Immune System - Cells and Organs

Epigenetic Changes

• Innate immune system cells can be trained by past infections, vaccines (e.g., Bacillus Calmette-Guérin - BCG), or microbial components (e.g., LPS) to enhance their response to triggers.

• This trained state results from epigenetic reprogramming of transcriptional pathways, not gene recombination.

• Monocytes and neutrophils have short lifespans, but hematopoietic stem cells (HSCs) in the bone marrow can conserve epigenetic memory of previous infections.

• HSCs are long-lived with self-renewal properties, ensuring lifelong production of innate immune cells.

Cells of the Innate Immune System

• A core group of cells plays a primary role in innate immunity.

• "Professional" phagocytes (neutrophils, monocytes, macrophages, and eosinophils) are critical effector components.

• Dendritic cells express pattern recognition receptors (PRRs) and originate as undifferentiated, innate cell types.

• As principal antigen-presenting cells, dendritic cells link innate and adaptive immunity.

Phagocytes

• Phagocytes (neutrophils and macrophages) ingest and destroy microbes and remove damaged tissues.

• Functions:

  • Recruitment to infection sites

  • Recognition and activation by microbes

  • Ingestion of microbes via phagocytosis

  • Destruction of ingested microbes

  • Communication with other cells through direct contact and cytokine secretion to promote or regulate immune responses

Distinguishing Properties of Neutrophils and Macrophages

• Neutrophils:

  • Origin: HSCs in bone marrow

  • Lifespan in tissues: 1-2 days

  • Responses to activating stimuli: Rapid, short-lived enzymatic activity

  • Phagocytosis: Rapid ingestion of microbes

  • Reactive oxygen species: Rapidly induced by assembly of phagocyte oxidase (respiratory burst)

  • Nitric oxide: Low levels or none

  • Degranulation: Major response, induced by cytoskeletal rearrangement

  • Cytokine production: Low levels per cell

  • NET formation: Rapidly induced, by extrusion of nuclear contents

  • Secretion of lysosomal enzymes: Prominent

• Macrophages:

  • Origin: HSCs in bone marrow (in inflammatory reactions); many tissue-resident macrophages from stem cells in yolk sac or fetal liver (early development)

  • Lifespan in tissues: Inflammatory macrophages - days or weeks; tissue-resident macrophages - years

  • Responses to activating stimuli: More prolonged, slower, often dependent on new gene transcription

  • Phagocytosis: Prolonged ability to ingest microbes, apoptotic cells, tissue debris, foreign material

  • Reactive oxygen species: Less prominent

  • Nitric oxide: Induced following transcriptional activation of iNOS

  • Degranulation: Not prominent

  • Cytokine production: Major functional activity, large amounts per cell, requires transcriptional activation of cytokine genes

  • NET formation: No

  • Secretion of lysosomal enzymes: Less

Neutrophils vs. Monocytes/Macrophages

• Neutrophils:

  • Circulating phagocytes

  • Short-lived

  • Rapid response, not prolonged defense

• Monocytes/Macrophages:

  • Monocytes circulate in blood, become macrophages in tissues

  • Provide prolonged defense

  • Produce cytokines that initiate and regulate inflammation

  • Phagocytose pathogens

  • Clear dead tissue and initiate tissue repair

  • Macrophages develop along two different pathways

Neutrophils Characteristics

• Most abundant circulating white blood cells, principal cell type in acute inflammatory reactions.

• Cytoplasm contains two types of membrane-bound granules:

  • Specific granules: Contain enzymes like lysozyme, collagenase, and elastase.

  • Azurophilic granules: Contain enzymes (e.g., myeloperoxidase) and microbicidal substances (defensins and cathelicidins).

• Production is stimulated by:

  • Granulocyte colony-stimulating factor (G-CSF)

  • Granulocyte-macrophage colony-stimulating factor (GM-CSF)

• Migrate rapidly to infection sites, function for 1-2 days in tissues, then die.

Neutrophil Chemotactic Factors

• Attracted by four major chemotactic factors at infection sites:

  • N-formyl bacterial oligopeptide

  • Complement-derived C5a

  • Leukotriene B4 (secreted by numerous immune cells)

  • Interleukin (IL) 8 (neutrophil chemokine secreted by activated innate immune cells and epithelial cells)

Leukocyte Adhesion Cascade

• Rolling: Mediated by Sialyl-Lewis X-modified glycoprotein interacting with P-selectin and E-selectin on endothelial cells.

