MCB 150: Molecular Today’s game-plan Immunologymcb.berkeley.edu/courses/mcb150/lecture1/Lecture1.pdf · MCB 150: Molecular Immunology Spring 2007 Prof. Ellen Robey Prof. Robert

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MCB 150: MolecularImmunology

Spring 2007Prof. Ellen Robey

Prof. Robert BeattyProf. Laurent Coscoy

Today’s game-plan

• Structure of the course and administrative

issues

• Overview of the immune system

• Begin: Innate Immunity

MCB 150 Spring 2007

Innate Immunity Humoral ImmunityB cells, antibody, complementPhagocytes, Toll-like receptors

Cellular ImmunityT cells, TCR, development, selection, tolerance, NK cells

Immune Responses

inflammation, allergy, autoimmunity, infection

Course InstructorsLecturers:

Ellen Robey471 LSA 2-8669Office hours: Tues 11-12

Laurent Coscoy451 LSA 3-4128Office hours: TBA

Robert Beatty176 LSA 2-0671Office hours: Tues 3-4

GSIs:

Dina [email protected] hours: TBA

Tim [email protected] hours: TBA

Course Components

• Lecture series• Discussion sections (not required, but highly

recommended)• Reading: Text (Kuby 6th addition), Journal Articles• Problem sets (posted on web, these are not graded, but

are to help reinforce what you learn in class)• Exams-- two mid-terms, plus final exam

Grading

• Mid-terms: 25% each• Final 50%

Half of the material final is a cumulative reviewand half focuses on the last third of the class.

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Course Web Site

• www.mcb.berkeley.edu/courses/mcb150• All lecture notes, problem sets, answers will

be posted for viewing or download• Powerpoint presentations shown in lecture

will be posted for your review

Getting Help!!!•Web site:www.mcb.berkeley.edu/courses/mcb150

•Discussion groups / GSIs

•Office Hours

•After lecture-- very brief questions only

•No Discussion sections this week.

•Sign up sheets available in class today

•You may attend any or all of the 4discussion sections.

•Problem set/reading material fordiscussion will be posted on website

Overview of the Immune system

Microbes: why they are formidable foes.

Gross anatomy of the immune system

Cells of the immune system

Effector mechanisms: how the immune system protects

Immune recognition of pathogens: innate vs adaptive immunity

Cytokines and the inflammatory response

Microbes are ubiquitous in nature, extraordinarily diverse,rapidly evolve to exploit opportunities to infect hosts and to

evade their immune systems.

Exponential Growth

1

10

100

1000

10000

100000

1000000

10000000

100000000

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

Time (minutes/10)

# of bacteria

8 hours = 280 trillion bacteria!!!!

Exponential growth

Num

ber o

f bac

teria

Time (hrs)

Many pathogens can expand rapidly in the nutrient-richenvironment of the host.

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Some microbes hijack cellular machinery toreplicate and spread. Intracellular pathogens

include viruses (influenza, HIV) and intracellularbacteria (listeria) and intracellular parasites

(malaria, toxoplasma).

Listeria bacteria using the actin cytoskeleton ofthe host cell to spread from cell to cell.(Portnoy lab)

Toxoplasma parasites (red) and dendritic cells(green) within a mouse lymph node. (Robeylab)

Pathogens rapidly evolve to avoid the host immune response

Virally encoded decoy receptors








First some key definitions:

Pathogen: microbe that causes disease

Antigen: material (from a pathogen) that induces an immune response

Innate (natural) immunity: rapid, non specific immune response

Adaptive (acquired) immunity: slower, specific immune response

Leukocytes: blood cells

Lymphocytes: specialized blood cells that mediate adaptive immunity(e.g. T and B cells)

The cells of the immune systemcirculate through the body via

lymph and blood. Pathogens andtheir antigens are transported from

tissues via lymphatic vessels tothe lymph nodes where they

encounter immune cells.

The cells of the immune systemspend much of their time in

lymphoid organs. They develop(arise) in primary lymphoid

organs, and they interact withantigens in secondary lymphoid

organs.

Thymus: primary lymphoid organfor T cell development

Bone marrow: primary lymphoidorgan for B cell development

Lymph nodes: collect antigensfrom tissues

Spleen: collects antigens fromblood stream

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Many different types of blood cells participate inthe immune response to microbes:

Innate immune cells: “phagocytes”macrophage, neutrophils, dendritic cells

Adaptive immune cells: “lymphocytes”T cells, B cells

Most blood cellsact to fightinfection.

AdaptiveimmunityInnate

immunity

Blood cells lineages.

Lymphocytes of the adaptive immune system

T helper cells: regulate other immune cellsT cytotoxic (killer) cells: kill infected cellsB cells: produce antibodies (immunoglobulin)

Dendritic cells and macrophage: directly kill microbes by phagocytosis and othermechanisms. They also help to activate T cells (connection between innate and adaptiveimmunity)NK cells are lymphocytes that have characteristics of innate and adaptive immunity.






