Introduction to Immunology and Innate Immunity

Immunology

studying defense mechanisms the body has against infection

• how to recognize and eliminate infections/ diseases while making sure immune system doesn’t attack us

Primary Immune Organs

1. Bone Marrow

2. Thymus

Bone Marrow

Site of hematopoiesis (RBC, WBC being formed), origin of all immune cells, site for B cell development and maturation while origin for T-cells but they mature in thymus

Thymus

Site of T cell maturation and selection

• selection

  • positive selection: can T cells see MHC molecules that the antigen might be presented on cause T cells can’t see freely floating antigens

  • negative selection: does t cells bind strongly to self antigens and if it does, can risk autoimmunity and deleted

Secondary Immune Organs

1. Lymph Nodes

2. Spleen

3. Mucosa Associated Lymphoid Tissues (MALT)

Lymph Nodes

• filter lymph

• here is where the antigens are presented on the MHC molecules

• here is where both T and B cells are activated for immune response

Spleen

• filters blood

• responds to blood borne pathogens

• contains red and white pulp

  • red pulp (filters blood and rbc screening)

  • white pulp (immune response and screen blood for pathogens)

Mucosa Associated Lymphoid Tissues (MALT)

• provides immune defense at mucosal surfaces which are distributed through respiratory tract, lungs, guts

• contain components like tonsils, adenoids, Peyer’s patch and appendix which help in producing unique antibodies

• first line of defense

Three Functions of Immune System

• Defending against pathogens: identifying and removing harmful microorganisms

• Neutralizing harmful substances: detects and neutralizes toxins or allergens

• Eliminating diseased cells: identifies and removes abnormal or mutated cells including cancer cells

How Immune System is Activated

• by antigens (molecules body recongizes as foregin)

Epitope

specific region of antigen that is recongized and where immune cells bind

Immunogen

A type of antigen that triggers an immune response

• all immunogens are antigens

• not all antigens are immunogens because not all trigger immune response

Allergen

specific type of antigen that triggers hypersensitivity or allergic reaction

Two types of antigens

Exogenous and Endogenous Antigens

Exogenous Antigens

• originate outside of body and are foreign to host

  • allergens, vaccine antigens

Endogenous Antigens

produced within body during metabolism or intracellular bacterial/ viral infection

• tumor antigens

• once virus affects cells can be part of our body cause the origin of the virus is in our cells

Complete Antigens

Triggers full immune response including both B and T cell activation without using carrier proteins

Incomplete Antigens/ Haptens

cannot generate full immune response on its own and are non protein substances that require a carrier protein to evoke immunity

Innate Immunity

• rapid non specific first line of defense including physical, chemical and biological barriers preventing pathogen entry like mucosa, tears, (within minutes to hours)

• relies on barriers like skin and immune cells including phagocytes and NK cells to contain and eliminate threats before causes harm

• react in same way every time encounter pathogen (no memory)

• immediate, non specific as targets general features of pathogens such as bacterial cell wall

• after pathogens bypass initial barriers including innate immune cells, 2nd line of defense begins

Adaptive Immunity

• slower but highly specific response

• develops memory that helps in long term protection

• rapid recognition of previous pathogens

• dendritic cells branch between innate and adpative immunity

First line of defends - Skin

• First line of defence

• Physical barrier

• Stratum corneum: forms a tough keratinized layer to block pathogens

• Keratinization: skin cells produce keratin as mature causing a dense, water resistant and protective barrier

• Dynamic defence : rapid healing and regeneration after minor Kim damage to stop pathogens from getting in

• Skin shedding outmost cells helps get rid of debris so continuous barrier

First Line of Defense - Mucosal barrier

• acts as physical barrier: epithelial lining of respiratory, GI, and urogenital tracts block pathogens entry

• Mucus secretion: traps microbes and debris for clearance through secreting mucus when coughing or sneezing and mucociliary activity

  • mucocililiary activity - how mucus moves

• Mucus contains anti microbial molecules like lysozymes, defensins, and secretory antibodies (IgA) to neutralize pathogens by actions such as breaking down bacterial cell wall