• Integrin activation: Chemokines activate integrins on the leukocyte surface.

• Stable adhesion: Integrins (high-affinity state) bind to integrin ligands (ICAM-1) on endothelial cells.

• Migration through endothelium: Leukocytes migrate through the endothelium, guided by chemokines and interacting with PECAM-1 (CD31).

Functions of Neutrophils

• Phagocytosis of microbes, especially opsonized microbes, and products of necrotic cells.

• Secretion of granule contents.

• Extrusion of nuclear contents, forming neutrophil extracellular traps (NETs), which immobilize and kill extracellular microbes but may also damage healthy tissues.

Mononuclear Phagocytes

• The mononuclear phagocyte system includes:

  • Circulating bone marrow–derived cells called monocytes.

  • Macrophages that differentiate from monocytes upon migrating into tissues.

  • Tissue-resident macrophages, initially derived from yolk sac or hematopoietic precursors during fetal life.

Development of Macrophages and Monocytes

• After birth, monocyte-macrophage lineage cells arise from committed precursor cells in the bone marrow, driven by monocyte (or macrophage) colony-stimulating factor (M-CSF).

• Precursors mature into monocytes, circulate in the blood for 1-7 days.

• Most macrophages at inflammation sites are monocyte-derived.

• Long-lived tissue-resident macrophages are derived from yolk sac or fetal liver precursors during fetal development.

• These cells have self-renewal capacity, maintaining stable numbers.

Origin and Tissue Specificity of Macrophages

• Monocyte-derived macrophages in inflammation: Originate from bone marrow monocytes activated in infected or injured tissue.

• Tissue-resident macrophages in homeostasis: Originate from fetal hematopoietic organs like the yolk sac and fetal liver; differentiate into macrophages in various tissues.

• Examples:

  • Brain: Microglial cells

  • Lung: Alveolar macrophages

  • Liver: Kupffer cells

  • Skin: Dermal macrophages

  • Heart: Myocardial macrophages

  • Spleen: Sinusoidal macrophages

  • Intestines: Lamina propria macrophages

  • Bone: Osteoclasts

Factors Shaping Macrophage Tissue Specificity & Functions

Monocyte Characteristics

• Monocytes are 10 to 15 μm in diameter.

• They have bean-shaped nuclei and finely granular cytoplasm containing lysosomes, phagocytic vacuoles, and cytoskeletal filaments.

• All human monocytes express class II major histocompatibility complex (MHC) molecules.

Macrophage Polarization (M1 vs. M2)

Macrophage Functions

• Sacrificial death to alert the immune system.

  • Example: Salmonella infects a macrophage, macrophage attempts phagocytosis, Salmonella escapes the phagosome, inflammasome activated.

• Promote repair of damaged tissues by stimulating new blood vessel growth (angiogenesis) and synthesis of collagen-rich extracellular matrix (fibrosis).

• These functions are mediated by cytokines secreted by macrophages that act on various tissue cells.

Granulocytes

• Neutrophil

• Eosinophil

• Basophil

• Mast cell

Mast Cells

• Function: Release granules filled with chemicals, such as histamine, that cause inflammation.

  • Inflammation increases blood flow, allowing more immune cells and other helpful particles to reach a site of infection or injury more easily.

• Disease: The inflammatory chemicals released by mast cells can cause allergy symptoms when the immune system reacts inappropriately to otherwise harmless substances.

  • Persistent inflammation can occur in mastocytosis (too many mast cells).

• Location: Reside outside the bloodstream in tissues, especially in skin, lung tissue, lymph nodes, the liver, and the spleen.

  • Basophils, another immune cell type involved in allergies, are located in the blood.

Allergies and Mast Cells

1. Special B cells recognize allergens, activate, and produce IgE antibodies.

2. Mast cells bind IgE antibodies like a magnet.

3. The allergy "bomb" is now armed.

4. When IgE antibodies on the mast cell connect to the allergen again, the mast cell releases chemicals, especially histamine.

Basophil Characteristics

• Function: Loaded with granules released by inflammatory, infectious, and allergic triggers.

