BIOS 372 - UNIT 1

4 different types of pathogens

bacteria, viruses, fungi, and parasites

Why is sanitation and clean water important to prevent infection?

Dirty water can cause chronic, low grade gut inflammation and reduce the efficacy of oral vaccines

How does nutrition fuel the immune system?

Vitamin A = mucosal architect, Proteins build antibodies, Micronutrients aid in catalysis

Innate vs. Adaptive immune system

• Innate - nonspecific, fast-acting

• Adaptive - specific to antigen, slow-acting, retains memory of infection

  • Humoral immunity - B cells produce antibodies

  • Cell-mediated immunity - T cells kill infected cells or recruit other cells to bolster immune response

Active vs. Passive immunity

• Active - individual produces their own antibodies after pathogen exposure

• Passive - individual receives antibodies from another source 

Types of immune dysfunction

• Hypersensitivity (e.g. allergies, asthma)

• Autoimmune (body attacks self)

• Immunodeficiency (weakened immune system)

  • Primary (genetic)

  • Secondary (acquired)

• Immune imbalance (uncontrolled inflammation)

What cell types are in the myeloid vs. lymphoid lineages?

• Myeloid lineage: RBCs, platelets, monocytes/macrophages, granulocytes, dendritic cells

• Lymphoid lineage: T cells, B cells, innate lymphoid cells, dendritic cells

Key transcription factors in hematopoiesis

• GATA 1 - promotes erythrocyte (RBC) and megakaryocyte (platelet) development

• PU.1 - initiates myeloid lineage

• IKAROS - initiates lymphoid lineage

Neutrophils

• Phagocytic

• Release AMPs to destroy bacterial pathogens

• Promote tissue remodeling after damage (collagenase)

• Most numerous WBC

Eosinophils

• Phagocytic

• Destroy large parasites

• Destroys viruses via ribonucleases

• Attract other WBCs by releasing cytokines and chemokines

Basophils

• Target parasites

• Modulate adaptive immune response via release of cytokines

• Promote vasodilation and inflammation via release of histamine

Mast cells

• Target parasites

• Promote vasodilation and inflammation via release of histamine

Difference between basophils and mast cells

Mast cells reside in the body’s tissues and have a longer lifespan than basophils, which circulate in the bloodstream and have a very short lifespan

Monocytes

• Migrate into tissues and differentiate into a diverse array of phagocytic cells

• Two categories:

  • Inflammatory - rapidly enter tissues to respond to infection

  • Patrolling - crawl along inside of blood vessels to clear cellular debris and repair tissue

Macrophages

• Can form from monocytes or progenitor cells

• Specialize according to the tissue they reside in

• Express receptors for antibodies

• High phagocytic activity

Dendritic cells

• Functions are still being clarified

• Can be antigen-presenting or antigen-capturing depending on location

• Two types:

  • Conventional dendritic cells (cDCs) - present antigens to T cells to bridge the innate and adaptive immune systems

  • Plasmacytoid dendritic cells (pDCs) - produce large amounts of antiviral cytokines

How do we differentiate between B and T cells?

Appear identical under a microscope - must identify pattern of proteins on cell surface (CD proteins)

B cells

• Mature in bone marrow

• Functions: antibody production, antigen presentation, immunological memory

• Types of B cells

  • Naive B cells, plasma cells, memory B cells

T cells

• Originate in bone marrow, mature in thymus

• Functions: kill infected cells, coordinate other immune cells, immunological memory

• Types of T cells

  • Helper T cells (CD4, recognizes antigen-MHC II)

    • Coordinate other immune cells

    • 4 types: Th1, Th2, Th17, Thf

  • Cytotoxic T cells (CD8, recognizes antigen-MHC I)

    • Kill infected cells

  • Regulatory T cells

    • Suppress excessive immune response

  • Memory T cells

Innate lymphoid cells

• Lack antigen specific receptors

• Three subtypes based on varying cytokine secretion:

  • ILC1 (includes NK cells)

    • Defends against intracellular pathogens, tumor surveillance

    • Secretes IFN-y

    • Similar to Th1

  • ILC2

    • Responds to parasites and allergens, repairs tissue

    • Secretes IL-4, IL-5, IL-13

    • Similar to Th2

  • ILC3

    • Responds to extracellular bacteria and fungi, maintains gut barrier integrity

    • Secretes IL-17, IL-22

    • Similar to Th17

Functions of the lymphatic system

• Keeps fluid levels balanced

• Transports immune cells

• Monitors body for potential threats (pathogen detection occurs at lymph nodes, where immune cells reside)

How does the lymphatic system keep fluid levels balanced?

