Immunology Flashcards
what is immunity?
immunity is the state of being insusceptible or resistant to a noxious agent or process, especially a pathogen of infectious disease
what types of organisms or bodies may pathogens be?
- Bacteria
- Fungi
- Parasites
- Foreign bodies
- Foreign tissues
- Unwanted cells e.g. necrosis, apoptosis, cancer
what is the body’s first line of defence? give examples:
physical and chemical barriers that are always ready and prepared to defend the body from infection:
- skin
- tears, mucus, saliva
- cilia
- stomach acid
- urine flow
- friendly bacteria
how is skin part of the body’s first line of defence?
- biggest organ in our body and can self-renew
- barrier function – waterproof
- its own micro-biome: competes with pathogens
- the lining of the gut is also an epithelium with barrier functions
how are tears, mucus and saliva part of the body’s first line of defence?
- ‘openings’ are potential entry points for pathogens and are protected by secretions
- many contain anti-microbial peptides (defensives) or enzymes such as lysozyme that digest bacterial cell walls
- pathogens transported out of the body or into the stomach and killed
how are cilia part of the body’s first line of defence?
- very fine hairs (cilia) lining our windpipe move mucus and trapped particles away from your lungs.
- Particles can be bacteria or material such as dust or smoke
- cystic fibrosis is caused by mutation of a chloride ion channel that results in thickened mucus that cilia can no longer move leading to lung infections
how is stomach acid part of the body’s first line of defence?
HCl secreted by parietal cells lowers the pH, activating proteases such as pepsin in the stomach and killing pathogens
how is urine flow part of the bod’s first line of defence?
- regularly flushes out pathogens from the bladder and urethra
how are friendly bacteria part of the body’s first line of defence?
- naturally occurring ‘friendly bacteria’ form a microbiome in our guts, skin, mouth, vagina etc acts as competition to reduce the ability of pathogens to colonise and grow
- BUT, use of antibiotics, anti-bacterial soaps etc can disrupt the microbiome and leave areas for colonisation by pathogens
what is the body’s second line of defence?
innate immunity
how can the body distinguish between the pathogen and all the self-cells?
by recognising molecules pathogens have that we do not:
- e.g. Lipopolysaccharides (LPS) which are components of the Gram-negative bacterial cell wall or peptides containing formylated-methionine, an amino acid only used by bacteria
these are called pathogen-associated molecular patterns (PAMPs)
how are damaged self-cells recognised by the innate immune system?
by identifying damage-associated molecular patterns (DAMPs)
what is the largest family of innate receptors that recognise PAMPs?
the largest family of receptors that detect PAMPs are members of the Toll family collectively known as Toll-like Receptors (TLRs)
what are Toll-like receptors (TLRs)?
- 10x TLRs in humans and are highly expressed by macrophages, dendritic cells and neutrophils to recognise PAMPs
- TLRs are a molecular signalling cascade that signal through downstream effectors such as the Jun/Fos transcription factors and NFkB and ultimately change gene expression
- Upregulate proinflammatory gene pathways
what leukocytes in our blood provide innate protection?
myeloid cells
what leukocytes in our blood provide adaptive protection?
lymphoid cells
what do haematopoietic stem cells (HSCs) in the bone marrow differentiate to?
- 100,000-200,000 haematopoietic stem cells at birth, 40-50 HSCs in 80 year olds
- Differentiate to either common myeloid progenitor or common lymphoid progenitor for white blood cells
what are myeloid cells?
Leukocytes of the innate system
- myeloid cells such as macrophages and dendritic cells (both derived from monocytes) and neutrophils express TLRs (as well as other receptors that detect pathogen profiles)
- cells that are activated because they recognise a pathogen-associated molecular patterns (PAMPs) secrete molecular ligands that attract additional cells of the innate immune system
what 2 things does activation of myeloid cells trigger?
- inflammation - dilation of local blood vessels, pain, redness, heat, swelling
- recruitment of specialist phagocytic cells
what is triggered during innate inflammation?
- dilated vessels become permeable and endothelial cells become sticky so ‘catching’ white blood cells and facilitating their access.
- further pro-inflammatory cytokines are released including prostaglandins, histamines and cytokine from mast cells
- fever inhibits pathogen proliferation and speeds chemical reactions used by antimicrobial peptides, complement cascade etc
how may innate inflammation responses become dangerous?
- responses appropriate locally can be dangerous systemically (e.g. in response to sepsis)
- This is a shock: loss of plasma volume, crash of blood pressure, clotting, cytokine storm
what types of phagocytic cells are recruited during the innate response?