  • The granules contain various proteins and chemicals.

  • Histamine increases blood flow during an inflammatory response.

  • May play a role in controlling parasites and insect vectors of disease.

• Disease: In some people, an otherwise harmless substance (e.g., tree pollen or peanut) can make basophils release chemicals and proteins, causing allergy symptoms.

  • Severe allergies: Basophils contribute to inflammation that can cause airway tightening and low blood pressure (anaphylaxis).

• Location: Make up less than 1 percent of the immune cells in the blood.

  • Mast cells are located in the body's tissues.

Eosinophil Characteristics

• Function: Contain granules full of molecules that kill cells the immune system has marked for destruction.

  • Help clear parasitic infections and mediate inflammation.

• Disease: Several immune disorders involve too many or overactive eosinophils.

  • These include eosinophilic esophagitis, which causes difficulty swallowing, nausea, and vomiting.

  • Eosinophils are also believed to contribute to asthma.

• Location: Circulate in the blood and then migrate to tissues that interact with the outside environment, like the lungs and the lining of the gastrointestinal tract.

Antibody-Dependent Cellular Cytotoxicity (ADCC)

• A method of killing that depends on the ability of the immune cell to recognize specific antibody bound to a cell and trigger the death of that cell without the use of complement.

Dendritic Cells (DCs)

• Tissue-resident and circulating cells that detect microbes and initiate innate immune defense reactions.

• Capture microbial proteins for display to T cells to initiate adaptive immune responses.

• Subsets of DCs are defined by cell surface markers, transcription factors, development from different precursor cells, tissue localization, and functions.

Dendritic Cell Subsets

• Classical DCs (cDCs): Major type of DC involved in capturing protein antigens of microbes that enter through epithelial barriers and presenting them to T cells.

• Plasmacytoid DCs (pDCs): Produce the antiviral cytokine type I interferon (IFN) in response to viruses and may capture blood borne microbes and carry their antigens to the spleen for presentation to T cells.

• Monocyte-derived DCs (MoDCs): Cells with functions similar to those of cDCs but are derived from monocytes that were recruited into tissue inflammatory sites.

• Langerhans cells: DCs found in the epidermis that share functions with cDCs but are developmentally related to tissue-resident macrophages, arising from embryonic fetal liver and yolk sac precursors.

Follicular Dendritic Cells (FDCs)

• Have a dendritic morphology but are not derived from bone marrow precursors.

• Do not present protein antigens to T cells.

• Involved in B cell activation in the germinal centers of secondary lymphoid organs.

• Should not be confused with DCs.

Lymphocytes

• B lymphocyte.

• Helper T lymphocyte.

• Cytotoxic T lymphocyte (CTL).

• Regulatory T lymphocyte.

Life of Lymphocytes

• Naive lymphocytes typically live for 1 to 3 months.

• Their survival requires signals from antigen receptors and cytokines.

Lymphocyte Effector Functions

• B lymphocyte: Produces antibodies for neutralization of microbes, phagocytosis, and complement activation.

• Helper T lymphocyte: Activates macrophages and causes inflammation.

• Cytotoxic T lymphocyte (CTL): Induces killing of infected cells.

• Regulatory T lymphocyte: Suppresses other lymphocytes.

Antigen Recognition Molecules of Lymphocytes

• Each cell of the lymphoid lineage is clinically identified by the characteristic surface molecules that it possesses.

• Mature, naive B lymphocytes express two isotypes of antibody or immunoglobulin called IgM and IgD within their surface membrane.

• Mature, naive T cells express a single genetically related molecule, called the T-cell receptor (TCR), on their surface.

Antigen Receptors of Mature Lymphocytes

• Mature B Lymphocyte: Expresses IgM and IgD.

• Mature T Lymphocyte: Expresses Alpha and Beta Chain.

B-Lymphocyte Antigen Recognition Molecule (Membrane-Bound Immunoglobulin)

• The antigen receptor of the B lymphocyte, or membrane-bound immunoglobulin, is a 4-chain glycoprotein molecule that serves as the basic monomeric unit for each of the distinct antibody molecules destined to circulate freely in the serum.

• This monomer has 2 identical halves, each composed of a heavy chain and a light chain.

• Flexibility of movement is permitted between the halves by disulfide bonds forming a hinge region.

