13_failures_of_host_defense.md

Failures of Host Defense Mechanisms

Severe Combined Immunodeficiencies

Mutation in IL2RG gene on X chromosome (common gamma chain, \gamma_c) causes SCID:

• T-cells unable to develop
• B-cells are able to develop but are unable to function without T-cells

Variants:

• somewhat ablated RAG1/RAG2 lead to Omenn's syndrome. Limited T-cell repertoire somehow becomes very autoreactive leading to symptoms resembling graft vs. host disease. (called hypermorphic mutation)

• "radiation sensitive" SCID is when defects in DNA repair proteins (eg. Artemis) cause reduced somatic hypermutation that also increase susceptibility to radiation / general DNA damage

SCID can be caused by pathologies in the purine salvage pathways

• ADA (adenosine deaminase)
• PNP (purine nucleotide phosphorylase)

Purines - pyrimidine fused to imidazole Defficiency in purine salvage lead to accumulation of toxic purines and kill lymphocytes.

What does purine salvage do? Purine bases are used all over the place, not just in DNA:

• metabolism (cyclic AMP, ATP, cofactor for NADP, CoA)
• cell signaling (GTP used in G-protein signaling,
• protein synthesis (tRNA loading)

T-cell based SCID (development)

• "Nude" mice/people lack proper thymus epithelial formation (FOXN1).
• DiGeorge syndrome caused by large deletion of chrom 22 leading to similar thymic underdevelopment
• MHC-II deficiency is caused by at least 4 upstream regulatory genes
• MHC-I deficiency is generally caused by dysfunctional peptide transport proteins (TAP1/TAP2) but otherwise normal levels of mRNA + surface MHC-I. People with this are generally healthy indicating alternative ways of displaying peptide
• Dysfunction in thymal epithelial peptide presentation (AIRES) leads to autoimmunity

B-cell based SCID (development)

• Characterized by inability to fight bacteria with polysaccharide membrane components that need opsonization

• Ogden Bruton (1957) characterized X-linked absence of antibodies

• Bruton's Tyrosine Kinase (BTK) is essential in pre-BCR signaling. It is one of the downstream proteins when the heavy and nascent/decoy light chain assemble needed to show that it functions

• XLA X-linked agammaglobulinemia

• Women randomly deactivate one chromosome early in embryonic development, creating mosaic patchworks of cells. In XLA, only the B cells that receive the functional copy develop

Other components can be dysfunctional in rarer versions of XLA, in order or frequency: 1/ Igu 2/ lambda light chain 3/ Ig\alpha/Ig\beta (heterodimer with ITAMs necessary for internal signaling of BCR) 4/

T-cell / B-cell activation based defficiencies

Defects in class switching - hyper-IgM syndrome

On set grouped together by pathologies of CD40L - CD40 pathway:

• Most common is CD40L (on activated T-cells), necessary for eg. AID via CD40
• CD40L defficiencies also prevent crosstalk with macrophages / dendritic cells, dampening ILC1 response
• truly "combined" susceptability to pyogenic bacteria and intracellular bacteria

CD40 itself NEMO

Severe Variable ID are characterized by late onset, smaller issues usually with just a single isotype and scoped to B-cell:

• Mutations with TACI (interacts with APRIL and BAFF produced by T cells)
• Mutations with ICOS (present on activated T cells and necessary for B cell)
• Hyper IgE production (Jobs syndrom) - STAT3 dysfunction, leading to reduced ICL3 module. Lack of T_H17 cells might prevent inhibition of T_H2 and too much IgE

Immune Module Cytokine Defficiencies

• IL-12 + IFN-\gamma receptor mutation -> susceptibility to Salmonella, Mycobateria, Listeria

• IL-17F / IL-17RA mutation -> susceptibility to Staphylococcus aureusa and Candida albicans

Malfunctions with cytolytic pathway

Shows the complexity and number of moving pieces with effective release of eg. perforin:

1/ Acivation 2/ Polarization (movement of endosome to membrane) 3/ Docking 4/ Priming (making content of membrane "fusion competent") 5/ Fusion (of endosome with membrane)

Defects with intracellular trafficking:

• Chediak-Higashi syndrome
• Griscelli syndrome

Also cause issues with melanocytes (skin pigment) and vision (eye pigment) in many cases. Many

The lack of active immunity stimulates macrophages. Macrophages cause so much inflammation that they start eating blood cells

hemophagocytic lymphohemocytosis

Failure to curb EBV

• Epstein-Barr Virus infects 95% of people
• Usually reduced to a latent state within B-cells by healthy NK / T / NKT response
• XLP (X-linked lymphoproliferative) causes expansion of EPV infected B/T cells + lack of antibodies

T-cell <> antigen presenting cell NK-cell <> target cell SLAM mediates interaction dysfunctional SAP prevents SLAM

Dendritic cells

T cells suffer

The two population validated genetic targets are:

GATA2

Kind of unclear but probably involved in maintaining stem cell progenitors.

