ADVANCED MOLECULAR IMMUNOLOGY
AND CELL BIOLOGY
Master Biomedical Sciences
VU Amsterdam
2024-2025
Contents
Lecture introduction immunology ...............................................................................2
Lecture Dendritic cells in tailored adaptive immunity .........................................6
Lecture T cell priming..................................................................................................... 16
Lecture Immunometabolism ....................................................................................... 22
Lecture The spatial tumor microenvironment in lung cancer ....................... 29
Lecture Antibodies in health and disease .............................................................. 35
Lecture immune responses to glycolipids and polysaccharides .................. 41
Lecture lymphoid organ development ................................................................... 52
Lecture Neuro-immunology ........................................................................................ 57
,Lecture introduction immunology
Adaptive
- B cells
- T cells
Innate
- Macrophages
- Dendritic cells
- Neutrophils
- Eosinophils
- Basophils
- Mast cells
o Have Fc receptors
Co-stimulation
DC presents an antigen to the T cell with MHC class + CD80/CD86 (B7) The T cell activates
this co-stimulation via CD28.
- The DC got the CD receptor to the surface via the TLR signalling.
Complement
Antibodies recognize and cover the bacteria, so that macrophages can evolve even more
receptors and recognize the bacteria better, so that it can phagocyte them. this is via Fc
receptors (for the immunoglobulins).
The constant region determines the isotype of the antibody (5 types).
In the additional presence of complement, the opsonization and phagocytosis is even more
efficient.
Complement is in most liquids of the body, everywhere where there is extracellular fluid.
They are synthesized by the liver, which gets signalled to make
more when there is an infection
Three different pathways: that all lead to complement
activation of C3.
1. Alternative pathway
2. Lectin pathway
3. Classical pathway
a. Only can start with the adaptive immunity
(because it has to react to the antibody)
Cleavage of C3 into C3a and C3b leads to
- Recruitment of inflammatory cells
- Opsonization of pathogens, facilitating uptake and killing by phagocytes
- Perforation of pathogen cell membranes
2
,B&T cell receptors
RAG enzymes that regulate the diversity of the B and T cell receptors. They cut the DNA and
nucleate the gene segments together.
B → antibodies
T → cytokines (soluble factors)
Specificity antigen receptor: different for each lymphocyte
Receptors on individual lymphocytes: identical
B-cells
Igβ and Igα are necessary for signalling when bound antibodies bind to an antigen.
T-cells
T cell receptor associates with CD3 co-receptors.
Only lymphocytes express RAG enzymes !!
B cells can later in their response, further change that B cell receptor. This is called
somatic hypermutation. This is only possible in the antigen recognition domain.
→ high-affinity antibodies are selected.
→ it occurs during maturation in the germinal center.
B lymphocytes divert into a plasma cell or memory cell. The memory cells are stored in the
lymph organs, sometimes also in the bone marrow
T cell receptor diversity
- By gene rearrangement
- Only 5% make it out
- Can only recognize an antigen/peptide via an MHC molecule!!
- Donor matching with allografts is always done with MHC matching?
MHC class I and II presentation
Antigenic peptides are situated in antigen-binding sites non-
covalently. Peptides in antigen binding site: 9 amino acids on average.
MHCII gets antigens/peptides derived from the phagosomes →
lysosomes → class II compartment.
The peptide groove red dots are where the peptides bind, while the
‘border’ is where the T cell binds.
A great diversity of HLA types is necessary to be protected against
some diseases.
3
,T and B cell activation
HEV, specialized blood vessels that express adhesion molecules and chemokines
where naïve T and B cells have receptors for and get therefore drawn to the lymph
node.
T cells need two signals to get activated:
- Recognition of the peptide in MHC
- Co-stimulation via B7 (CD80/CD86)
T cells that recognize self-antigens in the absence of co-stimulation become
anergic!
Signal 3 are cytokines that can specify the T cells into 5 different T cells.
