Lecture 26 - Evolutionary Immunology - Adaptive Flashcards
In which organisms is adaptive immunity present?
Only higher organisms (vertebrates)
What are Ig superfamily domains?
Give examples of where they are found
Examples
- BCR
- TCR
What are VLRs?
Where were they first found?
What is their structure?
What is their function?
Variable lymphocyte receptors
- Found in Hagfish and Lampreys
- Large number of unique transcripts found that encoded LRR modules (leucine rich repeat)
Structure:
- Made up of leucine rich repeat domains
- similar to TLRs
- stalk region
- Arch shaped
Function
- Recognise VLR antigen on the concave surface
- VLRB+
- VLRB+ lymphocytes recognise their Ag →
- Lymphocyte proliferates
- Soluble VLRB+ secreted
- Analogous to B cells
- VLRB+ lymphocytes recognise their Ag →
- VLRA+
- VLRA+ lymphocytes recognise their Ag →
- Lymphocyte proliferation
- Release of cytokine homologues
- Analogous to T cells
- VLRA+ lymphocytes recognise their Ag →
- VLRC+
- Analogous to γδ T cells
- Found in epithelia (epidermal and intestinal)
What are FREP and Dscam?
In which organisms are they found?
What is structurally significant?
Describe their function in Drosophila
Highly diverse PRRs, but they are not part of the adaptive immune response:
- No expansion
- No memory
FREP: Fibrinogen related proteins
- Molluscs
Dscam: Down syndrome cell adhesion molecules
- Arthropods (eg. Drosophila)
Structure
- Contain Ig SF domains
- FREP
- Fibrinogen domain at C terminus
- 1-2 Ig domains at N terminus
Function in Drosophila:
- Produced in haemocytes (ie fat body cells)
- Secreted into haemolymph
- Bind and opsonise pathogens
Describe gene encoding of VLRs
Describe gene assembly
How does it differ from assembly of BCRs and TCRs in higher order organisms?
Encoded by:
- 3 types of VLR gene
- A, B, and C
- VLRA
- VLRB
- VLRC
- A, B, and C
- The loci of the VLRs do not encode the repeats that end up in the middle of the protein
- Multiple LRR gene cassettes present elsewhere in the genome
Gene assembly
- Only occurs at one locus
- VLRA, VLRB, or VLRC
- Only one allele used (analogous to allelic exclusion)
-
Gene conversion
- Addition of repeats from elsewhere in the genome within the VLR N and C terminal domains
- Recombination between homologous sites in the chromosome:
- CDA (cytidine deaminase) creates nicks in the DNA
- Induction of DNA repair
- Differences:
- No random addition of nucleotides at the ends (N regions), since there is no TdT
What is CDA?
What is it evolutionarily related to?
Cytidine deaminase
- Introduces nicks in DNA for gene conversion for assembly of VLRs
- Followed by induction of DNA repair
- Two types:
- CDA1 ⇒ VLRA
- CDA2 ⇒ VLRB
Related to AID
State the homologues of the following:
- B cells
- T cells
- γδ T cells
What is the evidence?
- Development
- Effector function
- Markers
B cells: VLRB+ lymphocytes
T cells: VLRA+ lymphocytes
γδ T cells: VLRC+ lymphocytes
Evidence:
- Marker expression
- VLRB+ lymphocytes express B cell markers
- BLIMP
- PAX5
- VLRA+ lymphocytes express T cell markers
- GATA3
- CCR7
- CTLA4
- VLRC+ lymphocytes express γδ T cell markers
- VLRB+ lymphocytes express B cell markers
- Function
- The observed function of these VLR lymphocytes reflects the function of the various mammalian lymphocytes respectively
- VLRA+ cells
- Proliferation and expression of surface VLRA and effector cytokines after stimulation
- Release of molecules onto VLRB+ cells: crosstalk analogous to T cell help
- Recognition of processed antigen
- VLRB+ cells
- Secretion of soluble VLRB after activation
- Recognition of native antigen
- Development
- VLRA+ cells develop in thymoid tissue in gills
- VLRB+ cells develop in haematopoietic tissue in kidney
When do γδ T cells split from the conventional T cell lineage?
At the DN stage (ie whilst the TCR is being arranged)
In which organisms are VLRA/B/C+ cells found?
