Human Autoinflammatory Diseases Mediated by NLRP3-, Pyrin-, NLRP1-, and NLRC4-Inflammasome Dysregulation Updates on Diagnosis, Treatment, and the Respective Roles of IL-1 and IL-18

Abstract

Recent research has led to novel findings in inflammasome biology and genetics that altered the diagnosis and management of patients with autoinflammatory syndromes caused by NLRP3-, Pyrin-, NLRP1-, and NLRC4-inflammasomes and spurred the development of novel treatments. The use of next-generation sequencing in clinical practice allows for rapid diagnosis and the detection of somatic mutations that cause autoinflammatory diseases. Clinical differences in patients with NLRP3, pyrin, and NLRP1 inflammasomopathies, and the constitutive elevation of unbound free serum IL-18 that predisposes to the development of macrophage activation syndrome (MAS) in patients with gain-of function mutations in NLRC4 led to the screening and the characterization of novel diseases presenting with constitutively elevated serum IL-18 levels, and start to unravel the biology of "high IL-18 states" that translate into the use of biomarkers that improve diagnosis and monitoring of disease activity and investigations of treatments that target IL-18 and IFN-gamma which promise to improve the management and outcome of these conditions. Lastly, advances in structural modeling by cryo-electron microscopy (cryo-EM) of gasdermin, and of NLRP3- and NLRC4-inflammasome assembly, and the characterization of post-translational modifications (PTM) that regulate inflammasome activation, coupled with high-throughput screening (HTS) of libraries of inflammasome-inhibiting compounds, promise a new generation of treatments for patients with inflammasome-mediated diseases.

Keywords: GSDMD; NLRC4; NLRP1; NLRP3; autoinflammatory diseases; inflammasome; pyrin.