- neutrophils
- macrophages
- eosinophils
what are neutrophils?
short-lived phagocytic abundant in blood but not tissues, respond and migrate to sites of infection (neutrophils make up most ‘puss’ within wounds, spots etc)
what are macrophages?
long-lived professional phagocytes abundant in areas likely to be exposed to pathogens (e. g. airways, guts)
what are eosinophils?
are specialists in attacking objects too large to engulf
what cells can link the innate and adaptive immune systems?
dendritic cells
what are dendritic cells?
specialist phagocytic cells derived from monocytes
- express a large variety of recognition receptors (TLRs etc)
- dendritic cells are central to activating the adaptive response
how do dendritic cells in the innate system activate the adaptive system?
- dendritic cells phagocytose pathogens, and cleave them into peptides which are bound to MHC proteins (Major Histocompatibility Complex)
- dendritic cells display the MHC-peptides on their surface for T cell recognition
- DCs migrate to lymphoid tissues (e.g. lymph nodes), activate and stimulate T-cells of the adaptive immune system
- T cells develop TCRs which are highly specific for that pathogen peptide/antigen
what is adaptive immunity?
- can generate highly specific responses to specific pathogens
- can identify, target and destroy vast range of pathogens / toxins
- but it’s important to direct AI against foreign targets and NOT host ‘self’ molecules/proteins
what happens if our self-cells are recognised as foreign?
accidental targeting of ‘self’ as ‘foreign’ can be lethal
how does the immune system avoid attacking harmless molecules that enter our body?
- harmless molecules enter our bodies and do not warrant a response
- innate immunity plays key role in recognising targets to attack
- inappropriately targeting harmless molecules can also cause trouble
what are lymphoid cells?
Lymphoid cells (aka Lymphocytes) generate adaptive immune responses
- Lymphocytes develop within the thymus and bone marrow (primary lymphoid organs)
- they then migrate to secondary lymphoid organs where they are exposed to foreign antigens (the skin and respiratory system are also secondary sites)
- Lymph ultimately drains into the bloodstream and cells circulate
what are the 3 main types of lymphoid cells?
- B cells
- T cells
- natural killer cells
where do B cells develop?
bone marrow
where do T cells develop and where are they matured ?
Bone marrow
Thymus
what are natural killer cells?
- participate in early defence against foreign cells and autologous cells undergoing various forms of stress, such as microbial infection or tumour transformation
- Lymphoid cells BUT considered part of the innate immune response
what are antibodies?
- antibodies (aka Immunoglobulins or Ig) are essential for adult survival and make up around 20% of the protein in blood plasma
- secreted soluble immunoglobulins of various types that bind to antigens
- produced by B-lymphocytes and ultimately secreted by plasma cells
- initially antibody receptors, and when plasma cells are differentiated they become soluble antibody
what is cell-mediated immunity?
- adaptive immunity carried out by T cells which trigger cellular level responses
what are the 3 subtypes of T cells?
- cytotoxic T cells
- helper T cells
- regulatory T cells
what are cytotoxic T cells?
- directly kill infected host cells by inducing apoptosis
what are helper T cells?
they activate macrophages, dendritic cells, B cells and cytotoxic T cells by secreting cytokines and displaying co-stimulatory proteins on their surface
what are regulatory T cells?
use cytokines to inhibit the function of helper T cells, cytotoxic T cells and dendritic cells
- tunes the immune system so that it is not excessively active
how is adaptive immunity activated?
- the body randomly generates a ‘library’ of lymphocytes most of which remain dormant
- when an antigen is presented (e.g. by dendritic cells or T-helper cells) those that have some binding affinity to the antigen of interest become ‘activated’
- binding of antigen to activated cells leads to their proliferation and clonal expansion
- expansion triggers differentiation into effector cells
- an expansion round occurs every time an antigen is encountered
- subsequent encounters stimulate the memory cells made previously so building a bigger pool of cells able to bind
- the body can now respond to multiple antigens at once, specifically
what is immune tolerance?
- adaptive immune system needs to identify and respond to an almost infinite range of unknown antigens but simultaneously ignore a huge range of very similar ‘self’ antigens
- adaptive immune system can ‘learn’ not to respond to self-antigens.
- Cells/organs transplanted between adults will be rapidly destroyed by the hosts T-cell response
- cells transplanted into a newborn host will survive and be ‘accepted’ as self as the immune system is still naive.
- Future transplants from the same source will be treated as self and survive
how can immune tolerance be studied experimentally?