TH1 → activates macrophages to help better kill bacteria
- IL-12
- IFN-y
TH17 → enhances neutrophil responses (phagocytosis)
- IL17
- IL-6
TH2 → activates cellular and antibody response to parasites
- IL-4
- IL-5
TFH → activate B cells maturation of antibody response
- IL-21
Treg → Suppress other effector T cells.
- TGF-B
- IL-10
All the T cells have a defining transcription factor that induces their
specification. And those transcription factors have their own cytokines
that induce differentiation. The cells that express the cytokines that
induce the differentiation are Dendritic cells and stromal cells in the
lymph nodes (microenvironment)
Bacteria are being taken by macrophages, but if a T cell doesn’t help it,
it will become a granuloma.
Co-stimulation is only required during activation of naïve T cells. After recognition, they start
to proliferate and differentiate to which then they will perform their effector function.
TFH cell has already received signal 1 and signal 2. Upon recognition, it releases the cytokines
that then further help the B cells to become more activated. Most B cells need their help.
Two waves of plasma cell formation at 2 different sites
1st. expansion of B and Tfh cells: medulla | plasma cells → IgM
2nd expansion in follicle → germinal center reaction. Here: affinity maturation and isotype
switching
4
,Cytokines regulate which isotype occurs. Some inhibit some isotypes and some induce some
isotypes
IGM can activate the complement system via the classical pathway due
to its pentameric shape, it can bind to the C3 porous complex(?).
The gut microbiota are important for
- Synthesis of clotting factors in the liver
- Release of small molecules that can be used in metabolism and
biosynthesis
- Degradation of toxins
- Limitation of pathogen species
- Establishment of the gut-associated lymphoid tissue.
Difference between systemic and mucosal immune defense:
- In systemic defense, inflammatory cytokines are being produced and also an
inflammatory response.
- In mucosal defense, bacteria gain access to the lamina propria by endocytosis,
activate macrophages but do not cause inflammation.
Summary
- Cells of the immune system: innate and adaptive
- Innate cells: pattern recognition receptors
- Adaptive cells: antigen receptors
- Complement: important for pathogen removal
- B- & T- cell receptors: diverse and specific
- MHC class I and II presentation: antigens from different cellular compartments
- T cell activation: 2 signals for activation and signal 3 for differentiation
- B cell activation: need help from T cells → plasma cells
- Antibody effector functions are determined by Fc tail
- Mucosal immune system: in close contact with bacteria!
5
,Lecture Dendritic cells in tailored adaptive immunity
Function of PRR (pathogen recognition receptors) and DC in shaping adaptive immunity
1. DC are important in the activation of adaptive immune responses
2. PRR (pattern recognition receptors) expressed by DC allow for sensing of infection
and induction of tailored immunity
3. DC specific PRR can be targeted for (therapeutic) vaccination
PART I: INNATE AND ADAPTIVE IMMUNITY (dendritic cells)
The immune system consists of multiple components together regulating
health and disease. Three main phases are initiated upon first infection with a
pathogen:
1. Innate immunity (0-4 hours)
a. Macrophages and other immune cells
2. Early induced innate response (4-96 hours)
a. Here the complement system is activated.
3. Adaptive immune response (>96 hours (week))
Just remember that the 3 phases are kind of like this: first macrophages, then
the complement system, then the adaptive immune response.
The effector cells need co-stimulation whereas naïve cells don’t. naïve cells
need the 3 signal paradigm to proliferate:
1. The presentation of the antigenic peptide
a. Necessary for activation of the TCR and clonal expansion of Ag-
specific T cells
2. Provided via costimulatory molecules that are upregulated on APCs only
when the Ag is associated with a PAMP.
a. PAMPs are pathogen-associated molecular patterns that recognize
‘nonself’ conserved microbial components.
3. Consists of innate cytokines that are produced as a result of PRR activation.
The complement system consists of pre-formed factors which respond immediately
upon infection.
6
, - Anaphylatoxins (C3a)
o Increased vascular permeability
o Leukocyte recruitment
▪ Neutrophils
▪ Degranulation of mast cells and basophils
- Opsonization (C3b)
o Enhanced phagocytosis
▪ Via complement receptor (CR) binding
o Membrane Attack Complex formation
▪ Bacterial Lysis
Phagocytes are important for clearance of invading pathogens. Macrophages and dendritic
cells (DC) are phagocytes of the innate immune system with different functions.