Figure 1

Domain structure and activation of inflammasomes that cause human diseases. (A) The inflammasome sensors are tripartite proteins with an amino-terminal PYRIN (PYD), CARD, or BIR domain, a nucleotide-binding NACHT domain, and a carboxy-terminal leucine-rich repeat (LRR) domain. Intracellular sensors, including NLRP3, NLRP1, Pyrin, and NLRC4/NAIP, oligomerize upon stimulation and recruit and activate pro-Caspase-1 (pro-Casp-1), which cleaves proinflammatory cytokines (pro-IL-1β, pro-IL-18, not shown), and gasdermin-D (GSDMD). All sensors except for pyrin, have a “NACHT domain” that includes an NBD, an HD1, a WHD1 and a HD2 domain (shown in black box). (B) The 3D cryo-EM structure of the gasdermin D pore is shown (left panel); 27 cleaved N-terminal gasdermin fragments assemble a 27-multimeric ring, the gasdermin pore. The cryo-EM structures of NLRP3 (middle panel) and NLRC4-NAIP (right panel) demonstrate assembly of 11 or 12 NLRP3 or NLRC4/NAIP monomers through self-oligomerization into a disc-like structure. NLRP3 binds to NIMA-related Kinase 7, NEK7; NLRC4 binds to NAIP, which is a sensor of microbial flagellin, and of components of the bacterial Type III injection system. (C) Inflammasome activation. Canonical NLRP3 inflammasome activation requires a first or “priming” step which encompasses pattern recognition receptor/cytokine induced transcriptional upregulation of pro-IL1B and genes of some NLRP3 inflammasome components. The second step that leads to NLRP3 activation can be K+ efflux-dependent or independent and eventually leads to mitochondrial stress and the production of oxidized mitochondrial DNA (Ox-mtDNA); its production is controlled by the rate-limiting enzyme UMP-CMPK2. Non-canonical inflammasome activation is triggered by caspase-4/5 in humans (and caspase-11 in mice) that cleave GSDMD but not the pro-inflammatory cytokines and induces pyroptosis without priming step 1. Furthermore, activation of the RIPK3-MLKL pathway mediates necroptosis and alternative activation through FADD-Caspase-8 induces apoptosis and triggers inflammatory cytokine release through NLRP3 activation. One hypothesis to reconcile how different NLRP3 activating signals activate the inflammasome is through the common generation of mitochondrial distress and the release of Ox-mtDNA. (D) Post translational modifications of NLRP3 and ASC control inflammasome activation and have become targets for drug development. In resting macrophages, the LRR domain of NLRP3 is ubiquitylated. Deubiquitylation by the deubiquitinating enzyme (DUB) BRCC3, and dephosphorylation by protein tyrosine phosphatase, PTPN22 promote NLRP3 oligomerization while the E3 ubiquitin ligases, MARCH7, and FBXL2, ubiquitinate the NLRP3 LRR domain to inhibit NLRP3 inflammasome activation. The NACHT domain is modified by phosphorylation and dephosphorylation at serine residues, p.S194 and p.S293 by JNK1, and PKD, respectively, which activate, while phosphorylation or ubiquitylation at sites modified by PKA and ARIH2, respectively, inactivate the NLRP3 inflammasome. Modifications of the PYD domain at a Lys48-linked ubiquitylation site by the E3 ubiquitin ligase, TRIM31, cause proteasomal degradation of NLRP3 whereas dephosphorylation at p.S5 by PP2A and desumoylation by SENP6/SENP7 promote NLRP3–ASC, NLRP3 PYD–PYD interactions and inflammasome activation. Six conserved sumoylation loci keep NLRP3 in a resting state; desumoylation by SENP6/7 promotes NLRP3 activation. (E) Presumed drug-NLRP3 interaction sites are depicted. The MCC950 mechanism of action is unknown, while Tranilast, a tryptophan analog binds to the NACHT domain and inhibits NACHT-NACHT interaction between NLRP3 monomers. Oridonin binds to the NACHT domain and blocks NLRP3 and NEK7 interaction. A group of direct NLRP3 inhibitors including OLT1177 (Dapansutrile), a β-sulfonyl nitrile compound, block the NACHT ATPase activity. Residue numbers refer to human protein (ENST00000336119). (A,B): B, Pyrin B-box; B30.2, Pyrin B30.2 domain; BIR, Baculovirus IAP-repeats; CARD, Caspase Recruitment Domain; Casp-1, Caspase 1; C-C, coiled-coiled domain; CT, C- terminal domain of gasdermin; FIIND, Function to Find Domain; HD1, Helical Domain 1; HD2, Helical Domain 2; LRR, Leucine Rich Repeat; NACHT, NAIP/C2TA/HET-E/TP1; NBD, nucleotide-binding domain; NT, N- terminal domain of gasdermin; PYD, pyrin domain; P20, protein 20; P10, protein 10; WHD, Winged Helix Domain. (C): CASP1, caspase-1; CASP4/5, caspase-4/5; CASP8, caspase-8; FADD, Fas-Associated protein with Death Domain; GM-CSF, Granulocyte-monocyte colony stimulating factor; GSDMD, Gasdermin D; LPS, Lipopolysaccharide; MLKL, mixed-lineage kinase domain-like protein; NFkB, nuclear factor-kB; NOD2, nucleotide-binding oligomerization domain-containing protein 2; oxPAPC, oxidized phospholipid 1-palmitoyl-2-arachidonoyl-sn-glycerol-3-phosphorylcholine; P2X7, purinoceptor 7; PRR, Pattern recognition receptor; RIP1, receptor-interacting protein 1; RIPK3, receptor interacting protein kinase 3; TLR, Toll-like receptor; TNFR1, tumor receptor factor receptor 1; TNFR2, tumor receptor factor receptor 2; UMP-CMPK2, Cytidine Monophosphate Kinase 2. (D,E): ARIH2, Ariadne homolog 2; BRCC3, BRCA1/BRCA2-containing complex subunit 3; FBXL2, F- box/LRR- repeat protein 2; JNK1, c-Jun N-terminal kinase 1; MARCH7, membrane-associated RING finger protein 7; NEK7, NIMA related kinase 7; PKA, protein kinase A; PKD, protein kinase D; PP2A, protein phosphatase 2A; PTPN22, protein tyrosine phosphatase, non-receptor type 22; SENP6/SENP7, Sentrin/SUMO-specific protease 6/7; TRIM31, tripartite motif containing protein 31.

