1. Immunocomputing The natural immune system and its computational metaphors by Ian Nunn, inunn@digitaldoor.net, 2002inunn@digitaldoor.net

2. Organization of This Lecture Overview of the Immune System (IS): –The innate IS –The adaptive IS –The immune response –Antibodies and the Clonal Selection principle –Immune network theory The key computational aspects The symbol ↓ means significant explanatory text or diagram follows later

3. Views of the Immune System A collection of lymphoid organs, cells principally leukocytes ( lymphocytes ↓ and phagocytes ↓), and molecules that are interrelated in function A related collection of bodily defenses: –Physical barriers (skin, mucous membranes) –Physiology (temperature, ph, enzymes in secretions) –Innate IS ↓(phagocytes) ~ cellular level –Adaptive IS ↓(lymphocytes) ~ molecular level The innate IS and the adaptive IS are interactive It’s all molecular chemistry: proteins and peptides

4. Anatomy of the Immune System 1 Primary lymphoid organs (black/red) Secondary lymphoid organs (blue/yellow)

5. The Antagonists Infectious foreign agents called pathogens: –Viruses (cold, influenza, smallpox) –Bacteria (anthrax, E. coli) –Multi-cellular parasites (malaria) –Fungi Foreign proteins and toxins Pathogens express cell surface and soluble proteins called antigens (Ag) Agent identification problem: how to detect and remove pathogens or harmful non-self elements without attacking beneficial self elements (autoimmune reaction)

6. Immune Defense 1 Response of various ‘subsystems’ to pathogens

7. The Innate Immune System System available at birth, non-adaptive in makeup, providing an immediate response to invasion Principal components are: –Complement ↓ system, a class of ~25 blood proteins –Phagocytes that are scavenger cells including macrophages ↓ ingest foreign material and assist the adaptive immune response –Natural Killer (NK) ↓ Cells, a type of lymphocyte

8. The Complement System Proteins that bind to the surface of certain types of bacteria Promotes two mechanisms ↓ of elimination after binding: –lysis: the complement ruptures the cell membrane –opsonization: the bound complement marks the pathogen for destruction by macrophages Self cells have surface regulatory proteins that prevents complement binding

9. Macrophages Scavenger role Have receptors for: –Certain types of bacteria directly –Complement on opsonized bacteria Activated partly by Th1 cell ↓ lymphokine ↓IL-2 Known as antigen presenting cells ↓(APC): –ingest and then digest pathogens and antigens –present the Ag peptides at their surface to T cells ↓ via class II major histocompatibility complex (MHC) molecules that are contained only in IS cells

10. Macrophage Bacterial Ingestion 1 Step 1: an opsonized antigen is ingested Step 2: antigen peptides are bound by class II MHC molecules Step 3: MHC/peptide complex presented on surface

11. Macrophages (cont.) Secrete cytokines (IL-1) ↓ after activation: Cytokines are a class of signalling molecules that: –Induce inflammatory response, physiological changes that facilitate the activity of IS cells: Elevated temperature Increased blood flow and blood vessel permeability –Trigger liver to produce acute phase protein (ATP) a complement molecule which binds to bacteria activating a macrophage response

12. Natural Killer Cells Bind to carbohydrates on surface of self cells Can’t recognize specific antigens unlike Tk cells ↓ or killer cells of the adaptive immune system Healthy self cells express an inhibitory signal Virus-infected cells may lose inhibitory ability thus activating NK cells Activated NK cell injects chemicals that trigger apoptosis ( programmed cell death) or lysis

13. The Adaptive Immune System Characterized by a two-phase, primary and secondary response to pathogens ↓ Principal components are ~ 10 12 short-lived (4 – 7 days) lymphocytes created in bone marrow at the rate of 10 7 per day: –T-cells ↓ which mature in the thymus gland –B-cells ↓(majority) which mature in bone marrow

14. Lymphocyte Growth Pleuripotent or common haemopoietic stem cells in bone marrow at birth Differentiate into progenitor cells including: –Myeloid type → phagocytes –Lymphoid type → B and T lymphocytes These grow into immature precursor cells in bone marrow Precursor cells mature in primary lymphoid organs Mature cells: –Activate and differentiate in bodily tissue –Some (B cells ↓) multiply in secondary lymphoid organs

