Immunocomputing

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

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 System1 • 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 Defense1 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 • Phagocytesthat 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 Ingestion1 Step 1: an opsonized antigen is ingested Step 3: MHC/peptide complex presented on surface Step 2: antigen peptides are bound by class II MHC molecules

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 ~ 1012 short-lived (4 – 7 days) lymphocytes created in bone marrow at the rate of 107 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 (~1016 possible varieties) • Lymphocytes have (~105) identical secretable surface protein receptors called antibodies (Ab) ↓ • At any time the immune system has a set of ~108 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 Paratopes1 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 Ve of complementary epitopes with which it can bind called its recognition region • eis called the affinity threshold↓

20. Shape-Space1 • Paratopes (•), epitope complements (x) and affinity thresholds (ε) in shape-space (V)

21. Spatial Distance • Measures degree of interaction (affinity) • For Ag(ag1, ag2 ,…,agL) and Ab(ab1, ab2 ,…,abL) expressed as vectors in shape-space: Euclidean: Manhattan: Hamming:

22. Affinity Threshold (ε) • Distance or match score is inversely proportional to complementarity or affinity for binding • The affinity threshold ε is that value of distance above which which binding actually occurs • 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 Functions1 • Threshold (step) binding function • 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 Antigens3

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 Bafter primary response to A: • Similar to secondary response to A but less pronounced. Called immunological cross-reaction

27. Primary and Secondary IR1

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 Tolerization3

33. Tk Cell Activation3

34. T Cell Activation2

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 Principle1

40. B Cell Adapted Population Diversity3

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 Infection1 • Macrophage ingests Ag, presents MHC/peptide at surface, releases IL-1 • T cell binds MHC/peptide and IL-1, activates • Activated T cell develops, releases IL-2 • B cell binds antigen and IL-2, activates • Activated B cell clones, differentiates into plasma and memory cells • 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 constantregion ↓ 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 Molecule1 • Heavy (H) and light (L) chains; variable (V) and constant (C) regions of the antibody molecule • The V, D and J gene libraries from which the antibody DNA is assembled

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 misalignmentif 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 ~5x107

47. Somatic Hypermutation • Expressed in B cell (somatic) clonal reproduction • Mutation rate 109 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 ~108, ~107 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