Immunology Resources
- Murphy, K.B, Travers, P., and Walport M. Janeway’s Immunobiology: 9th edition, 2016.
- Abbas, AK et al. Cellular and Molecular Immunology 9th edition, 2018
- Further reading recommended by lecturers
- Review articles from Immunology Journals
Overview of immune response
• 3 components: (1) recognition (innate and adaptive), (2) amplification and regulation, (3)
effector mechanisms.
• Host response initiated by recognition of PAMPs/DAMPs by germline-encoded PRRs.
• PAMPs are common to many different pathogens, can be used as adjuvants to activate
responses to antigens, and activate effector function by innate immune cells and are also
required for myeloid cells to instruct adaptive immunity.
• PRRs are presented by all immune cell types.
• PRR forms: cell membrane-associated receptor proteins (including TLRs, NLRs, CLRs, RIGs -
present in all immune cells), organelle membrane-associated, cytosolic receptors (detect
nucleic acid motifs), circulating plasma proteins (e.g. C reactive protein, C1q, factor XII)
• Innate (rapid) immunity: granulocytes (neutrophils, eosinophils, basophils), DCs, mast cells,
macrophages, NK cells, complement, yd T cells, NK T cells.
• Adaptive (slow) immunity: T cells (CD4+ and CD8+), B cells, antibodies, yd T cells, NK T cells.
• Yd T cells are active in both innate and adaptive responses. They have a semi-variant
ydTCR, which acts as a PRR to recognise bacterial metabolites and stressed cells. They
produce cytokines and cytotoxic molecules and become an APC. They have the potential for
memory.
• NK T cells are also active in both innate and adaptive responses. They are a subtype of aB T
cells that possess a specific semi-invariant TCR that recognises lipid antigen. They can be
sub-divided into Group 1 iNKT cells with CD1d-restricted TCR or Group 2 with a more diverse
TCR. They do not have memory.
• To avoid immunopathology:
•
• Factors determining whether an infection leads to immunopathology:
• Pathogen factors: dose, virulence, inflammatory capacity
• Host factors: age, genetics of HLA/cytokines etc., ability to cleave virus
• See week 8 Immunopathology for specific immunopathology examples e.g:
, • Dengue: febrile, critical, recovery phases, immunopathology (fever to shock, cytokine storm
leading to vascular pathology and multiorgan failure, pro-inflammatory mediators TNF, IFNy,
anti-inflammatory IL-10, cross-reactive T cells)
• Cross-reactive T cells: CD8+ T cells have high affinity for different DENV subtypes. Type I
cross-reactive T cells recognise dengue-infected cells and produce cytokines. Type II
granulate and kill the cell. Type III have low avidity and are non-functional. These cross-
reactive T cells can either be helpful for the response or immunopathogenic.
• Streptococcus: bacterial, molecular mimicry of self-antigen (autoimmunity)
Innate myeloid/lymphoid cell subsets and inflammation
• Innate responses are rapid (0-4hrs of pathogenic infiltration) because PRR forms are widely
distributed + innate does not rely on cellular proliferation (unlike adaptive).
• Innate responses are broadly specific: many PRRs but each PRR binds a specific
PAMP/ligand/motif shared by many microbes.
• Innate immune receptors (PRRs) are expressed by all nucleated cells.
• TLRs allow innate immune cells to specifically detect pathogens.
• Innate responses recognise non-self and self.
• All innate immune cells are derived from bone marrow multipotent haematopoietic stem
cells -> self-renewal + common myeloid progenitor (mast cells, myeloblast, basophil,
neutrophil, eosinophil, monocyte, macrophage, dendritic cell, platelets) OR common
lymphoid progenitor (natural killer cell, ChILP, ILC1, ILC2, ILC3, LTi, adaptive T/B cells).
