Induced Innate Immune Responses Study Notes

PRRs are essential components in the innate immune system that recognize pathogen-associated molecular patterns (PAMPs).

Kinase: A type of enzyme that adds phosphate groups to other molecules, typically proteins.
Phosphorylation: The process of adding a phosphate group to a molecule, often used in cellular signaling.
Ubiquitination and Proteasomal Degradation: Ubiquitination is a process where a ubiquitin protein is attached to a substrate protein, marking it for degradation by the proteasome.
Adaptor Proteins: Proteins that mediate protein-protein interactions, facilitating signaling cascades.
Scaffold Proteins: Proteins that provide a platform for the assembly of signaling complexes.
Transcription Factors: Proteins that bind to specific DNA sequences to regulate gene expression.

Innate Immunity (Pattern Recognition Receptors) vs. Adaptive Immunity (Antigen Receptors)
Receptor Characteristic:
- Specificity inherited in the genome: Yes (Antigen Receptors), No (Pattern Recognition Receptors)
- Triggers immediate response: Yes (Pattern Recognition Receptors), No (Antigen Receptors)
- Recognizes broad classes of pathogens: Yes (Pattern Recognition Receptors), No (Antigen Receptors)
- Encoded in multiple gene segments: No (Pattern Recognition Receptors), Yes (Antigen Receptors)
- Requires gene rearrangement: No (Pattern Recognition Receptors), Yes (Antigen Receptors)
- Clonal expression: No (Pattern Recognition Receptors), Yes (Antigen Receptors)
- Capable of discriminating between closely related molecular structures: Yes (both)

Four Canons of Inflammation:
- Pain
- Redness
- Heat
- Swelling
Mechanisms of Inflammation:
- Dilation of local blood vessels increases blood flow.
- Activation of endothelial cells to express adhesion molecules.
- Increase in vascular permeability promotes migration of leukocytes into tissue and the leakage of effector proteins and molecules.
- Blood clotting acts as a physical barrier.
- Induced by pro-inflammatory cytokines produced by tissue macrophages.

Types of Leukocytes: Neutrophils migrate first, followed by monocytes.
Attraction: Leukocytes are attracted by lipid mediators, cytokines, and chemokines.
Process:
- Extravasation: Monocytes bind to adhesion molecules on the vascular endothelium near the infection site and receive chemokine signals.
- Monocytes migrate into surrounding tissue and differentiate into inflammatory monocytes at the infection site.

Localization of PRRs: Found at cell surfaces/endosomes as well as cytosolic.
Ligands: PAMPs that activate signaling pathways.
Ultimate Outcomes:
- Activation of transcription factors leading to pro-inflammatory cytokine production.
- Activation of pro-inflammatory caspases leading to cytokine maturation and secretion, and pyroptosis.
Specific PRRs:
- Toll-like receptors (TLRs), identified in the 1990s and 2000s.
- RIG-I-like receptors (RLRs), discovered 2005-2006.
- NOD-like receptors (NLRs), identified in the 2000s.
- AIM2-like receptors (ALRs), discovered in 2009.
- cGAS-STING axis, discovered between 2008 and 2012-2013.

Recognized for contributions to the understanding of the innate immune response by researchers Bruce A. Beutler and Jules A. Hoffman.
Role in innate immune recognition includes:
- TLR-1:TLR-2 heterodimer: Recognizes lipomannans from mycobacteria.
- TLR-2:TLR-6 heterodimer: Recognizes diacyl and triacyl lipopeptides from bacteria.
- TLR-3: Recognizes double-stranded RNA from viruses.
- TLR-4: Recognizes lipopolysaccharides (LPS) from Gram-negative bacteria.
- TLR-5: Recognizes flagellin from bacteria.
- TLR-7 and TLR-8: Recognizes single-stranded RNA from viruses.
- TLR-9: Detects DNA with unmethylated CpG from bacteria and DNA viruses.
- TLR-10 (human only) and TLR-11, TLR-12, TLR-13 (mouse only) have specific ligand interactions yet to be defined.

Induces TLR dimerization or conformational change in pre-formed dimers to initiate signaling.

First Step: LPS-binding protein extracts LPS from Gram-negative bacteria outer membrane; LPS is transported to TLR4-MD2 complex through co-factor CD14.
Second Step: LPS binding induces TLR4 dimerization, facilitating downstream signaling.
Recruitment: Dimerized TLR4 recruits adaptor proteins (MyD88 and/or MAL) via TIR interactions.
Oligomerization: MyD88 oligomerizes, recruiting serine/threonine kinases (IRAK1 and IRAK4) through death domain interactions.
Further Recruitment: Active IRAKs recruit E3 ligase (TRAF6) and heterodimeric E2 (Ubc13/Uev1A).
TAK1 Activation: K63-polyubiquitinated TRAF6 serves as a platform to recruit and activate TAK1 kinase, phosphorylating MAPK, leading to the activation of the AP-1 transcription factor.
IKK Complex Recruitment: IKK/NEMO is recruited by binding to K63-polyubiquitin chains; TAK1 phosphorylates IKKβ, leading to the degradation of IκB (inhibitor of NFκB).
Translocation: Phosphorylated IκB degrades through K48 ubiquitination, allowing NFκB to translocate to the nucleus and induce expression of pro-inflammatory cytokines, chemokines, and antimicrobial peptides.

TLR3 Activation: Significantly recruits adaptor protein TRIF instead of MyD88, activates TRAF3 for K63 polyubiquitin chain production, leading to TBK1 activation which phosphorylates IRF3 to initiate type I interferon gene transcription.
RLRs: RIG-I and MDA5 act as intracellular sensors of viral RNA, promoting production of cytokines and interferons.
- RIG-I binds to 5’-triphosphate viral RNA; MDA5 binds to long viral dsRNA.
CGAS-STING Axis: Intracellular sensors respond to dsDNA from viruses, activating cGAMP production, which triggers STING signaling, leading to IRF3 phosphorylation and type I interferon expression.
NLRs (NOD-like Receptors): Detect peptidoglycan and initiate NF-κB signaling to manage bacterial infections.
- NLR Inflammasomes: Intracellular sensors that mediate stress responses, activate caspase-1 for IL-1 and IL-18 secretion, also triggering pyroptosis.

Gasdermins exist as autoinhibited forms in cells; upon cleavage by inflammatory caspases, they form pores in the plasma membrane, allowing the release of cytokines and other cellular contents.