• Constant secretion and movement prevent pathogens from taking over

First line of defense - tears and saliva

• Action: wash away pathogens from exposed surfaces (over eyes, mouth)

• Lysozyme is found in saliva and degrades bacterial cell wall specifically in gram positive bacteria

• IgA antibodies neutralize pathogens preventing them from sticking

• Lactoferrin: binds free iron reducing bacterial growth and replication because bacteria are not getting the iron they need to survive

First line of defense - Commensal Flora (non harmful microorganisms)

• occupies physical areas on skin, gut, and mucosal surfaces preventing pathogens from settling down onto the tissues

• Competes with microbes for nutrients and space preventing pathogens from growing

• Produces antimicrobial compounds such as bacteriocins, shirt chain fatty acids, that are toxic to pathogens

• Helps immune maturation and immune tolerance (not attacking our own cells)

  • DEFINE????.?.?.

Innate Immunity

• 2nd line of defense that is activated after pathogens pass the barriers mentioned above

• It involves innate cells including monocytes/ macrophages, dendritic cells, NK cells, neutrophils, eosinophils, basophils, mast cells

• It also involves soluble factors

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Granulocytes (Make sure you can differentiate between the types)

• innate cells containing cytoplasmic granules

• Four types

  • Neutrophils (50-70%): rapid and phagocytose and kill microbes using enzyme and reactive oxygen species

    • disappears really quick cause high levels cause inflammation

  • Eosinophils (1-4%): target parasites by releasing cytotoxic granules and help with allergic and inflammatory responses

  • Basophils (<1%): cells that release histamine and inflammatory mediators during allergic reactions (DIFFERENCE BETWEEN EOSINOPHILS AND BASOPHILS)

  • Mast cells (rare): cells in tissue not blood unlike basophils, that release histamine and cytokines during allergy, anaphylaxis, and wound healing

Monocytes (difference between this and neutrophils???????)

• circulate in blood and phagocytic

• Makes up about 5-10% of WBC

• Key functions

  • Surveilliance: monitor blood to see if there is any infection or tissue damage

  • Migration: can rapidly move into tissue once sense inflammatory signals

  • Differentiation: can become macrophages and dendritic cells but once leaves blood stream and enters tissue, will differentiate into this

Macrophages (one of most versatile)

• phagocytosis (engulf and destroy pathogens, debris, and apoptotic cells

• Cytokines secretion: release signalling molecules called cytokines that recruit and activate other immune cells

• Antigen presentation: display pieces of the pathogen to the T cells and shows the connection between innate and adaptive immunity

• Tissue repair: promotes wound healing and lowering inflammation after infection

Macrophage polarization

• M0 macrophages can differentiate into either M1 or M2 macrophages depending on the signals they receive from the environment

• M1 Macrophages: classically activated and are pro inflammatory so induce inflammation but if too severe can cause tissue damage as M1 can attack your body

  • fight against Tumor cells

  • tissue specific antigen presentation: process antigens and using the MHC class 2 molecules located on surface of the M1 macrophages present them to T cells

• M2 macrophages

  • anti inflammatory

  • Protect Timor cells from being attacked because mistake tumour cells for wound healing ??.??????

  • Secrete anti inflammatory cytokines to stop inflammation

  • Can get immune suppression if too many

Macrophages Tissue Types (DO!)

Dendritic Cells (DC)

• bridge between innate and adaptive immune system

• Comes from monocytes

• Immature DC

  • found in peripheral tissues (skin, mucosa, lymphoid organs)

  • Specialized in capturing antigens from pathogens or damaged cells

    • strong capacity to take up antigens but have to become mature to be able to present those antigens

  • Activated by pathogen signals and cytokines

• Mature DC

  • Efficient at antigen processing and presentation to T cells

  • Activate naive T cells (have never seen the antigen yet)

  • Mature DC have already taken up antigen

• Maturation Process

  • dendritic cells mature in peripheral tissue upon seeing danger signals and migrate to lymph nodes

    • develop extended dendrites (branches) to interact with T cells

Dendritic cell Subsets (DO)

