abs are selected.
- During maturation in germinal centers.

BC activation can lead to plasma cells or memory cells (in a secondary infection these will turn into
plasma cells > memory response).
TC needs MHC and antigenic peptides to get activated, which BC can already recognize.
TC recognizes Ag peptides and HLA (MHC), when it’s the wrong MHC molecule the TC gets activated
and you get an allo-response like in graft-vs-host diseases.

,MHC I and II
Antigenic peptides are situated in Ag-binding sites non-covalently. Peptides in the
Ag-binding site are on average 9 amino acids.
MHC I recognize CD8 > every cell except for erythrocytes, and intracellular
peptides (viruses). 9 amino acids, HLA class one. Many self-peptides end up here,
when TC binds to that they get silenced.
MHC II recognizes CD4 > extracellular peptides (phagocytosis). 15 amino acids,
HLA class two. Phagosomes > lysosomes > class II compartment.
There are only certain peptides in the sequences that can bind to the MHC
receptor. The other part of the sequence can vary.

TC/BC activation
DC takes up Ag and transports them to a draining lymph node to activate an adaptive response. Naïve
TC circulates in the secondary lymph node and recognizes the Ag presented on the DCs. Extravasation
is hard because blood has a high velocity > DC starts rolling over the endothelium walls to slow down
and can recognize cytokines.

TC needs 3 signals:

1. Peptide recognition in MHC molecule
2. Co-stimulation (CD28 on naïve cell + B7 (CD80/CD86) on DC)
a. Missing > cell anergy (can’t do anything anymore) and stays anergic. This is to
activate TC only at the right time.
3. Cytokines that determine which Th subset is activated (Th specification). Only required during
activation.
a. Th1 > makes IL-12 and IFN-g > activate MQ. T-bet is determining transcription factor
b. Th2 > makes IL-4 and IL-5 > activate cellular and Ab responses to parasites.
c. Th17 > makes IL17 and IL-6 > enhance neutrophil response
d. ThFH > makes IL-21 > activated BC maturation of Ab response
e. Treg > makes TGF-b and IL-10 > suppress other effector TC




CD8 TC > kill virus-infected (and tumor cells).
CD4 TC > can transform in BC. Most BCs need the help of the ThFH to become activated.

- DiGeorge syndrome: no thymus

There are two ‘waves’ of plasma cell formation at 2 different sites:

1. Expansion of BC and ThFH in the medulla (plasma cells produce IgM);
2. In follicle > germinal center reaction. Here: affinity maturation and isotope switching.

, Plasma cells (effector BC)
Plasma cells make one type of Ab.
Cytokines regulate which isotype switch occurs.

Internal organs are protected by IgM, IgG, and IgA via FcRn transport > tissues.

- IgA protects the mucosa against bacteria that want to enter the epithelium. It forms a sort of
shield.
- IgE protects against parasitic infections by activation of mast cells, eosinophils, and basophils
that secrete mediators that expel parasites from the body.
- Neutralising Ab: an important defect mechanism (vaccination), making pathogens not
dangerous anymore.

Opsonization is covered in Ab to make the pathogen more attractive to the immune cells.

Mucosal immune system
More or less our microbiome. However, there is a difference between the skin and mucosal organs
(respiratory-, gastrointestinal;- and urogenital tract); the skin is very thick whereas e.g. the lung
epithelium is only one cell layer thick.
Beneficial role for gut microbiota:

- Cofactor for the synthesis of clotting factors in the liver;
- Release of small molecules that can be used in metabolism and biosynthesis;
- Degradations of toxins into harmless components that can be used by the human body;
- Limitation of pathogens species to small numbers that are not harmful;
- Establishment of the gut-associated lymphoid tissues.




Epithelial cells contribute to mucosal defense. This can happen by activation of TLR or activation of
NOD1/2 (when the bacteria has entered the cytosol)  activation of NF-kB, inducing the epithelial
cell to express inflammatory cytokines, chemokines, and other mediators. These recruit and activate
neutrophils and monocytes.
M cells can take up and transport Ag to present them to DCs and other lymphatic cells > effector TC
production + plasma cell makes specific secretory Ab.
DC can extend processes across the epithelial layer to capture Ag from the lumen of the gut.

Summary:

- Cells of the immune system: innate and adaptive;

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