15. Lymphocyte Maturation

16. Cell Structure Each antigen exhibits many unique structural regions called epitopes (~10 16 possible varieties) Lymphocytes have (~10 5 ) identical secretable surface protein receptors called antibodies (Ab) ↓ At any time the immune system has a set of ~10 8 different Ab types called its repertoire An antibody exhibits a unique structural region or binding site called a paratope expressing a range of affinities ↓ for binding a specific set of epitopes

17. Ag Epitopes and Ab Paratopes 1 Antigen (Ag) showing epitopes and B cell lymphocytes showing antibody (Ab) paratopes (receptors)

18. Protein Structure (Folding) Courtesy www.stanford.edu/group/pandegroup/Cosm/

19. Shape-Space Representation Factors affecting Ab/Ag binding include: –Molecular shape of paratopes and epitopes –Charge distribution –Relationship of corresponding chemical groups –Not covalent (chemical) bonding A binding site parameterizes an L-dimensional shape- space ↓ A paratope is at the center of a volume V  of complementary epitopes with which it can bind called its recognition region  is called the affinity threshold ↓

20. Shape-Space 1 Paratopes (), epitope complements (x) and affinity thresholds (ε) in shape-space (V)

21. Spatial Distance Measures degree of interaction (affinity) For Ag(ag 1, ag 2,…,ag L ) and Ab(ab 1, ab 2,…,ab L ) expressed as vectors in shape-space: Euclidean: Manhattan: Hamming:

22. Affinity Threshold (ε) The affinity threshold ε is that value of distance above which which binding actually occurs Distance or match score is inversely proportional to complementarity or affinity for binding A binding function measures affinity or strength of binding: –Its domain is the set of possible distances –Its range is the set of binding values

23. Affinity Binding Functions 1 a)Threshold (step) binding function b)Sigmoid binding function

24. Activation Threshold A lymphocyte may bind multiple antigens (epitopes) of the same type A lymphocyte may also bind multiple antigens of related type A lymphocyte can’t become activated before the number of receptors bound exceeds an activation threshold Different cell types have different activation thresholds Different cell types behave differently on activation

25. Lymphocyte Binding Different, Structurally Related Antigens 3

26. The Adaptive Immune Response Immune response (IR) in the adaptive immune system has two phases ↓ : –Primary response to antigen A (some Ab present): Initial lag phase Ab concentration then increases, levels off and falls –Secondary response to antigen A: Short lag phase faster buildup to greater maximum level with slower drop off –Response to a new unknown but related antigen B after primary response to A: Similar to secondary response to A but less pronounced. Called immunological cross-reaction

27. Primary and Secondary IR 1

28. The Adaptive Immune Response (cont.) Demonstrates adaptation, reinforcement learning and associative memory needed for immunization - called a generalization capability Characteristics of an associative memory ↓ are: –Robust both to noise (binding occurs over a range of antigen types) and component failure (destruction of individual lymphocytes) –Stored data recovered by reading same or similar data (IR) Restricted by Th cell dependency ↓

29. The T Cell A lymphocyte that along with B cells ↓ are the major elements of the adaptive immune system Three major subclasses: –Helper (CD4, T4 or Th ) T cells ↓ assist a range of leukocytes in antigen identification –Cytotoxic (killer or Tk) T cells ↓ destroy pathogens by lysis –Suppressor (CD8) T cells express a negative effect on immune cell generation preventing autoimmune reaction Population diversity created in thymus by combinatorial rearrangement of genes but no somatic mutation ↓

30. Th Cell Functioning Binds (recognizes) only linear conformations of epitopes on unfolded (digested) antigen peptide/MHC complex on a macrophage Secrete IL-2 lymphokines on activation and express IL-2 receptors IL-2 promotes cellular growth, activation and regulation - particularly of self, B cells and macrophages Th cells differentiate into: –Th1 cells that activate Tk cells and macrophages inducing an inflammatory response –Th2 cells that activate B cells

