Phylogeny of the Immune System

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Phylogeny of the Immune System
Yufang Shi yufang.shi_at_umdnj.edu
Evolution of Adaptive Immunity by M. F.
Flajnik http//www.ivis.org/proceedings/ACVP/2004/
Flajnik/IVIS.pdf http//www.youtube.com/watch?v8-
TUG084GW4
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Phylogeny of the Animal Kingdom
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Protozoa
http//www.cartage.org.lb/en/themes/Sciences/Zoolo
gy/Animalclassification/Polygenetic/phylogenetictr
ee/phylogenetictree.htm
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Annelida Mollusca Arthropoda Echinodermata Chordat
a
Body Organization
Platyhelminthes
Nematoda
Cnidaria
Parazoza Sponge
3-germ layers No body cavity
2-germ layers
Pseudocoelom
Eucoelom
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Kinship of Chordates
Adaptive immunity
http//cas.bellarmine.edu/tietjen/images/Evolution
_of_chordata.gif
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Lancelets
Sea Squirt
Shark
Lamprey
Jawless Fish
Bonny fish
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Big Events in the Evolution of the Immune System
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Approaches

• Compare with important evolution events/stages
• Cellular analysis
• Allograft recognition
• Genome Analysis
• gene duplication
• domain shuffling

Ag Receptors, MHC, TLR, Complements, Cytokines
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(No Transcript)
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"Big Bang" of gene duplication

• Jawless fish to jawed fish
• Make the formation of vertebra and tissue
  specificity possible
• (form gene clusters such as HOX genes)
• Mechanisms
• 1. Whole Genome Duplication (not fully supported
  by genome sequencing)
• Tendon or segmental duplication
• Continuous small scale gene duplication.

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Phylogeny of Chordates and the Major Events in
the Evolution of Adaptive Immunity

Genome Duplication Large-scale gene duplication
and subsequent reshuffling of exons lead the
emergence of new genes
TRENDS in Immunology Vol.25 No.2 February 2004
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• In jawless vertebrate (lamprey hagfish),
  protochordate (amphioxus and sea squirt) and
  other invertebrates

variable lymphocyte receptors, TCR-like protein,
Lymphocyte -like cells (Nature, 2004)
lamprey
vertebrate
V region-containing chitin-binding protein
family, proto-MHC region (Nat Immuol Nat Genet,
2002)
amphioxus
innate immunity related molecules, proto-MHC
region. Protocytokines
sea squirt
invertebrate
arthropod
Immunoglobulin Domain
mollusk
Immunoglobulin Domain
TLRs expansion and innate immunity (Science,
2006)
sea urchin
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Types of Immune Recognition
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Self and non-self Recognition
Every organism is capable of innate defense.

• Exist in both animals and plants
• In some plants
• Plants developed more and longer lateral roots
  towards neighboring roots of different plants
  than towards other roots of the same plant. Het
  recognition.
• Pollen recognition, self-incompatibility
  (prevent inbreeding) s-locus polymorphism
• In animals
• Define the characteristics of individual
  organisms from those of similar kind.
• Identify self and prevent self-reactivity.
  Defend organisms from their predators
• Recognize and destroy viruses, bacteria or
  infected cells.
• Recognize Pathogen Associated Molecular
  Patterns (PAMPS) through Pattern Recognition
  Receptors (PRRs)

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Pattern Recognition Receptors
Strategies of Immune Reaction in Invertebrates

• Anti-microbial peptides
• Interference RNA
• Phagocytic cells/cytolytic cells
• Lysozymes
• Production of toxic oxygen and nitrogen
  metabolites
• The most advanced defense mechanisms are C3 and
  Toll receptors.

• Critical for self-nonself discrimination, even
  exist in Amoeba
• Complement in Cnidaria
• Toll receptors are well described in Drosophila.
  Recognition of infecting micro-organisms
• Activation of intracellular signaling cascades,
  especially the NFkB pathway, which leads to the
  expression of a vast array of antimicrobial
  effector molecules that attack microorganisms at
  many different levels.

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Immunoglobulin Domain

• An IgG molecule consists of a total of 12
  immunoglobulin domains. Found in many other
  proteins that play key roles in the immune
  system.
• Consist of a pair of ß sheets, each built of
  antiparallel ß strands. A single disulfide bond
  bridges the two sheets.
• Most prevalent domains encoded by the human
  genome. Can be found in nemotodes.
• The conserved beta barrel structures making up
  each immunoglobulin domain along with the beta
  turns and helical turns at the ends of the beta
  strands
• Key for Ig, TCR, costimulation molecules and MHC

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MHC Origin

• Origin not known
• Class II first?
• Class I first as a result of a recombination
  between an immunoglobulin-like
• C-domain and the peptide-binding domain of an
  P70 heat-shock protein
• Not in jawless fish, but both class I and class
  II can be seen in shark.
• Generation of polymorphism
• (1) a high mutation rate
• (2) gene conversion or interlocus genetic
  exchange
• (3) overdominant (balancing) selection
• (4) frequency-dependent selection.
• Maintenance of polymorphism
• (1) Pathogen-driven
• (2) Non-pathogen-driven
• inbreeding depression
• mate selection
• selective fertilization