• Neutrophils/granulocytes: large, uneven-shaped, first innate responder recruited form
BM/blood to tissue (rolling, adhesion, crawling, transmigration), most abundant, tightly
controlled with rapid response and short half-life (circulate for 1/2 days before dying). Input:
Respond to complement component C3a and C5a, products of other leukocytes IL-8, and
PRRs activation by PAMPs/DAMPs. Output: Phagocytosis (killing by: respiratory burst,
NADPH oxygenase-dependent mechanisms (ROS) or intracellularly/extracellularly-acting
antibacterial proteins (cathepsins, defensins, lactoferrin, lysozyme), degranulation (non-
specific) – release of pro-inflammatory proteins, release neutrophil extracellular traps (NETs)
which immobilise pathogens preventing their spread and allowing subsequent phagocytosis
and kill directly with antimicrobial histones/proteases, chemokine production to recruit
other immune cells (monocytes, dendritic cells, natural killer cells, Th1 cells), pro-
inflammatory cytokine (IL-1, IL-6, TNFa, MIF) production.
• Neutrophil respiratory burst:
•
• Monocytes: small, round-shaped, released from BM, precursor of macrophages and
dendritic cells. Respond to PAMPs and cytokines. 3 monocyte lineages, all have PRRs:
CD14+/CD16- classical monocytes 85% of circulating monocyte pool (high CCR2 – needed for
, monocytes to leave BM and reach inflamed tissue, functional plasticity - differentiate into
dendritic cells and macrophages, produce pro-inflammatory cytokines IL-6, IL-10, TNFa,
undergo phagocytosis, migrate to lymph nodes to present antigen to T cells, tissue
remodelling in response to wounding), CD14+/CD16+ intermediate monocytes (less CCR2),
CD14-/CD16+ (very little CCR2, differentiate and remain in blood, patrol vessel removing
debris, recruiting and activating neutrophils, being antiviral).
• Macrophages: resident cells in all tissues with differing functions e.g. kidney Kupffer cells for
iron and cholesterol recycling, brain microglia for synaptic pruning and debris clearing. They
are long-lived (years, very slowly self-renewing). Responsive to local environment. In an
inflammatory environment, they receive stimulation from TLR agonists, TNFa, IFNy, iNOS, IL-
6, IL-23 = bactericidal and have role in inflammation and immunomodulation = anti-tumour
activity. In an anti-inflammatory environment, they receive stimulation from IL-4/13, TGFB,
IL-10, Arg, PD-L1 = play a role in tissue repair, angiogenesis, immunosuppression = pro-
tumour activity. Input: opsonised cells (Ab/C3b-coated), necrotic cells or pathogens via
PRRs, or uptake of apoptotic cells. Output: phagocytosis of bacteria and debris, rapid killing
by ROS/RNS, promoted by IFNy, present antigens to T cells in periphery, produce pro-
inflammatory (IL-1, IL-6, TNFa) and anti-inflammatory (IL-10, TGFB) cytokines. Pro-
inflammatory IL-6 stimulates Tfh cells to release IL-21 to stimulate neutrophils and B cells.
• Basophils: reside in blood, respond to parasite infection. Input: cytokine input (IL-3, IL-5, G-
CSF), complement (C3a, C5a), IgE-coated particles. Output: release of heparin (prevent
clotting), release of histamine (recruit), produce IL-4 to promote Th2 response to parasite.
• Eosinophils: rare in blood, respond to parasite infection, must be tightly-controlled – must
be pre-activated for stimulation of granule release. Input: cytokine input (IL-3, IL-5, G-CSF),
IgE-coated particles binding to eosinophil Fce receptor. Output: release toxic granules to
destroy parasite, amplify cytokine signal.
• Dendritic cells: arise from BM, circulate blood, reside in infected tissue in immature
(unlicensed) form to pick up antigen. They express TLRs and other receptors that recognise
microbial molecules and respond by secreting cytokines that recruit and activate innate cells
at the infection site. 2 types of highly conserved myeloid dendritic cell lineages arise from
pre-dendritic cells: if the pre-DC expresses Irf8 TF, it differentiated into cDC1 which produce
high IL-12 to stimulate cytotoxic and Th1 cells. If the pre-DC expresses Irf4 TF, it
differentiated into cDC2 which stimulate Th2 responses. Plasmacytoid dendritic cells (pDC)
take on dendritic morphology upon activation (may derive from lymphoid lineage) – impart
rapid response against viruses by stimulating release of high Type 1 IFNs. Output:
Phagocytosis. Immature DCs have antigen uptake receptors for cytosolic antigens that are
presented via MHC class I to CD8+ T cells, and exogenous antigens presented via MHC class II
to CD4+ T cells. Cross-presentation of MHC-peptide complexes by cDC1, which takes an
exogenous antigen and transfers it from extracellular pathways to intracellular endosomes
to present on MHC class I for CD8+ T cell response. Cross-presentation is important for viral
infections as viruses infect DCs and disable MHC class I pathways, stopping activation of
CD8+ T cells. (Cross-presentation is essential for the initiation of immune responses to
pathogens that do not infect APCs.) When activated by PAMPs, immature dendritic cells
migrate out of infected tissue to draining lymph node where they mature to licensed
dendritic cells and activate naïve T cells (adaptive). These licensed dendritic cells undergo
reduced phagocytosis and antigen processing, loaded antigens are presented on surface
MHC I and II and co-stimulatory CD80/86 and CD40 are upregulated and cytokines produced.