Has two forms:

• autosomal recessive (two bad copies)
• autosomal dominant negative (one bad copy)

IRF8

Specific defect with dendritic cells rather than progenitor. DNA binding transcription factor.

Complement

Recall pathways

• Classic
• Mannose binding lectin
• Alternative (constant, low-rate "tick over" that provides blood surveillance)

All converge to C3 cleavage and membrane attack components C5-9.

Different complement disease

C3 - increased susceptibility to pyogenic bacteria

Membrane attack proteins (C5-C9) result almost exclusively in susceptibility to Neisseria

• Japan population - 1 / 2e6 -> 1/200 risk when these proteins are mutated

classic complement - more immune complexes (eg. clumps of matter in kidney? SLE)

MBL - (common, ~5% of population) more risk of bacterial infection

control proteins - complement covers self cells, eg. blood cells in paroxysmal nocturnal hemoglobinuria

Phagocytic cells

These are generally bad. Four major types:

1/ Development 2/ Adhesion 3/ Activation 4/ Killing

Development

• Severe Congenital Neutropenia (SCN)
• Cyclic Neutropenia

With SCN, 3-5 * 10^9 per liter to like 0.5 * 10^9

ELA2/neutrophil elastase.

• Mostly caused by defects in the "primary" granules (azurophilic granules, stained blue with Romanowsky/ methylene blue stains)

• autosomal dominant mutation causes one form of SCN

• Still don't undertand what causes the cycles (~21 day, 3 week periods?) in the cyclic flavor.

Variety of autosomal recessive variants

• Kostmann's disease

Can also gain neutropenia with therapies - eg. chemo, cancer, aplastic anemia (condition of bone marrow that cause defficiency in immune cell production) OR part of other combined ID.

Adhesion

The migration to infection is a multi step process and any damaging any component can lead to problems

Rolling -> Firm adhesion -> activation and "lock" of integrin

LAD2 -> LAD1 -> LAD3

1/ glycosylated ligands needed for selectin mediated rolling 2/ missing piece of \beta integrin (CD18) 3/ induction of high affinity state of \beta integrin

Activation

TLRs play central role. High amount of redundancy and remarkably only defects with TLR3 actually cause problems. Susceptibility to HSV and can cause brain swelling (encephalitis).

Also other PRR (pattern recognizing receptors)

Killing / Ingestion

Defects in the ROS. Result in chronic granulomatous disease.

Actually showed that oxides themselve are insufficeint to kill but create a low pH environment that allow true microbicidal peptides to kill.

Regulators of inflammation

Pyrin:

• apoptosis of inflammatory cells
• inhibit secretion of IL-1\beta

Inflammasome:

Functions:

• releases inflammatory cytokines, by processing eg. pro IL-1\beta into active form
• causes programmed cell death, via cleaved caspase

Structure:

• NLRP3 is a "sensor" protein
• forms a pinwheel structure

Diseases:

• Familial Mediterranean Fever - lack of pyrin.
• pyogenic arthritis, pyoderma gangrenosum and acne (PAPA) - another lack of pyrin
• TNF-receptor associated periodic syndrome - lack of TNF receptor, high TNF-\alpha. Treated by TNF blockers, like those developed for RA.
• Muckle-Wells / familial cold autoinflammatory syndrome (FCAS) - defects in NLRP3, causing inflammasome to be "on" more than it should

HSC transplantation

You can get autoimmunity in two broad directions, mostly caused by MHC mismatches:

• graft vs host: when immune cells from transplant attack host
• host vs graft: where immune cells in the graft attack transplant

Depletion by chemotherapy is common, but the extent or use of cytotoxic pre treatment depends on the disease. Some diseases require complete elimination of immune cells because they were already dysfunctional.

(like XLA, the B-cell abnormality that leads to HSV)

Somatic gene therapy began by the use of retroviruses to insert corrections. However, strong enhancers in genetic cargo misinserted upstream of proto-oncogenes, causing leukemia.

Broad corrections:

• ex-vivo editing, driven by iPSC reprogramming to make new HSC
• expression systems that can be shut down

How different pathogens evade immune system

• HIV. virus
• tuberculosis (Mycobacterium). bacteria.
• malaria (Plasmodium falciparum). protozoa

Extracellular evasion strategies

Gram negative. LPS. TLR-4. Gram positive. Peptidoglycan. TLR-2 + NOD1/NOD2.