Natural Killer Cells

• cytotoxic lymphocytes (toxic to cells and can kill them)

• Detect and kill virus infected or tumor cells by releasing perforin and granzymes to induce apoptosis

• Different from T cells cause can act fast without prior exposure

• Do not rely on specific antigen receptors like T cells or B cells

  • T cells need antigen receptors to recognize antigens present on MHC molecules

  • B cells need antigen receptors to bind to free antigens

How are NK cells similar to adaptive immunity

• release cytokines (IFN-gamma) to recruit and activate adaptive immune cells

• Some NK cells can respond more effectively to repeated viral exposure

Second Line of Defense - Soluble Factors (watch video)

• Complement system made up of soluble factors usually being proteins

  • definition: a network of proteins circulating in the blood and tissues in an inactive form

• Once system detects presence of antigen, cause a cascade of events involving proteins being activated

  • once proteins are triggered some become enzymes that cut and activate other proteins, amplifying immune response

Complement system specifics

• nine main complement proteins named C1, C2, etc

• Multiple complement fragments can come together to form a enzyme complex called convertase that will cleave other complement proteins amplifying response

• Once complement proteins are cleaved they can be given a or b (ex. C1 a)

  • a fragment = anaphylatoxin (alarm signal) that recruits neutrophils and monocytes to site of infection

  • B fragment = binding fragment (sticks to surface of pathogen marking it for immune system to destroy such as by phagocyte

Complement Activation Pathways (Watch video), don’t understand?

• Classical Pathway (triggered by antigen-antibody complexes linking adaptive and innate immunity)

• Lectin Pathway: recognizes sugar molecules on bacteria, faster cause doesn’t rely on antibodies but can only bind to sugar molecules

• Alternative Pathway: spontaneous activation on pathogen surfaces

• 3 different alarms/ pathways but all lead to tagging and recruiting immune cells

Key outcomes of Complement Activation (DO)

Clinical relevance of Complement System

• C3 deficiency leads to severe frequent bacterial infections because negatively impacts opsonization

• Over activation of complement system can cause tissue damage as seen in PNH which is a rare blood disorder where red blood cells are destructed due to complement system and RBC not having protective proteins on their surface due to mutation

  • C5 inhibitors prevent this

Second Line of Defense in Soluble Factors (cytokines)

• Cytokines: small signalling proteins secreted by immune and non immune cells, help communicate with immune system

Key functions of cytokines

• inflammation: promote and regulate inflammatory responses

• Cell recruitment: guide immune cells (ex. Neutrophils, monocytes, lymphocytes) to sites of infection

• Cell activation and differentiation: stimulate immune cells and help immune cells to differentiate

• Help activate T cells and B cells for targeted response

Autocrine action

• cytokines act on cell secreting it

Paracrine action

Cytokines act in nearby cells locally

Endocrine action

Cytokines travel through blood to act on distant cells

Cytokines examples

• pro inflammatory cytokines

  • ex. IL-1, TNF-alpha, IL-6)

  • Amplify inflammation and fever cause recruit more immune cells to the area

• Anti inflammatory cytokines

  • IL-10, TGF-Beta

  • Help limit and resolve excessive immune responses

  • Reduce inflammation

• Interferons

  • Type 1: IFN alpha, IFN beta, Type 2 IFN-gamma

  • Enhance antiviral defences

  • Warn neighbouring cells about infection

  • IFN gamma also activate macrophages and support adaptive immunity

Clinical relevance of cytokines

• cytokines storms

  • too many inflammatory cytokines at once can cause dangerous inflammation as seen in COVID 19 and sepsis and damage tissues and organs

  How to reduce storms

  • IL-6 inhibitors: block IL-6 signalling to calm down immune activation

  • JAK inhibitors: indirect cytokines signalling blockers that suppress inflammation pathways

Clinical relevance of cytokines - autoimmune dieases

• cytokines overrreacting can cause diseases

  • rheumatoid arthritis

    • secrete high amounts of TNF alpha cytokines causing inflammation in joints

  • Crohn’s disease

  • Psoriasis

• Cytokines can disrupt intestinal barriers

• To reduce/ block TNF alpha inhibitors

  • Block

Clinical relevance of cytokines - Cancer Therapy (Video)