• As blood moves through the circulatory system, blood capillaries leak fluid

• Most interstitial fluid is pulled back into blood capillaries, remaining fluid is absorbed by lymphatic capillaries and called lymph

• Lymph cannot get out once it is in (flaps of endothelial cells snap shut)

Movement of lymph

• Lymphatic capillary → Vessel → Trunk → Duct → Circulatory system

• Uneven drainage into right duct (right upper quadrant of body) and thoracic duct (rest of body)

• Powered by:

  • Skeletal muscle contractions

  • Pressure changes from breathing

  • Valves prevent backflow

Primary lymphoid organs

• Include bone marrow and thymus

• Boot camps where immune cells develop and learn the rules (attack invaders, but don’t touch the body’s cells)

Secondary lymphoid organs

• Include lymph nodes and spleen

• Filter stations, where lymph and blood are exposed to immune cells that respond to potential pathogens

Components of bone marrow

• Specialized cells create a niche (highly organized environment) that influences blood cell differentiation:

  • Perivascular cells - release cytokines, growth factors, display surface molecules that influence stem cell behavior

  • Osteoblasts provide a niche for developing B cells

Structure of thymus

• Organized into lobes, each with specialized microenvironments that guide T cell development

• Microenvironments:

  • Cortex: densely populated with immature T cells

  • Medulla: sparsely populated with mature T cells

  • Corticomedullary junction: entry and exit point for T cells as they move to and from the bloodstream

Main vessels that serve the lymph nodes

• Afferent lymphatic vessels: entrance for lymph, antigens, some immune cells

• High endothelial venules (HEV): site where naive lymphocytes circulating in the blood enter lymph node

• Efferent lymphatic vessels: carry cells out of lymph nodes

Three main regions of lymph nodes

• Cortex: B cells reside in follicles and germinal centers, with macrophages and dendritic cells helping trap antigens

• Paracortex: rich in T cells and antigen presenting cells

• Medulla: contains antibody producing plasma cells, exit point for cells via the efferent lymphatic vessel

Flow of blood through spleen

Splenic artery → Arterioles → Vascular sinusoids (where immune cells survey blood for pathogens) → Splenic vein

Structure of spleen

• Red pulp: rich in RBCs, surrounds sinusoids and removes old RBCs

• White pulp: forms periarteriolar lymphoid sheath (PALS) around the arterioles, populated by T cells

  • Contains lymphoid follicles, which are rich in B cells

• Marginal zone: boundary between red and white pulp, contains specialized macrophages and B cells, traps antigens

What are MALT?

• Mucosa Associated Lymphoid Tissue

• Contain secondary lymphoid tissue (e.g. T cell zones and lymphoid follicles) outside the lymph nodes and spleen

• Found in barrier tissues (e.g. skin, mucosal membranes of the digestive, respiratory, urogenital tracts) that represent the main entry points for pathogens

What are tertiary lymphoid organs?

• Form in non-lymphoid tissues in response to chronic inflammation

• Resemble secondary lymphoid organs in structure and function

• Can be simple clusters or highly organized with B/T compartments, germinal centers, lymphatic vessels, and HEV

• Enable localized immune responses at site of injury

Sequence of development from HSCs

Long term HSCs → Short term HSCs → Multipotent progenitors → Myeloid/Lymphoid lineages

Physical barriers of the innate immune system

• Skin

  • Covers outside of body

  • Contains multiple layers of epithelial cells

• Mucous membranes of the respiratory, digestive, and urogenital tracts

  • Single layer of epithelial cells covered with mucus

• Can be enhanced by chemical additions like low pH, AMPs, mucus.