Role of DCs in 3 signals: Signal 1 – DC present Ag via MHC class I/II with peptide to naïve T
cell via CD8/CD4+ TCR. Signal 2 – DC co-stimulation ligands bind to CD80/86 and CD40 on T
, cell, activating T cell to become effector T cell. Signal 3 – DCs secrete cytokines: myeloid DCs
are activated by TLR-PAMPs to produce IL-12, TNFa, IL-6, IL-10. pDCs activated by TLR7/9-
viral PAMPs to produce Type I antiviral IFN (TNFa/B).
• Herpes simplex virus infects DCs and inhibits its ability to stimulate T cell proliferation, which
delays initiation of the adaptive response.
• Natural killer (NK) cell:
• Input: Recognise and kill virally infected (instant decision), Ab-coated, stressed, missing-self
(fail to express MHC class I) or cancerous cells. There is tonic (continuous background)
activation between NK cells and target cells. Self-MHC class I on target cells is recognised by
inhibitory receptors expressed on NK cells: KIR (inhibitory and activating) binds to top of
MHC class I groove, CD94-NKG2A (inhibitory) binds non-classical MHC class 1 molecule HLA-
E, LILRB1 (inhibitory) binds broad-range of MHC class I, NKG2D (activating) recognises
ligands associated with stressed epithelial cells (MICA, MICB, ULBPs), NKp44/46 (activating)
recognised viral haemagglutinins on virus-infected host cell surfaces and viral envelope
glycoproteins, CD16 (activating) binds IgG allowing NK cells to kill any Ab-coated cells.
Usually there is balance between these activating and inhibitory signals. But if the target
cells (cancerous/virus-infected) downregulated MHC class I, the inhibitory signal will be lost,
leaving only an activating signal, leading the NK cell to kill the target cell.
• Output: Kill by inducing apoptosis by releasing cytokines (TNFa, IFNy) or cytotoxic granules
(with perforin and granzyme) or ligating death receptors: perforin forms a pore in the
membrane to allow entry of granzymes. Intrinsic pathway (granzyme-dependent): granzyme
A induces caspase-independent pathway of apoptosis by slicing at the nuclear DNA causing
loss of nuclear structure, granzyme B promotes apoptosis via caspase 3, 7 and 8 and
mitochondrial dependent pathway. Extrinsic pathway: Target cell expresses TNFR/TRAIL
receptor/FasL and NK cell expresses TNFa/TRAIL/Fas, activation of caspase 8 and 10, induces
apoptosis. NK cells cause onward signalling by releasing IFNy and IL-12, which polarises the
immune response to a type 1 antiviral state via stimulating Th1 to release IFNy and TNFa.
• ILC1: macrophages and dendritic cells release IL-12 which activate Tbet ILC1, which release
IFNy, inducing type 1 antiviral response.
• ILC2: epithelial cells release IL-33 which activate GATA3 ILC2, which release IL-4, IL-5, IL-13
for a type 2 response and contribute to antigen presentation by expressing MHC class II.
• ILC3: dendritic cells release IL-23 which activate RoRyt ILC3, which release IL-22 for epithelial
integrity and contribute to antigen presentation. ILC3 also require commensal bacterial for
their development.
• LTi (lymphoid tissue inducer cell): most active in foetal life, LTi cells induce secondary
lymphoid tissue formation (lymph nodes) for adaptive response.
