Immunology Study Guide c12-17

Mechanisms of mAb against cancer

1. Mediating antibody-dependent cellular cytotoxicity (ADCC) effector cell responses 2. Releasing inhibition of T cells 3. Targeted delivery of drugs to cancer cells 4. Targeted concentration of radiation

Understand that A, B, O are slight variations of a short (4-5 ring) polysaccharide chain anchored by a lipid (thus a glycolipid) to the cell membrane of an RBC. Whether an individual has an allelic variation of a sugar transferase protein that adds a Gal-NAc (N-Acetylgalactosamine), a galactose, or fails to add another sugar ring at all to the glycolipid determines if the blood type is A, B, or O respectively. (You don't have to memorize these specifics, but it's interesting!)

ABO blood groups are variations of RBC antigens • RBC have many surface antigens that interact with immune system • most important for transfusions are ABO and Rh typing • A, B, O are variations on a specific surface glycolipid • a polymorphic sugar transferase enzyme adds sugar groups: ∵ version that adds Gal-NAc to end yields Type A ∵ version that adds Gal to end yields Type B ∵ heterozygous people have both Type AB ∵ recessive for inactive enzyme "leaves" Type O

Why DON'T we normally have IgG already in our bodies against other HLA types? (Hint: in order for memory IgG to be present, what must have happened in the past?) Why is an acute Type IV tissue rejection much stronger than typical anti-pathogen response? (Think about how many potential T cell clones could be involved)

Acute Type IV rejection via direct T cell activation • patient unlikely to have antibodies recognizing donor's tissue right away - NOT a Type I (IgE) or Type II (IgG) allergy situation • donor's dendritic cells will migrate into secondary lymphoid tissues • patient's CD8 T cells will see wrong HLA and activate • because MHC itself is "wrong", in days following surgery numerous T cell clones in recipient become effectors and attack donated tissue • resulting reaction is much stronger than typical pathogen response

Summarizing acute tissue rejection model

Acute tissue rejection by host T cell activation • host's T cells never tolerance-tested against donor HLA (MHC) • many host T cells will improperly allo-activate against MHC I and II • activated CD4 T cells will cause inflammation • activated CD8 T cells will directly attack donor tissues • within days graft is rejected

Recognize that every day the cells of our immune system process and assess vastly more examples of normal "self" antigens from healthy cells than abnormal "non-self" antigens from disease or pathogens. Consider the importance of tolerance training for both B cells and T cells in order for this to be an OK situation. Review Fig 16.5 describing several mechanisms that support self-tolerance (we learned these in the lectures about B cell and T cell development)

Adaptive immunity depends on "self" tolerance Every day our body's tissues present the immune system with far more healthy "self" antigens than pathogenic antigens.

Immunosuppressive medication: IgG-based

Alemtuzumab (Anti-CD52) • IgG-based drug • binds CD52 on leukocytes • causes C3 opsonization • reduction in WBC count

Why do the majority of foods and environmental antigens fail to trigger immune responses? (Hint: think about the nature of our skin and how mucosal layers selectively allow antigens to pass through. Also think about the role of inflammation in amplifying immune responses)

Allergic reactions are termed hypersensitivity • most foods & environmental antigens don't trigger immune response • tissues avoid inflammation against benign molecules • sometimes harmless molecules do trigger a response • sensation of illness when no infection really exists • tissue reaction can be mild and annoying, or deathly serious

Understand the term hypersensitivity and how it describes allergies Understand that both innate and adaptive immune factors may be involved in hypersensitivity, but in general allergies are considered "mistakes" of our adaptive immune system

Allergies are due to adaptive immune responses • hypersensitivity is your adaptive system making a "mistake" • harmless antigens are treated as though they are pathogens • such environmental antigens are termed allergens • atopic individuals have a predisposition to allergies • affects approximately 40% of people in developed countries • children in these countries have more allergies than parents • what is the cause of this epidemic of allergy?

Explain the concept that developing a Type 1 allergy requires involvement of adaptive memory

Allergies develop from adaptive memory • most Type I allergens are proteins (such as in pollen grain) • often desiccated (dry) and airborne, easily enter respiratory tract • first exposure has no reaction, subsequent exposures triggers response

What is meant by a haploidentical transplant in reference to HLA type? Why might alloreactive NK cells from intentionally mismatching HLA (keep in mind, not too far mismatched) be useful in attacking remaining leukemia cells?

Alloreactive NK cells from intentional HLA mismatch • selecting a haploidentical donor can help patient clear remaining cancer left after radiation treatment • NK cells replenish before T cells → killing residual cancer cells • termed Graft-Versus-Leukemia (GVL) effect

Understand that tissue graft (transplant) rejection mirrors Type II, III and IV allergic reactions. (Tip: review examples of these from our lectures on allergies) Why are hyperacute reactions so quick compared to acute or chronic reactions? Which are due to ABO mismatch, and which are due to HLA mismatch?

Anti-solid tissue graft reactions mirror allergies • called allorecognition: allo = other, as in other "normal" antigen • follow Type II, Type III, and Type IV hypersensitivity models • Type I not common, because IgE memory against graft is unlikely

What are bacterial superantigens and how do they disable the immune system?

Bacterial proteins disable the immune system • some bacteria secrete highly toxic proteins effective in any amounts • these superantigens intentionally stimulate T cell activation • cause non-specific TCR-to-MHC binding of CD4+ T cells Superantigens overload the immune system • non-specific T cell response (up to 20% of contacted CD4 T cells!) • flood of cytokines (IL-12, IFN-γ, TNF-α) cause severe inflammation • food poisoning often due to superantigens • normal immune signals crippled so bacteria can multiply

How do bacterial proteins such as SSLP7 interfere with IgA function?

Bacterial proteins interfere with IgA function • Staphylococcal superantigen-like protein 7 (SSLP7) binds IgA and C5 • prevents phagocytosis and blocks C5-mediated MAC formation

Be comfortable with nomenclature of distinguishing different γ:δ T cell types based on what V blocks make them (the idea that the sequences of different V blocks may lend themselves to make TCR that preferentially bind different antigen families).

Be familiar with the 3 examples of γ:δ T cell types discussed in class in terms of their V:V name, their targets, and what situations the T cell is involved in. • Vγ9:Vδ2 T cells bind cell surface phosphoantigens predominant in blood. • Vγ4:Vδ5 T cells sense viral infections and tumors. • Vγ:Vδ1 T cells sense glycolipid antigens in mucosa.

Immunosuppressive medication: synthetic peptide

Belatacept • chimeric peptide • blocks B7 from binding CD28 • inhibits T cell activation

Why are ABO differences between a pregnant mother and developing baby not as big of a concern compared to Rh D +/- differences?

Blood incompatibilities during pregnancy • blood Type O mothers can certainly carry Type A,B babies (baby's father is Type A,B) • normally maternal and fetal blood do not mix, and amount of IgG being transferred through placenta is low (any IgM made cannot cross placenta) • Rh D +/- is more serious, mother's exposure to baby's blood during delivery can generate strong adaptive memory (raise mother's IgG titer against Rh D) • complications may then arise in second pregnancy • prophylactically treatable with anti-Rh D IgG during pregnancy to suppress mother's IgG production

Why is blood transfusion incompatibility considered a Type II hypersensitivity?

Blood incompatibility is Type II hypersensitivity • sugars on A,B type glycolipids and/or presence of Rh D protein on mismatched blood leads to IgG attack on donated RBCs • IgG-mediated agglutination and RBC destruction leads to: fever, chills, shock, renal failure, death

What would such antibodies used as drugs not "cure" a patient who has HIV, but may be useful in "preventing" infection in high-risk individuals?

CCR5 mutations provide immunity to HIV / AIDS • approx 1% of Caucasians are homozygous for CCR5-Δ32 mutation • their CCR5 proteins are truncated & non-functional • CCR5-Δ32 individuals are mildly immunocompromised against some diseases • but they have resistance to HIV infection! • in 2008 Timothy Brown, an HIV-infected patient suffering from AIDS-related leukemia, received a stem cell transplant from a CCR5-Δ32 donor in Berlin • Brown was cured of leukemia AND had HIV eliminated • in 2018 a second patient in London received same treatment and also was cured. • to date these two patients are the only people ever "cured" of HIV

Understand that some viruses such as HPV can have long-term persistent infections whereby host cells that have integrated viral DNA into the human genome in random ways that don't lead to viral production. In these cells, the disrupted human genome may express genes aberrantly, potentially including oncogenes that lead to transformation and eventually cancer.