31. Th Cells and Self-Tolerance Most self epitopes occur in the thymus and bone marrow An immature Th cell activated by binding a self epitope suffers apoptosis (clonal deletion or negative selection) Process called central tolerance Some may still be auto(self)reactive. A second mechanism, costimulation is required: –Signal I occurs when activation threshold exceeded –Signal II IL-1cytokines provided by innate IS Signal I without II triggers apoptosis, a negative selection or down-regulatory signal

32. T Cell Tolerization 3

33. Tk Cell Activation 3

34. T Cell Activation 2

35. The B Cell Two major subclasses: –Plasma cells ↓ that produce and secrete antibodies (no lymphokines), a defense reaction –Memory cells ↓ that express the associative memory characteristic Antigen processing: Plasma cells digest bound antigens and present Ag peptides at their surface via class II MHC molecules

36. B Cells and Self Tolerance Initial tolerization occurs in bone marrow Affinity maturation ↓ may produce autoreactive clones through somatic hypermutation ↓ Distributed tolerance (occurs in lymph nodes throughout body) by costimulation: –Signal I occurs when activation threshold exceeded –Signal II provided by Th2 cell IL-2 lymphokines during antigen processing Signal I without II triggers apoptosis

37. B Cell Antigen Processing B cells digest bound antigens and present Ag peptides at their surface via class II MHC molecules A Th2 cell binds to the peptide/MHC complex and returns a signal II IL-2 lymphokine contributing to the B cell’s activation Activated B cells travel to the secondary lymphoid organs as part of the affinity maturation process

38. B Cell Affinity Maturation Affinity maturation is a cyclical process involving plasma B cells: –Selection: activation by Th2 cell lymphokines and threshold regulated antigen binding –Proliferation: clonal division in lymph nodes expressing somatic hypermutation ↓and receptor editing ↓ –Differentiation: after leaving lymph node, into plasma and memory cells

39. The Affinity Maturation Principle 1

40. B Cell Adapted Population Diversity 3

41. The Memory Problem B cells live only a few days (10 max) How is memory effected? Theories: –A long-lived variety of B cell –Restimulation by long lived (years) traces of antigens in the body - a kind of low level chronic infection –Both

42. Intracellular Pathogenesis Intracellular pathogens (viruses, some bacteria) are invisible to B cells Viral antigen is captured by a macrophage, presented to a Th cell which releases IL-2 lymphokines Non-IS cells contain class I MHC molecules that transport internal viral peptides to the cell surface Class I MHC/peptide complexes are bound by killer T cells which are activated in part by costimulation by IL-2 Tk cells kill infected cells by exercising an effector function (lysis, apoptosis induction, toxic chemical injection)

43. The Adaptive Immune System’s Response to Infection 1 I.Macrophage ingests Ag, presents MHC/peptide at surface, releases IL-1 II.T cell binds MHC/peptide and IL-1, activates III.Activated T cell develops, releases IL-2 IV.B cell binds antigen and IL-2, activates V.Activated B cell clones, differentiates into plasma and memory cells VI.Plasma cell releases antibodies which bind antigens

44. The Antibody Molecule A soluble form of leukocyte receptor also called an immunoglobulin (Ig) Two identical light (L) and heavy (H) chains ↓ A constant region ↓ responsible for IS cell binding and available in a few varieties called isotypes that determine effector selection – there are 5 Ig classes A variable region ↓ responsible for Ag binding Variable region is a concatenation of three genes, V (Variability), D (Diversity) and J (Joining) each from a separate gene library ↓ Binding is Ab paratope to Ag epitope

45. The Antibody Molecule 1 b)The V, D and J gene libraries from which the antibody DNA is assembled a)Heavy (H) and light (L) chains; variable (V) and constant (C) regions of the antibody molecule

46. Combinatorial And Junctional Diversity Occurs in the bone marrow when lymphocytes are first created Expressed by random combinatorial joining of a D and J gene followed by a V gene in the VH chain Junction misalignment if amino acids don’t line up causing some to be dropped (Frame shift). Many are non- translatable or unproductive and are dropped Productive recombinations result in cells which repeat with V and J genes of VL chain Estimated combinatorial diversity from both chains ~5x10 7

