Molecular mechanisms of emerging inflammasome complexes and their activation and signaling in inflammation and pyroptosis

Abstract

Inflammasomes are multi-protein complexes that assemble within the cytoplasm of mammalian cells in response to pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns (DAMPs), driving the secretion of the pro-inflammatory cytokines IL-1β and IL-18, and pyroptosis. The best-characterized inflammasome complexes are the NLRP3, NAIP-NLRC4, NLRP1, AIM2, and Pyrin canonical caspase-1-containing inflammasomes, and the caspase-11 non-canonical inflammasome. Newer inflammasome sensor proteins have been identified, including NLRP6, NLRP7, NLRP9, NLRP10, NLRP11, NLRP12, CARD8, and MxA. These inflammasome sensors can sense PAMPs from bacteria, viruses and protozoa, or DAMPs in the form of mitochondrial damage, ROS, stress and heme. The mechanisms of action, physiological relevance, consequences in human diseases, and avenues for therapeutic intervention for these novel inflammasomes are beginning to be realized. Here, we discuss these emerging inflammasome complexes and their putative activation mechanisms, molecular and signaling pathways, and physiological roles in health and disease.

Keywords: PANoptosis; PANoptosome; autoimmunity; autoinflammation; bacteria; cancer; caspase‐1; caspase‐11; caspase‐4; caspase‐5; cell death; cytokines; gasdermin D; immunity; infection; inflammatory caspases; interferons; lipopolysaccharide; parasites; pattern‐recognition receptors; viruses.

FIGURE 1

Inflammasome‐forming proteins and related molecules in humans. Proteins that have been demonstrated to form an inflammasome are indicated by an orange‐colored wheel‐like symbol. The nucleotide‐binding domain and leucine‐rich repeat (LRR) containing gene family (NLR) are grouped based on their N‐terminal domains. At least 22 NLRs have been identified in humans. NLRA is defined by an acetyl‐transferase activity or acidic transactivation domain and has the sole member Class II, major histocompatibility complex, transactivator (CIITA). NLRB is defined by a baculoviral inhibitory repeat (BIR)‐like domain. The NLRB subfamily has one member called NLR family member apoptosis inhibitory protein (NAIP). NLRC is defined by a caspase recruitment domain (CARD) or a CARD‐like disordered region. This family contains five members: Nucleotide‐binding oligomerization domain containing 1 (NOD1, also known as NLRC1), nucleotide‐binding oligomerization domain containing 2 (NOD2, also known as NLRC2), NLRC3, NLRC4, and NLRC5. NLRP is defined by a pyrin domain (PYD). This family contains 14 members in humans: NLRP1, NLRP2, NLRP3, NLRP4, NLRP5, NLRP6, NLRP7, NLRP8, NLRP9, NLRP10, NLRP11, NLRP12, NLRP13, and NLRP14. NLRX is an NLR family with the sole member NLRX1 that carries an N‐terminal domain with no strong homology to the N‐terminal domain of any other NLR subfamily member. The N‐terminal region carries a mitochondrial localization signal (MLS). The AIM2‐like receptor (ALR) family contains the founding member called absent in melanoma 2 (AIM2). The tripartite motif‐containing (TRIM) family is defined by an N‐terminal set of domains known as the RING, B‐box‐type, coiled‐coil (CC) motif. This family has one inflammasome‐forming protein called Pyrin (also known as Mediterranean fever, MEFV or TRIM20). A CARD‐containing protein called CARD8 can form an inflammasome. The Dynamin family of large GTPases contains an inflammasome‐forming protein called Myxovirus resistance protein 1 (MxA, also known as MX1). Inflammasome assembly requires the adaptor protein called apoptosis‐associated speck‐like protein containing a CARD (ASC, also known as PYCARD). The proteases that induce proteolytic cleavage of inflammasome substrates in humans are caspase‐1, caspase‐4 and caspase‐5. bZIP, Basic Leucine Zipper domain; FIIND, Function‐to‐Find Domain; FISNA, Fish‐specific NACHT‐associated domain; GED, GTPase effector domain; HIN‐200, Hematopoietic IFN‐inducible Nuclear proteins with a 200‐amino acid motif; NACHT, Domain present in NAIP, CIITA, HET‐E, and TP‐1; SPRY, SPla/Ryanodine receptor domain; UPA, UNC5, PIDD, and Ankirins domain; ZU5, ZO‐1, and UNC5 domain. The domain structures are annotated based on UniProt, NCBI, and the published literature.