Agnathan fish (lampreys, hagfish)
Describe the function of RAG in higher order organisms
RAG: recombinase activating gene
- Recognise RSSs (recognition signal sequences) adjacent to segments in BCR and TCR genes
- Forms a 12-23 hairpin between segments
- Cleaves DNA between the segments
- → DNA repair machinery + TdT
What are transposons?
Describe the process
Mobile elements that integrate into the chromosome
Transposases:
- Enzymes that excise and integrate elements into the DNA
- Encoded by transposase genes
Integration/exision DNA sequences
- There are the targets of the transposases
In which organisms did BCRs and TCRs emerge?
Gnathans (jawed fish)
Which sorts of domains are found in diverse receptors?
Give examples of receptors in which these domains are found
- Ig domains
- BCRs
- TCRs
- Dscams (Drosophila)
- FREP (Molluscs)
- Leucine rich repeats (LRRs)
- TLRs
- VLRs
Describe the diversity of FREPs
How does this come about?
More diversity than is encoded in the germ line
Mechanism
- Not known
- Hypothesised mechanisms of introduction of point mutations and somatic hypermutation
Describe how diversity of Dscam is generated
Gene:
- Multiple exon clusters
- Each cluster contains many segments
Diversification:
- Alternate splicing selects one of the many segments in each exon
- Generates many different combinations
Compare the features Dscam, VLRs and FREP
Dscam & FREP:
- Very diverse, but not adaptive
- No expanision or memory
- Contain Ig domains
VLRs
- Highly diverse
- Adaptive (memory)
- Experimentally shown second set rejection of skin grafts in Lamprey
- Contain LRR domains
Describe the structure of VLRs
Made up of LRRs
Repeats form a solenoid shape
(similar to TLRs)
Slight curve in the solenoid
Compare CDA expression in the different VLR cells in agnathans
(Cytidine deaminase)
(Agnathans = jawless fish)
VLRA+ cells: CDA1
VLRB+ cells: CDA2
Compare development of the following cells in agnathans:
- VLRA+ cells
- VLRB+ cells
What is the tissue distribution of VLRC+ cells?
VLRA+ cells: thymoid tissue in gill tips
VLRB+ cells: haematopoietic tissue in kidney and thyphylosole
VLRC+ cells:
- Similar distributino to VLRA+ cells
- Presumeable using CDA1 expression in the thymoid organs for VLRC generation
Describe the proposed mechanism of evolution of diversity of BCRs
Two mechanisms: convergent evolution
- RAG1/2
- Developed from transposons
- Transposon inserted into Ig SF gene member, disrupting the gene
- Seperation of RAG-1 and RAG-2 onto another locus in the genome over time, but the excision sites remained within the gene
- Expansion of regions in Ig SF genes that could be acted upon by RAG-1 and RAG-2
- RAG-1/2 could still act on all these regions
- Chicken BCR diversification
- Little diversity in BCR V, D and J genes
- However, many Pseudogenes for V region segments
- Invariant BCR assembled from genes and expression of this on the surface of immature B cell
- This triggers proliferation and gene conversion of Ig genes
- AID dependent incorporation of pseudogene segments into the genes for BCR chains
- Functional sIg ⇒ survival
- Non-functional sIg ⇒ death
- Mature B cells express diverse Ig
What is CRISPR?
Where are they found?
Describe the mechanism of generation of CRISPR
CRISPR: Clustered regularly interspaced short palindromic repeats
- Repeats in genome
- Contained genomic DNA from viruses
- Encoded near Cas locus
Found in Bacteria and Archaea
Generation:
- Cas proteins mediated insertion of viral DNA into the genome
- CRISPR expressed as only long transcript
- Transcripted cleaved into hairpin structures
- When the virus is encountered again, the viral DNA plasmids bind the hairpin structures
- Cas then cleaves the viral DNA
Describe adaptive immune responses in bacteria and archaea
CRISPR arrays
- Adaptive: remembering past infections
- Not, however, anticipatory
Describe the CRISPR/Cas9 system
CRISPR:
- Produces sgRNA
- Guide RNA for targeted gene
Cas 9
- Enzyme that causes ds nicks in target DNA
- Together, these molecules allow precise disruption of DNA at a certain location
- Once the disruption has taken place:
- Homology-directed recombination
- Precise insertion of genetic material
This system has much potential
- Generation of KO and knock-in animal models
- Clinical applications: gene therapy?