Can you vaccinate against cancer? • human papillomavirus (HPV) linked to cancers • most common cause of sexually transmitted disease • around 50% of sexually active individuals are infected • majority of infections clear in 1-2 years • in longer cases, viral DNA integrates permanently into cells and may initiate transformation • leading to cervical and other genital cancers (both sexes)

If the cell itself is the body's first line of defense then our immune system is our second line of defense Consider: every day our immune system is dealing with protecting us against our own defective cells as well as outside pathogens!

Cancer and our immune system • a single cell that cannot stop itself from dividing should be detected and destroyed before it forms a tumor • the immune system is our second line of defense • consider: our immune system protects us from external pathogenic threats AND internal threats from our own defective cells! • such immune responses are just like attacking foreign antigens

Understand how the lab mouse experiment Fig 17.7 demonstrates the importance of our immune system in protecting against cancer

Cancer cells evade immunity • for cancer to develop, it must escape detection/attack by immune system • if tumor cells from lab mouse are injected into healthy genetically identical mouse, tumor cells grow • if tumor cells are injected into mouse of different MHC type, no tumor grows this is why cancers are not contagious... the recipient's body WILL see the foreign cells as a pathogen!

How does Type III reaction lead to chronic graft rejection?

Chronic Type III rejection via indirect T cell activation • donor's HLA peptides presented by patient's own APCs may not trigger massive CD8 T cell response • however, low-level CD4 T cell activation over time encourages B cell selection for Ig made against donor HLA • after many years, constant inflammation damages donated organ

Summarizing chronic tissue rejection model

Chronic tissue rejection by host B cell activation • donor HLA peptides are processed and presented by host's own APCs • because HLA is normal human peptide, CD4 T cell activation is modest • gradually, naïve B cells with "close enough" IgM activated • build-up of resulting IgG damages transplanted tissue • after several years graft is rejected

Why does it make sense that many common allergens resemble parasite antigens - especially protease enzymes?

Common allergens resemble parasitic antigens • many antigenic proteins from parasites are proteases • common allergens are often structurally similar • allergies may result by antibodies cross-detecting harmless antigen

Immunosuppressive anti-T cell drugs from microbes

Cyclosporin: isolated from fungus T. inflatum; blocks TCR signals from reaching nucleus Tacrolimus (FK506): isolated from soil bacteria S. tsukabaensis; blocks TCR signals from reaching nucleus Rapamycin: isolated from soil bacteria S. hygroscopicus; prevents IL-2 receptor from activating T cell

Recognize there are several complement pathway proteins that have mutations identified in disease. Review how the seven groups of complement proteins work so you could discuss how innate immune functions get compromised.

Defects in complement pathway genes. all the effector functions that antibodies recruit to clear pathogens and their antigens are facilitated by complement activation. • C3: an opsonin that promotes the efficient elimination of bacteria by phagocytes. • C5-C9: the terminal complement components of the membrane attack complex (MAC). • immune complexes are mainly transported by erythrocytes, which capture the complexes with their CR1 complement receptor that binds to C4b and C3b; deficiencies in C1-C4 impair the formation of C4b and C3b. • deficient in factor I leads to unchecked conversion of C3 to C3b and supplies of C3 are quickly depleted. • properdin (factor P): plasma protein that enhances the activity of the alternative pathway by stabilizing the C3 convertase; reduced C3 deposition impedes formation of the MAC. • deficiency in decay accelerating factor (DAF) or CD9, mean cells activate the alternative pathway of complement willy-nilly. • deficiency of complement regulator C1 inhibitor (C1INH) have overactive classical pathway, causing abnormally low levels of C2 and C4 and high production of C2a fragment.

Understand that since we inherit regions of chromosomes as blocks of genes from our parents (crossing-over during meiosis), we get our HLA genes in blocks. Therefore certain risk-associated HLA are recognized as "haplotypes".

Diversity of HLA polymorphic allotypes • there are thousands of HLA polymorphisms • diversity reflects our species' immune evolution • specific polymorphisms are given labels such as HLA-A*02:04 • top 6 most common allotypes for select HLA shown (attached) • example: Top 3 most common HLA-A families are A2, A24, A68

Understand that this A,B,O glycolipid is structurally similar to lipopolysaccharide (LPS) structures on surface of bacteria, and therefore a person will invariably have immune memory IgG already present that recognize other ABO types than their own. (What processes prevent a person from having IgG against their own blood type released in their circulation?)

Donor/recipient compatibility of ABO groups • immune system is very responsive to ABO antigens • likely because they resemble lipopolysaccharides of common pathogens • thus we develop tolerance (no antibodies) against own ABO type but invariably have IgM against other types • actual function of A,B,O variations still unknown *green = combinations of donor and recipient groups that allow blood transfusion *red = combinations of donor and recipient groups that result in immune reactions and should avoid blood transfusion. self-tolerance: T-cells and B-cells (which release IgG) receive "training" or education to learn not to attack our own cells

Understand how in Fig 16.27 the different polymorphic variations of specifically HLA-DR B1*04 influence peptide binding. How does this explain both elevated risk with some alleles and protection conferred by other alleles? (Hint: Imagine HLA-DR is the guy with the blue raincoat in the chicken cartoon - how might the amino acid substitutions in Fig 16.27 affect his ability to carry the chicken foot? What is the chicken foot in this case? What happens if he cannot present the chicken foot on the plate very well?)

Genetics of rheumatoid arthritis • HLA-DRB1*04 alleles preferentially present citrullinated peptides • in table, BLUE amino acid increase risk, while RED are actually protective (decrease risk)

Important concept: why might a specific HLA-D isotype, in this case HLA-DR, give a person a higher risk of developing rheumatoid arthritis? (Hint: what kind of specifically modified peptide is associated with this disease, and how might HLA-DR be relevant to the mechanism by which this peptide causes disease? Think about the chicken cartoon again, and what class of MHC this HLA-DR belongs to!)

Genetics of rheumatoid arthritis • peptidyl arginine deaminase (PAD): a normal enzyme that removes arginines from peptides, making them citrullinated • PAD usually expressed in response to tissue damage • smoking increases PAD in lung tissue, resulting in immune system seeing many citrullinated peptides that activate naïve T cells • aging joints activate PAD, leading to T cells attacking joint tissue • MHC class II polymorphisms involving HLA-DR4 allotype favor binding and presentation of citrullinated peptides to T cells

IgG may autoactivate receptors leading to disease

Graves' disease: hyperthyroidism caused by antibodies activating thyroid stimulating hormone (TSH) receptor • uncontrolled release of thyroid hormones regulating metabolism • symptoms: enlarged thyroid, sweating, nervousness, irregular heart rate Myasthenia gravis: IgG binds to neurotransmitter receptors at neuronmuscle synapse • prevents nerve signals from reaching muscle cells • leads to loss of muscle responsiveness

Discuss how the introduction of HAART treatment regimens has impacted life with HIV

HIV escapes the immune response and develops resistance to antiviral drugs by rapid mutation • HIV rapidly mutates and escapes from individual anti-viral drugs • before 1997, vast majority of HIV patients would progress to AIDS • highly active anti-retroviral therapy (HAART) in 1997 is a combination of drugs that attacks several HIV variations at once • HIV patients on HAART can live with infection for 50+ years • but virus is never eliminated, and patients live with many health conditions and lifestyle restrictions

Why can there be a period of many years between infection with HIV and development of full-blown AIDS?

HIV progression to AIDS is slow • first infects macrophages and dendritic cells • increasing CD4 T cell infection as immune response occurs • this is why T cell depletion occurs over many years • AIDS progresses once T cells too few to fight normal infections

Understand the importance of CD4 and CCR5 as receptors that bind HIV

HIV replication cycle: HIV virions bind to the CD4 receptor and CCR5 co-receptor on host cells. • the gp120 envelope protein of the virus binds to CD4 T cell, enabling gp120 to also bind the chemokine co-receptor. • this binding releases gp41, causing fusion of the viral envelope with the plasma membrane and release of the viral core into the cytoplasm. • RNA genome is released and reverse transcribed into double-stranded DNA. • this DNA migrates to the nucleus in association with the viral integrase and becomes integrated into the cell genome as a provirus. • activation of the CD4 T cell causes low level transcription of the provirus that directs the synthesis of the early proteins Tat and Rev. • these expand and change the pattern of provirus transcription to produce mRNA encoding the protein constituents of virion and RNA molecules corresponding to the HIV genome. • envelope proteins travel to the plasma membrane, other viral proteins and viral genomic RNA assemble into nucleocapsids. • new virus particles bud from the cell, acquiring the T cell's membrane as their envelope.