FIGURE 2

Inflammasome‐forming proteins and related molecules in mice. Proteins that have been demonstrated to form an inflammasome are indicated by an orange‐colored wheel‐like symbol. The nucleotide‐binding domain and leucine‐rich repeat (LRR) containing gene family (NLR) are grouped based on their N‐terminal domains. At least 34 NLRs have been identified in mice. NLRA is defined by an acetyl‐transferase activity or acidic transactivation domain and has a single‐member Class II, major histocompatibility complex, transactivator (CIITA). NLRB is defined by a baculoviral inhibitory repeat (BIR)‐like domain. This subfamily has seven members of NLR family member apoptosis inhibitory protein (NAIP): NAIP1, NAIP2, NAIP3, NAIP4, NAIP5, NAIP6, and NAIP7. NLRC is defined by a caspase recruitment domain (CARD) or a CARD‐like disordered region. This family contains five members: Nucleotide‐binding oligomerization domain containing 1 (NOD1, also known as NLRC1), nucleotide‐binding oligomerization domain containing 2 (NOD2, also known as NLRC2), NLRC3, NLRC4, and NLRC5. NLRP is defined by a pyrin domain (PYD), however, of the 20 members in mice, four do not carry a PYD. This family contains NLRP1a, NLRP1b, NLRP1c, NLRP2, NLRP3, NLRP4a, NLRP4b, NLRP4c, NLRP4d, NLRP4e, NLRP4f, NLRP4g, NLRP5, NLRP6, NLRP9a, NLRP9b, NLRP9c, NLRP10, NLRP12, and NLRP14. NLRX is an NLR family with the sole member NLRX1 that carries an N‐terminal domain with no strong homology to the N‐terminal domain of any other NLR subfamily member. The N‐terminal region carries a mitochondrial localization signal (MLS). The AIM2‐like receptor (ALR) family contains the founding member called absent in melanoma 2 (AIM2). The tripartite motif‐containing (TRIM) family is defined by an N‐terminal set of domains known as the RING, B‐box‐type, coiled‐coil (CC) motif. This family has one inflammasome‐forming protein called Pyrin (also known as Mediterranean fever, MEFV or TRIM20). Inflammasome assembly requires the adaptor protein called apoptosis‐associated speck‐like protein containing a CARD (ASC, also known as PYCARD). The proteases that induce proteolytic cleavage of inflammasome substrates in mice are caspase‐1 and caspase‐11. bZIP, Basic Leucine Zipper domain; FIIND, Function‐to‐Find Domain; FISNA, Fish‐specific NACHT‐associated domain; HIN‐200, Hematopoietic IFN‐inducible Nuclear proteins with a 200‐amino acid motif; NACHT, Domain present in NAIP, CIITA, HET‐E, and TP‐1; UPA, UNC5, PIDD, and Ankirins domain; ZU5, ZO‐1, and UNC5 domain. The domain structures are annotated based on UniProt, NCBI and the published literature.

FIGURE 3

A high‐level overview of inflammasome assembly and activation in mammalian cells. Inflammasome sensors can interact directly with their target ligand or respond to a variety of physiological changes. Following activation, most inflammasome sensors recruit an adaptor protein called apoptosis‐associated speck‐like protein containing a caspase‐recruitment domain (also known as ASC or PYCARD) and the cysteine protease caspase‐1. Activated caspase‐1 cleaves gasdermin D to release the N‐terminal domain which induces pyroptosis. Caspase‐1 also cleaves pro‐interleukin (IL)‐1β and pro‐IL‐18 into their biologically active forms which are released through gasdermin D pores.

FIGURE 4

The NLRP6 inflammasome. The expression of NLRP6 is induced by microbial ligands, type I interferons (IFN‐α) and peroxisome proliferator‐activated receptor‐γ (PPARγ) agonist, rosiglitazone. These ligands activate mammalian cells via their respective cell‐surface receptors: Toll‐like receptors (TLRs), Interferon alpha/beta receptor (IFNAR), or PPARγ. The metabolites histamine and spermine attenuate the activation of the NLRP6 inflammasome, whereas the metabolite taurine promotes the activation of the NLRP6 inflammasome. NLRP6 can undergo liquid–liquid phase separation upon interaction with double‐stranded (ds)RNA from enteric viruses or lipoteichoic acid (LTA) from Gram‐positive bacteria leading to inflammasome activation. In the context of the activation of NLRP6 by LTA, NLRP6 drives the recruitment of caspase‐1 and caspase‐11 to the same inflammasome complex.