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Generation of Antigen Receptor Diversity Most
vertebrate animals use the way as humans. In
all animals, antigen receptors require RAG
proteins. TCR in most species uses similar
rearrangement strategies. There are differences
in the ways Ig molecules are generated. In
chickens and rabbits, the recombined V region is
diversified by gene conversion (one piece of DNA
is donated from one chromosome to another) in the
bursa of Fabricius (in chickens) or another
intestinal lymphoid organs (in rabbits). Sheep,
in its ileal Peyer's patch, generates diverse
repertoire by somatic hypermutation of a fairly
invariant recombined V region. Sharks have
multiple copies of discrete VL-JL-CL and
VH-DH-JH-CH cassettes, and activate rearrangement
in different copies.
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• Evolution of the Adaptive Immune Response.
• The evolution of adaptive immunity is one of the
  greatest biological mystery.
• Adapt genes for MHC, immunoglobulin, RAG and TCR
• By the invasion of a putative immunoglobulin-like
  gene by a retroposon with the ability to undergo
  gene rearrangement. The T-cell receptor a, ß, ?,
  and d chain loci and the immunoglobulin H, ?, and
  ? loci
• The Key is the RAG genes (lack introns), which
  was recently found to catalyze transposition
  events. It was found that the stretch of DNA
  containing the recombination signal sequences was
  being inserted into other DNA fragments!!
• Adaptive immunity appears abruptly in jawed fish
  and thus can mount an adaptive immune response.
• Hagfish and lampreys lack all signs of an
  adaptive immune system no lymphoid tissue, no
  primary immune responses, and no immunological
  memory.

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Major steps of the phylogeny of the immune system
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Level 1 Cell or species-specific aggregation
plants, sponges and protozoans. Level 2
Specific immunorecognition/ immunoimcompatibility
Cnidaria not MHC mediated differentiated
leucocytic cells exist Level 3 cell-mediated
immunity with at least short-term memory
annelids, arthropods, echinoderms and possibly,
mollusks. Level 4 Integrated cell and humoral
antibody immunity first evolved in advanced bony
fishes. helper T cells and B cells capable of
producing two or more molecular classes of
antibodies thymus found in fish and
amphibians Bursa of Fabricius in the
reptilian-avian branch of the phylogenic
tree Level 5 multiple classes and subclasses of
immunoglobulins and heterogeneous T and B
repertoires birds and mammals.
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Sponge

• Protozoa
• Amoeba
• Pattern recognition Food particles, not other
  amoeba or own pseudopods
• Prototype of Macrophages?

Mouse macrophage
Amoeba
http//cellmotility.genebee.msu.ru/images/foto/pic
-3.jpg

• Sponge
• 1. Separated cells aggregate only with their
  own kind. Thus are able to distinguish between
  "self" and "non-self,"
• 2. Phagocytes

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Cnidaria

• Clonal animals, such as sea anemones, can attack
  individuals belonging to different genetic clones
  while avoiding attacking individuals of the same
  clone
• Phagocytes and Cnidocyste for defense.
• C3 like molecules can be detected in some species

Nematoda

• Pattern Recognition
• Constitutive components anti-microbial or
  digestive peptides
• Inducible Components a TGFb-like pathway, a p38
  kinase pathway, a programmed cell death pathway,
  and an insulin receptor-like pathway
• Related to Stress?

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Annelida
In earthworms, the coelomocytes (leukocytes)
located in the coelomic cavity. Humoral
agglutinins
Arthropoda, Example Drosophila

• Defense response can be activated by TOLL
  (Activate NFkB) or Imd (a family of TNFR like
  molecules).
• Primarily through the secretion of antimicrobial
  peptides.
• Lectins and serine proteases in hemolymph
  function like complement and blood-clotting. 
  Coagulation in response to LPS (horseshoe crab)
• Very beginnings of complement-mediated immunity
  as well as blood-clotting
• molecules capable of making covalent linkages to
  pathogens called TEPs. Able to induce
  opsonization. Thus opsonization may be the oldest
  function of complements.

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The Similarity between TOLL Receptors and
TOLL-like Receptors

• Drosophila Toll recognize fungi, 18wheeler
  recognize bacteria
• TOLL Like Receptors and IL-1 receptor in mammals
  share
• strong homology to TOLL

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Echinoderms

• C3/C4/C5-like gene was discovered in sea urchin.
  Can be upregulated upon exposure to LPS.   Act
  primarily as an opsonin.
• C2/Bf-like gene was also identified
• The prototype of the alternative complement
  pathway. The alternative pathway is the oldest
•   Therefore, the first appearance of a
  complement-mediated immune system.  Thus, possess
  effective phagocytosis.
• TLR

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Urochordates (sea squirt)

• C3/C2 homologues have been identified and can
  opsonize.
• The complement system seems to be more complete
  due to the existence of MASP, a component of the
  lectin pathway
• (TNF) and IL-8 homologue was found.