• cytokines like IL-2 can boost immune system to help fight cancer and used in cancer treatments

  • IL-2 stimulates growth of T cells which fight against cancer

  • However treatment can increase IL-2?? And cause hypertension and toxicity so used in specialized cases

Clinical Relevance of Cytokines (Viral Infections) (Video)

• Type 1 interferons help the body fight viruses like flu or hepatitis by turning on antiviral defences

  • type 1 interferons block viral replication and spread of virus

  • Infected cells warn surrounding cells to prepare

• Treatment option

  • Pegasys

    • helps treat chronic hepatitis B and c infections

    • Polymer and being in blood longer????

Chemokines

• specialized group of cytokines responsible for guiding movement of immune cells to infection, inflammation, and injury sites (Chemotaxis)

• Direction of chemotaxis is pathway that leads to increasing concentrations of chemokines

• Types of chemokines

  • CXCL8: attracts neutrophils to infection sites to start clearing

  • CCL2: recruits monocytes during inflammation to eliminate threat

Clinical Relevance of Chemokines

• maraviroc is a CCR5 antagonist

  • CCR5: chemokine receptor on immune cells that HIV uses as a co-receptor to enter and infect cells

  • by blocking it, virus cannot bind to cell and slow HIV replication

How Innate Immunity is Activated

• relies on sensors (Pattern Recognition Receptors - PRRs) that detect signals from microbes or damaged cells and send an alert to trigger an immune response

• What signals are detected

  • PAMPs: Pathogen assoicated molecular patterns (molecules only bacteria carry)

  • DAMPs: Damage associated molecular patterns (signals from injured or dying cells)

• How it works

  • When PPR’s (found on membrane or cytoplasm), bind to DAMPs or PAMPs. activate transcription factors turning on genes for cytokines and other immune molecules causing inflammation, and activating immune cells

Major Types of PRRs - TLRs

• toll like receptors

• dectect bacterial lipids and viral DNA

• found on surface or inside cell

Major types of PRRs - NLRs

• NOD like receptors

• sense bacterial cell wall components inside cells

• location: inside cell'

• mutations can cause over immunity

Major Types of PRRs - RLRs

• RIG-1-like receptors

• Dectect viral RNA inside cytoplasm

• found in cytoplasm of cells

Major Types of PRRs - CLRs

• C-type Lectin Receptors

• recognize fungal pathogen sugars

• found mainly on cell surface

Major types of PRRs - cGAS-STING pathway

• dectects viral or bacterial DNA floating inside cytoplasm

• Boost antiviral defense and protect body against tumor cells

• in cytoplasm

PAMPs

• pathogen associated molecular patterns

• unique parts found on microbes but not human cells so immune system can recognize it quickly and lead to activation of T cells

• Doesn’t need previous memory to work, see and recongize instantly

• Common examples

  • Bacteria: Lipopolysaccharides (LPS)

  • Viruses: Double stranded RNA, single stranded RNA, unmethylated CpG DNA (cytosine (C) is followed by a guanine (G), linked by a phosphate bond (p).)

  • Fungi: carbohydrate structures like B glucans and mannans

DAMPs

• damage associated molecular patterns

• molecules released by damaged or dying host cells even when no pathogen leading to inflammation

• located within own cell

• Common examples

  • HMGB1 (high mobility group box 1)

  • ATP

  • DNA/ RNA outside nucleus or mitochondria

  • uric acid crystals

Clinical relevance of PAMPs and DAMPs

• PAMPs

  • LPS in gram negative bacteria binds to TLR-4 receptors (toll like receptors) causing lots of cytokine release and can cause septic shock if uncontrolled (low bp, organ failure, or leaky vessels)

• DAMPs

  • ATP and DNA from dead cells are released causing sterile inflammation (inflammation without pathogens being involved) due to triggers such as ischemia reperfusion injury, autoimmune disease)

    • ex: gout flares due to uric acid crystals being released