• Heavy Chain: VH, C{H1}, C{H2}, C{H3}.

• Light Chain: VL, CL.

Idiotype and Isotype

• The unique structure of the antigen binding site is called the idiotype of the molecule.

• Although two classes (isotypes) of membrane immunoglobulin (IgM and IgD) are coexpressed on the surface of a mature, naive B lymphocyte, only one idiotype or antigenic specificity is expressed per cell (although in multiple copies).

• Each individual is capable of producing hundreds of millions of unique idiotypes.

T-Lymphocyte Antigen Receptor

• Composed of 2 glycoprotein chains, a beta and alpha chain that are similar in length.

• The antigen-binding site is formed between the 2 chains, whose 3-dimensional shape will accommodate the binding of a small antigenic peptide complexed to an MHC molecule presented on the surface of an antigen presenting cell.

• There is no hinge region present in this molecule, and thus its conformation is quite rigid.

B-Cell vs. T-Cell Receptors

• The membrane receptors of B lymphocytes are designed to bind unprocessed antigens of almost any chemical composition, i.e., polysaccharides, proteins, lipids, whereas the TCR is designed to bind only peptides complexed to MHC.

• Also, although the B-cell receptor is ultimately modified to be secreted antibody, the TCR is never released from its membrane-bound location.

Lymphocyte Activation

• When a lymphocyte binds to an antigen complementary to its idiotype, a cascade of messages transferred through its signal transduction complex will culminate in intracytoplasmic phosphorylation events leading to activation of the cell.

B- versus T-Lymphocyte Antigen Receptors

Natural Killer (NK) Cells

• Innate immune cells with unique features.

• Lymphoid cells that do not express antigen-specific receptors derived from exposure to specific antigens, such as T cell receptors or surface immunoglobulin on B cells.

• Can alter their behavior based on prior exposure to particular antigens, including after viral infection, by a mechanism different from that of T and B cells.

• Play an important role in controlling infection by herpesviruses and flaviviruses (eg, Dengue and Zika), and influenza, hepatitis C, human immunodeficiency virus 1 (HIV-1), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses.

NK Cell Function and Receptors

• Express a broad array of activating and inhibitory receptors, including TLRs 2, 3, 4, 5, 7, and 8.

• Activating receptors are central to the "killer" function, responding to viral infections and malignant tumors by recognizing damaged or "stressed" host cells for elimination.

• Have granules with perforins and granzymes that, upon activation, are released into the interface between target and effector NK cells, disrupting target cell membranes and inducing apoptosis.

• Distinguish and avoid healthy host cells through receptors that recognize major histocompatibility complex (MHC) class I molecules expressed on all normal healthy cells.

• Inhibitory receptors on NK cells are counterbalanced by activating receptors that recognize "stress" ligands expressed on cell surfaces in response to intracellular DNA damage.

• Play a critically important role in maintaining the balance between protecting the placenta against infection without rejecting the half-foreign fetus.

NK Cell Activation and Inhibition

• Normal Cell: Class I MHC binds to inhibitory receptor on NK cell, preventing killing.

• Virus-Infected Cell: Reduced or absent Class I MHC, activation signal predominates, leading to killing.

NK Cells and Disease

• Serious herpesvirus infections are sustained by patients lacking functional NK cells.

• NK cells are reduced in number, metabolically stressed, and functionally deficient in children with obesity, which could relate to the increased rates of cancer in this population.

• The "immunosenescence" that occurs with aging is regularly associated with a decrease in the number and function of NK cells.

• Exercise has been experimentally shown to increase the number and cytolytic capacity of NK cells in this population.

Innate Lymphoid Cells (ILCs)

• A diverse group of lymphocytes found in many tissues, particularly the skin and the mucosal barriers of the lungs and gastrointestinal tract.

• Develop from the common lymphoid progenitor but do not express antigen receptors or expand into a clone when stimulated.

• React quickly to signals from infected or injured tissues by releasing an array of cytokines, including IFN-gamma, IL-5, and IL-17, which direct the immune response to the source of ILC stimulation.

• Some have cytolytic potential and can act directly to kill tumor cells.

• Limit T cell adaptive responses to intestinal commensal bacteria.

• Continuously produce IL-5, which regulates eosinophil homeostasis.