Receptors
- Specific receptors for recognition of self-versus non-self via associated molecular
patterns
o Pathogen (PAMP)
o Danger (DAMP)
o Self (SAMP)
- Direct (PAMP) or indirect (whole pathogen) binding
o Phagocytosis
o Intracellular signalling
▪ A.o. cytokine production
MHC class II is on APC (macrophages, DC, B cells). Macrophages stay in the tissues, dendritic
cells move.
T cells are activated first, later the humoral response is being activated. PRR enable to
distinguish the self from non self receptors.
DC are the bridge between innate and adaptive immunity via activation and skewing of naïve
T cells.
- In a mature DC the MHC molecules go up to the cell surface
7
, - Only mature DC can activate naïve T cells for induction of adaptive immunity upon
recognition of pathogens
What happens during DC maturation?
• Phagocytosis ↓
• Antigen processing & presentation ↑
o MHC expression ↑
o Co-stimulatory molecules ↑
• Migration ↑
• Inflammatory cytokines ↑
Pathogen binding via specific receptors enables DC to shape adaptive immune responses
- Receptor binding for phagocytosis
o Signal 1 antigen presentation T cell can never bind to
▪ MHC I CD8+ cytotoxic T cells intact pathogens, so they
▪ MHC II CD4+ helper T cells
need MHC molecules!
- Receptor binding for signaling
o Signal 2 co-stimulation
▪ Proliferation
▪ Activation vs inhibition
o Signal 3 cytokine secretion
▪ T helper cell differentiation.
Pathogen can bind
Indirect → opsonized pathogen
Direct → via PAMP/DAMP
Receptors
Fc Receptors
Fc receptors can activate or inhibit immune cells by binding of
immune complexes. When indirect binding to Fc happens, they cannot induce intracellular
signals!
C-type Lectin receptors
C-type lectin receptors (CLRs) are a diverse family of receptors important for antigen uptake,
presentation and signaling. They only recognize the sugars on pathogen surfaces. They are
very specific and use it to internalize the pathogen/antigen. They are also important for
phagocytosis.
They have a carbohydrate recognition domain (CRD)
- Calcium-dependent
- Recognition (pathogen) specific carbohydrate structures
o Antigen internalization
o Antigen presentation
o Adhesion
8
, • Intracellular signalling motifs: these molecules that interact with the receptors inside
the cell are necessary because otherwise the signalling won’t happen and the DC
doesn’t get the information.
Toll-like receptors (TLR)
TLRs are important signalling receptors leading to specific
cytokine secretion. 9 TLRs activate your cells. They induce
the cell to phagocytose. They can be used for all the types of
pathogens.
- They recognize different specified PAMPs
Only CLRs and TLRs can directly bind pathogens to induce
intracellular signaling cascades!
Context-dependent role of PRR in shaping adaptive immunity, since each pathogen requires
a different elimination strategy. The Pathogen recognition receptors give the distinguishment
Summary of PART I
phases of immunity keeping us healthy by fighting infection
1. Innate immunity
2. Early induced response
a. Activation of complement and phagocytes
i. Macrophages: inflammation
ii. Dendritic cells: adaptive immune activation
1. Tailored adaptive immunity via 3-signal paradigm skewing T cell
responses
2. Only provided by mature dendritic cells following PRR stimulation
3. Adaptive immunity
Innate immune cells recognize pathogens or danger via specific receptors and molecular patterns
- PAMP | DAMP | SAMP
- Receptors which indirectly bind to opsonized pathogen
o Complement and Fc receptors
- Receptors which directly bind to pathogen ligands: PRRs
o TLR, CLR, NLR, RLR: induction of phagocytosis and/or intracellular signaling
▪ CLR: phagocytosis and intracellular signaling (signal 1)
▪ TLR: signaling for inflammatory cytokine production (signal 2/3)
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