Why is HLA matching so important for stem cell transplant? (Hint: understand what the cartoon Fig 15.33 is showing - why does the new immune system fail to fight infection?)

HLA matching is important for stem cell transplant • donor thymocytes developing in host's thymus will be trained to work with host's MHC (HLA) as they mature to T cells • but APCs in lymph nodes also came from donor and present antigen using donor's "self" MHC (not the hosts!) • if donor/recipient HLA are too different, rebooted system won't generate adaptive immune responses! *none of the recipient's HLA (red) are same as donor's HLA (blue) → recipient could not reconstitute working T cell system and suffers severe immunodeficiency.

Understand that certain HLA polymorphisms are associated with higher risk of autoimmune disease. Be comfortable describing what the Major Histocompatibility Complex is (learned in previous chapters), how MHC genes represent different HLA isotypes, WHY we evolved to express multiple different HLA isotypes on our cells (hint: what do these HLA proteins do, and why is it good to have slightly different variations working together - think about the chicken / chicken pieces cartoon)

HLA polymorphisms and risk of autoimmune disease

Why is it much more difficult to match HLA profiles between donor/recipient compared to matching ABO and Rh +/-?

HLA polymorphisms make matching difficult • polymorphisms allow for diverse peptide presentation • but this means your "self" HLA profile is unique • grafted tissue with someone else's HLA may alert immune system

Just as with rheumatoid arthritis, understand the concept that Fig 16.35 is showing regarding both risk and protective alleles of HLA-DR. This is a bit tricky, but think about how the polymorphism might play a role in different people's immune responses against Coxsackie virus (think about the virus being phagocytosed and processed into different peptides and what certain (still unknown) normal peptides presented by insulin-producing pancreatic β cells might happen to look like.

HLA-DR associated with Type 1 Diabetes

Recognize that anti-HPV vaccines such as Gardasil represent the functional equivalent of an anti-cancer vaccine.

HPV vaccination protects against cancers • Gardasil formulation based on L1 proteins from HPV16/18 and other strains most likely to cause cancer • demonstrates 100% effectiveness in preventing pre-cancerous lesions of cervix • controversial because must be given before first HPV infection

Understand why it is being suggested that undergoing hematopoietic stem cell grafts during organ transplantation from the same donor may have clinical benefits.

Hematopoietic grafts may improve organ transplants • around 8% of non-identical twins share circulation in womb • such siblings will be exposed to each other's "non-self" HLA types • later in life, organ transplants between them yield no GVHD • possible that undergoing hematopoietic cell grafts during organ transplantation from same donor can improve recipient outcome and lessen the need for immunosuppressive drugs

What is myeloablative therapy and why is it a necessary step in immune stem cell transplantation?

Hematopoietic stem cell transplantation • usually donors are alive and healthy • patient receives cytotoxic drugs and radiation to destroy old system • called myeloablative therapy (ablates = destroys bone marrow) 1) avoids grafted cells from being attacked 2) makes room in host's bone marrow for new cells to grow • transplanted tissue is liquid delivered by intravenous infusion • within 2-3 weeks granulocytes and NK cells repopulate • B cells and T cells take longer to restore

Understand the active vs. latent cycle of herpesvirus, and understand the role of neurons in maintaining a chronic infection

Herpesvirus hides from immune response • for any viral infection to be cleared, CD8 T cells must see peptides presented by MHC I of infected cells • herpes simplex virus (cold sores) infects epithelium but spreads to neurons • neurons express very little MHC I, but not supportive of viral replication • thus herpes enters dormancy until stress, other illness, hormonal shift reactivates infection • chickenpox (also a herpes virus) behaves same way: reactivation as adult causes painful condition called shingles.

Consider the importance of regulating proliferation if there are roughly 11 trillion nucleated cells in us every day that could lose control (this is not counting the roughly 25 trillion red blood cells that DON'T have a nucleus and therefore cannot become cancerous)

How many cells are in the human body? the human body has around 11 trillion nucleated cells • each with the potential to divide under control of its genes • cancer arises when a cell loses control and is not stopped

Why is the CCR5-Δ32 mutation of such interest not only for understanding how HIV infects humans, but also how the human immune system is evolving?

How will human's evolve to beat HIV? Question: Why did the immuno-compromising CCR5-Δ32 mutation exist in European populations? Mutation likely gave some protection against bubonic plague and smallpox that ravaged the population. HIV will provide similar natural selection pressures for CCR5-Δ32 in Africa and other global populations as our immune defenses evolve against ever-present pathogens.

How do ABO mismatches contribute to hyperacute rejection of transplanted tissues? (Hint: this is particularly true for highly vascular tissues such a kidney)

Hyperacute tissue rejection from ABO mismatch • endothelial cells (walls of blood vessels) also present ABO groups • organs such as kidneys are highly vascularized • mismatched ABO typing leads to immediate attack on donated organ

Review Fig 14.9 and understand the unique nature of IgE binding FcεRI. Why is the strength of this conformation so important?

IgE binds FcεRI on granulocytes • IgE is not held in blood, but preferentially goes to tissues • IgE is held onto mast cells by FcεRI in folded conformation • this gives extremely strong attachment to mast cell • when IgE is cross-linked by antigen, signals degranulation • therefore careful control of IgE cross-linking is essential this conformation allows the antigen binding sites to project out from the surface of the mast cell and be in advantageous positions for capturing antigens.

Understand that there are four subclasses of IgG, and that IgG4 is the last and most refined antigen-specific version In the presence of a parasite infection, why is IgE made early and also late in the response? (Hint: consider antigen-binding affinity at different points)

IgE is produced early and late in immune response • in the primary response to an antigen, IgM is first switched to either IgG or IgE. • majority of B cells switch to IgG3 • switching to four IgG isotypes occurs in order that C region genes are located in heavy chain locus. • now favors specific-targeting over inflammation • as infection beaten, some B cells switch from IgG4 to IgE with highest affinity • elevated high-affinity IgE may be part of memory

Understand the normal role of IgE as it relates to fighting parasites How are sneezing, coughing, vomiting, diarrhea related to actions of IgE?

IgE normally defends against multi-cellular parasites • parasitic worms are biologically more similar to our cells than bacteria, fungus, viruses, thus less antigenic • CD4 TH2 cells encourage B cells to switch to IgE production • effector cells lead to sneezing, coughing, vomiting, diarrhea, scratching to try expelling parasites • all a result of severe inflammatory response

inhibition of activating FcγRIIA by inhibitory FcγRIIB

IgG1 binds identical epitopes with its Fab arms, whereas IgG4 can have two different Fab arms that bind different epitopes. when IgG4 binds to an allergen it can block the binding of IgE and so reduce the severity of allergic reaction → damps the immune response

Understand the concept that infections by pathogens may trigger autoimmune disease - what might our immune system get "confused" about?

Infections may trigger autoimmune disease • what if a pathogenic antigen that your adaptive immunity "learns" and "remembers" happens to look a lot like a normal self-antigen? • as with ABO blood mismatches, cells may be marked for destruction • but in this case, it's not from a donor, it's your own body!

Understand why Diabetes mellitus type 1 (Juvenile diabetes) is a Type IV autoimmune disease. How does pathogenic infection possibly play a role?

Juvenile onset diabetes • also called Diabetes mellitus type 1 • around 200,000 kids in USA affected • results from CD8 T cells destroying insulin producing Islet β cells of pancreas • disease likely triggered by infection

Why are diseases such as Kaposi's sarcoma considered strong indicators of AIDS?

Kaposi's sarcoma (KS) is one of the opportunistic diseases that made the public aware of AIDS. • healthy people rarely get KS. • symptoms include purplish lesions on face and neck • tumors of endothelial cells from lymph vessels (not true sarcoma)

many NK cell receptors recognize MHC I and related molecules

MHC I HLA proteins have different degrees of polymorphism. activating NK cell receptors tend to recognize related MHC I.