FIGURE 5

The NLRP7 inflammasome. The NLRP7 inflammasome is activated in human macrophages following infection with Listeria monocytogenes, Mycobacterium bovis, Staphylococcus aureus and Mycoplasma species. NLRP7 also senses the bacterial acylated lipoprotein of Mycoplasma species, followed by interaction with ASC and the recruitment of caspase‐1 to assemble a functional inflammasome complex.

FIGURE 6

The NLRP9 inflammasome. The mouse NLRP9b inflammasome is activated in intestinal epithelial cells during rotavirus infection. The double‐stranded (ds)RNA of rotavirus is recognized by the RNA sensor DEAH‐box helicase (DHX) 9, which binds to mouse NLRP9b, potentiating the activation of the inflammasome. In addition, human NLRP9 also co‐precipitates with dsRNA, DHX9 and ASC in HEK293T cells.

FIGURE 7

The NLRP10 inflammasome. NLRP10 senses mitochondria damage induced by the chemical 3 m3‐FBS and forms an inflammasome complex. In addition, the inflammation‐inducer dextran sodium sulfate, via an unknown mechanism, triggers the formation of an NLRP10 inflammasome in colonic epithelial cells of mice (not shown).

FIGURE 8

The NLRP11 inflammasome. NLRP11 forms a protein complex with NLRP3 and mediates NLRP3 inflammasome activation in human THP1 cells in response to the activators nigericin, adenosine triphosphate (ATP), silica, potassium ion (K⁺) efflux, and cytosolic lipopolysaccharide (LPS). Infection with the bacterium Shigella flexneri or Salmonella enterica serovar Typhimurium leads to the liberation of cytosolic LPS. LPS directly binds to both NLRP11 and caspase‐4, forming a complex. Caspase‐4 induces the proteolytic cleavage of gasdermin D that triggers pyroptosis.

FIGURE 9

The NLRP12 inflammasome and PANoptosome. Infection with Yersinia pestis and Plasmodium chabaudi triggers the formation of the NLRP12 inflammasome in mouse macrophages. The combination of the iron‐containing molecular component of the hemoglobin protein and pathogen‐associated molecular patterns (PAMPs) or cytokines tumor necrosis factor (TNF) triggers the activation of Toll‐like receptors (TLR) 2 and TLR4, driving the depletion of cytoplasmic nicotinamide adenine dinucleotide (NAD⁺). The depletion of NAD⁺ upregulates the expression of the innate immune sensor NLRC5 (indicated by an upward arrow) and induces mitochondrial stress leading to the production of reactive oxygen species (ROS) and the formation of a PANoptosome complex comprising NLRP12, NLRC5, NLRP3, ASC, caspase‐1, caspase‐8, and the serine/threonine‐protein kinase RIPK3. The PANoptosome complex triggers the activation of the lytic inflammatory cell death pathway called PANoptosis. The lytic nature of PANoptosis is mediated by membrane‐disrupting proteins called gasdermins allowing damage‐associated molecular patterns (DAMPs) to be released from the dying cell.

FIGURE 10

The CARD8 inflammasome. Under homeostatic conditions, CARD8 undergoes autoproteolysis and is restrained from activation following binding to the dipeptidyl peptidase DPP8 or DPP9. The enzymatic activity of viral proteases from HIV‐1 and Coxsackie virus triggers the proteolytic cleavage of the disordered region of CARD8, leading to the liberation of the C‐terminal fragment which recruits caspase‐1 and assembles the CARD8 inflammasome complex. The chemical Val‐boroPro (VbP) or stress releases DPP8 or DPP9, exposing the N‐terminal fragment for proteasomal degradation and liberating the C‐terminal fragment for inflammasome assembly.

FIGURE 11

The MxA inflammasome. The influenza A virus (IAV)‐derived nucleoproteins are recognized by human Myxovirus resistance protein 1 (also called MxA). The GTPase domain (also called the Dynamin‐type G domain) of MxA interacts with the adaptor protein apoptosis‐associated speck‐like protein containing a caspase‐recruitment domain (also known as ASC or PYCARD), leading to the oligomerization of ASC, resulting in the formation of the MxA inflammasome.