47. Somatic Hypermutation Expressed in B cell (somatic) clonal reproduction Mutation rate 10 9 times normal (hyper) Types of mutation in Ab V region (receptor): –Point mutations –Short deletions –Insertion of random gene sequence (receptor editing ~25%) Results: –Most non-functional or low affinity receptors eliminated by apoptosis (mechanism not understood) and negative selection –Some are autoreactive and eliminated by negative selection –A very few may have increased affinity due to conformational change and positive selection –Total coverage of antigen repertoire thought to be complete

48. The Clonal Selection Principle Governs generation of new lymphocytes by plasma cells: –Clonal copies of parents under somatic hypermutation –Elimination of autoreactive & unproductive clones –Proliferation and differentiation resulting from antigen activation of B cells –Autoimmune disease the result of autoreactive clones resistant to early elimination by self-antigens The total number of lymphocytes kept relatively constant over time by regulation Responsible for maintaining Ab repertoire diversity – recall: repertoire is ~10 8, ~10 7 replaced daily so complete replacement in 10 days

49. Combinatorial Diversity and Shape Space Coverage Generational diversity

50. Other Mutational Effects Clones may express different isotypes by recombination in the constant region of the antibody called isotype switching

51. Immune Network Theory A theory to explain the self-regulation and memory properties of the IS An Ab may display epitopes called idiotopes to distinguish them from Ag epitopes An Ab’s set of idiotopes called its idiotype An idiotope may be recognized by a set of antibody paratopes Direction of recognition results in activation or suppression in the network

52. The Immune Network 1 a)Cascading recognition: antibody view b)Cascading recognition: sets of idiotopes and paratopes

53. A Complex Adaptive System The IS is a complex adaptive system: –Large populations of several classes and sub-classes of agents with specific unique behaviors –No central control –Able to regenerate its (self) elements –Overall population is self-regulating –Able to adapt to any external influence through an ability to generate diversity A rich example of a multi-agent or swarm system

54. Features Of Computational Interest Pattern recognition: through affinity binding –Self-recognition by tolerization –Intrusion detection by lymphocyte / antigen receptor binding Feature extraction: through Macrophage and B cell antigen digestion and MHC/peptide (feature) presentation Reinforcement learning: –exhibited by the adaptive immune response (AIR) in response to repeated infection –Clonal selection selects for cells with higher affinity Memory: –AIR exhibits associative memory in the cross-reactive response. –A result of the affinity maturation principle by which high affinity long-lived memory cells are produced

55. Features Of Computational Interest (cont.) Self-Regulation: through AIR and lymphocyte population regulation Generation of diversity: –Part of affinity maturation process (clonal production) –One mechanism: Combinatorial gene recombination and junction editing in primary lymphoid organs –Another mechanism: Somatic hypermutation in secondary lymphoid organs Point mutations (explore local optima) Short deletions Random insertions or receptor editing (escape from local optima) Adaptation: IS can respond to novel conditions through AIR and ability to generate diversity

56. Features Of Computational Interest (cont.) Optimization: the immune response and clonal selection result in increasingly better response to stimulus over time through higher affinity clones Distributed and Collaborative processing: the various agents in the IS interact cooperatively with each performing a unique set of functions to achieve –Distributed detection –Distributed defense Robust and scalable: –Noise tolerant: due to affinity binding (recognition region) –Component failure tolerant : affinity maturation ensures a large population of agents that carry desirable characteristics Garbage collection: activity of phagocytes

57. Other Concepts Formalism: allow mathematical treatment –Shape space and identification parameters Binding functions and affinity threshold Stochastic nature of affinity binding –Can model with differential equations Neat concepts: –Negative selection –Costimulation and chemical signaling –Helper and suppressor functions –Threshold mechanisms (affinity and activation) –Cross-reactivity

58. References 1.de Castro, L.N. and Von Zuben, F.J. Artificial immune Systems: Part I – Basic Theory and Applications. Technical Report TR DCA 01/99, December, 1999. 2.Eales, L.J. Immunology For Life Scientists A Basic Introduction. John Wiley & Sons, Chichester, 1997. 3.Hofmeyr, S.A.Introduction to the Immune System. In Design Principles for the Immune System and Other Distributed Autonomous Systems. Oxford University Press, New York, 2001.