Understand that many NK receptors bind MHC I as a way to sense whether target cell is properly "displaying" its contents (the way our immune system monitors the health of our cells). How might infection lead to too little MHC I or too much MHC I being expressed? Why is NK cell interested in both situations?

MHC I presents peptides from infection. • presence of self-MHC I helps identify a normal cell that should be tolerated. • however, unhealthy cells may have altered MHC I expression levels (tumor cells, virus-infected cells). • infected cells may also overexpress MHC I as an alert to immune cells. • therefore NK cells use recognition of self-MHC and detect levels of MHC to decide whether to kill cell.

Understand the link between viral infections and many forms of cancer

Many cancers are caused by viral infection • around 30-40% of cancer types (not frequency!) are linked to viruses • viral genomes evolved to alter infected cell's normal regulation

Recognize that cancer begins with a single cell "going rogue"

Many tissue types give rise to cancer • contributes to public's vague perception (and fear) of disease • tissue variability presents unique challenges for treatment • every cancer begins with a single cell undergoing transformation

Be aware that variability in γ:δ T cell properties among different mammals leads to our poor understand of how this class of T cells work.

Many unknowns about γ:δ T cell evolution & function

Define the terms epidemic, pandemic, antigenic drift

Mutation allows flu virus to escape immunity • flu spreads quickly through populations of unprotected individuals • local outbreaks are called epidemics, in which virus spreads rapidly through a local population and then abruptly subsides. • RNA viruses such as influenza are highly mutation-prone • an immune person may be re-infected by virus mutating in a friend, this is termed antigenic drift (Fig 13.2), which causes mild and limited epidemics. • every 10-50 years a new strain causes worldwide pandemic.

NK cells normally need two or more receptors types to signal activation. However, NK cell binding IgG with its FcgRIIIA receptor is strongest and can work by itself - why do you think this is?

NK cell binding IgG is the strongest activating signal • normally, NK cell needs two different activating receptors triggered. • this prevents improper activation and killing of target cell. • but binding IgG alone through FcγRIIIA is a high confidence message. • confirmation from a second receptor is unnecessary because the pathogen specific antibody provides assurance that infection is truly present.

Understand that individual NK cell will have several different receptors on its surface, therefore giving different populations of NK cells with different targeting behaviors. All NK cells express CD56, used as a marker to distinguish from T cell.

NK cells express a range of activating and inhibitory receptors. • no single NK cell has all the receptors on its surface. • instead individual NK cells express a subset of the receptors, producing a diversity of NK cell phenotypes. • many of these receptors may be found on T cells as well. • all NK cells express CD56, because presence of CD56 without presence of a TCR identifies the cell as an NK cell when stained.

Main distinction is NK cell (more primitive) relies on diverse repertoire of surface receptors to decide fate of target, whereas T cell (evolutionarily newer) rely on unique T Cell Receptor (TCR) to determine target. Therefore an individual NK cell can target a broad range of cells as part of innate effector function, but T cell's limited specificity is the basis for adaptive effector function (and memory!).

NK cells target unhealthy and infected cells • the primitive form of T cells • both NK and T cells are cytotoxic, but major difference in specificity • unlike having a specific TCR, NK cells use an array of receptors • combinations of ~30 different NK receptors provide variability • individual NK cell expresses only a subset • receptor repertoire balances inhibitory and activating signals

Understand the functions of FcgRIIIA, NKG2D, CD94:NKG2A

NK cells use many activating and inhibitory receptors to distinguish unhealthy cells from healthy cells. activating receptor: FcγRIIIA receptor structure: Ig-like ligand: IgG ligand structure: immunoglobulin inhibitory receptor: NKG2D receptor structure: lectin-like ligand: MIC-A, MIC-B ligand structure: MHC I inhibitory receptor: CD94:NKG2A receptor structure: lectin-like ligand: HLA-E ligand structure: MHC I

Who are elite neutralizers? What is special about broadly neutralizing antibodies?

Natural antibodies that control HIV infection • a small minority (1 in 500) of HIV patients make antibodies that keep HIV levels very low in their bodies • termed elite neutralizers making broadly neutralizing antibodies • antibodies target gp120 on HIV envelope • however, these antibodies are made only after ~2yrs of HIV infection • they are the product of repeated secondary adaptive response leading to memory B-cells improving their IgG • therefore never eliminate HIV entirely • current clinical trials aimed at using these as immunoglobulin drugs prophylactically

Fig 13.31: understand that examples of different pathogens from all 4 main pathogen types pose serious threats to AIDS patients

Opportunistic infections characterize AIDS common opportunistic parasites, bacteria, fungi, and viruses kill AIDS patients in developed countries. malignancies are also the result of impaired responses to infectious agents.

define antigenic shift Why are pandemics most often caused by recombinant viruses? Understand the concepts of inter-species antigenic shift as presented by Fig 13.3.

Pandemics are caused by recombinant viruses • avian virus may bind human cells but cannot replicate (no threat) • simultaneous infection of secondary host (pig) by human and avian virus allows genetic mixing leading to antigenic shift • recombinant virus can bind AND replicate in human cells • new strain never seen previously in humans, so very dangerous!

Give some reasons why a pathogen such as smallpox can be completely eradicated from a population, whereas a pathogen such as influenza likely will never be

Pathogen strain variations block long-term immunity • high-affinity IgG against pathogen is the basis of long-term immunity • if pathogen rarely mutates, there is hope of eradicating specific disease (like smallpox) • many pathogens exist as many strains w/diverse mutations • such pathogens/diseases may never be wiped out • all part of co-evolving relationships between us and them!

Understand the differences between Direct Allorecognition of "too different" donor HLA versus Indirect Allorecognition. (Hint: Fig 15.12 nicely presents this - most important concept is whose cells are presenting the donor's HLA peptides, and to what cells are they being shown? In the figure, why are some MHC yellow and some orange?)

Patient's T cells activate against donor tissue • APCs (eg. dendritic cells) from donor are present in donated tissues • allorecognition of donor HLA leads to activation of patient's T cells • may happen directly (Acute Type IV) or indirectly (Chronic Type III) • direct allorecognition: donor MHC activates CD8 T cells, causing apoptosis of donor presenting cell. • indirect allorecognition: patient MHC presents donor peptide, causing activation of CD4 T cells and then B cells → antibodies for donor's HLA class created

Understand how IgE is passed from mother to baby - what are the benefits of this? How might this contribute to the child developing an atopic profile?

Predisposition to allergies passed by mom to baby • mother's IgE is found in amniotic fluid and in breast milk • during gestation and nursing, baby will ingest IgE • meant to defend against parasites, but transfers allergies as well

Describe the three main strategies for preventing and treating allergic reactions in atopic patients

Prevention and treatment of allergies 1) avoidance: changing patient's behavior (lifestyle) or their living environment. avoiding certain foods, cleaning house 2) pharmacological: using drugs that reduce the impact of allergen exposure. antihistamines, anti-IgE antibody treatment 3) immunological: retraining the immune system to be desensitized to allergen. administering increasing doses of antigen to increase tolerance

If our adaptive immune memory is so good, how can we catch bacterial pneumonia multiple times throughout our lives?

Repeated illness due to different strain exposure • you can catch pneumonia numerous times in your life • but you gain long-term immunity to strains you already survived! • consider: Why would infants and elderly have highest risk of pneumonia mortality? ∴ infants have not yet built up immunity. ∴ elderly have reduced thymus and can no longer create new T cells.

What is Rhesus (Rh) factor? Understand that Rhesus factor D is the most immunogenic of the C/D/E types, and that a person may or may not have an allele of the Rh D gene that expresses protein and thus you are either Rh D positive (+) or negative (-). Understand that between matching ABO and Rh +/- there are 64 different donor/recipient pairings, of which 27 are compatible (Fig 15.3) Be aware that frequency of blood types varies across different populations

Rh factors are RBC surface proteins • discovered when an injection of blood from a rhesus monkey into rabbits caused an antigenic reaction in the serum component of rabbit blood • Type D is the most immunogenic / relevant for compatibility: • if you have working Type D allele, you are Rh+ • if you have allele that doesn't work, you are Rh- • Rh- patients who receive Rh+ donor blood will generate anti-Rh IgG, making subsequent transfusions dangerous *green squares for compatible donor and recipient *bottom line gives the frequency in US population

Understand how rheumatoid arthritis represents a Type IV disease.