Outside:

• Modifications to LPS lipid-A base/core. TLR-4 antagonism instead of agonism.
• Modulation of peptidoglycan.
• Carbohydrate shell to both evade TLR-2 and opsinisation/phagocytosis.
• Significant carb variation on eg. Streptococcus
• DNA rearrangement on E coli, Neiserria leading to carb / pillus variation

Misc.:

• Blocking C3 cleavage
• Protein A. Fc-binding proteins that interfere with antibodies
• Factor H. Prevent complement binding. Decorated on bacterial surfaces.

Intracellular evasion strategies

• Prevention of phagolysosome formation

• Escape phagosome

• Resistance to microbicidal compounds

• Listeria escape into cytosol. Hijack actin push membrane bound packets to other cells.

• Salmonellaa release factors to prevent destruction of their vacuole

• Tuberculosis prevents fusion with phagosome

Two types of lepropsy, with different response types:

• Tuberculoid lepropsy
• Lepromatous lepropsy

Protozoans

Theme here is evasion

• Trypanosoma brucei constantly cycle the glycoprotein they express allowing variants to survive under selection of antibody. Cycles of antigen clearance eventually lead to coma ("sleeping sickness")
• Plasmodium moves from the liver to the blood cells, creating moving target for disease
• Leishmania major prevents release of IL-12 by macrophage host, suppressing NK activation + T_H1 differentiation in type-1 response

RNA virus

• plasmacytoid DCs + NK cells before T_H1 + CD8 T cells are ready
• RNA polymerases have higher error rate -> viral chromosome is smaller
• RNA chrom also tend to be segmented
• antigenic drift - mutation of epitope
• antigenic shift - exchange of segmented

Influenza - Hepatitis C virus (HCV), leading cause of liver cirrhosis

• CD81 binding glycosylated protein that is difficult to bind to

DNA virus

• Lower mutation rates -> larger genomes -> more machinery to evade/subvert
• Many enter latency allowing them to escape recognition for long periods with cyclic reactivation

9/10 people are infected by the 5 common types of herpesvirus:

• HSV-1 (mouth)
• HSV-2 (genitals)
• EBV (mononucleosis / "mono")
• varicella-zoster
• cytomegalovirus (CMV)

Evasion Mechanisms

immunoevasins are class of proteins preventing peptide display

• Disrupting various steps of loading and presenting antigens (redirect to degradation in the ER) 1/ TAP transport/peptide entry to ER 2/ movement of MHC to cell surface 3/ dislocation (degradation of MHC)

Inhibiting cytolysis by NK cells normally caused by lack of MHC expression with decoy MHCs.

Cytokine disruption:

• Decoy receptors
• Receptor inhibitors
• JAK/STAT inhibition
• expression inhibition
• cyotkine induced TF inhibition
• direct antagonism of cytokine itself
• decoy cytokines, eg. cmvIL-10

Chemokine disruption:

• Decoy receptors (herpesvirus + poxvirus display >40 homologs)

CMV / HCV shown to increase PDL1.

Recall cheomkine receptors are exclusively GPCR (7 transmembrane spanning). While cytokine receptors are single transmembrane protein (also associated with STAT).

AIDS

Zoonotic infection with at least four crossover events, two of which were in the early 1900s, likely from lowland gorillas or chimpanzees.

HIV-1/HIV-2

Structure

3 major genes

gag

pol (alone encodes replication tools)

• reverse transcriptase
• integrase
• viral protease

env gp120 + gp41 (trimers alongside the envelope)

6 regulatory genes Tat + Rev are essential for early replication Nef Vif Vpr Vpu are necessary for efficient viral production

What determines if it enters latent or actively replicating state? Maybe determined by the state of the infected cell itself

CD4 cells are long lived in contrast to macro + DCs. Difference in state there provide clues for quiescence

Replication mechanics

NFkB + NFAT both used to induce expression of proviral genes (nuclear factor of activated T cells) Recall:

• NFkB is common across most immune cell types
• NFAT is specific to T cells and primarily induced by direct TCR stimulation

(Bind directly to the promoters in the proviral LTR - these are functional!, not just scars for integrase recognition)

Tat and Rev reveal important eurkaryotic replication components:

• Tat phosphorylates RNA polymerase (in combination with cyclin T1 + CDK9), to enable the enzyme to produce full length transcripts
• Rev is necessary to shuttle unspliced mRNA for later viral components out of the nucleus. It binds to motifs on later unspliced transcripts and recruits

The smaller regulatory genes:

• decrease expression of surface proteins like MHC I/II, allowing invasion
• prevent cytidine deaminase (APOBEC) from mutating transcript

Where in the body replication happens

Usually in sex fluid or blood. Free virus or within one of the cells listed.

genital + gastrointenstainal mucosae are primary sites of sexual transmission

• initial contact with memory T cells + DCs
• spread to lymph
• from the lymph the entire bloodstream

Tropism

Variants have affinity for CCR5 or CXCR5. (a la R5 or X4).