- knock out a gene encoding a ‘self’ protein
- allow animal to grow, then reintroduce KOed self-protein
- host now mounts immune response as it hasn’t ‘learnt’ this is self
- this shows host CAN mount attack against self-antigens - remove ‘self’ protein from adult animal
- reintroduce after several weeks / months
- host now mounts immune response to removed protein
- the system can ‘forget’ what it has previously learnt
what are the 5 classes of antibody?
- IgG
- IgM
- IgA
- IgD
- IgE
each have different heavy chains, dinge and tail structures, so have unique characteristics and functions
what is the most common antibody in the body?
IgG
what is the structure of IgG?
- made up of two copies of two proteins (4 in total) linked by covalent di-sulphide bonds
- 2x Heavy chains (around 440aa) and 2x Light chains (around 220aa)
- Antigen-binding site at N-terminus of heavy and light chains
- each chain consists of variable and constant domains
- both light & heavy chains are made up of repeating 110aa domains as Immunoglobulin domains, each containing an internal di-sulphide bond. Likely to be the result of gene duplications during evolution
- antigen-binding region consists of two variable domains made up of a single modified Ig domain and containing three hyper variable regions
what is the role of the constant domain of IgG?
constant domains interact with other parts of the immune system (e.g. Innate immune & complement systems)
what is the role of the variable domain of IgG?
- variable domains make up the antigen-binding sites
- antigen-binding region consists of two variable domains made up of a single modified Ig domain and containing three hypervariable regions
how do the structures of hypervariable domains of antibodies vary and why?
3D structure of the hyper variable domains vary following in vivo evolution:
- selects the best structure to best interact with the antigen
- variable domain has barrel structure formed by beta-sheets, that makes it specific to antigen
- by mutating amino acids in the loops produces 3D pockets/grooves which antigens can bind to
- somatic hypermutation
how is the constant domain of an antibody encoded for?
- the Ig domains that make up the constant part of the heavy chain are each encoded by a single exon
what is the primary antibody repertoire?
a naive, unchallenged human immune system can generate around 1x10^12 different antibody molecules
how many antibodies are generated in the primary antibody repertoire?
1x10^12
how many antibodies can a mature immune system generate?
a mature immune system can make antibodies able to bind to essentially any antigen (essentially infinite flexibility)
how is the variable domain of an antibody encoded for?
- in the germline a k-light chain gene variable domain contains 40x V domains, 5x J domains and a single C domain
- and a heavy chain gene variable domain contains 40x V domains, 25x D domains, 6x J domains and 5x C domains
- In developing B-cells these are recombined in a process known as VJ or V(D)J recombination
what domains does the variable k-light chain gene contain?
k-light chain gene variable domain contains 40x V domains, 5x J domains and a single C domain
what domains does the variable heavy chain gene contain?
heavy chain gene variable domain contains 40x V domains, 25x D domains, 6x J domains and 5x C domains
what process generates the primary antibody repertoire?
V(D)J recombination
how is the primary antibody repertoire generated in development?
developing B cells join together separate gene segments in DNA in order to create the genes that encode the primary repertoire of low-affinity antibodies:
- during the development of a B cell a coding sequence joining a V to a J segment is assembled by removing the intervening DNA (in this case joining V3 to J3)
- transcription starts immediately upstream of the fused V segment (in this case V3) which lies immediately upstream of a J region (J3 in this case).
- Extra downstream J segments (J4 & J5) are transcribed but edited out of the mRNA transcript via splicing
- An mRNA is translated containing V3, J3 and C
what is the process of V(D)J recombination?
The process of V(D)J recombination joins separate antibody gene segments together to form a functional VL- or VH-region coding sequence
- DNA splicing is driven by the V(D)J recombinase enzyme (encoded by RAG1 & RAG2 genes)
- Has recombinase and ligase (joining) activity
what does V(D)J recombination generate?
fully formed primary antibody repertoire
what is junctional diversification?
during joining of gene segments a variable number of nucleotides are often lost or inserted from the ends of the recombining gene segments.
- This is called junctional diversification.
- in many cases, this will shift the reading frame to produce a non-functional gene.
- These developing B cells never make a functional antibody molecule and die in the bone marrow.
- 2/3s of B cells cannot make a functional antibody
- B cell survival depends on its ability to make antibody, so if it can’t it is apoptosed
what is allelic exclusion?
- Developing B & T-cells are diploid (one maternal & one paternal copy) but chose just one allele to recombine (this is known as allelic exclusion)
- Further increases antibody diversity
what does a mutation in recombinase enzyme genes RAG1 and RAG2 result in?