Rheumatoid arthritis • most common "rheumatic" disease (from Greek rheuma = body fluid) • affects 1-3% of US population, women 3:1 over men • starts between age 20 - 40 • painful swelling of joints such as fingers leading to severe bone damage, disfigurement, loss of use of appendage • Type IV autoimmunity (T cell mediated) • many patients go on to produce IgG against joint antigens

What is SCID? Why are SCID phenotypes some of the most serious inherited immunodeficiency diseases?

Severe Combined Immune Deficiency (SCID): lack T-cell dependent antibody responses & T cell effector response. • B cells contribute only to the antibody response, but T cells function in all aspects of adaptive immunity. • this means that inherited defects in the mechanisms of T cell development and T cell function have a general depressive effect on the immune system's capacity to respond to infection. • T cell development and function depend on the action of many proteins, so SCID can arise from defects in any of a number of genes.

Recognize that some level of GVHD might actually be helpful in certain disease situations

Some GVHD helps prevent cancer relapse • completely removing T cells from graft prior to transplant discourages GVHD, but leads to higher failure rate and cancer relapse (consider inflammation's stimulatory role) • physicians may select a donor that has one copy of HLA allele identical to patient, but other copy different. • this is termed a haploidentical transplant

What are three strategies for successful tissue transplantation?

Strategies to encourage successful transplantation I. Matching HLA as close as possible • looking for a donor within the patient's family • twins are an ideal situation II. Anti-inflammatory medications • steroid such as prednisone reduce presence of activated dendritic cells, T cells and cytokines III. Immunosuppressive medications • target leukocytes to inhibit effector responses • some are IgG-based or synthetic peptide • several different drugs derived from microbes

Why are systemic allergic reactions potentially dangerous? Understand some of the physiological responses that combine to create anaphylactic shock - how does epinephrine counter-act this?

Systemic allergic reactions can be life threatening • widespread mast cell degranulation leads to inflammation, constriction of airways, irregular heart beat, loss of blood pressure → this can cause anaphylactic shock, which could be fatal • highly sensitized individuals may need to carry auto-injector of epinephrine (adrenalin: stimulates heart, relaxes airways, reduces fluid loss from blood vessels)

If recruiting α:β T cells is your goal, understand how exciting newer technologies such as adoptive-T-cell transfer works

T cells are extracted from the patient, genetically modified and cultured in vitro and returned to the same patient. Provenge is an antigen-dendritic cell fusion drug

Understand the situation known a GVHD

T cells present in graft will attack new host • T cells from donor will likely allo-recognize patient's HLA differences • this may trigger systemic Graft-versus-host disease (GVHD) • high levels of cytokines causes inflammation • fortunately, relative number of participating T cells means GVHD can run its course within first few months following transplant

Review how we end up making γ:δ T cells compared to α:β T cells (remember it has to do with what pair of peptide chains makes up the TCR)

Thymocyte development leads to α:β and γ:δ T cells. T cell receptor gene rearrangements in double negative thymocytes can lead to expression of either a γ:δ or a pre-T-cell receptor. the β, γ, and δ genes rearrange. if successful γ and δ chain rearrangement occurs first, then a γ:δ receptor is expressed and the cell is signaled to differentiate into a mature γ:δ cell. the more frequent outcome is for a productive β chain gene rearrangement first. if successful β chain rearrangement is made first, a pre-T-cell receptor assembles and signals the cell to proliferate, express CD4 and CD8, and become a pre T cell. at this stage the pre T cell turns on the recombination machinery to rearrange the α, γ, and δ genes.

Compare/contrast the factors contributing to blood transfusion failure and organ transplant failure

Tissue rejection follows Type II-IV hypersensitivities Type II: existing IgG against wrong ABO blood Type III: development of new IgG against wrong HLA forms immune complexes Type IV: activation of T cells against wrong HLA results in effector cells targeting tissue Consider: • majority of antigens in graft are near-identical to patient's own "self" antigens, most proteins encoded by our genes are not radically different between individuals • exceptions are ABO and HLA types which are highly immunogenic and activate alloimmunity because: - location on cell membrane makes them easy to detect intact - patient already has elevated IgG titer for wrong AB antigens - HLA is the specific protein that T cells are designed to bind

Recognize there are several scenarios in Fig 17.9 by which abnormal presentation of peptides by MHC of transforming cells can alert the immune system to something wrong happening

Transformed cells present abnormal peptides

Understand how the nature of organ donation leads to inflammation and ischemia of tissues, which contribute to heightened patient immune response

Transplant delays contribute to immune responses • inflammation of organs due to trauma will damage tissue • ischemia (lack of oxygen) suffered by donated organ also damaging • patient awaiting operation suffers medication-induced inflammation • these factors heighten immune sensitivity during/after surgery

Type I: Binding of antigen to IgE-equipped granulocytes (such as mast cells) Recognize that antigen must cross-link two or more FcεRI-IgE receptors to stimulate degranulation of a mast cell Why is Type I also called immediate hypersensitivity?

Type I hypersensitivity: Binding of antigen to surface IgE Mechanism: • antigen binds allergen-specific IgE held by FcεR1 receptor on mast cells, basophils, eosinophils • receptors cross-link to send signal into cytoplasm • cells degranulate and release mix of inflammatory molecules Examples: • hay fever, animal fur allergies, food allergies, bee sting allergy • also called immediate hypersensitivity because reaction is very fast • can be life-threatening

Type II: IgG-mediated attack on host cells - what is role of B cells and macrophages?

Type II hypersensitivity: IgG-mediated attack on cells Mechanism: • small chemicals introduced into body may covalently interact with surface proteins of healthy cells • result is altered presentation of cell antigens • naïve B cells recognize antigen as "non-self" and initiates IgG production • macrophages attack self cells resulting in tissue damage Example: Penicillin allergy

Type III: Why would the body's IgG be more likely to bind an infused therapeutic IgG, causing a large immune reaction, compared to inappropriately binding another of the body's IgG types? (Hint: think about amount of IgG involved)

Type III hypersensitivity: Improper immune complexes of antigen and specific IgG that form deposits in the walls of small blood vessels or the alveoli of lungs. Mechanism: • antibodies such as IgG cross-react and form complexes in blood • may attach to tissues and result in improper fixation of complement, which activated and inflammatory response plus targeting by effector cells causes tissue damage. Example: • therapeutic immunoglobulins made in other species may cross-react with patient's immune system • unlikely to occur spontaneously by own antibodies due to high concentrations required

Type IV: Mediated by T cells. Understand why this mechanism doesn't involve antibodies but still represents the adaptive immune system making a mistake, what is the immune system attacking? Why might this NOT be considered as life-threatening as some Type I mechanisms?

Type IV hypersensitivity: mediated by T cells, not antibody unlike Types I, II, III. also called delayed type hypersensitivity because only apparent 1-3 days after exposure to antigen; slower than the few hours or less of Types I, II, III. not considered as life-threatening as Type I Mechanism: • external molecules form adducts with normal proteins, altering their form • when altered proteins are presented to CD4 TH1 cells, TH1 cells activate and induce phagocytosis and CD8 T cell attack of presenting cells Examples: • metals like nickel form adducts with histidine residues that then get incorporated into misshapen proteins • allergies to some pieces of jewelry result

Understand that cancer is, in its simplest definition, a loss of control over cell proliferation. If every nucleated cell in our body has the same genome of 20+ thousand human genes, how do we get so many different types of cells in our body?