- Murphy, K.B, Travers, P., and Walport M. Janeway’s Immunobiology: 9th edition, 2016.
- Abbas, AK et al. Cellular and Molecular Immunology 9th edition, 2018
- Further reading recommended by lecturers
- Review articles from Immunology Journals
Overview of immune response
• 3 components: (1) recognition (innate and adaptive), (2) amplification and regulation, (3)
effector mechanisms.
• Host response initiated by recognition of PAMPs/DAMPs by germline-encoded PRRs.
• PAMPs are common to many different pathogens, can be used as adjuvants to activate
responses to antigens, and activate effector function by innate immune cells and are also
required for myeloid cells to instruct adaptive immunity.
• PRRs are presented by all immune cell types.
• PRR forms: cell membrane-associated receptor proteins (including TLRs, NLRs, CLRs, RIGs -
present in all immune cells), organelle membrane-associated, cytosolic receptors (detect
nucleic acid motifs), circulating plasma proteins (e.g. C reactive protein, C1q, factor XII)
• Innate (rapid) immunity: granulocytes (neutrophils, eosinophils, basophils), DCs, mast cells,
macrophages, NK cells, complement, yd T cells, NK T cells.
• Adaptive (slow) immunity: T cells (CD4+ and CD8+), B cells, antibodies, yd T cells, NK T cells.
• Yd T cells are active in both innate and adaptive responses. They have a semi-variant
ydTCR, which acts as a PRR to recognise bacterial metabolites and stressed cells. They
produce cytokines and cytotoxic molecules and become an APC. They have the potential for
memory.
• NK T cells are also active in both innate and adaptive responses. They are a subtype of aB T
cells that possess a specific semi-invariant TCR that recognises lipid antigen. They can be
sub-divided into Group 1 iNKT cells with CD1d-restricted TCR or Group 2 with a more diverse
TCR. They do not have memory.
• To avoid immunopathology:
•
• Factors determining whether an infection leads to immunopathology:
• Pathogen factors: dose, virulence, inflammatory capacity
• Host factors: age, genetics of HLA/cytokines etc., ability to cleave virus
• See week 8 Immunopathology for specific immunopathology examples e.g:
, • Dengue: febrile, critical, recovery phases, immunopathology (fever to shock, cytokine storm
leading to vascular pathology and multiorgan failure, pro-inflammatory mediators TNF, IFNy,
anti-inflammatory IL-10, cross-reactive T cells)
• Cross-reactive T cells: CD8+ T cells have high affinity for different DENV subtypes. Type I
cross-reactive T cells recognise dengue-infected cells and produce cytokines. Type II
granulate and kill the cell. Type III have low avidity and are non-functional. These cross-
reactive T cells can either be helpful for the response or immunopathogenic.
• Streptococcus: bacterial, molecular mimicry of self-antigen (autoimmunity)
Innate myeloid/lymphoid cell subsets and inflammation
• Innate responses are rapid (0-4hrs of pathogenic infiltration) because PRR forms are widely
distributed + innate does not rely on cellular proliferation (unlike adaptive).
• Innate responses are broadly specific: many PRRs but each PRR binds a specific
PAMP/ligand/motif shared by many microbes.
• Innate immune receptors (PRRs) are expressed by all nucleated cells.
• TLRs allow innate immune cells to specifically detect pathogens.
• Innate responses recognise non-self and self.
• All innate immune cells are derived from bone marrow multipotent haematopoietic stem
cells -> self-renewal + common myeloid progenitor (mast cells, myeloblast, basophil,
neutrophil, eosinophil, monocyte, macrophage, dendritic cell, platelets) OR common
lymphoid progenitor (natural killer cell, ChILP, ILC1, ILC2, ILC3, LTi, adaptive T/B cells).