Amphioxus (lancelets)

• The closest relative to the vertebrates. 
• A C3-like gene and a C6-like gene were found.
• C6 like protein is involved in the lysis of
  foreign pathogens
• Some prototype cytokines MIF, TNF, IRF
• Death Domain
• Lymphocyte like cells, V and C domains
• Several TLRs

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Jawless Fish (lampreys and hagfish)

• most ancestral vertebrates. 
• no rearranging antigen receptors or MHC genes
  have been found.  No Rag. V and C domains
  exist.
• No adaptive immune system
• Have a C3 homologue, a Bf/C2 homologue, and a
  MASP homologue (All vertebrates except jawless
  fish share the human complement systems)
• Have CD59, an inhibitor of the lytic pathway of
  the complement system
• No secondary lymphoid organ. May have
  lymphocytes, but since lymphocytes in all other
  vertebrates utilize rearranging antigen
  receptors, their role in lamprey immunity remains
  unclear. Immunization lead to increase in
  proteins in lymphocytes containing leucine-rich
  repeats (LRR). Existence of an adaptive immunity?
  (Nature. 2004 Jul 8430(6996)174-80. )

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Rearranging antigen receptors of jawless and
jawed vertebrates.
The lamprey mature VLR gene consists of the
signal peptide (SP), N-terminal LRR (LRRNT),
first 18-residue LRR (LRR1), variable number of
24-residue LRR (LRRV), a connecting peptide (CP),
C-terminal LRR (LRRCT) and threonine/proline-rich
stalk. Portions of LRRNT and LRRCT that are not
encoded in the germline VLR are hatched.
Gnathostome antibody genes are assembled via
random joining of Ig gene fragments consisting of
variable (V), diversity (D) and joining (J)
elements, and Ig constant (C) domains.
--Zeev Pancer, University of Maryland
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• Cartilaginous Fish
• Oldest animals have Ig/TCR/MHC/Rag based adaptive
  immune response.
• Their B cells resemble CD5 B cells and T cells
  resemble gamma/delta T cells.
• Mostly IgM some IgNAR (new antigen receptor) and
  IgW
• Heavy-chain genes in the cluster-type
  organization (V, 2 - 3 D, 1 J and C). Gene
  rearrangement seems to occur only within a
  cluster. High levels of N-region addition.
• Three L chain isotypes, also in the cluster
  organization.
• IgNAR is a covalently linked dimer without L
  chains. The V domains in the dimer are free and
  flexible and each V interacts with antigen.
• TCR genes. Secondary lymphoid tissue has
  segregated into discrete T and B cell zones. TCR
  genes are in the translocon organization (not
  multicluster).
• Polymorphic MHC class I/II molecules
• No known cancer.

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Ontogeny of thymus

• During ontogeny, thymic epithelial cells are
  derived from the third endodermal pharyngeal
  pouch and the third ectodermal branchial cleft.
• The ectodermal cells proliferate extensively to
  cover the endodermal cells.
• Thus, cortex epithelial cells are ectodermal
  origin, while the medulla is endoderm
  derived.

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• Teleost Fish
• IgM (in a tetrameric form).
• Some species have IgD
• No class switch. Alternative splicing leads to
  IgD from IgM.
• Heavy-chain genes are in the same organization as
  primates/rodents. Light-chain genes are cluster
  organization like that in the cartilaginous fish
  (cluster organization is more primitive?). There
  2 to 4 light-chain isotypes.

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• Amphibians
• IgM and IgY (four C-domains) isotypes-IgY emerged
  in an immediate ancestor of the amphibians).
• Start to have the isotype switch,
• very low MHC class II polymorphism.
• Some species such as Xenopus have high MHC
  polymorphism and robust T-dependent responses.
• IgX in the intestine, mucosal immunity? IgM and
  IgX are present in thymectomized animals, while
  IgY production is strictly T-dependent.
• Major changes during metamorphosis, prevention of
  autoimmunity?

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• Reptiles
• IgM and IgY.
• Turtles have a large number of V genes. Thus,
  the generation of diversity more like
  primates/rodents than birds.
• All ectothermic vertebrates have no germinal
  centers. Thus no affinity maturation and no high
  affinity antibodies.
• Need more studies.

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• The Endotherms Birds and Mammals
• Gut-associated lymphoid tissue (GALT) species
  chickens, rabbits, sheep, cows, and pigs. A small
  number of V genes (only one in birds) is
  rearranged and then modified by gene conversion
  or somatic hypermutation. There are dedicated
  organs for B cell development the bursa and
  appendix.
• B cells are continually produced throughout life
  in the primates/rodents group, but only during
  early in development in the GALT species (bursa
  and appendix degenerate afterward).
• In all jawed species, T cell development is
  conserved all rearange the TCR gene families (a,
  ß, ?, and d). The GALT species have more g/d T
  cells

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The Mammalian Type Adaptive Immune System

• Ig and TCR as antigen receptors
• RAG-Mediated Recombination
• Primary and secondary lymphoid organs
• MHC
• Somatic mutation
• Memory
• Cytokines
• Do not exist in invertebrates or jawless fish.
  Might start in placoderms.

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Camel antibodies
VH-D-D-J-Cn L-J-Cn,
Shark IgNAR
Chicken IgY