What is cancer? A loss of control over cell proliferation • every nucleated cell in our body contains a complete copy of the human genetic blueprint • selective expression of genes determines specific cell type and function • genes also control when a cell should divide and when it should not • a normal cell is either in the process of dividing or performing its assigned job, but not both • thus the majority of nucleated cells in our body at a given time are differentiated and no longer proliferating

X-linked defects in antibody production

X-linked agammaglobulinemia (XLA) • mutation in BTK gene that lets Pre-B cell know Ig has been made • in affected individuals, immature B cells never develop • without antibodies, innate immunity OK but no adaptive Ig function • females have two X chromosomes, cell randomly inactivates one • therefore in heterozygous female 50% of developing B cells are OK • no appearance of XLA disease because still have good B cells

Asthma results from IgE stimulation

acute attack: when specific allergen is inhaled triggering mast cells. chronic asthma: when TH2 cells continue to activate long term

Be comfortable explaining the "hygiene hypothesis"

allergy is prevalent in countries where parasite infections have been eliminated

Understand how the prefix "allo-" is used to describe actions directed against normal antigen from an outside source (for example normal healthy tissue transplanted from someone other than the patient). Words such as "alloimmunity", "alloreactivity", "allo-antibody", "allorecognition" all fit this meaning.

allo = other, as in other "normal" antigen

Understand how "autoimmunity" can be thought of as failed self-tolerance. Recognize that autoimmune diseases likely arise from a combination of genetic, developmental, and environmental factors.

autoimmunity: a failure of "self tolerance" if we routinely generated Ig or TCR against our own body's antigens, our health would always be compromised • over 100 different autoimmune diseases identified • more common in affluent, industrialized countries • body engaged in a "civil war" making the origin of disease difficult to determine • little understanding of how "self tolerance" lost • likely combination of genetic, developmental and environmental factors (including infectious agents)

Recognize the various examples of innate and adaptive cells/factors working together to generate allergic responses

cells involved in Types I - IV hypersensitivities

You do NOT need to memorize names/functions of different KIR receptors, but understand why we have several types - how have NK cell receptors for detecting MHC evolved to deal with this variation?

each KIR detects one of four main shapes of HLA • NK cell receptors have a disadvantage of insensitivity to diverse, highly polymorphic HLA-A, -B, and -C. • CD94:NKG2A is expressed first, followed by KIRs. • through random process, NK cells express different numbers of KIR genes in different combinations. • KIRs are inhibitory NK receptors that recognize polymorphic determinants of HLA-A, -B, and -C, used to complement CD94:NKG2A.

Understand how the term serotype relates to descriptions of a pathogen

example: Streptococcus pneumoniae has many strains w/diverse mutations. • causes bacterial form of pneumonia • over 90 different strains identified • called serotypes because antibody tests used to ID • differ in their capsular polysaccharides

Consider the 4 categories of allergens (inhaled materials, ingested materials, injected materials, and contacted materials) in terms of what kinds of antigens might be involved, what body tissues are exposed, and what kinds of immune effector cells/molecules are behind the allergic response Understand there are four distinctive hypersensitivity types based on underlying effector mechanisms

four distinctive types of hypersensitivity reactions involve different effector mechanisms of adaptive immunity Type I: inhaled and ingested materials • antigens: proteins (plant pollen, dust mite feces, food particles) • body tissues exposed: mucosal layers of respiratory tract • immune effector cells/molecules: IgE + mast cell Type II: injected materials • antigens: chemicals that covalently interact with cell surface proteins, like penicillin • body tissues exposed: tissue self cells • immune effector cells/molecules: naive B cells initiate IgG and macrophages attack self cells Type III: injected materials • antigens: therapeutic Ig • body tissues exposed: walls of small blood vessels or alveoli of lungs • immune effector cells/molecules: complement fixation and phagocyte attack. Type IV: contracted materials • antigens: external molecules (metals) • body tissues exposed: skin • immune effector cells/molecules: helper CD4 TH1 cells and CD8 cytotoxic T cells

Understand how mutations may lead to surface signals such as MIC being altered in cancer cells to avoid detection by γ:δ T cells Understand how mutations leading to loss of MHC I expression by cancer cells can really help them hide from our immune system.

improperly processed peptides hide a cancer cell. human epithelial tumors inhibit the response of lymphocytes expressing NKG2D. cancer cells lose MHC I expression.

Understand the example in Fig 17.11 of how mutations may lead to peptide fragments generated by the proteasome sticking together to create "non-self" antigenic signals (signals our T cells never developed tolerance against)

improperly processed peptides identify a cancer cell production of tumor specific antigens by 'cutting and pasting' peptides from self proteins

Understand that T cells and NK cells arise from the same lymphocyte precursor, and therefore have very similar cytotoxic effector capabilities on target cells.

lineages of innate and adaptive immune cells • innate immunity is present in both vertebrates and invertebrates. • adaptive immunity is found only in vertebrates. • origin of innate immunity was 600 mya • adaptive immunity was 400 mya • immunoglobulin and T cell receptor genes rearrange, a property that distinguishes them from all other lymphocytes, believed to be 200 mya

Understand the mechanisms of therapeutic monoclonal antibody (mAb) action that we discussed. How can a mAb help our innate effector cells such as NK cells target tumor cells? Why is it not accurate to imagine these mAb drugs recruiting α:β T cells in the same way? (I mention this because often people describe mAb drugs working this way through T cells, and this isn't really correct...think about how T cells interact with targets and you'll realize why).

mAbs "highlight" cancer so effector cells see it • mAbs specific for tumor antigens can help focus the attention of NK cells and γ:δ T cells to target cancer • mAbs bind to FcγRIII receptors and activate NK cell cytotoxicity • consider you cannot directly recruit α:β T cells via antibody signaling this way because mAbs do not bind to MHC, which is the target of T cells. antibody-dependent cellular cytotoxicity (ADCC)

Understand that mAbs can be used to relieve inhibitory signals that usually limit T cell activity, thus enhancing the patient's existing adaptive immune response.

mAbs can relieve inhibition of effector cells • recall that naïve T cells need B7-CD28 co-stimulation to activate • normally CTLA4 competes against this to help limit T cell activity • anti-CTLA4 monoclonal antibody blocks this inhibition • existing T cell sensitivity is greatly enhanced

Understand examples of how mAb can also be used as targeting vehicles to deliver high effective dose (meaning systemically throughout the body the patient gets a low, easily tolerated dose, but the agent gets concentrated to lethal doses at the target) of cytotoxic compounds or radiation to cancer cells while sparing surrounding healthy cells.

mAbs deliver high-dose cytotoxins and radiation

Understand how mutations leading to upregulation of cytokines that stimulate Treg function are a mechanism for cancer cells to avoid being targeted by other T cells.

manipulation of the immune response by a tumor tumors can proect themselves from the immune response by secreting immunomodulatory cytokines, such as TGFβ, which supress the inflammatory response and recruit Treg into the tumor tissue. these combine to supress the actions of effector CD8 T cells and CD4 TH1 helper cells that are specific for tumor antigens.

Role of the immune system may be to tolerate infections that cannot be completely blocked or eliminated (example EBV)

many pathogens cause latent infections • Epstein Barr Virus (EBV) is a herpesvirus widespread in children, causing infectious mononucleosis in teenagers. • EBV binds B-cell co-receptor CR2, leading to over-activation of EBV-specific T-cells • after primary infection beaten, EBV enters latency and is present for rest of your life. • estimated 70% of adults carry the virus, but healthy immune system quickly defeats viral reactivation.

humanized mABs used in the treatment of cancer

monoclonal antibodies as anti-cancer therapies several different mechanisms involving mAbs: • aiding detection & targeting by effector cells • relieving existing inhibition of effector cells • delivering cytotoxins to targets • directing radiation against targets

Understand the concept that oncogenes and tumor-suppressor gene pathways are constantly acting against each other like the gas/brake pedals in a car. Individual cars must follow traffic signals telling them when to go/stop to keep traffic moving and avoid chaos, BUT it is ultimately up to the driver (the cell's genes) to determine which pedal gets pressed and how hard

oncogenes: mutated genes that cause cancer. • like pedals of a car, these gene groups work against each other to determine whether the cell moves forward with division or stops • as with a busy freeway, our body relies on individual cells regulating their own driving behavior

immunoglobulin like NK cell receptors recognize

polymorphic epitopes of HLA-A, HLA-B, and HLA-C MHC I HLA proteins have different degrees of polymorphism.

Understand what is meant by a primary versus secondary immunodeficiency disease

primary immunodeficiency disease: caused by inherited defects in genes. secondary immunodeficiency disease: caused by environmental factors (chemicals, pathogens). • prior to widespread use of antibiotics in 1940s, most individuals born with inherited defects died in infancy. • only since 1950s has identification of immunodeficiency diseases progressed due to medicine extending lives.