Needs to get to the CD4 immune cells in the lamina propria. So transcytosis through epithelial cells + traveling through "interdigitating" DCs.

• gp120 binds to proteins on both squamous and columnar epithelia
  • squamous -> vagina mucous, penis foreskin, ectocervix, rectum, oropharynx, esophagous
  • columnar -> endocervix, rectum, upper GI
• DC receptors:
• langerin (CD207)
• mannose receptor (CD206)
• DC-SIGN

1/ acute phase (influenza like illness

• rapid replication of virus in mostly CCR5+ CD4+ T cells
• population quickly declines
• immune cell depletion in GALT leads to further infection (in particular IL-17

• IL-22 no longer around to promote tight epithelia) 2/ asymptomatic phase (~10 years)

• seroconversion (first point antibodies detected)

Genetic resistance

Non function variant of CCR5 in Caucasians confers some resistance (not cure but decreases rate of progress) and suggests some past selection. Some suggest small pox and bubonic plauge provided selection.

Development of AIDS

After the initial depletion, T cells recover. But after the variable period, they start to decline again:

• CD8 T cells kill virus infected T cells
• latent virus awakening + killing T cells
• disruption of new T cell development in thymus

Immune activity does help. Type 1 response (IFN-\gamma + granzyme B) inversely correlated with viral presence in blood ("viral load"). The irony is these are the very cells the virus kills off slowly...

Anti-retrovirals are somewhat effective

Neutralizing antibodies do develop but generally later (after first year). Vaccines therefore might be promising

ADCC mediated (non-neutralizing) antibodies also recruit NK, macrophage, neutrophils.

Virus mutates a lot, making antibody mediated response challenging

Reservoir in lymph tissues

• Within CD4 T cell, macrophage, neutrophil (latter are shorter lived and not major holders)
• Immune complexes actully form on the surface of follicular DCs in lymph

Genetic resistance

Some people (1 / 300) live with latent virus and never progress to AIDS. Strongest loci are HLA traits, presumably enhancing presentation of virus and preventing their silent latent state.

What kinds of diseases

• Candida (oral fungal infection)
• tuberculosis

Cancers:

• EBV induced lymphomas
• Kaposi sarcoma (induced by HIV)

In both cancers, the viruses don't actually introduce mutation but induce survival that select for oncogenetic mutation)

How do we treat it?

Target:

• reverse transcriptase
• integrase
• protease (required for creating functional product)

HAART (Highly active anti-retroviral therapy)

Can prevent infection of new cells. But cannot remove integrated provirus.

Combination therapy, eg. a cocktail of different inhibitors, called HAART. Showed success starting in 1995. Must take for life.

• Releases T cells trapped in lymph tissue
• Decreases CD4 cell killing by CD8 T cells
• Somehow new T cells emerge from thymus

Can detect these with TRECs (T cell receptor excision circles) - the little loops that form during somatic hypermutation.

New drugs also target viral integration + cDNA creation. Do not deplete latent reservoir

Targeting reservoirs

• Try to tease out virus by activating provirus. (Clincal data does not show efficacy over HAART alone)
• Cytokines (TNF-\alpha, IL-1) or histone acetylation to active proviral genes

Berlin patient HCST to inject T cells with CCR5 mutation. Progression free for 5 years. Risk of CXCR4-tropic variant mutation. Also impractical as population level cure.

Vaccines are difficult

Two types of vaccines:

• Prophylactic. What variant to you target? If you do generate antibodies, it is hard for them to bind glycoproteins on HIV.
• Already infected. If you increase antibody + CD8 T cell response, still hard to clear virus.

Other vaccines use broken viruses of the type they are treating. Cannot do this with HIV because of high mutation rate + risk of recombination Use "canary" virus - AAV, vaccinia

delivery gag,pol,env genes with canarypox vector:

• only vaccine that has any efficacy
• data shows type of response useful - non-neutralizing for ADCC. (this is good because neutralizing kind are hard to develop)