RAG1 or RAG2 mutants have a severe combined immunodeficiency phenotype (SCID).
how is the primary antibody repertoire encoded for, when the entire genome only encodes 25,000 genes?
- The process of V(D)J recombination
- the gain or loss of nucleotides during recombination – junctional diversification
- choice of one allele – allelic exclusion
these processes enable the random combination of domains of genes to generate a diverse array of antibodies in development
how is the primary antibody repertoire of 1x10^12 increased to infinite antibodies?
by antigen-driven somatic hypermutation
what is affinity maturation?
over time after initial immunisation there is a progressive increase in affinity of the antibodies to the antigen
what happens to B cells genes during affinity maturation and antigen stimulation?
- Accumulation of point mutations in both heavy and light chain V-region coding sequences of the B cells that are being amplified
- This happens AFTER recombination has assembled the gene segments
- After B cells have been stimulated by antigen and helper T cells in a peripheral lymphoid organ, some of the activated B cells proliferate rapidly in the lymphoid follicles and form structures called germinal centres.
what is somatic hypermutation?
B cells mutate at the rate of about one mutation per V-region coding sequence per cell generation
- Every time the cell divides, each V-region mutates
- Approximately 1 million times faster than ‘background’ mutation rate
- this is termed somatic hypermutation
what enzyme drives somatic hypermutation?
activation-induced deaminase (AID), which is expressed in the germinal centres of B cells
what stimulates B cell clonal expansion
Developing B cells present their antibodies on their surface and binding of antigen stimulates their proliferation
how is B cell survival determined in somatic hypermutation?
- most somatic mutations will have no effect or will make the antibody worse. This will stop antigen binding, remove stimulus, and these B cells will apoptose
- B cells containing mutations that increase affinity of the antibody to the antigen will increase the stimulus.
- These clones will survive and proliferate (especially as antigen levels get very low)
- in vivo evolution that selects cells with beneficial mutations
why are V(D)J recombination and somatic hypermutation dangerous?
Normally cells experiencing double-stranded breaks (e.g. during V(D)J recombination) and high levels of DNA damage [eg somatic hypermutation] will apoptose via the p53 pathway that acts as a ‘watch keeper’ to kill cells with potentially oncogenic mutations
- may generate oncogenic mutations
how is the p53 pathway inhibited in V(D)J recombination and somatic hypermutation?
- BCL-6 is a transcriptional repressor expressed in germinal centres of B cells
- BCL-6 binds to sites in the p53 promoter switching off expression
- leaves GC without ‘watch keeper’ oversight.
- high risk (may cause oncogenic mutation)/ high reward (specific antibody with high affinity produced)
B cells and antbody summary:
- VJ and V(D)J recombination shuffles the light & heavy chain genes in the region encoding the variable domains
- nucleotide lost /gain in recombining gene segments creates junctional diversification
- initial ‘primary repertoire’ library of 1x1012 B-cells
- affinity maturation via ‘in vivo evolution’ based on binding of antigens
- this selects amongst variations induced by somatic hypermutation
how are T cells activated?
T cells are activated by partly degraded antigens displayed on the surface of antigen-presenting cells
- MHC proteins on antigen-presenting cells bind to the peptide fragments and carry them to the cell surface where T cells can recognise them via their TCRs
how can antigen-presenting dendritic cells activate T cells?
activating DCs present three proteins: MHC with a foreign antigen, stimulating ligands and cell-cell adhesion molecules
how can antigen-presenting dendritic cells tolerise T cells?
tolerising DCs present self-antigens on their MHCs but do NOT include the co-stimulatory activator protein
- T cells will be exposed to the antigen but will not trigger adaptive immunity processes
how do T cells recognise APCs?
T cells bind to MHCs on APCs via their T-cell Receptors (TCRs)
what is the structure of TCRs?
TCRs are immunoglobulins and contain variable domains and hypervariable loops much like antibodies
how are TCRs diverse?
TCR diversity generated by V(D)J-like recombination & junctional diversification in the thymus to give diversity of 1x108 (this decreases with age by 2-5 fold)
give 3 examples of pathogens which can evade/harness the immune system:
- Candida albicans
- Staphylococcus aureus
- HIV
how does Candida albicans evade the immune system?
Candida albicans: a yeast that usually lives on skin, mouth gut, vagina without issues, but can become pathogenic.
- Grows as several forms including ‘normal’ yeast cells and pseudohyphal filamentous forms
- Phagocytosis by macrophages can induce switch to hyphae form
- in hyphae form they can break out of the phagocyte
how does Staphylococcus aureus evade the immune system?