Recognize some features of inhaled allergens that encourage the IgE response (Fig 14.22). You don't have to memorize the table, but make sure these descriptions make sense to you.

properties of inhaled allergens

The immune system responding to tissue transplants

rejection of tissue may be due to blood or solid tissue incompatibility • for thousands of years people have attempted transplantations, most of the time with failure • very first successful organ transplant (kidney) performed by Dr. Joseph Murray in 1954

How can we therapeutically "boost" the immune system to better target and destroy cancer cells?

remember: patient's immune system may be perfectly fine, but tumor cells have stumbled upon combinations of mutations that allow them to "evade" proper immune attack. monoclonal antibodies (mAbs) directed against cancer antigens can be introduced into the patient's body to alert the immune system and generate a response.

What is an atopic individual?

someone with a genetic predisposition to allergy atopy = out of place

Understand the role of the 3 main HIV genes: gag, pol, env (be aware that gp120 and gp41 are coded by env)

the gag, pol, env genes are common to all retroviruses • gag: core proteins and matrix proteins • pol: enzymes: reverse transcriptase, protease, and integrase • env: viral spike envelope: gp120 and gp41 glycoproteins, CD4 receptor. ∴ gp120 component of spike binds tightly to human CD4, enabling virons to attach to CD4 expressing cells; before virus can enter the cell, gp120 must also bind a co-receptor in the host cell membrane → once bound, the gp41 component of the envelope glycoprotein fuses the viral membrane with the host cell membrane, allowing the viral genome and associated proteins to enter the cytoplasm of the now infected cell.

Be familiar with Fig 12.20 - don't need to memorize numbers, but be comfortable commenting on how γ:δ T cells and α:β T cells compare/contrast using the criteria in the table.

γ:δ T cells are not governed by same rules as α:β T cells

APD disease caused by defective AIRE alleles

• Autoimmune Polyglandular Disease results from body's lack of proper T cell negative selection in thymus • AIRE transcription factor activates expression of diverse tissue antigens in thymus for thymocytes to screen against • people who don't express AIRE have T cells that are not fully trained and autoreact to many potential tissue targets

Remember that HLA proteins that make MHC complexes can be highly polymorphic - how have NK cell receptors for detecting MHC evolved to deal with this variation? (Hint: why would using HLA-E levels as a proxy for overall MHC levels be a good choice?)

• HLA-E is a conserved HLA class I molecule with ubiquitous tissue distribution like HLA-A, -B, and -C but a distinctive specificity for binding to peptides derived from the leader sequences of HLA-A, -B, and -C heavy chains. • the amount of HLA-E on a cell's surface provides a measure of the total amount of HLA-A, -B, and -C being made by the cell. when HLA-E on healthy cell engages NK cell CD94:NKG2A, the NK cell is inhibited; dephosphorylated Vav inactivates pathways of NK cell activation. when same NK cell responds to a virus infected cell; target cell expresses MIC and CD48, which engage the NK cell activating receptors, NKG2D and 2B4 → the phosphorylated Vav initiates further signaling and mobilization of NK cell effector function.

Understand the concept of diseases such as HIV jumping from another species to humans (compare/contrast with earlier example of human and avian flu recombining in pig). What feature(s) of HIV infection are consistent with it being a lentivirus?

• Human Immunodeficiency Virus (HIV), first identified as the virus causing AIDS in 1983 • two types of HIV: ∴ HIV-1: main cause of AIDS in most countries ∴ HIV-2: much slower in progressing to AIDS, mainly in West Africa and Asia • HIV jumped from primates to humans in the 1950s • likely from chimps and monkeys in West Africa: chimpanzee origin of HIV-1 and sooty mangabey origin of HIV-2 • local people exposed to blood from hunting infected animals • Simian Immunodeficiency Virus (SIV) does not cause widespread illness (non-human primates live with SIV without developing AIDS-like symptoms). • HIV is a retrovirus family member, meaning its genome is RNA and must be reverse-transcribed in infected host cells • belongs to the lentivirus genus because HIV causes slowly progressing chronic disease • HIV infects CD4 T cells, macrophages, dendritic cells • in almost all infected individuals, the immune system cannot eliminate HIV

Systemic Lupus (Type III autoimmune disease)

• Lupus occurs when IgG is improperly made against a variety of cellular proteins • immune complexes of IgG-antigens are not cleared away, causing severe inflammation • can lead to heart attack, stroke, organ failure • ninety percent (90%) of patients are women between 15-44 years old • no cure, can treat symptoms with anti-inflammatory drugs • affects ~1.5 million people in US

Understand what is meant by "NK-cell education". Why can this also be considered NK cell calibration? How does this relate to NK cell's role in sensing MHC levels on surfaces of normal cells?

• NK cells acquire inhibitory receptors for MHC I at late stages of their development in bone marrow. • NK cell must express one inhibitor receptor that recognizes a self MHC I, this can be either CD94:NKG2A or KIR. • NK cells test inhibitory receptors against the MHC I of bone marrow cells; if inhibitory receptor finds a cognate MHC I then it signals initiated NK cell education that makes the NK cell sensitive to loss of self-MHC I. • the inhibitory signaling molecules produced during this initial interactions create a level balance between the activating and inhibitory signals. • in this situation, where the NK cell is interacting with a healthy cell expressing normal levels of self-MHC I, the cell does not respond because signaling from the activating receptors is cancelled out by signaling from inhibitory receptors.

Multiple sclerosis (Type IV autoimmune disease)

• TH1 CD4 cells activate against myelin sheaths of neurons • inflammatory IFNγ recruits macrophages and destroy myelin • result in scar-like plaques (sclera) that impede nerve conduction • symptoms: loss of sensory skills, muscle weakness, coordination • disease usually presents between age 20-50 • patients are twice as likely to be women than men

Hemolytic anemia (Type II autoimmune disease)

• Type II: hypersensitivity mediated by antibodies directed against components of cell surfaces or ECM.

How does this Rhesus (Rh) factor differ from ABO antigens?

• antigen of ABO blood groups are LPS. • antigens of Rh blood groups are proteins, Rh⁻ people don't have antibodies against RhD until exposed to it.

inherited disease

• around 200 known primary immunodeficiency diseases • those with severe phenotypes are very rare (natural selection) Dominant: child inheriting one copy of defective gene enough to cause disease - effects of mutant allele interfere with normal allele. Recessive: healthy parents who are carriers may pass two copies of bad allele to child, who is then affected by disease. X-linked: gene in question is on X chromosome, so disease mainly seen in males who inherit from mother. (Females must get two copies to be affected).

V(D)J loci arose from ancestral genome duplication

• believed that two whole genome duplications occurred prior to vertebrates • divergence of V(D)J genes allowed for specialized immune functions • dedication of γ:δ loci for innate TCR functions • T cell α:β and B cell Ig chain loci developed for adaptive immunity

HIV / AIDS is a global pandemic

• current estimates are over 37 million people infected with HIV • over 2 million new infections per year • tens of millions expected to die from AIDS in next few years

Tumor specific antigens contain tumor specific mutations

• five are peptide tumor antigens containing a point mutation (in magenta) • three are peptides derived from the novel protein produced by fusion

Eosinophils

• found in tissues underlying respiratory, GI and urogenital tracts • present but rare in blood • stain pinkish red with eosin (acidic stain) • highly toxic pre-formed compounds released 1st to attack microbes • followed by cytokine production and secretion for inflammation • eosinophil action is highly damaging to surrounding tissues, so numbers are limited

Celiac disease similarities to autoimmune disease

• gluten proteins in wheat are rich in glutamine • due to charge, peptides bind strongly to MCH II HLA-DQ2 and DQ8 allotypes • intestinal epithelial cells transporting peptides from lumen become targeted • once gluten consumption stops, disease eliminated

Vγ:Vδ1 T cells sense glycolipid antigens in mucosa

• glycolipids of human and microbial origin may indicate disease • sulfatide secretion abundant in intestinal epithelium • carried by CD1d (similar to MHC I) and presented to γ:δ T cells

Preferential T cell Vγ and Vδ blocks used in tissues

• goal of α:β T cells is to anticipate infinite possible peptides • goal of γ:δ T cells is flexibility to bind variations of certain "themes" • "themes" means certain types of molecules acting as signals: microbial metabolites, phospholipids, glycolipids • these antigens either don't belong in human body or increased levels indicate disease (eg. tumors).

What is histamine? What molecule is it derived from? How do antihistamine drugs work?