• Neutrophils/granulocytes: large, uneven-shaped, first innate responder recruited form
BM/blood to tissue (rolling, adhesion, crawling, transmigration), most abundant, tightly
controlled with rapid response and short half-life (circulate for 1/2 days before dying). Input:
Respond to complement component C3a and C5a, products of other leukocytes IL-8, and
PRRs activation by PAMPs/DAMPs. Output: Phagocytosis (killing by: respiratory burst,
NADPH oxygenase-dependent mechanisms (ROS) or intracellularly/extracellularly-acting
antibacterial proteins (cathepsins, defensins, lactoferrin, lysozyme), degranulation (non-
specific) – release of pro-inflammatory proteins, release neutrophil extracellular traps (NETs)
which immobilise pathogens preventing their spread and allowing subsequent phagocytosis
and kill directly with antimicrobial histones/proteases, chemokine production to recruit
other immune cells (monocytes, dendritic cells, natural killer cells, Th1 cells), pro-
inflammatory cytokine (IL-1, IL-6, TNFa, MIF) production.
• Neutrophil respiratory burst:
•
• Monocytes: small, round-shaped, released from BM, precursor of macrophages and
dendritic cells. Respond to PAMPs and cytokines. 3 monocyte lineages, all have PRRs:
CD14+/CD16- classical monocytes 85% of circulating monocyte pool (high CCR2 – needed for
, monocytes to leave BM and reach inflamed tissue, functional plasticity - differentiate into
dendritic cells and macrophages, produce pro-inflammatory cytokines IL-6, IL-10, TNFa,
undergo phagocytosis, migrate to lymph nodes to present antigen to T cells, tissue
remodelling in response to wounding), CD14+/CD16+ intermediate monocytes (less CCR2),
CD14-/CD16+ (very little CCR2, differentiate and remain in blood, patrol vessel removing
debris, recruiting and activating neutrophils, being antiviral).
• Macrophages: resident cells in all tissues with differing functions e.g. kidney Kupffer cells for
iron and cholesterol recycling, brain microglia for synaptic pruning and debris clearing. They
are long-lived (years, very slowly self-renewing). Responsive to local environment. In an
inflammatory environment, they receive stimulation from TLR agonists, TNFa, IFNy, iNOS, IL-
6, IL-23 = bactericidal and have role in inflammation and immunomodulation = anti-tumour
activity. In an anti-inflammatory environment, they receive stimulation from IL-4/13, TGFB,
IL-10, Arg, PD-L1 = play a role in tissue repair, angiogenesis, immunosuppression = pro-
tumour activity. Input: opsonised cells (Ab/C3b-coated), necrotic cells or pathogens via
PRRs, or uptake of apoptotic cells. Output: phagocytosis of bacteria and debris, rapid killing
by ROS/RNS, promoted by IFNy, present antigens to T cells in periphery, produce pro-
inflammatory (IL-1, IL-6, TNFa) and anti-inflammatory (IL-10, TGFB) cytokines. Pro-
inflammatory IL-6 stimulates Tfh cells to release IL-21 to stimulate neutrophils and B cells.
• Basophils: reside in blood, respond to parasite infection. Input: cytokine input (IL-3, IL-5, G-
CSF), complement (C3a, C5a), IgE-coated particles. Output: release of heparin (prevent
clotting), release of histamine (recruit), produce IL-4 to promote Th2 response to parasite.
• Eosinophils: rare in blood, respond to parasite infection, must be tightly-controlled – must
be pre-activated for stimulation of granule release. Input: cytokine input (IL-3, IL-5, G-CSF),
IgE-coated particles binding to eosinophil Fce receptor. Output: release toxic granules to
destroy parasite, amplify cytokine signal.
• Dendritic cells: arise from BM, circulate blood, reside in infected tissue in immature
(unlicensed) form to pick up antigen. They express TLRs and other receptors that recognise
microbial molecules and respond by secreting cytokines that recruit and activate innate cells
at the infection site. 2 types of highly conserved myeloid dendritic cell lineages arise from
pre-dendritic cells: if the pre-DC expresses Irf8 TF, it differentiated into cDC1 which produce
high IL-12 to stimulate cytotoxic and Th1 cells. If the pre-DC expresses Irf4 TF, it
differentiated into cDC2 which stimulate Th2 responses. Plasmacytoid dendritic cells (pDC)
take on dendritic morphology upon activation (may derive from lymphoid lineage) – impart
rapid response against viruses by stimulating release of high Type 1 IFNs. Output:
Phagocytosis. Immature DCs have antigen uptake receptors for cytosolic antigens that are
presented via MHC class I to CD8+ T cells, and exogenous antigens presented via MHC class II
to CD4+ T cells. Cross-presentation of MHC-peptide complexes by cDC1, which takes an
exogenous antigen and transfers it from extracellular pathways to intracellular endosomes
to present on MHC class I for CD8+ T cell response. Cross-presentation is important for viral
infections as viruses infect DCs and disable MHC class I pathways, stopping activation of
CD8+ T cells. (Cross-presentation is essential for the initiation of immune responses to
pathogens that do not infect APCs.) When activated by PAMPs, immature dendritic cells
migrate out of infected tissue to draining lymph node where they mature to licensed
dendritic cells and activate naïve T cells (adaptive). These licensed dendritic cells undergo
reduced phagocytosis and antigen processing, loaded antigens are presented on surface
MHC I and II and co-stimulatory CD80/86 and CD40 are upregulated and cytokines produced.