Commensal microbes functions

• Use up metabolic resources/occupy binding sites to prevent other organisms from inhabiting the human body

• Produce AMPs to kill invading microbes

• Aid in digestion

• Synthesize vitamins and neurotransmitters

Structure of the skin

• Epidermis

  • Stratum basale (innermost layer): source of dividing keratinocytes

  • Stratum spinosum: cells appear spiny due to keratin deposits, houses Langerhans cells

  • Stratum granulosum

  • Stratum corneum (outermost layer): sheds layers of dead cells, keratin deposits create dry and impermeable surfaces

• Dermis

  • Contains structural molecules like elastin and collagen

  • Contains macrophages and mast cells

  • Contains sweat glands, sebaceous glands

Chemical barriers of the skin

• Sweat glands: release acidic electrolytes, flush out dirt/debris, produce dermcidin (AMP)

• Sebaceous glands: release sebum, maintain acidic environment of skin, deliver AMPs

• Keratinocytes and other immune cells produce defensins and cathelicidins (AMPs)

• Lacrimal glands: rinse the eyes, loaded with lysozyme

Structure of mucous membranes

• Can only be a single layer of epithelial cells (need to be thin in order to also handle the functions of absorption and secretion)

• Coated in mucus - a sticky, protein rich layer made by goblet cells

  • Traps pathogens

  • Contains commensal microbes that produce AMPs and compete with invaders

How does the structure of mucus vary by location?

• Single, thin layer in small intestine to avoid blocking absorption of nutrients

• Stomach and colon have two layers:

  • Dense inner layer for protection against pathogen invasion

  • Loose outer layer that provides nutrients and attachment sites for commensal microbes

What is the complement system?

• 2nd line of defense in the innate immune system

• Collection of proteins produced by the liver, circulate in an inactive form, unless activated by a pathogen or antigen-antibody complex

How is the complement system activated?

• Signaling cascade

• Signal is amplified with each step in the pathway

Outcomes of the complement system

• C5b → creates membrane attack complex (MAC), which creates a pore in pathogen cell membrane, causing cellular contents to leak out

• C3b → opsonizes (coats) pathogen to make phagocytosis easier

  • Activates itself, generating a positive feedback loop that amplifies the complement response

• C3a + C5a → acts as chemoattractants that recruit neutrophils and monocytes

How does the complement system avoid destroying host tissues?

• Classical pathway and lectin pathway are only initiated by binding to markers on the surface of a pathogen

• C4b can bind to surface proteins or carbohydrates indiscriminately, but if it doesn’t bind to the pathogen surface, it is inactivated

What happens to complement proteins that don’t become a part of the convertase enzymes?

• Bind to receptors on phagocytes to enhance phagocytosis

• Bind to receptors on endothelial cells → increase production of adherins → cause immune cells to stick to blood vessels, also increase permeability of vessels to transport immune cells to infection site

• Bind to receptors on mast cells to promote release of inflammatory molecules

Convergence point for complement pathways

• Creation of C5 convertase, which cleaves C5 into C5a and C5b

• Final steps involve C6 - C9

• Ultimately results in formation of membrane attack complex

Classical Pathway

Lectin Pathway

Alternative Pathway

What are cytokines?

• Small proteins, released by both immune and non-immune cells

• Act as signals to inform cells regarding the location, strength of the immune response

IL1 family of cytokines

• Secreted by dendritic cells, monocytes, macrophages

• Proinflammatory, regulate inflammation

Class 1 (hematopoietin cytokine)

• Secreted by a diverse array of cells

• Regulates hematopoiesis and antibody secretion

Class 2 (interferon cytokines)

• Secreted by activated macrophages, DCs, activated T cells, NK cells, virally infected cells

• Antiviral, immune modulation

Tumor Necrosis Factor

• Secreted by activated macrophages, non-immune cells

• Immune system development, effector function, homeostasis

IL17 family of cytokines

• Secreted by activated T cells

• Proinflammatory, promote neutrophil accumulation

Chemokines

• Direct migration of other immune cells (function as chemoattractants) by acting on G protein coupled receptors

  • Direct other cells via concentration gradients (concentration of chemokines is highest at the site of infection)

5 properties of cytokines

• Pleiotropy: single cytokine can act on multiple cell types and have different effects

• Redundancy: multiple cytokines perform the same function

  • Ensures immune system can adapt if one pathway is disrupted

• Synergy: two or more cytokines combine their actions to enhance an immune response

• Antagonism: one cytokine can inhibit the effect of another

• Cascade induction: one cell releases cytokines to stimulate a target cell to release additional cytokines, creates a domino effect to amplify the immune response