Immune recognition: innate and adaptive

Cytokines and inflammation

Immune Effector Mechanisms:

Cell-mediated immunity:Phagocytosis (cellular eating)cytotoxcity (cellular killing)

Humoral immunity:complement: group of serum proteins that can directly kill

pathogens.antibodies: (also called immunoglobulin) proteins secreted

by B cells that bind directly and specifically to pathogens.Antibodies target pathogens by marking them for destruction byother components of the immune system.

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Macrophage fight microbes by engulfing anddigesting them (phagocytosis or cellullar eating).

A macrophage engulfing yeast

Bacteria fight back againstphagocytosis

A macrophage attempting toengulf a bacterium Streptococcuspneumoniae, that is covered with

a slimy coat.

Target cell killing by a cytotoxic (killer) lymphocyte

A cytotoxic T lymphocyte (CTL) killing a cellthat has been infected by a virus. NK cells use a

similar mechanism to eliminate tumor cells.






innate and adaptive immunity


Found in:

Substancesthat trigger:

Receptors:

all multicellullar organisms

A limited number ofpathogen-associatedmolecular patterns (PAMPs)

A limited number of PatternRecognition Receptors(PRRs) expressed on manycells types

Vertebrates only

Virtually any component ofpathogens

Highly variable receptors of2 types: antibody made by Bcells and TCR made by Tcells

Comparison of innate and adaptive immune recognition

Receptors that mediateinnate immune recognition: Toll-like receptors (TLR)

Receptors that mediate adaptive immune recognition:Antibody and the T cell receptor (TCR)

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The genes encoding the T cell antigen receptor (TCR) are assembledby DNA rearrangement as T cells develop in the thymus

TCR ! locus:structure in germline

TCR ! locus:structure in T cells

DNA rearrangement(rag1, rag2)

transcriptionRNA splicingtranslation

T cell

!"

V segments D J C

The genes encoding the antigen receptors of T and B cells areassembled by DNA rearrangement as these cells develop. As aresult of V(D)J recombination, every B and T cells expresses aunique version of the antigen receptor.






Immune recognition: innate and adaptive


Cytokines: (also called interleukins)

Small secreted peptides that used forintracellular communication between cellsof the immune system

Can turn on or off immune responses

Mediate inflammation

Chemokines: subset of cytokines thatspecialize in regulating cell motility

Inflammation: a complex series ofevents induced by tissue damage(described in medical literature in 1500s)

• Redness (rubor)

• Pain (dolor)

• Swelling (tumor)

• Heat (calor)

Infection can induce inflammation, but even sterile injuries can besufficient to induce inflammation.

Inflammation occurs when injured tissues release mediators that promotevasodialation (increased blood flow) and chemotaxis (directed migration)

of leukocytes. Inflammation causesblood cells to move

from blood stream tosite of injury

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Blood cells (leukocytes) travel from the blood stream intotissues by a process known as extravasation

Blood cells can also be attracted to sites of infection byproducts produced by pathogens, as well as by

chemoattractants made by host (chemokines, inflammatorymeditators).

Neutrophils (a type of white blood cell) are attracted to bacterialproducts. Here they are moving toward a gradient of the

bacterial peptide fMLP.

Why study the immune system?Importance of the immune system in human health

Provides model systems for studies of:gene regulationmolecular recognitionsignal transductionetc, etc

Provides powerful techniques for use in medicine and science

Diseases associated with immunesystem dysfunction

• Autoimmunity (SLE, Arthritis,Myasthenia gravis, Graves disease)

• Immunodeficiency (inherited, acquired)• Allergy (environment, drugs)• Cancer (Leukemia, Lymphoma)

Myasthenia gravis

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Asthma & AllergyTherapeutics

• Vaccination• Adoptive immunotherapy• Transplantation

Vaccination: THE major successCases per

100,000population

Cases per100,000

population

Cases per100,000

population

Diphtheria

Polio

Measles

year

Treating cancer

Tissue Transplantation Powerful methods for detecting andquantitating proteins and cells based onthe highly specific binding of antibodies

(immunoglobulins)

• ELISA: enzyme-linked immunosorbant assay(measures small amounts of hormones, drugs,microbes in body fluids)

• Western blot (detects disease associated proteins)• Flow cytometry (quantifies various cell types in

mixed population-- HIV patients)

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Western Blot

•Separate proteins by size using PAGE gel

•Transfer gel to blotting membrane•Probe membrane with antibody

specific for protein of interest•Detect bound antibody by

chemiluminesence

ImmunofluoresenceImmunofluoresence

Flow Cytometry: QuantitativeSingle-cell Immunofluoresence

Innate (natural) immunity

Found in:

Substancesthat trigger:

Receptors:

all multicellular organisms

A limited number ofpathogen-associatedmolecular patterns (PAMPs)

A limited number of PatternRecognition Receptors(PRRs) expressed on manycells types

Vertebrates only

Virtually any component ofpathogens

Highly variable receptors of2 types: antibody made by Bcells and TCR made by Tcells

Innate ImmunityInnate immune effector mechanisms

Physical and biochemical barriers (defensins)Phagocytosis and reactive oxygenCell autonomous defenses

ApoptosisInterferons and PKR

Innate immune recognitiondiscovery of the Toll-like receptorsmammalian TLRs and their ligandsnon-TLR recognition of PAMPs

Connections between adaptive and innate immunity

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Physical & Biochemical barriers

Defensins

• Originally isolated from frog skin based on their ability tokill bacteria

• Small polypeptides (<10kDa) secreted at mucosal surfaces• Direct bacteriocidal properties• Insertion into biological membranes leading to target cell

lysis• Inhibited by cholesterol (specificity)

Hanging out with Tolstoy 1909

In 1882, the Russian scientist Ilya Mechnikov was working in Messina, Italy, studying thelarvae of the sea star. When he inserted a thorn into a larva, something weird happened.Mechnikov noticed strange cells gathering at the point of insertion. The cells surrounded thethorn, eating any foreign substances that entered through the ruptured skin. Mechnikov wasthrilled. He decided to name these new cells phagocytes from the Greek words meaning"devouring cells."

Phagocytosis was discovered by Ilya Mechnikov in 1882

Phagocytosis “cellular eating”

3. Phagosome fuses withlysosome.

1. Bacterium attaches tomembrane

2. Bacterium is ingested, formingphagosome,

4. Lysosomal enzymesdigest the bacteria.

5. Digested material isreleased from cell.

Phagocytes: macrophage,neutrophils, dendritic cells

Phagocytes use a variety of methods to destroy ingested microbes.

(household bleach)

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Macrophage fight microbes by phagocytosis andproduction of toxic molecules

A macrophage produces reactive oxygenspecies to aid in destruction of the microbe

Reactive oxygen is revealed by the blue dye,NBT


Physical and biochemical barriers (defensins)Phagocytosis and reactive oxygen speciesCell autonomous defenses


Innate immune recognitiondiscovery of the Toll-like receptorsmammalian TLRs and their ligandsnon-TLR recognition of PAMPs


Some microbes hijack cellular machinery to replicateand spread. Intracellular pathogens include viruses(influenza, HIV) and intracellular bacteria (listeria)and intracellular parasites (malaria, toxoplasma).

cell-autonomous defense:cell produces an immuneresponse that acts on itself

Apoptosis: Cellular Suicide

•Nuclear fragmentation•Proteolysis•Blebbing•Death

Remnantsundergophagocytosis

Apoptosis versus Necrosis•Tidy: contents of cellsdegraded from within,producing small cellular“blebs”

•Programmed from inside thecell

•Messy: contents of cellreleased.

•Induced by external insult

Cell death by necrosis is more likely to produce inflammation.

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Interferons are cytokines that areproduced in response to viral infection.

Produce an “anti-viral state” in targetcells.

Acts on cell that produces it, as well asneighboring cells.

Together with dsRNA, act to triggeringthe Protein Kinase R(PKR) pathway.

Shuts down protein synthesis machineryof cells, thus preventing viral replication.

Cells can avoid being hijacked by viruses by activating the ProteinKinase R (PKR) pathway. PKR is triggered by dsRNA and interferon. Protein Kinase R:

Interfering with Infection

RNA-bindingdomain

Kinasedomain

dsRNAor

interferon

PKR

eIF2a

PhosphorylatedPKR

(active)

PhosphorylatedeIF2a

(inactive)


Physical and biochemical barriers (defensins)Phagocytosis and reactive oxygenCell autonomous defenses


Innate immune recognitiondiscovery of the Toll-like receptorsTLRs and their ligandsnon-TLR recognition of PAMPs


Comparison of the adaptive and innate immune responses

innate adaptive

Response time hours days

Response to identical to primary stronger response uponrepeat infection second exposure

Receptors that pattern recognition receptors antibodies and T cell antigen receptors (TCR)Mediate pathogen Toll-like receptors (TLR)Recognition limited diversity, unlimited diversity

fixed in germline generated by V(D)J recombination

Ligands Pathogen associated molecular virtually any component of pathogenpatterns (PAMPs)

Documents

MCB 150: Molecular Today’s game-plan Immunologymcb.berkeley.edu/courses/mcb150/lecture1/Lecture1.pdf · MCB 150: Molecular Immunology Spring 2007 Prof. Ellen Robey Prof. Robert