Role of DCs in 3 signals: Signal 1 – DC present Ag via MHC class I/II with peptide to naïve T
cell via CD8/CD4+ TCR. Signal 2 – DC co-stimulation ligands bind to CD80/86 and CD40 on T
, cell, activating T cell to become effector T cell. Signal 3 – DCs secrete cytokines: myeloid DCs
are activated by TLR-PAMPs to produce IL-12, TNFa, IL-6, IL-10. pDCs activated by TLR7/9-
viral PAMPs to produce Type I antiviral IFN (TNFa/B).
• Herpes simplex virus infects DCs and inhibits its ability to stimulate T cell proliferation, which
delays initiation of the adaptive response.
• Natural killer (NK) cell:
• Input: Recognise and kill virally infected (instant decision), Ab-coated, stressed, missing-self
(fail to express MHC class I) or cancerous cells. There is tonic (continuous background)
activation between NK cells and target cells. Self-MHC class I on target cells is recognised by
inhibitory receptors expressed on NK cells: KIR (inhibitory and activating) binds to top of
MHC class I groove, CD94-NKG2A (inhibitory) binds non-classical MHC class 1 molecule HLA-
E, LILRB1 (inhibitory) binds broad-range of MHC class I, NKG2D (activating) recognises
ligands associated with stressed epithelial cells (MICA, MICB, ULBPs), NKp44/46 (activating)
recognised viral haemagglutinins on virus-infected host cell surfaces and viral envelope
glycoproteins, CD16 (activating) binds IgG allowing NK cells to kill any Ab-coated cells.
Usually there is balance between these activating and inhibitory signals. But if the target
cells (cancerous/virus-infected) downregulated MHC class I, the inhibitory signal will be lost,
leaving only an activating signal, leading the NK cell to kill the target cell.
• Output: Kill by inducing apoptosis by releasing cytokines (TNFa, IFNy) or cytotoxic granules
(with perforin and granzyme) or ligating death receptors: perforin forms a pore in the
membrane to allow entry of granzymes. Intrinsic pathway (granzyme-dependent): granzyme
A induces caspase-independent pathway of apoptosis by slicing at the nuclear DNA causing
loss of nuclear structure, granzyme B promotes apoptosis via caspase 3, 7 and 8 and
mitochondrial dependent pathway. Extrinsic pathway: Target cell expresses TNFR/TRAIL
receptor/FasL and NK cell expresses TNFa/TRAIL/Fas, activation of caspase 8 and 10, induces
apoptosis. NK cells cause onward signalling by releasing IFNy and IL-12, which polarises the
immune response to a type 1 antiviral state via stimulating Th1 to release IFNy and TNFa.
• ILC1: macrophages and dendritic cells release IL-12 which activate Tbet ILC1, which release
IFNy, inducing type 1 antiviral response.
• ILC2: epithelial cells release IL-33 which activate GATA3 ILC2, which release IL-4, IL-5, IL-13
for a type 2 response and contribute to antigen presentation by expressing MHC class II.
• ILC3: dendritic cells release IL-23 which activate RoRyt ILC3, which release IL-22 for epithelial
integrity and contribute to antigen presentation. ILC3 also require commensal bacterial for
their development.
• LTi (lymphoid tissue inducer cell): most active in foetal life, LTi cells induce secondary
lymphoid tissue formation (lymph nodes) for adaptive response.
