Cedars-Sinai researchers have identified the NLRP11 gene that plays an essential role in the innate human immune system


Cedars-Sinai investigators have identified a gene that plays an essential role in the innate human immune system. The gene, NLRP11, helps activate the inflammatory response that tells the body’s white blood cells to go on the attack against a foreign presence.

The findings, published in Nature Immunology, bring medical science closer to understanding a biological process that can both help and harm the body.

“Chronic inflammation is an underlying cause of innumerable human diseases,” said Christian Stehlik, Ph.D., a co-senior author of the study and director of Pathology Research at Cedars-Sinai. “If you study the molecular mechanisms involved in how inflammation occurs and how it is regulated, you find something that can be applied very broadly.”

When the immune system senses a bacteria, virus, toxin or other foreign presence in the body, it sends white blood cells to surround the unwanted substance and release chemicals to attack it. This response leads to inflammation, which causes redness, pain, warmth and swelling in the affected area as the body heals itself.

Sometimes this defensive response lasts longer than it should, resulting in chronic inflammation. Or, the immune system may mistakenly attack healthy cells, leading to autoimmune disease.

“Acute inflammation is necessary and beneficial to eradicate infection and initiate wound healing,” said Andrea Dorfleutner, Ph.D., co-senior author of the study and associate professor in the departments of Academic Pathology and Biomedical Sciences at Cedars-Sinai. “Chronic, long-term, uncontrolled inflammation, however, is detrimental and can damage the body’s organs and tissues.”

The key to controlling the inflammatory response and preventing chronic inflammation may lie in being able to influence the expression of the NLRP11 gene.

The investigators used a gene-editing system called CRISPR/Cas9 to remove genes or introduce gene mutations in human white blood cells called macrophages. They observed that when they deleted NLRP11, it prevented an immune system sensor called the NLRP3 inflammasome from being activated and launching the inflammatory response.

When the investigators restored the NLRP11 gene, the NLRP3 inflammasome sent its attack signals, which triggered the typical inflammatory process. The investigators chose to focus on this gene in particular because it is not expressed in mice, which led them to hypothesize that it was integral to the complex immune system that exists in humans.

“Now that we have a better picture of the mechanisms behind inflammation, we can come up with completely new strategies to target it that have not been possible before,” Dorfleutner said.

The first authors of the study are Anu Gangopadhyay, Savita Devi, Ph.D., and Shivendra Tenguria, Ph.D., all investigators in the Stehlik and Dorfleutner Laboratory.

Here, we identified NLRP11 as an essential component of the NLRP3 inflammasome in human macrophages, which was required for caspase-1 activation, release of IL-1β and IL-18 and pyroptosis. NLRP11 bound to ASC through homotypic PYD–PYD interactions, which was required for nigericin-induced ASC polymerization. NLRP11 also independently interacted with NLRP3, which involved the NLRP11LRR and the NLRP11NACHT domains and facilitated NLRP3 oligomerization.

The NLRP11NACHT did not specifically interact with NLRP3 in HEK293 cells. This unspecific affinity of NACHT domains when expressed in HEK293 cells has been reported earlier30. In THP-1 cells, the interaction between NLRP11 and NLRP3 occurred after NLRP3 activation. Therefore, we speculate that in macrophages additional unknown signals may be required to confer specificity to NLRP11NACHT domain interactions. Additional specificity is provided by the NLRP11LRR, which interacted with NLRP3, but not with NLRC4. Taken together, it is very likely that the NLRP11LRR and the NLRP11NACHT domains both contributed to the specific interaction between NLRP3 and NLRP11, reminiscent of the interaction between NLRP3 and NEK7 (ref. 23).

Other NACHT domain-mediated NLR hetero-oligomerizations have been described, including NLRC4-NLRP3 (refs. 28,35), NAIP-NLRC4 (refs. 36,37) and Nod2-NLRP1 (ref. 38). NLRC5 also interacts with the NLRP3NACHT to regulate NLRP3 by an unknown mechanism39 but has more recently been linked to major histocompatibility complex class I transactivation40,41.

