Pattern-recognition Pattern recognition and anti-viral anti viral innate immunity

1. Introduction
(1). Immunity innate and adaptive

Self and non-self Specific and non-specific Protective and non-protective

(2). Host anti-viral immunoresponse

Innate a e immunity: u y co common o to o all viruses-why

adaptive immunity: specific to individual viruses

(3) Viral Replication Cycle (3).

Common molecular patterns of viral and host origin produced during replication of an RNA virus: RNA (ssRNA and dsRNA) Viral glycoproteins Host RNA modified Others

(4) Anti (4). Anti-viral viral innate immunity

I t f Interferon (IFN)
Group 1: IFN-a and IFN-b Group 2: IFN-g

Proinflammatory response
Cytokines Chemokines Other soluble factors

2. Pattern-recognition receptor (PRR) signaling (1). Summary of the pathways

Viral nucleic acid

(2). ( ) Two main PRR families

Toll-like (TLR): TLR3, 7, 9 RIG-I-like (RLR): RIG-I ( retinoic-acid-inducible gene I) Mda5 (melanoma differentiation-associated gene 5) LGP2 (laboratory of genetics and physiology 2)

(3). Sensing of different classes of viruses

Viruses with a double-stranded DNA (dsDNA) genome
-dsDNA-TLR9 and presumably other cytoplasmic DNA receptors. -dsRNA dsRNA (by convergent transcription)-TLR3 transcription) TLR3, PKR, PKR MDA5 and/or RIG-I RIG I

Viruses with a dsRNA genome

-TLR3, MDA5.

Single-stranded RNA (ssRNA) viruses with a positive-sense RNA genome

-produce a dsRNA intermediate during replication -MDA5 in the cytoplasm (picornaviruses, such as poliovirus and hepatitis A virus). -RIG-I (flaviviruses, such as, hepatitis C virus and West Nile virus) -either either RIG RIG-I I or MDA5 (SARS (SARS-CoV) CoV)

Retroviruses (such as HIV-1 and human T-lymphotrophic virus)

-a special group of positive-sense ssRNA viruses that reverse transcribe their RNA into DNA, which is then integrated g into the host g genome) ) -HIV-1 ssRNA is sensed by TLR7 and TLR8. -a role for RLRs or possibly cytoplasmic DNA receptors has not yet been investigated.

Negative-sense ssRNA viruses (such as influenza virus)

-produce produce very limited amounts of dsRNA during their life cycle -ssRNA genome can activate RIG-I.

3. IL-1 receptor/TLR superfamily

(1). Subgroup 1: interleukin 1 receptor

(2). Subgroup 2: TLR

(3). ( ) Adaptor p protein p

(4) Th (4). The TLR d domain i

(5). Conserved mechanisms for signaling in IL IL-1R/TLR 1R/TLR superfamily

(6). Viral evasion of TLR signaling

4. RIG-I-like receptor (RLR) family

(1). RIG-I ligands
- 9 types of ligands, 3 groups. - some ligand types are specific to type of virus.

(2). Main domains and adaptor of RIG-I

The main adaptor adaptor: MAVS (also known as VISA, IPS1 and Cardif)

(3) S (3). Structure of fC C-terminal i l domain d i of f RIG-I RIG I

The core of the structure is formed by a sheet comprised of six central antiparallel st strands a ds (3 3-8). 8) Another ot e a antiparallel t pa a e s sheet eet (b (b1,2,9) , ,9) is s located ocated o on top o of t the e ce central ta sheet and flanks 1 and 2 together with the central b sheet.

(4). Binding specificity of C-terminal domain of RIG-I

(5) RNA-binding (5). RNA binding sites in C-terminal C terminal domain of RIG-I RIG I

dsRNA-binding sites

5ppp ssRNA-binding sites

(6). Working model 1: activation of RIG-1 by binding to viral RNA

(7). Working model 2: enhanced activation of RIG-1 by binding to viral RNA and unanchored K63 polyUb

(8). Self-control: regulation by LGP2 (1)

(8) Self (8). Self-control: control: regulation by LGP2 (2)

(9). Viral evasion of RLR signaling

(10). Viral inhibition of IRF3/IRF7

(11). Multiple functions of viral proteins

(12). Example-RIG-I recognition of HCV RNA (1)

(12). Example-RIG-I recognition of HCV RNA (2)

5. Intracellular DNA recognition

(1) Recognition of intracellular DNA triggers (1). two pro-inflammatory pathways

(2). DAI and RLR family in recognition of intracellular DNA

(3). Recognition of DNA-containing immune complexes p

(4). Summary of the proposed mechanisms of intracellular DNA sensing

6. Interferon-inducible antiviral effectors

(1) I (1). Interferon f receptor signaling i li

(2). Domain structure of antiviral proteins

(3). ISG15 ubiquitin-like pathway

(4). MxGTPase pathway

MxA (myxovirus-resistance A)