JAK-STAT pathway

• Intracellular signaling pathway activated by cytokines

• Ligand binds to cell surface receptor

• JAK adds Pi to receptor

• Two STAT proteins bind to the Pi on the receptor and are thus phosphorylated

• STAT proteins dimerize, enter nucleus to act as transcription factors

MAP-K pathway

• Intracellular signaling pathway activated by cytokines

• Cytokine binds to its receptor, receptor is phosphorylated and proteins are recruited → Ras is activated → Raf (MAPKKK) is activated → MEK (MAPKK) is activated → Erk (MAPK) is activated → Erk enters nucleus to phosphorylate transcriptional regulators of cell proliferation, differentiation, and survival

NFkB signaling pathway

• Intracellular signaling pathway activated by cytokines

• Cytokine binds to receptor → Adaptor proteins bind to receptor to form a signaling complex → Signaling complex activates IKK complex → IKK phosphorylates IkB, marking it for degradation and releasing active NFkB → Active NFkB translocates to nucleus

GPCR pathway

• Intracellular signaling pathway activated by cytokines

• Ligand binds to GPCR, which undergoes a conformational change

• Associated G protein exchanges GDP for GTP on alpha subunit

• Alpha-GTP subunit dissociates from GBy dimer

• Ga and GBy interact with downstream effectors

• Ga hydrolyzes GTP to GDP, Ga reassociates with GBy to terminate the signal

What are PAMPs?

• Pathogen Associated Molecular Patterns

• Include molecules shared by many microbes, but not produced by host cells

• Allow innate cells to quickly recognize microbes as a non-self threat

What are DAMPs?

• Damage Associated Molecular Patterns

• Found in the intracellular compartments of host cells and released due to damage caused by infection

What are DAMPs and PAMPs recognized by?

Pattern Recognition Receptors (PRRs) on immune cells

What are TLRs?

• Toll-Like Receptors are a type of PRR that can detect many different kinds of pathogens at the cell surface or intracellularly (in endosomes/lysosomes)

  • Ligand binding domain contains LRRs (leucine rich repeats)

• Generalized signaling pathway: TLR binds ligand → Receptor dimerization → Recruit adaptor proteins → Activation of kinase cascade → Nuclear translocation

Different types of PRRs

• TLRs - recognize extracellular pathogens on cell surface/extracellular pathogens that have been endocytosed

  • Localized to cell surface and endosomes

• CLRs - recognize only extracellular pathogens (fungal glucans)

  • Localized to cell surface

• RLRs - recognize only intracellular pathogens (viral dsRNA)

  • Localized to mitochondria membrane

• STING & cGAS - recognize only intracellular pathogens (DNA)

  • Localized to endoplasmic reticulum

• ALRs - recognize only intracellular pathogens (DNA & RNA)

  • Localized to cytoplasm

• NLRs - recognize extracellular pathogens that have been endocytosed

  • Localized to cytoplasm

What is extravasation?

• WBCs leave blood vessels to fight infection at the site of injury

• Residents DCs and macrophages release cytokines that promote vasodilation

• Endothelial cells produce adherins that tether WBCs to blood vessel walls, slowing the cells to initiate rolling

• WBCs squeeze through gaps between endothelial cells and leave the blood vessel in a process called diapedesis

Process of phagocytosis

PRR binds PAMP or opsonin receptors detect opsonin-coated extracellular pathogen → internalization creates phagosome → phagosome fuses with lysosome → microbe is killed → contents are released or displayed on surface

Process of autophagy

Isolation membrane forms around intracellular pathogen to form an autophagosome → fusion with lysosome → breakdown of autolysosome contents

Apoptosis vs. Necrosis

• Apoptosis - noninflammatory, controlled cell death

  • Cell contents are neatly enclosed and disposed of through phagocytic digestion

• Necrosis - inflammatory, uncontrolled cell death

  • Abrupt loss of membrane integrity and discharge of cell contents into the environment

What is NETosis?

• A form of neutrophil cell death that also serves to trap and kill pathogens

• Neutrophils are activated by the binding of cytokines/other chemical signals → NADPH oxidase produces ROS and intracellular membranes break down → Chromatin decondenses, AMPs are released from granules → Plasma membrane ruptures and releases a web of DNA and AMPs into the extracellular space