Staphylococcus aureus: a Gram-positive spherically bacterium, frequently found in the upper respiratory tract and on the skin.
- produces Protein A (A for aureus) - a 42 kDa cell [wall] surface protein that binds to the constant domain of IgGs.
- Bacteria are covered with ‘self’ proteins and no longer recognised by innate immune system
how does HIV evade the immune system?
Human Immunodeficiency Virus (HIV) : an RNA lentivirus that specifically infects T-helper cells, dendritic cells and macrophages expressing the CD4 receptor.
- infected immune cells no longer function AND trigger immune responses that trigger T-cells to target cells absolutely required for adaptive immune system function
- resulting immune deficiency leads to infections (e.g. Candida and Aspergillus) and cancers rarely seen in those with intact immune systems
what is Kaposi’s sarcoma?
Kaposi’s sarcoma is caused by herpesvirus 8 (HHV-8), a relatively common virus, that only causes cancer in people with a weakened immune system e.g. HIV infection
what are examples of autoimmune diseases?
- type 1 diabetes
- multiple sclerosis (MS)
- autoimmune inflammatory diseases such as rheumatoid arthritis
how is type 1 diabetes an autoimmune disease?
In Type 1 diabetes the immune system develops killer T-cells that attack insulin producing beta-cells within the Islets of Langerhans within the pancreas
how is MS an autoimmune disease?
In Multiple Sclerosis the immune system responds to proteins within the myelin sheath of neurons within the CNS.
- Associated with a range of symptoms, progressive loss of myelination can ultimately be fatal
what are examples of autoimmune inflammatory diseases and how are they triggered?
- Autoimmune inflammatory diseases: rheumatoid arthritis, psoriasis, Crohn’s disease, inflammatory bowel disease (IBD), ulcerative colitis
- defects in the ‘self-tolerance’ process leading to the production of antibodies that trigger inflammatory responses by the innate immune system
how are immunity and cancer linked?
immune competence decreases with age - “immunosenescence” - implying that decreased immunosurveillance against cancer contributes to increased disease in the elderly (age is the biggest risk factor for cancer)
can the immune system recognise and attack tumours?
In mouse transplantation models, tumours are rejected in syngeneic (immunologically compatible) hosts, while transplantation of normal tissues are accepted.
- So confirming the existence of tumour-specific antigens which can be recognised as non-self
- Overall, there seems to be compelling evidence that our immune systems identify and kill cancerous [and pre-cancerous] cells
how can the immune system detect cancers?
tumour-infiltrating lymphocytes (TILs)
what are the 3 phases of cancer immunoediting?
- the elimination phase, tumour cells are killed by NK, CD4+ and CD8+ cells
- a state of equilibrium between immune and tumour cells
- When the immune system is unable to destroy the tumour, tumour cells ‘escape’ leads to clinically detectable tumours
can the adaptive immune system be used to attack cancers?
Yes:
- stimulating, or boosting, the immune system so it is more effective at identifying and attacking cancer cells
- approaches to help restore or improve how the immune system works to find and attack cancer cells
how is the immune system limited in fighting cancer by itself?
- the immune system doesn’t see the cancer cells as foreign because the cells aren’t different enough from normal cells.
- the immune system recognizes the cancer cells, but the response might not be strong enough to destroy the cancer.
- cancer cells themselves can also give off substances that keep the immune system from finding and attacking them.
what cancer immunotherapies may be useful in treating cancer?
- checkpoint inhibitors: takes the ‘brakes’ off the immune system
- cytokines: to stimulate the immune cells to attack cancer
- immunomodulators: boosts parts of the immune system
- cancer vaccines: vaccines that direct an immune response designed to prevent a specific cancer epitope or cancer causing pathogen (e.g. HPV)
- monoclonal antibodies (mAbs): directed against cancer specific antigens
- oncolytic viruses: viruses that have been modified in a lab to infect and kill certain tumour cells
- chimeric antigen receptor (CAR) T-cell therapy
what is chimeric antigen receptor (CAR) T-cell therapy?
this approach takes the patients T cells and infects them (ex vivo) with a recombinant virus that causes the expression of a TCR with an antibody-derived variable (antigen binding) domain specific to a tumour antigen. This generates T-cells able to attach to tumour cells. These are transfused back into the patient so they can find, attach to and kill the cancer
what is graft versus host disease (GVHD)?
a relatively common side effect of heterologous haematopoietic stem cell / bone marrow transplantation where transplanted T cells will attack and kill the new host