• histamine derived from amino acid histidine • allergies involve H1 receptors on smooth muscle & endothelium • variety of physiological effects: inflammation, sleep cycle antihistamine drugs block H1 receptor binding • early generation drugs (Benadryl/diphenhydramine) crosses blood brain barrier and causes drowsiness • second generation drugs (Zyrtec/certirizine, Allegra/fexofenadine) less likely to enter brain.

Understand how blood vs tissue distribution of γ:δ T cells differs from α:β T cells.

• in blood, γ:δ T cells are the minority at only 2-5% to total T cells. • majority of γ:δ T cells are in tissues.

Consider how the innate and adaptive sides of our immune system are co-evolving - examples of crossing-over include how T cells help macrophages, and how antibodies (our newest "invention") help innate effector cells.

• inflammatory response of innate immunity is a necessary prelude to making good antibodies of adaptive immunity. • as adaptive immunity (RAG proteins and receptors encoded by rearranging genes) developed after innate immunity, it would occur in context of existing innate system. • classical pathway of complement activation: antibodies hook up with preexisting complement components of innate immunity.

NK cells are educated about reacting to conditions

• like a student driver first learning about accelerating and braking in a suitable environment. • once on your own, inhibitory signals in real-world setting limit ability to accelerate. • if inhibitory signals absent, you can really let loose.

Mast cells

• located in tissues such as mucosal and epithelium (not in blood) • detect infection, stimulate inflammation, repair damage • contain 50-200 well-defined granules with proteases & cytokines • Histamine is a strong inflammatory cytokine • Heparin is an anti-coagulant (blood thinner) two mast cell populations: mucosal mast cells - release tryptase against microbes connective tissue mast cells - release chymotryptase to remodel tissue

Describe some reasons why ABO and HLA antigens are particularly highly immunogenic, and understand why this is consistent with them being the main priority for matching in blood and organ transplantation.

• location on cell membrane = easily accessible • patient already has elevated titer for wrong ABO • HLA is the specific protein that comes in to contact with T cells to bind

Disease caused by IFNγ mutations

• macrophages depend on IFNγ signals from NK cells and CD4 T cells • without it, monocytes don't differentiate into macrophages • existing macrophages are not encouraged to phagocytose bacteria Recessive form of IFNγ deficiency: two bad alleles for IFNγR1 Dominant form: one bad allele of IFNγR1 gene leads to defective receptor that interferes with signaling by good allele.

How do mutations in the CD40 ligand affect CD4 T cell function? What broader impact does it have on how our adaptive immune system works?

• mutations in CD40 ligand prevent CD4+ T cells from activating B cells • results in very low IgG, IgA, IgE production • but abnormally high IgM levels • called X-linked hyper-IgM syndrome • macrophages also do not get activated by impaired T cells • therefore neutrophils don't get signal to help fight infections • termed neutropenia

Understand the terms: mutation, tumor, benign vs. malignant, metastasis, transformation, oncogene, tumor-suppressor gene

• mutations in genes may be silent or lead to loss/gain of function • cells dividing out of control lead to tumors, may be solid tissue or liquid (hematopoietic tumors) • benign (non-cancerous) tumors do not have mutations that allow them to spread beyond their normal tissue micro-environment. • malignant (cancer) tumors gained necessary mutations to spread • the spreading of malignant tumor is called metastasis normal cells (proto-oncogenes) undergo transformation to become cancer cells (oncogenes) • some gene mutations encourage this more than others • two most important categories of cancer-associated genes: ∵ oncogenes (and proto-oncogenes) drive cell division forward; examples: myc, ras ∵ tumor-suppressor genes halt cell division; examples: p53, PTEN

HLA is the "self" ID card of your cells

• nearly all your cells display HLA proteins (specifically MHC Class I) • like presenting ID to the guard to show you belong in building • not just your photo (peptide) but ID card itself (HLA) must be right

Understand that autoimmune diseases also follow Type II, III and IV hypersensitivity models (just like rejection of mismatched donor tissue)

• no autoimmune disease is mediated by IgE (Type I). • Type II: hypersensitivity mediated by antibodies directed against components of cell surfaces or ECM. • Type III: hypersensitivity mediated by soluble immune complexes deposited in tissues. • Type IV: hypersensitivity mediated by effector cells.

Vγ9:Vδ2 T cells bind cell surface phosphoantigens

• presence of HMBPP in body indicates microbial infection • presented on surface of our cells by BTN3A1 (similar to B7 and MHCI) • IPP is a normal human phosphoantigen • T cells are sensitive to levels of IPP indicative of disease • note the binding of γ:δ TCR is very different than α:β TCR binding

"Epitope spreading" broadens list of self-targets

• proteins and protein complexes contain many different antigens • improper B cell or T cell detection of one epitope can lead to processing, presentation, and sensitivity to other associated epitopes • result is spread of systemic autoimmunity against many self-targets and increasing severity of disease / extreme toll on health *autoreactive CD4 T cells specific for one epitope of a macromolecular complex can provide help to B cells specific for other accessible epitopes of the complex. *B cell that internalizes a macromolecular complex can present antigens to T cells specific for any one of the proteins on the complex.

Trypanosomes change surface antigens

• protozoan parasite Trypanosome brucei causes sleeping sickness • have over 1000 genes that each code for different surface protein • at any time, 1 of these Variable Surface Glycoproteins (VSG) is used • parasite switching through VSG heavily wears down immune system

Basophils

• rarest of the circulating leukocytes • move between blood and tissue • stain with basic dyes such as hematoxylin • basophils and eosinophil production is reciprocally balanced in bone marrow • similar innate effector functions as eosinophils • in addition, aids B cell and TH2-biased T cell differentiation

What is a syndrome? Why is AIDS considered a syndrome?

• syndrome means a set of medical symptoms that occur together • Acquired Immune Deficiency Syndrome (AIDS), first described in the early 1980s • characterized by greatly reduced CD4 T cell count in patient • accompanied by severe infection from opportunistic pathogens that normally do not make healthy people sick • all patients with AIDS will die of opportunistic infections

Understand that IgG4 has unique property of swapping arms with other IgG4 in blood circulation, resulting in two different antigen binding specificities - why is this useful?

• thus most IgG4 have two different antigen-binding sites (Fab) • IgG4 is particularly good at cross-linking different targets • IgG4 can no longer help fix complement to targets • the "stem" (Fc) of IgG4 preferentially binds the inhibitory receptor FcγRIIB on macrophage surfaces • this inhibits cytokine production from macrophages, reducing inflammation • when IgG4 binds to an allergen it can block the binding of IgE and so reduce the severity of allergic reaction → damps the immune response

Link between developed countries and allergies

• underdeveloped countries have highest parasitic infections (red) • people in those places have elevated IgE levels, but no allergies • regions such as N. America and Europe have highest allergy rates • What is the link?

How is hematopoietic stem cell transplantation conceptually different than blood transfusion or solid organ transplantation?

• unlike blood transfusion or organ grafts replacing missing function, stem cell transplantation reprograms immune system • used to treat genetic diseases of blood and hematopoietic cancers • additional challenges beyond ABO and HLA compatibility: - recipient's "old" immune system must first be eliminated (otherwise allo-reactions would be intolerable) - transplant graft must be adequately enriched for stem cells (must minimize time patient is without immune protection) - must control attacks made by "new" system on host's body (rebooted system must develop proper host tolerance)

How do the γ and δ chain gene loci compare to the α and β loci?

• unlike α:β chains, the γ:δ chains have fewer V(D)J blocks • therefore γ:δ TCR have much less antigen-binding variability • binding classes of antigen rather than specific antigen • γ:δ T cells are involved in tissue maintenance and immune response. • δ chain locus is small and squeezed within α chain locus on Chr 14. • γ chain locus is bigger than δ chain locus but still smaller than α or β chain loci; γ chain locus on Chr 7, though nowhere near β chain locus.

Vγ4:Vδ5 T cells sense viral infections and tumors

• viral-infected & tumor cells secrete Endothelial Protein C Receptor (EPCR) • protein C, an anti-coagulant in blood • expression of EPCR may indicate spread of disease/infection • Vγ4:Vδ5 T cells release cytokines and are cytotoxic

Understand that γ:δ T cells are more involved in tissue maintenance (more of an innate response) than adaptive specificity/memory.

• γ:δ T cells are less diverse than α:β T cells • γ:δ T cells do not recognize peptide agents but a wider range of chemical structures that distinguish distressed cells and secrete cytokines and growth factors that promote the repair of damaged tissue.