Even though NLRP11 and NLRP3 did not interact through their PYDs, the NLRP11PYD was still crucial for complex formation, because deletion of the PYD prevented NLRP11 recruitment to the NLRP3 inflammasome, NLRP3 oligomerization and NLRP3 inflammasome responses, which required an intact NLRP11 protein. NLRP3 can nucleate ASC polymerization in vitro, and we observed this ability in HEK293 cells, but only if NLRP3 was overexpressed.

Increasing the expression of NLRP3 during inflammasome priming contributes to, but is not sufficient for, inflammasome activation3,4,5. Low-level expression of NLRP3 did not nucleate ASC polymerization in HEK293 cells, and even priming-induced elevation of NLRP3 expression was insufficient in THP-1 cells in the absence of NLRP11. NLRP11 was required for NLRP3 inflammasome responses in a dose-dependent manner, but NLRP11 expression was not able to compensate for the loss of NLRP3, indicating that NLRP11 alone could not assemble an inflammasome under these conditions.

This mode of activation is unique, because NLRP11 interacted with NLRP3 as well as ASC, and all three were required for NLRP3 inflammasome assembly in THP-1 cells. Other described mechanisms for inflammasome activation require bridging of the NLRP3–ASC interaction by GBP524, or bridging NLRP3 molecules through NACHT-LRR interaction by NEK7 (ref. 23). NLRP11 uniquely combines these mechanisms. NLRP11 was required for the response to all tested soluble and crystalline NLRP3 triggers, supporting its essential role within the NLRP3 inflammasome.

NLRP11 is encoded in humans and absent from mice42, but whether this mechanism is unique to human macrophages will require additional studies. Nevertheless, several other examples exist for increased complexity of inflammasome regulation in humans, including the family of PYD- and CARD-only proteins43. In addition to its function in NLRP3 inflammasome activation, NLRP11 could potentially function as an inflammasome sensor.

Arguably, this would require the ability of NLRP11 to nucleate ASC polymerization, and based on our ASCEGFP polymerization assays in HEK293 cells, some NLRP11-mediated ASC polymerization was possible, especially in cells with sufficiently high NLRP11 expression. However, expression of NLRP11 in THP-1 cells failed to polymerize ASC in the absence of activated NLRP3, suggesting that physiological amounts of NLRP3 require the cooperation between NLRP3 and NLRP11, even though macrophages are the cells with the highest expression of NLRP3 (ref. 44).

Little is known about NLRP11, and there are conflicting reports on its role in type I interferon (IFN) or NF-κB signaling26,27,45. NLRP11 causes degradation of TRAF6 to inhibit TLR-mediated NF-κB activation27, and we observed slightly elevated TNF release in NLRP11KO cells. However, NF-κB-dependent IL-6 release and IL1B transcription were not impacted. NLRP11 also binds to DDX3X and inhibits IFN-β and reduces caspase-1 activity in HEK293T cells46. siRNA-mediated silencing of NLRP11 in THP-1 cells slightly elevates Sendai virus-induced IFN-β production and does not affect IL-1β release45, but Sendai virus already completely prevents NLRP3 inflammasome assembly47.

Several other NLRs, including NLRP2, NLRP3, NLRP6, NLRP7, NLRP12 and NLRC5, have been linked to inflammasomes, as well as transcriptional responses through regulating NF-κB, mitogen-activated protein kinase and IFN signaling48. Overall, our identification of NLRP11 as an essential adaptor or scaffold for NLRP3 inflammasome assembly and activation provides important insights into the still incompletely understood NLRP3 inflammasome response in humans.

NLRP3 is uniquely positioned as a central sensor for infections and cellular stress and has been implicated in a wide range of inflammatory diseases ranging from crystal arthropathies to hereditary autoinflammatory disorders49. NLRP11 may provide an important checkpoint control for NLRP3 inflammasome assembly. Intriguingly, NLRP11 is also necessary for NLRP3 inflammasome responses initiated by CAPS-linked NLRP3 mutations, which may have important clinical implications.

More information: Anu Gangopadhyay et al, NLRP3 licenses NLRP11 for inflammasome activation in human macrophages, Nature Immunology (2022). DOI: 10.1038/s41590-022-01220-3


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