• Promote glycosylation of the intestinal epithelial cell surface, which is required to allow survival of the gut microflora but prevent their invasion.

• Genetic impairment of ILC3 function may be involved in the pathogenesis of Crohn disease.

Lymphoid Organs

• Primary lymphoid organs:

  • Sites of lymphocyte formation

  • Bone marrow, Thymus

  • Create B and T cells

• Secondary lymphoid organs:

  • B cells and T cells proliferate

  • Lymph nodes

  • Spleen

  • Peyer’s patches

  • Tonsils

Lymph

• Interstitial fluid from tissues

• Drains into the lymphatic system

• Eventually drains into subclavian veins

Lymph Node Structure

• Follicle: Site of B-cell activation.

• Cortex: Contains follicles.

• Paracortex: Contains T cells activated by dendritic cells.

• Medulla: Contains medullary sinuses and cords.

• Afferent Lymph Vessel: Lymph enters.

• Efferent Lymph Vessel: Lymph exits.

• Artery/Vein: Blood supply.

Lymph Node Function

• Lymph fluid drains from site of infection.

• Dendritic cells activated:

  • Express MHC I, MHC II, B7

• Enter lymph carrying processed antigens.

• Free antigens also carried with lymph.

• Lymph enters nodes.

• Many B and T cells waiting for matching antigen.

• Dendritic cells present to T cells.

• APCs in lymph nodes to process antigen.

• B cells react to antigen.

• Result: Generation of adaptive immune response.

Lymphoid Follicles

• Found in the cortex of lymph nodes.

• Site of B-cell activation.

• Contain follicular dendritic cells (FDCs).

  • Different from tissue dendritic cells

  • Permanent cells of lymph nodes

  • Surface receptors bind complement-antigen complexes

  • Allows easy crosslinking of B cell receptors

  • Special note: FDCs important reservoir for HIV

    • Early after infection large amounts HIV particles in FDCs

Types of Lymphoid Follicles

• Primary follicles:

  • Inactive follicles

  • Follicular dendritic cells and B cells

• Secondary follicles:

  • “Germinal center”

  • B cell growth and differentiation, class switching

  • Nearby helper T cells can bind → more growth

Paracortex of Lymph Nodes

• Two key features:

  • #1: Contain T cells activated by dendritic cells and antigen

  • #2: Contain high endothelial venules

    • Vessels that allow B/T cell entry into node

• Engorged in immune response (swollen nodes)

• Underdeveloped in rare T-cell deficiency disorders

  • E.G: DiGeorge syndrome

Medulla of Lymph Nodes

• Medullary sinuses (cavities):

  • Contain macrophages

  • Filters lymph → phagocytosis

• Medullary chords (tissue between cavities):

  • Contain plasma cells secreting antibodies

Spleen

• Filters blood (no lymph)

• All blood elements can enter

• No high endothelial venules

• No selective entry T and B cells

Spleen Structure

• White pulp: Exposure to B and T cells, exposure to macrophages

• Red pulp: Filters blood in sinusoids, removes old RBCs (red), stores many platelets

White Pulp

• Marginal zone:

  • Macrophages remove debris

  • Dendritic cells process antigen

• Follicles: B cells

• Periarteriolar lymphocyte sheath (PALS): T cells

Sinusoids of Spleen

• Red pulp lined by vascular “sinusoids”

• Open endothelium → cells pass in/out

• Exit into splenic cords

• Cords contain macrophages (filtration)

Splenic Dysfunction

• Increased risk from encapsulated organisms.

• Loss of marginal zone macrophages → ↓ phagocytosis

• Also loss of opsonization: ↓ IgM and IgG against capsules (splenic B cells)

• Loss of IgG opsonization

• ↓ complement against encapsulated bacteria

• ↓ C3b opsonization

Encapsulated Organisms and Sepsis

• Strep pneumo is predominant pathogen for sepsis

  • Death in >50% of patients.

• Others: H. flu (Hib), Neisseria meningitidis

• Less common: Strep pyogenes, E coli, Salmonella

• Also malaria and babesia (RBC infections)

Howell-Jolly Bodies

• Nuclear remnants.

Target Cells

• Too much membrane for the amount of hemoglobin inside.

• Too little hemoglobin for the size of the cell wall.