(5). 2,5-oligoadenylate-synthetase (OAS1)di directed t d ribonuclease ib l L(RNaseL) L(RN L) pathway th

(6). Protein kinase R ( PKR) pathway

6. Regulation of adaptive immunity by innate immune system

(1). Cell-extrinsic recognition of pathogens

Optimal presentation on MHC class II Induction Ind ction of co-stimulatory co stim lator molec molecules les and c cytokines tokines for activation and differentiation of T lymphocytes

(2) Cell-intrinsic (2). C ll i t i i recognition iti of f pathogens th

Processing and presentation of viral proteins on MHC class I (ER path pathway) a ) or class II (a (autophagy) tophag ) Induction of co-stimulatory molecules and cytokines for activation and differentiation of T lymphocytes

(3) Cell (3). Cell-extrinsic extrinsic recognition of infected cells

activation

Processing and presentation of viral proteins on MHC class I ( (ER p pathway) y) or class II ( (autophagy) p gy) Induction of co-stimulatory molecules and cytokines for activation and differentiation of T lymphocytes (TLR signaling)

(4). ( ) Consequences q of TLR recognition g of exogenous and endogenous ligands

7. NLRP3 inflammasome: a sensor for virus and metabolic danger

8. Two unsolved issues

1 Commensal organisms 1. 2. Rules governing protective immunoresponse

9. An example from recent studies: Influenza virus activates inflammasomes via its intracellular M2 ion channel
Takeshi Ichinohe, Iris K Pang & Akiko Iwasaki
1Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA. 2Present address: Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan. Correspondence should be addressed to A.I. (akiko.iwasaki@yale.edu).

VOLUME 11 NUMBER 5 MAY 2010 nature immunology gy

(1). Experimental design

Influenza viral infection
Step1 TLR7 Step 2 M2 Membrane perturbations K+ efflux

Endosome Synthesis pro-IL-1 Pro-IL-18 Pro-IL-33

Caspase-1
NLRP3 Inflammasome

IL-1; IL-18

(2). Data interpretation

a Induction of NLRP3-dependent a. NLRP3 dependent proinflammatory response
Step1 TLR7 Step 2 M2 Membrane perturbations K+ efflux

Endosome Increase of pro-IL-1propro-IL-33 at IL-18 and p mRNA and protein levels

NLRP3 Inflammasome

Pro Caspase 1 Pro-Caspase-1

pro-IL-1 pro-IL-18 pro-IL-33 pro IL 33

Caspase 1 Caspase-1
IL-1 IL-18 IL 33 IL-33 (In cells and culture medium)

(2). Data interpretation

b. Induction of NLRP3-independent proinflammatory p y response p

Increase of IL-6 and TNF at both mRNA and p protein levels

(3). Activation of NLRP3 inflammasome by influenza virus

Infection of Bone marrow macrophages (BMMs)

(4). Induction of other proinflammatory responses by influenza virus (1)

(4) Induction of other proinflammatory (4). responses by influenza virus (2)

(5). Activation of step 1 by Influenza virus through TLR7 but not RIG

(6) Activation of signal 1 by live Influenza virus (6). and viral RNA components

(7). ( ) Activation of signal g 2 by y live Influenza virus but not viral RNA components

(8). The M2 channel activity of influenza virus is required for inflammasome activation (1)

(9). The M2 channel activity of influenza virus is required for inflammasome activation (2)

(10). Ectopic expression of M2 channel restores IL-1 production in cells infected with M2del2931 influenza virus

(11). M2 is sufficient to trigger signal 2 for inflammasome activation (1)

(12). M2 is sufficient to trigger signal 2 (12) for inflammasome activation (2)

(13). M2 is sufficient to trigger signal 2 for inflammasome activation (3)

(14). Influenza virus M2 protein stimulates IL-1 production from cells infected with HSV-2 or Sendai virus

(15). M2 triggers inflammasomes through (15) perturbation of ionic homeostasis of the Golgi (1)

(15). M2 triggers inflammasomes through perturbation of ionic homeostasis of the Golgi (2)

References
1. Saddle AJ and BRG Williams (2008) Interferon-inducible antiviral effectors. Nature reviews Immunology 8, 559-568. 2. Bowie AG and L Unterholzner (2008) Viral evasion and subversion of pattern-recognition receptor signalling. Nature reviews Immunology 8, 911-922. 3. Takahasi K et al (2008) Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses Molecular cell 29 responses. 29, 428 428-440. 440 4. Saito T et al. (2008) Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA. Nature 454,523-527. 5. Mueller K. (2010) Recognizing the first responders. Science 327, 283 (+other papers/reviews in the special section) 6. Hornung V and Latz E (2010). Intracellular DNA recognition Nature Reviews Immunology 10, 123-130. 7. Takeshi Ichinohe, Iris K Pang & Akiko Iwasaki (2010). Influenza virus activates inflammasomes via its intracellular M2 ion channel. Nature Immunology 11