Figure 2

Inflammasomes and inflammasomopathies. GOF mutations in Inflammasome sensors (NLRP3, Pyrin, NLRC4, NLRP1) cause systemic autoinflammatory diseases. While GOF mutations in NLRP3, pyrin, and NLRP1 lead to predominantly IL-1b activation (A), GOF mutations in NLRC4 lead to IL-1b activation and very high IL-18 levels (B). (A) GOF mutations in NLRP3 cause the cryopyrin-associated autoinflammatory diseases (CAPS) (images depict conjunctivitis, MRI with leptomeningeal enhancement in NOMID patient with aseptic neutrophilic meningitis and neutrophilic urticarial rash) and secondary NLRP3 inflammasome activation by recessive LOF mutations in LPIN2 has been linked to the generation of a metabolic triggers/stress () that cause Majeed syndrome (depicted is sterile osteomyelitis of the growth plates, the disease is not discussed in the text). Additive GOF mutations in pyrin cause familial Mediterranean fever (FMF) (depicted are abdominal adhesions that can develop in chronic sterile peritonitis and erysipelas-like erythema of the ankle in FMF) or Pyrin-Associated Autoinflammatory with Neutrophilic Dermatosis (PAAND) (depicted is cystic acne and pyoderma gangrenosum in a patient with neutrophilic dermatitis), and secondary pyrin inflammasome activation is caused by LOF mutations in MVK that cause Mevalonate kinase deficiency (MKD) (depicted is lymphadenitis and a papular rash). GOF mutations in NLRP1 cause NLRP1-Associated Autoinflammation with Arthritis and Dyskeratosis (NAIAD) (depicted is follicular dyskeratosis, hyperkeratosis of the soles and lesions on left hand). (B) GOF mutations in NLRC4 cause the NLRC4-Associated Autoinflammatory Disorders (NLRC4-AID) associated with often ultra-high serum IL-18 expression which predisposes to the development of MAS [images depict the rash from a patient with NLRC4-associated macrophage activation syndrome (MAS)]. Other high IL-18 states include CDC42 mediated autoinflammatory disease (depicted are mild facial dysmorphisms including frontal bossing and nasal bridge depression); IL-18 PAP-MAS (a subset of SOJIA-ILD), an autoinflammatory disease without known genetic defect (depicted are a chest CT scan with interstitial lung disease and clubbing of the fingernails). For the 2 latter diseases, increased NLRC4 inflammasome activation as cause of the high IL-18 has not been demonstrated. (A,B) Inflammatory markers during MAS and CAPS flares differ. Flare episodes in patients with CAPS (C) differ from flare episodes in patients with high IL-18 levels (shown in a patient with NLRC4-AID in D). ESR and CRP are similarly elevated in both diseases, in MAS other features include elevated ferritin and LDH, and cytopenias (leukopenia, thrombocytopenia); while in CAPS, ferritin and LDH increase little if at all and patients develop leukocytosis and thrombocytosis. (The shaded area shows longitudinal laboratory markers collected during a 2-week period during a disease flare). CAPS, Cryopyrin-Associated Periodic Syndrome; CDC42, Cell Division Control protein 42 homolog; FMF, Familial Mediterranean Fever; IL18-BP, IL-18 binding protein; IL-1Ra, IL-1 receptor antagonist; MKD or HIDS, Mevalonate Kinase Deficiency or Hyper-IgD Syndrome; NAIAD, NLRP1 Associated Autoinflammation with Arthritis and Dyskeratosis; NLRC4-AID, NLRC4-Associated Autoinflammatory Disorders; NOMID, Neonatal-Onset Multisystem Inflammatory Disease; PAAND, Pyrin-Associated Autoinflammatory with Neutrophilic Dermatosis; PAP-MAS, Pulmonary Alveolar Proteinosis-Macrophage Activation Syndrome; PRR, Pattern recognition receptor.